2024-03-28T10:02:22Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/902412019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Novel members of the family Micromonosporaceae, Rugosimonospora acidiphila gen. nov., sp. nov. and Rugosimonospora africana sp. nov.
Monciardini, Paolo
Cavaletti, Linda
Ranghetti, Anna
Schumann, Peter
Rohde, Manfred
Bamonte, Ruggiero
Sosio, Margherita
Mezzelani, Alessandra
Donadio, Stefano
Vicuron Pharmaceuticals, 21040 Gerenzano, Italy. paolo.monciardini@ktedogen.com
Two novel Gram-positive-staining, acidophilic strains were isolated from soil samples. Both show typical features of filamentous actinomycetes. On the basis of 16S rRNA gene sequence analysis, the strains are members of the family Micromonosporaceae. The two strains contain hydroxydiaminopimelic acid, glycine, alanine and glutamic acid in the peptidoglycan. Fatty acid profiles clearly differentiate the two strains: cyclohexyl C(17 : 0), i-C(16 : 0) and ai-C(17 : 0) are predominant in Delta1(T), while the major components for Delta3(T) are ai-C(17 : 0) and i-C(16 : 0). The two strains also differ in their major menaquinones, MK-9(H(8), H(4), H(6)) for Delta1(T) and MK-9(H(8), H(6)) for Delta3(T), and in phospholipid patterns; Delta1(T) displays phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, methyl phosphatidylethanolamine and an unknown aminophospholipid, while Delta3(T) also contains minor amounts of several unknown phospholipids in addition to these phospholipids. The whole-cell sugars of both strains are galactose, arabinose and xylose. The G+C content of the DNA is 72.7 mol% for Delta1(T) and 71.9 mol% for Delta3(T). On the basis of chemotaxonomic, physiological and phylogenetic data, we propose Rugosimonospora gen. nov. to accommodate the two strains, with the description of Rugosimonospora acidiphila gen. nov., sp. nov. (the type species; type strain Delta1(T) =DSM 45227(T) =NBRC 104874(T)) and Rugosimonospora africana sp. nov. (type strain Delta3(T) =DSM 45228(T) =NBRC 104875(T)).
2010-01-21T10:38:08Z
2010-01-21T10:38:08Z
2009-11
Article
Novel members of the family Micromonosporaceae, Rugosimonospora acidiphila gen. nov., sp. nov. and Rugosimonospora africana sp. nov. 2009, 59 (Pt 11):2752-8 Int. J. Syst. Evol. Microbiol.
1466-5026
19625428
10.1099/ijs.0.010231-0
http://hdl.handle.net/10033/90241
International journal of systematic and evolutionary microbiology
en
oai:repository.helmholtz-hzi.de:10033/2469512019-08-30T11:35:39Zcom_10033_338554col_10033_621050
Viral mediated redirection of NEMO/IKKγ to autophagosomes curtails the inflammatory cascade.
Fliss, Patricia M
Jowers, Tali Pechenick
Brinkmann, Melanie M
Holstermann, Barbara
Mack, Claudia
Dickinson, Paul
Hohenberg, Heinrich
Ghazal, Peter
Brune, Wolfram
Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
The early host response to viral infections involves transient activation of pattern recognition receptors leading to an induction of inflammatory cytokines such as interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα). Subsequent activation of cytokine receptors in an autocrine and paracrine manner results in an inflammatory cascade. The precise mechanisms by which viruses avert an inflammatory cascade are incompletely understood. Nuclear factor (NF)-κB is a central regulator of the inflammatory signaling cascade that is controlled by inhibitor of NF-κB (IκB) proteins and the IκB kinase (IKK) complex. In this study we show that murine cytomegalovirus inhibits the inflammatory cascade by blocking Toll-like receptor (TLR) and IL-1 receptor-dependent NF-κB activation. Inhibition occurs through an interaction of the viral M45 protein with the NF-κB essential modulator (NEMO), the regulatory subunit of the IKK complex. M45 induces proteasome-independent degradation of NEMO by targeting NEMO to autophagosomes for subsequent degradation in lysosomes. We propose that the selective and irreversible degradation of a central regulatory protein by autophagy represents a new viral strategy to dampen the inflammatory response.
2012-10-04T09:19:33Z
2012-10-04T09:19:33Z
2012-02
Article
Viral mediated redirection of NEMO/IKKγ to autophagosomes curtails the inflammatory cascade. 2012, 8 (2):e1002517 PLoS Pathog.
1553-7374
22319449
10.1371/journal.ppat.1002517
http://hdl.handle.net/10033/246951
PLoS pathogens
en
Archived with thanks to PLoS pathogens
oai:repository.helmholtz-hzi.de:10033/2810332019-08-30T11:32:17Zcom_10033_338554col_10033_621050
Noncanonical autophagy is required for type I interferon secretion in response to DNA-immune complexes.
Henault, Jill
Martinez, Jennifer
Riggs, Jeffrey M
Tian, Jane
Mehta, Payal
Clarke, Lorraine
Sasai, Miwa
Latz, Eicke
Brinkmann, Melanie M
Iwasaki, Akiko
Coyle, Anthony J
Kolbeck, Roland
Green, Douglas R
Sanjuan, Miguel A
Respiratory, Inflammation and Autoimmunity Research Department, MedImmune, Gaithersburg, MD 20878, USA.
Toll-like receptor-9 (TLR9) is largely responsible for discriminating self from pathogenic DNA. However, association of host DNA with autoantibodies activates TLR9, inducing the pathogenic secretion of type I interferons (IFNs) from plasmacytoid dendritic cells (pDCs). Here, we found that in response to DNA-containing immune complexes (DNA-IC), but not to soluble ligands, IFN-α production depended upon the convergence of the phagocytic and autophagic pathways, a process called microtubule-associated protein 1A/1B-light chain 3 (LC3)-associated phagocytosis (LAP). LAP was required for TLR9 trafficking into a specialized interferon signaling compartment by a mechanism that involved autophagy-related proteins, but not the conventional autophagic preinitiation complex, or adaptor protein-3 (AP-3). Our findings unveil a new role for nonconventional autophagy in inflammation and provide one mechanism by which anti-DNA autoantibodies, such as those found in several autoimmune disorders, bypass the controls that normally restrict the apportionment of pathogenic DNA and TLR9 to the interferon signaling compartment.
2013-04-12T12:07:26Z
2013-04-12T12:07:26Z
2012-12-14
Article
Noncanonical autophagy is required for type I interferon secretion in response to DNA-immune complexes. 2012, 37 (6):986-97 Immunity
1097-4180
23219390
10.1016/j.immuni.2012.09.014
http://hdl.handle.net/10033/281033
Immunity
en
Archived with thanks to Immunity
oai:repository.helmholtz-hzi.de:10033/2925592019-08-30T11:36:32Zcom_10033_338554col_10033_621050
Identification of the N-terminal domain of the influenza virus PA responsible for the suppression of host protein synthesis.
Desmet, Emily A
Bussey, Kendra A
Stone, Raychel
Takimoto, Toru
Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
Cellular protein synthesis is suppressed during influenza virus infection, allowing for preferential production of viral proteins. To explore the impact of polymerase subunits on protein synthesis, we coexpressed enhanced green fluorescent protein (eGFP) or luciferase together with each polymerase component or NS1 of A/California/04/2009 (Cal) and found that PA has a significant impact on the expression of eGFP and luciferase. Comparison of the suppressive activity on coexpressed proteins between various strains revealed that avian virus or avian-origin PAs have much stronger activity than human-origin PAs, such as the one from A/WSN/33 (WSN). Protein synthesis data suggested that reduced expression of coexpressed proteins is not due to PA's reported proteolytic activity. A recombinant WSN containing Cal PA showed enhanced host protein synthesis shutoff and induction of apoptosis. Further characterization of the PA fragment indicated that the N-terminal domain (PANt), which includes the endonuclease active site, is sufficient to suppress cotransfected gene expression. By characterizing various chimeric PANts, we found that multiple regions of PA, mainly the helix α4 and the flexible loop of amino acids 51 to 74, affect the activity. The suppressive effect of PANt cDNA was mainly due to PA-X, which was expressed by ribosomal frameshifting. In both Cal and WSN viruses, PA-X showed a stronger effect than the corresponding PANt, suggesting that the unique C-terminal sequences of PA-X also play a role in suppressing cotransfected gene expression. Our data indicate strain variations in PA gene products, which play a major role in suppression of host protein synthesis.
2013-05-21T14:14:21Z
2013-05-21T14:14:21Z
2013-03
Article
Identification of the N-terminal domain of the influenza virus PA responsible for the suppression of host protein synthesis. 2013, 87 (6):3108-18 J. Virol.
1098-5514
23283952
10.1128/JVI.02826-12
http://hdl.handle.net/10033/292559
Journal of virology
en
Archived with thanks to Journal of virology
oai:repository.helmholtz-hzi.de:10033/2962842019-08-30T11:33:05Zcom_10033_338554col_10033_621787
Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov.
Jogler, Mareike
Chen, Hong
Simon, Julia
Rohde, Manfred
Busse, Hans-Jürgen
Klenk, Hans-Peter
Tindall, Brian J
Overmann, Jörg
Bereich Mikrobiologie, Biologie I, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany.
A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585(T), was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585(T) was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis. Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T). The polar lipids of strain G1A_585(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585(T) was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585(T) ( = DSM 25081(T) = LMG 26646(T)). Because Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T) form a phylogenetic group together with strain G1A_585(T) that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151(T) = DSM 16223(T) = KCTC 12232(T)), Sphingorhabdus marina comb. nov. (type strain FR1087(T) = DSM 22363(T) = IMSNU 14132(T) = KCTC 12763(T) = JCM 14161(T)) and Sphingorhabdus litoris comb. nov. (type strain FR1093(T) = DSM 22379(T) = IMSNU 14133(T) = KCTC 12764(T) = JCM 14162(T)).
2013-07-17T10:50:20Z
2013-07-17T10:50:20Z
2013-04
Article
Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. 2013, 63 (Pt 4):1342-9 Int. J. Syst. Evol. Microbiol.
1466-5034
22798658
10.1099/ijs.0.043133-0
http://hdl.handle.net/10033/296284
International journal of systematic and evolutionary microbiology
en
Archived with thanks to International journal of systematic and evolutionary microbiology
oai:repository.helmholtz-hzi.de:10033/2970562019-08-30T11:33:05Zcom_10033_311624com_10033_6839com_10033_311308com_10033_338554col_10033_621787col_10033_311625col_10033_620777
Dengue-specific subviral nanoparticles: design, creation and characterization.
Khetarpal, Niyati
Poddar, Ankur
Nemani, Satish K
Dhar, Nisha
Patil, Aravind
Negi, Priyanka
Perween, Ashiya
Viswanathan, Ramaswamy
Lünsdorf, Heinrich
Tyagi, Poornima
Raut, Rajendra
Arora, Upasana
Jain, Swatantra K
Rinas, Ursula
Swaminathan, Sathyamangalam
Khanna, Navin
Recombinant Gene Products Group, International Centre for Genetic Engineering & Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India. swami@icgeb.res.in.
Dengue is today the most significant of arboviral diseases. Novel tools are necessary to effectively address the problem of dengue. Virus-like particles (VLP) offer a versatile nanoscale platform for developing tools with potential biomedical applications. From the perspective of a potentially useful dengue-specific tool, the dengue virus envelope protein domain III (EDIII), endowed with serotype-specificity, host receptor recognition and the capacity to elicit virus-neutralizing antibodies, is an attractive candidate.
2013-07-26T14:14:02Z
2013-07-26T14:14:02Z
2013
Article
Dengue-specific subviral nanoparticles: design, creation and characterization. 2013, 11 (1):15 J Nanobiotechnology
1477-3155
23706089
10.1186/1477-3155-11-15
http://hdl.handle.net/10033/297056
Journal of nanobiotechnology
en
Archived with thanks to Journal of nanobiotechnology
oai:repository.helmholtz-hzi.de:10033/2990822019-08-30T11:35:14Zcom_10033_338554col_10033_621787
Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand.
Montero-Calasanz, Maria del Carmen
Göker, Markus
Pötter, Gabriele
Rohde, Manfred
Spröer, Cathrin
Schumann, Peter
Klenk, Hans-Peter
Gorbushina, Anna A
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
A novel Gram-positive, multiloculated thalli-forming, aerobic, actinobacterial strain, CF9/1/1(T), was isolated in 2007 during environmental screening for xerophilic fungi in arid desert soil from the Sahara desert, Chad. The isolate grew best at a temperature range of 20-35 °C and at pH 6.0-8.5 and with 0-4% (w/v) NaCl, forming black-coloured and irregular colonies on GYM agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G+C content of the novel strain was 75.4 mol%. The peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, a not yet structurally identified aminophospholipid and a small amount of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose was a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C16:0 and iso-C15:0. The 16S rRNA gene sequence of the isolate showed 94.6-97.0% sequence similarities with those of five members of the genus: Geodermatophilus ruber DSM 45317(T) (94.6%), Geodermatophilus obscurus DSM 43160(T) (94.8%), Geodermatophilus siccatus DSM 45419(T) (96.2%), Geodermatophilus nigrescens DSM 45408(T) (96.7%) and Geodermatophilus arenarius DSM 45418(T) (97.0%). Based on the evidence from this polyphasic taxonomic study, a novel species, Geodermatophilus telluris sp. nov., is proposed; the type strain is CF9/1/1(T) (=DSM 45421(T)=CCUG 62764(T)).
2013-08-19T11:52:05Z
2013-08-19T11:52:05Z
2013-06
Article
Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand. 2013, 63 (Pt 6):2254-9 Int. J. Syst. Evol. Microbiol.
1466-5034
23159748
10.1099/ijs.0.046888-0
http://hdl.handle.net/10033/299082
International journal of systematic and evolutionary microbiology
en
Archived with thanks to International journal of systematic and evolutionary microbiology
oai:repository.helmholtz-hzi.de:10033/2991962019-08-30T11:35:13Zcom_10033_338554col_10033_621787
Geodermatophilus tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert.
Montero-Calasanz, Maria del Carmen
Göker, Markus
Broughton, William J
Cattaneo, Arlette
Favet, Jocelyne
Pötter, Gabriele
Rohde, Manfred
Spröer, Cathrin
Schumann, Peter
Klenk, Hans-Peter
Gorbushina, Anna A
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Three novel Gram-positive, aerobic, actinobacterial strains, CF5/2(T), CF5/1 and CF7/1, were isolated in 2007 during environmental screening of arid desert soil in the Sahara desert, Chad. Results from riboprinting, MALDI-TOF protein spectra and 16S rRNA sequence analysis confirmed that all three strains belonged to the same species. Phylogenetic analysis of 16S rRNA sequences with the strains' closest relatives indicated that they represented a distinct species. The three novel strains also shared a number of physiological and biochemical characteristics distinct from previously named Geodermatophilus species. The novel strains' peptidoglycan contained meso-diaminopimelic acid; their main phospholipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and a small amount of phosphatidylglycerol; MK-9(H4) was the dominant menaquinone. The major cellular fatty acids were the branched-chain saturated acids iso-C16:0 and iso-C15:0. Galactose was detected as diagnostic sugar. Based on these chemotaxonomic results, 16S rRNA gene sequence analysis and DNA-DNA hybridization between strain CF5/2(T) and the type strains of Geodermatophilus saharensis, Geodermatophilus arenarius, Geodermatophilus nigrescens, Geodermatophilus telluris and Geodermatophilus siccatus, the isolates CF5/2(T), CF5/1 and CF7/1 are proposed to represent a novel species, Geodermatophilus tzadiensis, with type strain CF5/2(T)=DSM 45416=MTCC 11411 and two reference strains, CF5/1 (DSM 45415) and CF7/1 (DSM 45420).
2013-08-20T09:24:48Z
2013-08-20T09:24:48Z
2013-05
Article
Geodermatophilus tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert. 2013, 36 (3):177-82 Syst. Appl. Microbiol.
1618-0984
23415483
10.1016/j.syapm.2012.12.005
http://hdl.handle.net/10033/299196
Systematic and applied microbiology
en
Archived with thanks to Systematic and applied microbiology
oai:repository.helmholtz-hzi.de:10033/3048112019-08-30T11:35:13Zcom_10033_338554col_10033_621787
Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger.
Tegtmeyer, Nicole
Rivas Traverso, Francisco
Rohde, Manfred
Oyarzabal, Omar A
Lehn, Norbert
Schneider-Brachert, Wulf
Ferrero, Richard L
Fox, James G
Berg, Douglas E
Backert, Steffen
Institute of Medical Microbiology, Otto von Guericke University Magdeburg, Magdeburg, Germany.
Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy) and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms) as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5-6 µm) and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers) from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections.
2013-10-31T10:23:00Z
2013-10-31T10:23:00Z
2013
Article
Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger. 2013, 8 (8):e71220 PLoS ONE
1932-6203
23940723
10.1371/journal.pone.0071220
http://hdl.handle.net/10033/304811
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3046032019-08-30T11:36:32Zcom_10033_338554col_10033_621050
Measurement of mouse cytomegalovirus-induced interferon-β with immortalized luciferase reporter cells.
Scheibe, Evgenia
Lienenklaus, Stefan
May, Tobias
Magalhães, Vladimir Gonçalves
Weiss, Siegfried
Brinkmann, Melanie M
Helmholtz Centre for Infection Research, Braunschweig, Germany.
The production of cytokines is a crucial element of the host response to viral and bacterial infections. To follow these events in vivo, transgenic mice have become a valuable tool to study cytokine production through induction of reporter genes. We describe here the generation and immortalization of cells derived from transgenic reporter mice for development of a high-throughput assay system for virus- or bacteria-induced cytokine induction. As an example we describe mouse cytomegalovirus (MCMV) infection of immortalized fibroblasts derived from mice expressing the firefly luciferase reporter downstream of the IFN-β promoter. Common methods to determine IFN-β production, including ELISA, quantitative real-time PCR (qPCR), and transient reporter assays using plasmid-based reporter constructs, have disadvantages and limitations. Transient transfections influence type I IFN responses in most cell types, and IFN-β ELISA as well as qPCR are both laborious and expensive. The method presented here is highly sensitive as well as cost-effective, and allows monitoring of a robust and dose-dependent induction of IFN-β upon virus infection in cell lysates as well as living cells.
2013-10-24T14:30:40Z
2013-10-24T14:30:40Z
2013
Article
Measurement of mouse cytomegalovirus-induced interferon-β with immortalized luciferase reporter cells. 2013, 1064:355-66 Methods Mol. Biol.
1940-6029
23996270
10.1007/978-1-62703-601-6_25
http://hdl.handle.net/10033/304603
Methods in molecular biology (Clifton, N.J.)
en
Archived with thanks to Methods in molecular biology (Clifton, N.J.)
oai:repository.helmholtz-hzi.de:10033/3064932019-08-30T11:29:15Zcom_10033_338554col_10033_621787
Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora
Stielow, Benjamin
Hensel, Gunnar
Strobelt, Dirk
Makonde, Huxley Mae
Rohde, Manfred
Dijksterhuis, Jan
Klenk, Hans-Peter
Göker, Markus
Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
2013-12-09T10:47:27Z
2013-12-09T10:47:27Z
2013-12-09
Article
Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora 2012, 12 (4):675 Mycological Progress
1617-416X
1861-8952
10.1007/s11557-012-0875-1
http://hdl.handle.net/10033/306493
Mycological Progress
http://link.springer.com/10.1007/s11557-012-0875-1
Archived with thanks to Mycological Progress
Springer
oai:repository.helmholtz-hzi.de:10033/3067612019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema.
Abt, Birte
Göker, Markus
Scheuner, Carmen
Han, Cliff
Lu, Megan
Misra, Monica
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mavromatis, Konstantinos
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Hauser, Loren
Jeffries, Cynthia D
Rohde, Manfred
Spring, Stefan
Gronow, Sabine
Detter, John C
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C
Woyke, Tanja
Klenk, Hans-Peter
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
2013-12-12T10:14:00Z
2013-12-12T10:14:00Z
2013-04-15
Article
Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. 2013, 8 (1):88-105 Stand Genomic Sci
1944-3277
23961314
10.4056/sigs.3096473
http://hdl.handle.net/10033/306761
Standards in genomic sciences
en
Archived with thanks to Standards in genomic sciences
oai:repository.helmholtz-hzi.de:10033/3108642019-08-30T11:30:30Zcom_10033_338554col_10033_621787
Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl.
Anderson, Iain
Teshima, Huzuki
Nolan, Matt
Lapidus, Alla
Tice, Hope
Del Rio, Tijana Glavina
Cheng, Jan-Fang
Han, Cliff
Tapia, Roxanne
Goodwin, Lynne A.
Pitluck, Sam
Liolios, Konstantinos
Mavromatis, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Rohde, Manfred
Lang, Elke
Detter, John C.
Göker, Markus
Woyke, Tanja
Bristow, James
Eisen, Jonathan A.
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C.
Klenk, Hans-Peter
Helmholtz Centre for Infection Research, Braunschweig, Germany
2014-01-03T13:06:20Z
2014-01-03T13:06:20Z
2014-01-03
Article
Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. 2013, 9 (1):83 Standards in Genomic Sciences
1944-3277
10.4056/sigs.4338002
http://hdl.handle.net/10033/310864
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4338002
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3109132019-08-30T11:30:26Zcom_10033_338554col_10033_621787
Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T)
Meier-Kolthoff, Jan P.
Lu, Megan
Huntemann, Marcel
Lucas, Susan
Lapidus, Alla
Copeland, Alex
Pitluck, Sam
Goodwin, Lynne A.
Han, Cliff
Tapia, Roxanne
Pötter, Gabriele
Land, Miriam
Ivanova, Natalia
Rohde, Manfred
Göker, Markus
Detter, John C.
Woyke, Tanja
Kyrpides, Nikos C.
Klenk, Hans-Peter
2014-01-06T14:57:41Z
2014-01-06T14:57:41Z
2014-01-06
Article
Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T) 2013, 9 (1):28 Standards in Genomic Sciences
1944-3277
10.4056/sigs.4207886
http://hdl.handle.net/10033/310913
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4207886
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3110792019-08-30T11:36:32Zcom_10033_338554com_10033_128109col_10033_621050col_10033_620747
Superior induction and maintenance of protective CD8 T cells in mice infected with mouse cytomegalovirus vector expressing RAE-1γ.
Trsan, Tihana
Busche, Andreas
Abram, Maja
Wensveen, Felix M
Lemmermann, Niels A
Arapovic, Maja
Babic, Marina
Tomic, Adriana
Golemac, Mijo
Brinkmann, Melanie M
Jäger, Wiebke
Oxenius, Annette
Polic, Bojan
Krmpotic, Astrid
Messerle, Martin
Jonjic, Stipan
Research group viral immune modulation, Helmholtz Centre for infection research, Braunschweig, Germany
Due to a unique pattern of CD8 T-cell response induced by cytomegaloviruses (CMVs), live attenuated CMVs are attractive candidates for vaccine vectors for a number of clinically relevant infections and tumors. NKG2D is one of the most important activating NK cell receptors that plays a role in costimulation of CD8 T cells. Here we demonstrate that the expression of CD8 T-cell epitope of Listeria monocytogenes by a recombinant mouse CMV (MCMV) expressing the NKG2D ligand retinoic acid early-inducible protein 1-gamma (RAE-1γ) dramatically enhanced the effectiveness and longevity of epitope-specific CD8 T-cell response and conferred protection against a subsequent challenge infection with Listeria monocytogenes. Unexpectedly, the attenuated growth in vivo of the CMV vector expressing RAE-1γ and its capacity to enhance specific CD8 T-cell response were preserved even in mice lacking NKG2D, implying additional immune function for RAE-1γ beyond engagement of NKG2D. Thus, vectors expressing RAE-1γ represent a promising approach in the development of CD8 T-cell-based vaccines.
2014-01-08T15:40:39Z
2014-01-08T15:40:39Z
2013-10-08
Article
Superior induction and maintenance of protective CD8 T cells in mice infected with mouse cytomegalovirus vector expressing RAE-1γ. 2013, 110 (41):16550-5 Proc. Natl. Acad. Sci. U.S.A.
1091-6490
24052528
10.1073/pnas.1310215110
http://hdl.handle.net/10033/311079
Proceedings of the National Academy of Sciences of the United States of America
en
Archived with thanks to Proceedings of the National Academy of Sciences of the United States of America
oai:repository.helmholtz-hzi.de:10033/3111442019-08-30T11:30:29Zcom_10033_338554col_10033_621787
Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)
Stackebrandt, Erko
Zeytun, Ahmet
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A.
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mavromatis, Konstantinos
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Chang, Yun-juan
Land, Miriam
Hauser, Loren
Rohde, M
Pukall, Rüdiger
Göker, Markus
Detter, John C.
Woyke, Tanja
Bristow, James
Eisen, Jonathan A.
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C.
Klenk, Hans-Peter
2014-01-09T13:58:29Z
2014-01-09T13:58:29Z
2014-01-09
Article
Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug) 2013, 8 (1):15 Standards in Genomic Sciences
1944-3277
10.4056/sigs.3507020
http://hdl.handle.net/10033/311144
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.3507020
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3111452019-08-30T11:29:45Zcom_10033_338554col_10033_621787
High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T)
Stackebrandt, Erko
Chertkov, Olga
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Han, Cliff
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A.
Bruce, David
Pitluck, Sam
Liolios, Konstantinos
Mavromatis, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Rohde, Manfred
Tindall, Brian J.
Göker, Markus
Woyke, Tanja
Detter, John C.
Bristow, James
Eisen, Jonathan A.
Markowitz, Victor
Hugenholtz, Philip
Klenk, Hans-Peter
Kyrpides, Nikos C.
Central unit for microscopy, Helmholtz Centre for infecton research,D38124 Braunschweig, Germany
2014-01-09T14:08:28Z
2014-01-09T14:08:28Z
2014-01-09
Article
High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T) 2013, 8 (1):37 Standards in Genomic Sciences
1944-3277
10.4056/sigs.3537045
http://hdl.handle.net/10033/311145
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.3537045
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3111462019-08-30T11:33:05Zcom_10033_338554col_10033_621787
Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva.
Stackebrandt, Erko
Chertkov, Olga
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mavromatis, Konstantinos
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Pan, Chongle
Rohde, Manfred
Gronow, Sabine
Göker, Markus
Detter, John C
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Woyke, Tanja
Kyrpides, Nikos C
Klenk, Hans-Peter
Central unit for microscopy, Helmholtz Centre for infecton research,D38124 Braunschweig, Germany
Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was established as a result of the reclassification of Leptospira parva Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella constitutes the family Leptospiraceae, within the order Spirochaetales. Here we describe the features of this free-living aerobic spirochete together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Turneriella and the 13(th) member of the family Leptospiraceae for which a complete or draft genome sequence is now available. The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
2014-01-09T14:37:49Z
2014-01-09T14:37:49Z
2013
Article
Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. 2013, 8 (2):228-38 Stand Genomic Sci
1944-3277
23991255
10.4056/sigs.3617113
http://hdl.handle.net/10033/311146
Standards in genomic sciences
en
Archived with thanks to Standards in genomic sciences
oai:repository.helmholtz-hzi.de:10033/3112902019-08-30T11:29:44Zcom_10033_338554col_10033_621787
Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements
Riedel, Thomas
Teshima, Hazuki
Petersen, Jörn
Fiebig, Anne
Davenport, Karen
Daligault, Hajnalka
Erkkila, Tracy
Gu, Wei
Munk, Christine
Xu, Yan
Chen, Amy
Pati, Amrita
Ivanova, Natalia
Goodwin, Lynne A.
Chain, Patrick
Detter, John C.
Rohde, Manfred
Gronow, Sabine
Kyrpides, Nikos C.
Woyke, Tanja
Göker, Markus
Brinkhoff, Thorsten
Klenk, Hans-Peter
Central unit for microscopy, Helmholtz Centre for infecton research,D38124 Braunschweig, Germany
2014-01-14T11:45:43Z
2014-01-14T11:45:43Z
2014-01-14
Article
Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements 2013, 8 (3):389 Standards in Genomic Sciences
1944-3277
10.4056/sigs.3858183
http://hdl.handle.net/10033/311290
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.3858183
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3113912019-08-30T11:30:29Zcom_10033_338554col_10033_621787
Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T
Freese, Heike M.
Dalingault, Hajnalka
Petersen, Jörn
Pradella, Silke
Davenport, Karen
Teshima, Hazuki
Chen, Amy
Pati, Amrita
Ivanova, Natalia
Goodwin, Lynne A.
Chain, Patrick
Detter, John C.
Rohde, Manfred
Gronow, Sabine
Kyrpides, Nikos C.
Woyke, Tanja
Brinkhoff, Thorsten
Göker, Markus
Overmann, Jörg
Klenk, Hans-Peter
2014-01-16T09:02:59Z
2014-01-16T09:02:59Z
2014-01-16
Article
Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T 2013, 8 (3):450 Standards in Genomic Sciences
1944-3277
10.4056/sigs.383362
http://hdl.handle.net/10033/311391
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.383362
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3262272019-08-30T11:35:14Zcom_10033_338554col_10033_621787
Production of infectious genotype 1b virus particles in cell culture and impairment by replication enhancing mutations.
Pietschmann, Thomas
Zayas, Margarita
Meuleman, Philip
Long, Gang
Appel, Nicole
Koutsoudakis, George
Kallis, Stephanie
Leroux-Roels, Geert
Lohmann, Volker
Bartenschlager, Ralf
With the advent of subgenomic hepatitis C virus (HCV) replicons, studies of the intracellular steps of the viral replication cycle became possible. These RNAs are capable of self-amplification in cultured human hepatoma cells, but save for the genotype 2a isolate JFH-1, efficient replication of these HCV RNAs requires replication enhancing mutations (REMs), previously also called cell culture adaptive mutations. These mutations cluster primarily in the central region of non-structural protein 5A (NS5A), but may also reside in the NS3 helicase domain or at a distinct position in NS4B. Most efficient replication has been achieved by combining REMs residing in NS3 with distinct REMs located in NS4B or NS5A. However, in spite of efficient replication of HCV genomes containing such mutations, they do not support production of infectious virus particles. By using the genotype 1b isolate Con1, in this study we show that REMs interfere with HCV assembly. Strongest impairment of virus formation was found with REMs located in the NS3 helicase (E1202G and T1280I) as well as NS5A (S2204R), whereas a highly adaptive REM in NS4B still allowed virus production although relative levels of core release were also reduced. We also show that cells transfected with the Con1 wild type genome or the genome containing the REM in NS4B release HCV particles that are infectious both in cell culture and in vivo. Our data provide an explanation for the in vitro and in vivo attenuation of cell culture adapted HCV genomes and may open new avenues for the development of fully competent culture systems covering the therapeutically most relevant HCV genotypes.
2014-09-18T08:44:32Z
2014-09-18T08:44:32Z
2009-06
Article
Production of infectious genotype 1b virus particles in cell culture and impairment by replication enhancing mutations. 2009, 5 (6):e1000475 PLoS Pathog.
1553-7374
19521536
10.1371/journal.ppat.1000475
http://hdl.handle.net/10033/326227
PLoS pathogens
en
Archived with thanks to PLoS pathogens
oai:repository.helmholtz-hzi.de:10033/3113922019-08-30T11:35:13Zcom_10033_338554col_10033_621787
Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).
Huntemann, Marcel
Stackebrandt, Erko
Held, Brittany
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mavromatis, Konstantinos
Mikhailova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Rohde, Manfred
Gronow, Sabine
Göker, Markus
Detter, John C
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Woyke, Tanja
Hugenholtz, Philip
Kyrpides, Nikos C
Klenk, Hans-Peter
Lapidus, Alla
Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.
2014-01-16T09:14:48Z
2014-01-16T09:14:48Z
2013
Article
Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). 2013, 8 (2):177-87 Stand Genomic Sci
1944-3277
23991250
10.4056/sigs.3637201
http://hdl.handle.net/10033/311392
Standards in genomic sciences
en
Archived with thanks to Standards in genomic sciences
oai:repository.helmholtz-hzi.de:10033/3114022019-08-30T11:35:14Zcom_10033_338554col_10033_621787
Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.
Liolos, Konstantinos
Abt, Birte
Scheuner, Carmen
Teshima, Hazuki
Held, Brittany
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Pagani, Ioanna
Ivanova, Natalia
Mavromatis, Konstantinos
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Rohde, Manfred
Tindall, Brian J
Detter, John C
Göker, Markus
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Woyke, Tanja
Klenk, Hans-Peter
Kyrpides, Nikos C
Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.
2014-01-16T09:35:44Z
2014-01-16T09:35:44Z
2013
Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. 2013, 8 (2):165-76 Stand Genomic Sci
1944-3277
23991249
10.4056/sigs.3607108
http://hdl.handle.net/10033/311402
Standards in genomic sciences
en
Archived with thanks to Standards in genomic sciences
oai:repository.helmholtz-hzi.de:10033/3114042019-08-30T11:30:30Zcom_10033_338554col_10033_621787
Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT)
Mavromatis, Konstantinos
Stackebrandt, Erko
Held, Brittany
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A.
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Rohde, Manfred
Spring, Stefan
Göker, Markus
Woyke, Tanja
Detter, John C.
Bristow, James
Eisen, Jonathan A.
Markowitz, Victor
Hugenholtz, Philip
Klenk, Hans-Peter
Kyrpides, Nikos C.
2014-01-16T10:17:36Z
2014-01-16T10:17:36Z
2014-01-16
Article
Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT) 2013, 8 (1):47 Standards in Genomic Sciences
1944-3277
10.4056/sigs.3547050
http://hdl.handle.net/10033/311404
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.3547050
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3113972019-08-30T11:29:16Zcom_10033_338554col_10033_621787
Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T)
Mavromatis, Konstantinos
Stackebrandt, Erko
Munk, Christine
Lapidus, Alla
Nolan, Matt
Lucas, Susan
Hammon, Nancy
Deshpande, Shweta
Cheng, Jan-Fang
Tapia, Roxanne
Goodwin, Lynne A.
Pitluck, Sam
Liolios, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Huntemann, Marcel
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Hauser, Loren
Rohde, Manfred
Gronow, Sabine
Göker, Markus
Detter, John C.
Bristow, James
Eisen, Jonathan A.
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C.
Klenk, Hans-Peter
Woyke, Tanja
2014-01-16T10:33:07Z
2014-01-16T10:33:07Z
2014-01-16
Article
Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T) 2013, 8 (1):26 Standards in Genomic Sciences
1944-3277
10.4056/sigs.3527032
http://hdl.handle.net/10033/311397
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.3527032
Archived with thanks to Standards in Genomic Sciences
oai:repository.helmholtz-hzi.de:10033/3169522019-08-30T11:31:18Zcom_10033_338554col_10033_621787
Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens
Dogs, Marco
Voget, Sonja
Teshima, Hazuki
Petersen, Jörn
Davenport, Karen
Dalingault, Hajnalka
Chen, Amy
Pati, Amrita
Ivanova, Natalia
Goodwin, Lynne A.
Chain, Patrick
Detter, John C.
Standfest, Sonja
Rohde, Manfred
Gronow, Sabine
Kyrpides, Nikos C.
Woyke, Tanja
Simon, Meinhard
Klenk, Hans-Peter
Göker, Markus
Brinkhoff, Thorsten
Central unit for microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
2014-05-14T13:59:47Z
2014-05-14T13:59:47Z
2014-05-14
Article
Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens 2013, 9 (2):334 Standards in Genomic Sciences
1944-3277
10.4056/sigs.4448212
http://hdl.handle.net/10033/316952
Standards in Genomic Sciences
http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4448212
Archived with thanks to Standards in Genomic Sciences
Michigan State University
oai:repository.helmholtz-hzi.de:10033/3260762019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Geodermatophilus poikilotrophi sp. nov.: A Multitolerant Actinomycete Isolated from Dolomitic Marble.
Montero-Calasanz, Maria Del Carmen
Hofner, Benjamin
Göker, Markus
Rohde, Manfred
Spröer, Cathrin
Hezbri, Karima
Gtari, Maher
Schumann, Peter
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
A novel Gram-reaction-positive, aerobic actinobacterium, tolerant to mitomycin C, heavy metals, metalloids, hydrogen peroxide, desiccation, and ionizing- and UV-radiation, designated G18(T), was isolated from dolomitic marble collected from outcrops in Samara (Namibia). The growth range was 15-35°C, at pH 5.5-9.5 and in presence of 1% NaCl, forming greenish-black coloured colonies on GYM Streptomyces agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for other representatives of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and small amount of diphosphatidylglycerol. MK-9(H4) was the dominant menaquinone and galactose was detected as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids iso-C16:0 and iso-C15:0 and the unsaturated C17:1 ω8c and C16:1 ω7c. The 16S rRNA gene showed 97.4-99.1% sequence identity with the other representatives of genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G18(T) is proposed to represent a novel species, Geodermatophilus poikilotrophi. Type strain is G18(T) (= DSM 44209(T) = CCUG 63018(T)). The INSDC accession number is HF970583. The novel R software package lethal was used to compute the lethal doses with confidence intervals resulting from tolerance experiments.
2014-09-12T14:17:46Z
2014-09-12T14:17:46Z
2014
Article
Geodermatophilus poikilotrophi sp. nov.: A Multitolerant Actinomycete Isolated from Dolomitic Marble. 2014, 2014:914767 Biomed Res Int
2314-6141
25114928
10.1155/2014/914767
http://hdl.handle.net/10033/326076
BioMed research international
en
Archived with thanks to BioMed research international
oai:repository.helmholtz-hzi.de:10033/3327252019-08-30T11:33:05Zcom_10033_338554col_10033_621787
Localization of MLH3 at the centrosomes.
Roesner, Lennart M
Mielke, Christian
Faehnrich, Silke
Merkhoffer, Yvonne
Dittmar, Kurt E J
Drexler, Hans G
Dirks, Wilhelm G
Mutations in human DNA mismatch repair (MMR) genes are commonly associated with hereditary nonpolyposis colorectal cancer (HNPCC). MLH1 protein heterodimerizes with PMS2, PMS1, and MLH3 to form MutLα, MutLβ, and MutLγ, respectively. We reported recently stable expression of GFP-linked MLH3 in human cell lines. Monitoring these cell lines during the cell cycle using live cell imaging combined with confocal microscopy, we detected accumulation of MLH3 at the centrosomes. Fluorescence recovery after photobleaching (FRAP) revealed high mobility and fast exchange rates at the centrosomes as it has been reported for other DNA repair proteins. MLH3 may have a role in combination with other repair proteins in the control of centrosome numbers.
2014-10-13T14:10:38Z
2014-10-13T14:10:38Z
2014
Article
Localization of MLH3 at the centrosomes. 2014, 15 (8):13932-7 Int J Mol Sci
1422-0067
25116689
10.3390/ijms150813932
http://hdl.handle.net/10033/332725
International journal of molecular sciences
en
Archived with thanks to International journal of molecular sciences
oai:repository.helmholtz-hzi.de:10033/3338342019-08-30T11:25:43Zcom_10033_338554col_10033_621787
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).
Frank, Oliver
Pradella, Silke
Rohde, Manfred
Scheuner, Carmen
Klenk, Hans-Peter
Göker, Markus
Petersen, Jörn
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.
2014-11-07T14:08:47Z
2014-11-07T14:08:47Z
2014-06-15
Article
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)). 2014, 9 (3):914-32 Stand Genomic Sci
1944-3277
25197473
10.4056/sigs.5179110
http://hdl.handle.net/10033/333834
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/3338902019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.
Breider, Sven
Teshima, Hazuki
Petersen, Jörn
Chertkov, Olga
Dalingault, Hajnalka
Chen, Amy
Pati, Amrita
Ivanova, Natalia
Lapidus, Alla
Goodwin, Lynne A
Chain, Patrick
Detter, John C
Rohde, Manfred
Tindall, Brian J
Kyrpides, Nikos C
Woyke, Tanja
Simon, Meinhard
Göker, Markus
Klenk, Hans-Peter
Brinkhoff, Thorsten
Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany .
Leisingera nanhaiensis DSM 24252(T) is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252(T) possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
2014-11-10T14:38:57Z
2014-11-10T14:38:57Z
2014-06-15
Article
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. 2014, 9 (3):687-703 Stand Genomic Sci
1944-3277
25197454
10.4056/sigs.3828824
http://hdl.handle.net/10033/333890
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/3344062019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring.
Göker, Markus
Spring, Stefan
Scheuner, Carmen
Anderson, Iain
Zeytun, Ahmet
Nolan, Matt
Lucas, Susan
Tice, Hope
Del Rio, Tijana Glavina
Cheng, Jan-Fang
Han, Cliff
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Liolios, Konstantinos
Mavromatis, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Hauser, Loren
Chang, Yun-Juan
Jeffries, Cynthia D
Rohde, Manfred
Detter, John C
Woyke, Tanja
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C
Klenk, Hans-Peter
Lapidus, Alla
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
2014-11-10T14:58:14Z
2014-11-10T14:58:14Z
2014-06-15
Article
Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. 2014, 9 (3):1105-17 Stand Genomic Sci
1944-3277
25197486
10.4056/sigs.3016383
http://hdl.handle.net/10033/334406
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/3338962019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia.
Göker, Markus
Lu, Megan
Fiebig, Anne
Nolan, Matt
Lapidus, Alla
Tice, Hope
Del Rio, Tijana Glavina
Cheng, Jan-Fang
Han, Cliff
Tapia, Roxanne
Goodwin, Lynne A
Pitluck, Sam
Liolios, Konstantinos
Mavromatis, Konstantinos
Pagani, Ioanna
Ivanova, Natalia
Mikhailova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Mayilraj, Shanmugam
Rohde, Manfred
Detter, John C
Bunk, Boyke
Spring, Stefan
Wirth, Reinhard
Woyke, Tanja
Bristow, James
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C
Klenk, Hans-Peter
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia of B acteria and Archaea project.
2014-11-10T15:24:49Z
2014-11-10T15:24:49Z
2014-06-15
Article
Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. 2014, 9 (3):1076-88 Stand Genomic Sci
1944-3277
25197484
10.4056/sigs.5138968
http://hdl.handle.net/10033/333896
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/3346512019-08-30T11:25:11Zcom_10033_338554col_10033_621787
Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium.
Kuever, Jan
Visser, Michael
Loeffler, Claudia
Boll, Matthias
Worm, Petra
Sousa, Diana Z
Plugge, Caroline M
Schaap, Peter J
Muyzer, Gerard
Pereira, Ines A C
Parshina, Sofiya N
Goodwin, Lynne A
Kyrpides, Nikos C
Detter, Janine
Woyke, Tanja
Chain, Patrick
Davenport, Karen W
Rohde, Manfred
Spring, Stefan
Klenk, Hans-Peter
Stams, Alfons J M
Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany.
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain Groll(T) together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
2014-11-11T14:39:01Z
2014-11-11T14:39:01Z
2014-06-15
Article
Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. 2014, 9 (3):821-39 Stand Genomic Sci
1944-3277
25197466
10.4056/sigs.5209235
http://hdl.handle.net/10033/334651
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/3379932019-08-30T11:36:33Zcom_10033_338554com_10033_128109col_10033_621050col_10033_620747
Age-dependent enterocyte invasion and microcolony formation by Salmonella.
Zhang, Kaiyi
Dupont, Aline
Torow, Natalia
Gohde, Fredrik
Leschner, Sara
Lienenklaus, Stefan
Weiss, Siegfried
Brinkmann, Melanie M
Kühnel, Mark
Hensel, Michael
Fulde, Marcus
Hornef, Mathias W
The coordinated action of a variety of virulence factors allows Salmonella enterica to invade epithelial cells and penetrate the mucosal barrier. The influence of the age-dependent maturation of the mucosal barrier for microbial pathogenesis has not been investigated. Here, we analyzed Salmonella infection of neonate mice after oral administration. In contrast to the situation in adult animals, we observed spontaneous colonization, massive invasion of enteroabsorptive cells, intraepithelial proliferation and the formation of large intraepithelial microcolonies. Mucosal translocation was dependent on enterocyte invasion in neonates in the absence of microfold (M) cells. It further resulted in potent innate immune stimulation in the absence of pronounced neutrophil-dominated pathology. Our results identify factors of age-dependent host susceptibility and provide important insight in the early steps of Salmonella infection in vivo. We also present a new small animal model amenable to genetic manipulation of the host for the analysis of the Salmonella enterocyte interaction in vivo.
2015-01-09T15:35:49Z
2015-01-09T15:35:49Z
2014-09
Article
Age-dependent enterocyte invasion and microcolony formation by Salmonella. 2014, 10 (9):e1004385 PLoS Pathog.
1553-7374
25210785
10.1371/journal.ppat.1004385
http://hdl.handle.net/10033/337993
PLoS pathogens
en
oai:repository.helmholtz-hzi.de:10033/3384692019-08-30T11:27:16Zcom_10033_338554col_10033_621787
Multiple mechanisms mediate resistance to sorafenib in urothelial cancer.
Knievel, Judith
Schulz, Wolfgang A
Greife, Annemarie
Hader, Christiane
Lübke, Tobias
Schmitz, Ingo
Albers, Peter
Niegisch, Günter
Genetic and epigenetic changes in the mitogen activated protein kinase (MAPK) signaling render urothelial cancer a potential target for tyrosine kinase inhibitor (TKI) treatment. However, clinical trials of several TKIs failed to prove efficacy. In this context, we investigated changes in MAPK signaling activity, downstream apoptotic regulators and changes in cell cycle distribution in different urothelial cancer cell lines (UCCs) upon treatment with the multikinase inhibitor sorafenib. None of the classical sorafenib targets (vascular endothelial growth factor receptor 1/-receptor 2, VEGFR1/-R2; platelet-derived growth factor receptor α/-receptor β, PDGFR-α/-β; c-KIT) was expressed at significant levels leaving RAF proteins as its likely molecular target. Low sorafenib concentrations paradoxically increased cell viability, whereas higher concentrations induced G1 arrest and eventually apoptosis. MAPK signaling remained partly active after sorafenib treatment, especially in T24 cells with an oncogenic HRAS mutation. AKT phosphorylation was increased, suggesting compensatory activation of the phosphatidylinositol-3-kinase (PI3K) pathway. Sorafenib regularly down regulated the anti-apoptotic myeloid cell leukemia 1 (Mcl-1) protein, but combinatorial treatment with ABT-737 targeting other B-cell lymphoma 2 (Bcl-2) family proteins did not result in synergistic effects. In summary, efficacy of sorafenib in urothelial cancer cell lines appears hampered by limited effects on MAPK signaling, crosstalk with further cancer pathways and an anti-apoptotic state of UCCs. These observations may account for the lack of efficacy of sorafenib in clinical trials and should be considered more broadly in the development of signaling pathway inhibitors for drug therapy in urothelial carcinoma.
2015-01-15T14:56:52Z
2015-01-15T14:56:52Z
2014
Article
Multiple mechanisms mediate resistance to sorafenib in urothelial cancer. 2014, 15 (11):20500-17 Int J Mol Sci
1422-0067
25387078
10.3390/ijms151120500
http://hdl.handle.net/10033/338469
International journal of molecular sciences
en
oai:repository.helmholtz-hzi.de:10033/3385552019-08-30T11:28:23Zcom_10033_338554col_10033_338544
The EHEC-host interactome reveals novel targets for the translocated intimin receptor.
Blasche, Sonja
Arens, Stefan
Ceol, Arnaud
Siszler, Gabriella
Schmidt, M Alexander
Häuser, Roman
Schwarz, Frank
Wuchty, Stefan
Aloy, Patrick
Uetz, Peter
Stradal, Theresia
Koegl, Manfred
Helmholtz Centre for infection research; Inhooffenstr. 7; D-38124 Braunschweig; Germany.
Enterohemorrhagic E. coli (EHEC) manipulate their human host through at least 39 effector proteins which hijack host processes through direct protein-protein interactions (PPIs). To identify their protein targets in the host cells, we performed yeast two-hybrid screens, allowing us to find 48 high-confidence protein-protein interactions between 15 EHEC effectors and 47 human host proteins. In comparison to other bacteria and viruses we found that EHEC effectors bind more frequently to hub proteins as well as to proteins that participate in a higher number of protein complexes. The data set includes six new interactions that involve the translocated intimin receptor (TIR), namely HPCAL1, HPCAL4, NCALD, ARRB1, PDE6D, and STK16. We compared these TIR interactions in EHEC and enteropathogenic E. coli (EPEC) and found that five interactions were conserved. Notably, the conserved interactions included those of serine/threonine kinase 16 (STK16), hippocalcin-like 1 (HPCAL1) as well as neurocalcin-delta (NCALD). These proteins co-localize with the infection sites of EPEC. Furthermore, our results suggest putative functions of poorly characterized effectors (EspJ, EspY1). In particular, we observed that EspJ is connected to the microtubule system while EspY1 appears to be involved in apoptosis/cell cycle regulation.
2015-01-19T15:02:33Z
2015-01-19T15:02:33Z
2014
Article
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. 2014, 4:7531 Sci Rep
2045-2322
25519916
10.1038/srep07531
http://hdl.handle.net/10033/338555
Scientific reports
en
oai:repository.helmholtz-hzi.de:10033/3385952019-08-30T11:25:43Zcom_10033_338554col_10033_621787
New insights into the antimicrobial effect of mast cells against Enterococcus faecalis.
Scheb-Wetzel, Matthias
Rohde, Manfred
Bravo, Alicia
Goldmann, Oliver
Helmholtz Centre for infection reseach,Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Enterococcus faecalis has emerged as an important cause of life-threatening multidrug-resistant bacterial infections in the hospital setting. The pathogenesis of enterococcal infections has remained a relatively neglected field despite their obvious clinical relevance. The objective of this study was to characterize the interactions between mast cells (MCs), an innate immune cell population abundant in the intestinal lamina propria, and E. faecalis. This study was conducted with primary bone marrow-derived murine MCs. The results demonstrated that MCs exerted an antimicrobial effect against E. faecalis that was mediated both by degranulation, with the concomitant discharge of the antimicrobial effectors contained in the granules, and by the release of extracellular traps, in which E. faecalis was snared and killed. In particular, the cathelicidin LL-37 released by the MCs had potent antimicrobial effect against E. faecalis. We also investigated the specific receptors involved in the recognition of E. faecalis by MCs. We found that Toll-like receptors (TLRs) are critically involved in the MC recognition of E. faecalis, since MCs deficient in the expression of MyD88, an adaptor molecule required for signaling by most TLRs, were significantly impaired in their capacity to degranulate, to reduce E. faecalis growth as well as to release tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6) after encountering this pathogen. Furthermore, TLR2 was identified as the most prominent TLR involved in the recognition of E. faecalis by MCs. The results of this study indicate that MCs may be important contributors to the host innate immune defenses against E. faecalis.
2015-01-20T13:24:43Z
2015-01-20T13:24:43Z
2014-11
Article
New insights into the antimicrobial effect of mast cells against Enterococcus faecalis. 2014, 82 (11):4496-507 Infect. Immun.
1098-5522
25114115
10.1128/IAI.02114-14
http://hdl.handle.net/10033/338595
Infection and immunity
en
oai:repository.helmholtz-hzi.de:10033/3442122019-08-30T11:31:49Zcom_10033_338554col_10033_621787
Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.
Huber, Katharina J
Wüst, Pia K
Rohde, Manfred
Overmann, Jörg
Foesel, Bärbel U
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H(T) and Ac_23_E3(T) were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H(T) and Ac_23_E3(T) were aerobic mesophiles with a broad range of tolerance towards pH (4.0-9.5 and 3.5-10.0, respectively) and temperature (15-44 and 12-47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H(T) and Ac_23_E3(T) were iso-C(15 : 0), summed feature 1 (C(13 : 0) 3-OH/iso-C(15 : 1) H), summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c) and anteiso-C(17 : 0). The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H(T) and Ac_23_E3(T) were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16(T), with 16S rRNA gene sequence identity of 93.2 and 93.3%, respectively. Strains A22_HD_4H(T) and Ac_23_E3(T) displayed 16S rRNA gene sequence similarity of 97.4% to each other. On the basis of the low DNA-DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4H(T) = DSM 26555(T) = LMG 27985(T)) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3(T) = DSM 26558(T) = LMG 27597(T)).
2015-02-05T10:51:47Z
2015-02-05T10:51:47Z
2014-06
Article
Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. 2014, 64 (Pt 6):1866-75 Int. J. Syst. Evol. Microbiol.
1466-5034
24573163
10.1099/ijs.0.060236-0
http://hdl.handle.net/10033/344212
International journal of systematic and evolutionary microbiology
en
oai:repository.helmholtz-hzi.de:10033/3464512019-08-30T11:31:49Zcom_10033_338554col_10033_621787
Belliella kenyensis sp. nov., isolated from an alkaline lake.
Akhwale, Juliah Khayeli
Göker, Markus
Rohde, Manfred
Schumann, Peter
Klenk, Hans-Peter
Boga, Hamadi Iddi
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 7 38124 Braunschweig, Germany.
A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164(T), was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella, with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698(T). Optimal growth temperature was 30-35 °C, at pH 7.0-12.0 in the presence of 0-4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164(T) were consistent with those of other members of the genus Belliella. The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella. The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164(T) ( = DSM 46651(T) = CECT 8551(T)).
2015-03-10T09:25:01Z
2015-03-10T09:25:01Z
2015-02
Article
Belliella kenyensis sp. nov., isolated from an alkaline lake. 2015, 65 (Pt 2):457-62 Int. J. Syst. Evol. Microbiol.
1466-5034
25385994
10.1099/ijs.0.066951-0
http://hdl.handle.net/10033/346451
International journal of systematic and evolutionary microbiology
en
oai:repository.helmholtz-hzi.de:10033/5509992019-08-30T11:31:49Zcom_10033_338554col_10033_621787
TatBC-Independent TatA/Tat Substrate Interactions Contribute to Transport Efficiency.
Taubert, Johannes
Hou, Bo
Risselada, H Jelger
Mehner, Denise
Lünsdorf, Heinrich
Grubmüller, Helmut
Brüser, Thomas
The Tat system can transport folded, signal peptide-containing proteins (Tat substrates) across energized membranes of prokaryotes and plant plastids. A twin-arginine motif in the signal peptide of Tat substrates is recognized by TatC-containing complexes, and TatA permits the membrane passage. Often, as in the model Tat systems of Escherichia coli and plant plastids, a third component - TatB - is involved that resembles TatA but has a higher affinity to TatC. It is not known why most TatA dissociates from TatBC complexes in vivo and distributes more evenly in the membrane. Here we show a TatBC-independent substrate-binding to TatA from Escherichia coli, and we provide evidence that this binding enhances Tat transport. First hints came from in vivo cross-linking data, which could be confirmed by affinity co-purification of TatA with the natural Tat substrates HiPIP and NrfC. Two positions on the surface of HiPIP could be identified that are important for the TatA interaction and transport efficiency, indicating physiological relevance of the interaction. Distributed TatA thus may serve to accompany membrane-interacting Tat substrates to the few TatBC spots in the cells.
2015-04-30T09:08:40Z
2015-04-30T09:08:40Z
2015
Article
TatBC-Independent TatA/Tat Substrate Interactions Contribute to Transport Efficiency. 2015, 10 (3):e0119761 PLoS ONE
1932-6203
25774531
10.1371/journal.pone.0119761
http://hdl.handle.net/10033/550999
PloS one
en
oai:repository.helmholtz-hzi.de:10033/5569262019-08-30T11:31:49Zcom_10033_338554col_10033_621787
An internal thioester in a pathogen surface protein mediates covalent host binding.
Walden, Miriam
Edwards, John M
Dziewulska, Aleksandra M
Bergmann, Rene
Saalbach, Gerhard
Kan, Su-Yin
Miller, Ona K
Weckener, Miriam
Jackson, Rosemary J
Shirran, Sally L
Botting, Catherine H
Florence, Gordon J
Rohde, Manfred
Banfield, Mark J
Schwarz-Linek, Ulrich
Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a 'chemical harpoon'. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions.
2015-06-15T14:10:13Z
2015-06-15T14:10:13Z
2015
Article
An internal thioester in a pathogen surface protein mediates covalent host binding. 2015, 4: Elife
2050-084X
26032562
10.7554/eLife.06638
http://hdl.handle.net/10033/556926
eLife
en
oai:repository.helmholtz-hzi.de:10033/5603312019-08-30T11:33:55Zcom_10033_338554col_10033_621787
Azithromycin Synergizes with Cationic Antimicrobial Peptides to Exert Bactericidal and Therapeutic Activity Against Highly Multidrug-Resistant Gram-Negative Bacterial Pathogens
Lin, Leo
Nonejuie, Poochit
Munguia, Jason
Hollands, Andrew
Olson, Joshua
Dam, Quang
Kumaraswamy, Monika
Rivera, Heriberto
Corriden, Ross
Rohde, Manfred
Hensler, Mary E.
Burkart, Michael D.
Pogliano, Joe
Sakoulas, George
Nizet, Victor
2015-07-13T14:14:51Z
2015-07-13T14:14:51Z
2015-06
Article
Azithromycin Synergizes with Cationic Antimicrobial Peptides to Exert Bactericidal and Therapeutic Activity Against Highly Multidrug-Resistant Gram-Negative Bacterial Pathogens 2015 EBioMedicine
23523964
10.1016/j.ebiom.2015.05.021
http://hdl.handle.net/10033/560331
EBioMedicine
http://linkinghub.elsevier.com/retrieve/pii/S2352396415300244
oai:repository.helmholtz-hzi.de:10033/5604062019-08-30T11:25:43Zcom_10033_338554col_10033_620574
The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation.
Kühn, Sonja
Erdmann, Constanze
Kage, Frieda
Block, Jennifer
Schwenkmezger, Lisa
Steffen, Anika
Rottner, Klemens
Geyer, Matthias
Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
Formins are actin polymerization factors that elongate unbranched actin filaments at the barbed end. Rho family GTPases activate Diaphanous-related formins through the relief of an autoregulatory interaction. The crystal structures of the N-terminal domains of human FMNL1 and FMNL2 in complex with active Cdc42 show that Cdc42 mediates contacts with all five armadillo repeats of the formin with specific interactions formed by the Rho-GTPase insert helix. Mutation of three residues within Rac1 results in a gain-of-function mutation for FMNL2 binding and reconstitution of the Cdc42 phenotype in vivo. Dimerization of FMNL1 through a parallel coiled coil segment leads to formation of an umbrella-shaped structure that—together with Cdc42—spans more than 15 nm in diameter. The two interacting FMNL-Cdc42 heterodimers expose six membrane interaction motifs on a convex protein surface, the assembly of which may facilitate actin filament elongation at the leading edge of lamellipodia and filopodia.
2015-07-14T14:34:49Z
2015-07-14T14:34:49Z
2015
Article
The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation. 2015, 6:7088 Nat Commun
2041-1723
25963737
10.1038/ncomms8088
http://hdl.handle.net/10033/560406
Nature communications
en
oai:repository.helmholtz-hzi.de:10033/6209022019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
Meier-Kolthoff, Jan P
Hahnke, Richard L
Petersen, Jörn
Scheuner, Carmen
Michael, Victoria
Fiebig, Anne
Rohde, Christine
Rohde, Manfred
Fartmann, Berthold
Goodwin, Lynne A
Chertkov, Olga
Reddy, TBK
Pati, Amrita
Ivanova, Natalia N
Markowitz, Victor
Kyrpides, Nikos C
Woyke, Tanja
Göker, Markus
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Abstract Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083T together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083T in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
2017-04-21T10:40:59Z
2017-04-21T10:40:59Z
2014-12-08
2015-09-04T08:25:00Z
Article
Standards in Genomic Sciences. 2014 Dec 08;9(1):2
http://dx.doi.org/10.1186/1944-3277-9-2
http://hdl.handle.net/10033/620902
en
Meier-Kolthoff et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6209532019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Sequencing and Characterization of Pseudomonas aeruginosa phage JG004
Garbe, Julia
Bunk, Boyke
Rohde, Manfred
Schobert, Max
Abstract Background Phages could be an important alternative to antibiotics, especially for treatment of multiresistant bacteria as e.g. Pseudomonas aeruginosa. For an effective use of bacteriophages as antimicrobial agents, it is important to understand phage biology but also genes of the bacterial host essential for phage infection. Results We isolated and characterized a lytic Pseudomonas aeruginosa phage, named JG004, and sequenced its genome. Phage JG004 is a lipopolysaccharide specific broad-host-range phage of the Myoviridae phage family. The genome of phage JG004 encodes twelve tRNAs and is highly related to the PAK-P1 phage genome. To investigate phage biology and phage-host interactions, we used transposon mutagenesis of the P. aeruginosa host and identified P. aeruginosa genes, which are essential for phage infection. Analysis of the respective P. aeruginosa mutants revealed several characteristics, such as host receptor and possible spermidine-dependance of phage JG004. Conclusions Whole genome sequencing of phage JG004 in combination with identification of P. aeruginosa host genes essential for infection, allowed insights into JG004 biology, revealed possible resistance mechanisms of the host bacterium such as mutations in LPS and spermidine biosynthesis and can also be used to characterize unknown gene products in P. aeruginosa.
2017-06-15T10:33:07Z
2017-06-15T10:33:07Z
2011-05-14
2015-09-04T08:25:12Z
Journal Article
BMC Microbiology. 2011 May 14;11(1):102
http://dx.doi.org/10.1186/1471-2180-11-102
http://hdl.handle.net/10033/620953
en
Garbe et al; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6209472019-08-30T11:31:23Zcom_10033_338554col_10033_621787
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae
Scheuner, Carmen
Tindall, Brian J
Lu, Megan
Nolan, Matt
Lapidus, Alla
Cheng, Jan-Fang
Goodwin, Lynne
Pitluck, Sam
Huntemann, Marcel
Liolios, Konstantinos
Pagani, Ioanna
Mavromatis, Konstantinos
Ivanova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Jeffries, Cynthia D
Hauser, Loren
Land, Miriam
Mwirichia, Romano
Rohde, Manfred
Abt, Birte
Detter, John C
Woyke, Tanja
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Göker, Markus
Kyrpides, Nikos C
Klenk, Hans-Peter
Abstract Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
2017-06-15T08:29:37Z
2017-06-15T08:29:37Z
2014-12-08
2015-09-04T08:24:43Z
Journal Article
Standards in Genomic Sciences. 2014 Dec 08;9(1):10
http://dx.doi.org/10.1186/1944-3277-9-10
http://hdl.handle.net/10033/620947
en
Scheuner et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6209572019-08-30T11:29:17Zcom_10033_338554col_10033_621787
The signaling pathway of Campylobacter jejuni-induced Cdc42 activation: Role of fibronectin, integrin beta1, tyrosine kinases and guanine exchange factor Vav2
Krause-Gruszczynska, Malgorzata
Boehm, Manja
Rohde, Manfred
Tegtmeyer, Nicole
Takahashi, Seiichiro
Buday, Laszlo
Oyarzabal, Omar A
Backert, Steffen
Abstract Background Host cell invasion by the foodborne pathogen Campylobacter jejuni is considered as one of the primary reasons of gut tissue damage, however, mechanisms and key factors involved in this process are widely unclear. It was reported that small Rho GTPases, including Cdc42, are activated and play a role during invasion, but the involved signaling cascades remained unknown. Here we utilised knockout cell lines derived from fibronectin-/-, integrin-beta1-/-, focal adhesion kinase (FAK)-/- and Src/Yes/Fyn-/- deficient mice, and wild-type control cells, to investigate C. jejuni-induced mechanisms leading to Cdc42 activation and bacterial uptake. Results Using high-resolution scanning electron microscopy, GTPase pulldowns, G-Lisa and gentamicin protection assays we found that each studied host factor is necessary for induction of Cdc42-GTP and efficient invasion. Interestingly, filopodia formation and associated membrane dynamics linked to invasion were only seen during infection of wild-type but not in knockout cells. Infection of cells stably expressing integrin-beta1 variants with well-known defects in fibronectin fibril formation or FAK signaling also exhibited severe deficiencies in Cdc42 activation and bacterial invasion. We further demonstrated that infection of wild-type cells induces increasing amounts of phosphorylated FAK and growth factor receptors (EGFR and PDGFR) during the course of infection, correlating with accumulating Cdc42-GTP levels and C. jejuni invasion over time. In studies using pharmacological inhibitors, silencing RNA (siRNA) and dominant-negative expression constructs, EGFR, PDGFR and PI3-kinase appeared to represent other crucial components upstream of Cdc42 and invasion. siRNA and the use of Vav1/2-/- knockout cells further showed that the guanine exchange factor Vav2 is required for Cdc42 activation and maximal bacterial invasion. Overexpression of certain mutant constructs indicated that Vav2 is a linker molecule between Cdc42 and activated EGFR/PDGFR/PI3-kinase. Using C. jejuni mutant strains we further demonstrated that the fibronectin-binding protein CadF and intact flagella are involved in Cdc42-GTP induction, indicating that the bacteria may directly target the fibronectin/integrin complex for inducing signaling leading to its host cell entry. Conclusion Collectively, our findings led us propose that C. jejuni infection triggers a novel fibronectin→integrin-beta1→FAK/Src→EGFR/PDGFR→PI3-kinase→Vav2 signaling cascade, which plays a crucial role for Cdc42 GTPase activity associated with filopodia formation and enhances bacterial invasion.
2017-06-16T08:14:22Z
2017-06-16T08:14:22Z
2011-12-28
2015-09-04T08:25:39Z
Journal Article
Cell Communication and Signaling. 2011 Dec 28;9(1):32
http://dx.doi.org/10.1186/1478-811X-9-32
http://hdl.handle.net/10033/620957
en
Krause-Gruszczynska et al; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6207592019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Single cell analysis applied to antibody fragment production with Bacillus megaterium: development of advanced physiology and bioprocess state estimation tools
David, Florian
Berger, Antje
Hänsch, Robert
Rohde, Manfred
Franco-Lara, Ezequiel
Abstract Background Single cell analysis for bioprocess monitoring is an important tool to gain deeper insights into particular cell behavior and population dynamics of production processes and can be very useful for discrimination of the real bottleneck between product biosynthesis and secretion, respectively. Results Here different dyes for viability estimation considering membrane potential (DiOC2(3), DiBAC4(3), DiOC6(3)) and cell integrity (DiBAC4(3)/PI, Syto9/PI) were successfully evaluated for Bacillus megaterium cell characterization. It was possible to establish an appropriate assay to measure the production intensities of single cells revealing certain product secretion dynamics. Methods were tested regarding their sensitivity by evaluating fluorescence surface density and fluorescent specific concentration in relation to the electronic cell volume. The assays established were applied at different stages of a bioprocess where the antibody fragment D1.3 scFv production and secretion by B. megaterium was studied. Conclusions It was possible to distinguish between live, metabolic active, depolarized, dormant, and dead cells and to discriminate between high and low productive cells. The methods were shown to be suitable tools for process monitoring at single cell level allowing a better process understanding, increasing robustness and forming a firm basis for physiology-based analysis and optimization with the general application for bioprocess development.
2017-01-27T08:52:31Z
2017-01-27T08:52:31Z
2011-04-15
2015-09-04T08:28:55Z
Journal Article
Microbial Cell Factories. 2011 Apr 15;10(1):23
http://dx.doi.org/10.1186/1475-2859-10-23
http://hdl.handle.net/10033/620759
en
David et al; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6207582019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium “Chlorochromatium aggregatum”
Liu, Zhenfeng
Müller, Johannes
Li, Tao
Alvey, Richard M
Vogl, Kajetan
Frigaard, Niels-Ulrik
Rockwell, Nathan C
Boyd, Eric S
Tomsho, Lynn P
Schuster, Stephan C
Henke, Petra
Rohde, Manfred
Overmann, Jörg
Bryant, Donald A
Abstract Background ‘Chlorochromatium aggregatum’ is a phototrophic consortium, a symbiosis that may represent the highest degree of mutual interdependence between two unrelated bacteria not associated with a eukaryotic host. ‘Chlorochromatium aggregatum’ is a motile, barrel-shaped aggregate formed from a single cell of ‘Candidatus Symbiobacter mobilis”, a polarly flagellated, non-pigmented, heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells of Chlorobium chlorochromatii, a non-motile photolithoautotrophic green sulfur bacterium. Results We analyzed the complete genome sequences of both organisms to understand the basis for this symbiosis. Chl. chlorochromatii has acquired relatively few symbiosis-specific genes; most acquired genes are predicted to modify the cell wall or function in cell-cell adhesion. In striking contrast, ‘Ca. S. mobilis’ appears to have undergone massive gene loss, is probably no longer capable of independent growth, and thus may only reproduce when consortia divide. A detailed model for the energetic and metabolic bases of the dependency of ‘Ca. S. mobilis’ on Chl. chlorochromatii is described. Conclusions Genomic analyses suggest that three types of interactions lead to a highly sophisticated relationship between these two organisms. Firstly, extensive metabolic exchange, involving carbon, nitrogen, and sulfur sources as well as vitamins, occurs from the epibiont to the central bacterium. Secondly, ‘Ca. S. mobilis’ can sense and move towards light and sulfide, resources that only directly benefit the epibiont. Thirdly, electron cycling mechanisms, particularly those mediated by quinones and potentially involving shared protonmotive force, could provide an important basis for energy exchange in this and other symbiotic relationships.
2017-01-27T08:50:13Z
2017-01-27T08:50:13Z
2013-11-22
2015-09-04T08:28:58Z
Journal Article
Genome Biology. 2013 Nov 22;14(11):R127
http://dx.doi.org/10.1186/gb-2013-14-11-r127
http://hdl.handle.net/10033/620758
en
Liu et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6207562019-08-30T11:29:47Zcom_10033_338554col_10033_621787
First genome sequences of Achromobacter phages reveal new members of the N4 family
Wittmann, Johannes
Dreiseikelmann, Brigitte
Rohde, Manfred
Meier-Kolthoff, Jan P
Bunk, Boyke
Rohde, Christine
Abstract Background Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far. Methods Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP). Results In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages. Conclusions Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.
2017-01-27T08:32:42Z
2017-01-27T08:32:42Z
2014-01-27
2015-09-04T08:29:21Z
Journal Article
Virology Journal. 2014 Jan 27;11(1):14
http://dx.doi.org/10.1186/1743-422X-11-14
http://hdl.handle.net/10033/620756
en
Wittmann et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/5810712019-08-30T11:30:58Zcom_10033_338554col_10033_621787
A Periplasmic Complex of the Nitrite Reductase NirS, the Chaperone DnaK, and the Flagellum Protein FliC Is Essential for Flagellum Assembly and Motility in Pseudomonas aeruginosa.
Borrero-de Acuña, José Manuel
Molinari, Gabriella
Rohde, Manfred
Dammeyer, Thorben
Wissing, Josef
Jänsch, Lothar
Arias, Sagrario
Jahn, Martina
Schobert, Max
Timmis, Kenneth N
Jahn, Dieter
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Pseudomonas aeruginosa is a ubiquitously occurring environmental bacterium and opportunistic pathogen responsible for various acute and chronic infections. Obviously, anaerobic energy generation via denitrification contributes to its ecological success. To investigate the structural basis for the interconnection of the denitrification machinery to other essential cellular processes, we have sought to identify the protein interaction partners of the denitrification enzyme nitrite reductase NirS in the periplasm. We employed NirS as an affinity-purifiable bait to identify interacting proteins in vivo. Results obtained revealed that both the flagellar structural protein FliC and the protein chaperone DnaK form a complex with NirS in the periplasm. The interacting domains of NirS and FliC were tentatively identified. The NirS-interacting stretch of amino acids lies within its cytochrome c domain. Motility assays and ultrastructure analyses revealed that a nirS mutant was defective in the formation of flagella and correspondingly in swimming motility. In contrast, the fliC mutant revealed an intact denitrification pathway. However, deletion of the nirF gene, coding for a heme d1 biosynthetic enzyme, which leads to catalytically inactive NirS, did not abolish swimming ability. This pointed to a structural function for the NirS protein. FliC and NirS were found colocalized with DnaK at the cell surface of P. aeruginosa. A function of the detected periplasmic NirS-DnaK-FliC complex in flagellum formation and motility was concluded and discussed.
2015-10-26T10:41:15Z
2015-10-26T10:41:15Z
2015-10-01
Article
A Periplasmic Complex of the Nitrite Reductase NirS, the Chaperone DnaK, and the Flagellum Protein FliC Is Essential for Flagellum Assembly and Motility in Pseudomonas aeruginosa. 2015, 197 (19):3066-75 J. Bacteriol.
1098-5530
26170416
10.1128/JB.00415-15
http://hdl.handle.net/10033/581071
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/5818112019-08-30T11:31:23Zcom_10033_338554col_10033_621787
Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.
Riedel, Thomas
Spring, Stefan
Fiebig, Anne
Scheuner, Carmen
Petersen, Jörn
Göker, Markus
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
2015-11-05T13:25:51Z
2015-11-05T13:25:51Z
2015
Article
Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. 2015, 10:17 Stand Genomic Sci
1944-3277
26203330
10.1186/1944-3277-10-17
http://hdl.handle.net/10033/581811
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5818082019-08-30T11:31:23Zcom_10033_338554col_10033_621787
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.
Hahnke, Richard L
Stackebrandt, Erko
Meier-Kolthoff, Jan P
Tindall, Brian J
Huang, Sixing
Rohde, Manfred
Lapidus, Alla
Han, James
Trong, Stephan
Haynes, Matthew
Reddy, T B K
Huntemann, Marcel
Pati, Amrita
Ivanova, Natalia N
Mavromatis, Konstantinos
Markowitz, Victor
Woyke, Tanja
Göker, Markus
Kyrpides, Nikos C
Klenk, Hans-Peter
Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
2015-11-05T12:10:32Z
2015-11-05T12:10:32Z
2015
Article
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. 2015, 10:46 Stand Genomic Sci
1944-3277
26380634
10.1186/s40793-015-0032-y
http://hdl.handle.net/10033/581808
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5839622019-08-30T11:27:46Zcom_10033_338554col_10033_621787
High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.
Choi, Dong Han
Ahn, Chisang
Jang, Gwang Il
Lapidus, Alla
Han, James
Reddy, T B K
Huntemann, Marcel
Pati, Amrita
Ivanova, Natalia
Markowitz, Victor
Rohde, Manfred
Tindall, Brian
Göker, Markus
Woyke, Tanja
Klenk, Hans-Peter
Kyrpides, Nikos C
Cho, Byung Cheol
Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535(T), was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535(T) was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535(T) did not form spore.
2015-12-15T15:36:09Z
2015-12-15T15:36:09Z
2015
Article
High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. 2015, 10:98 Stand Genomic Sci
1944-3277
26566423
10.1186/s40793-015-0088-8
http://hdl.handle.net/10033/583962
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5839632019-08-30T11:37:00Zcom_10033_338554col_10033_621787
Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.
Beyersmann, Paul G
Chertkov, Olga
Petersen, Jörn
Fiebig, Anne
Chen, Amy
Pati, Amrita
Ivanova, Natalia
Lapidus, Alla
Goodwin, Lynne A
Chain, Patrick
Detter, John C
Rohde, Manfred
Gronow, Sabine
Kyrpides, Nikos C
Woyke, Tanja
Simon, Meinhard
Göker, Markus
Klenk, Hans-Peter
Brinkhoff, Thorsten
In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564(T) was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
2015-12-15T15:39:39Z
2015-12-15T15:39:39Z
2013-07-30
Article
Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. 2013, 8 (3):403-19 Stand Genomic Sci
1944-3277
24501626
10.4056/sigs.3927623
http://hdl.handle.net/10033/583963
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5933282019-08-30T11:36:32Zcom_10033_338554col_10033_621787
Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions.
Poblete-Castro, Ignacio
Binger, Danielle
Oehlert, Rene
Rohde, Manfred
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Achieving a sustainable society requires, among other things, the use of renewable feedstocks to replace chemicals obtained from petroleum-derived compounds. Crude glycerol synthesized inexpensively as a byproduct of biodiesel production is currently considered a waste product, which can potentially be converted into value-added compounds by bacterial fermentation. This study aimed at evaluating several characterized P. putida strains to produce medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA) using raw glycerol as the only carbon/energy source.
2016-01-12T15:11:25Z
2016-01-12T15:11:25Z
2014
Article
Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions. 2014, 14:962 BMC Biotechnol.
1472-6750
25532606
10.1186/s12896-014-0110-z
http://hdl.handle.net/10033/593328
BMC biotechnology
en
oai:repository.helmholtz-hzi.de:10033/5935212019-08-30T11:31:19Zcom_10033_338554col_10033_621787
High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass
Laviad, Sivan
Lapidus, Alla
Han, James
Haynes, Matthew
Reddy, TBK
Huntemann, Marcel
Pati, Amrita
Ivanova, Natalia N
Mavromatis, Konstantinos
Lang, Elke
Rohde, Manfred
Markowitz, Victor
Woyke, Tanja
Klenk, Hans-Peter
Kyrpides, Nikos C
Halpern, Malka
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
2016-01-15T12:53:04Z
2016-01-15T12:53:04Z
2015-05-27
Article
High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass 2015, 10 (1) Standards in Genomic Sciences
1944-3277
26203340
10.1186/s40793-015-0010-4
http://hdl.handle.net/10033/593521
Standards in Genomic Sciences
http://www.standardsingenomics.com/content/10/1/29
oai:repository.helmholtz-hzi.de:10033/5944192019-08-30T11:36:33Zcom_10033_338554col_10033_621787
The signaling pathway of Campylobacter jejuni-induced Cdc42 activation: Role of fibronectin, integrin beta1, tyrosine kinases and guanine exchange factor Vav2.
Krause-Gruszczynska, Malgorzata
Boehm, Manja
Rohde, Manfred
Tegtmeyer, Nicole
Takahashi, Seiichiro
Buday, Laszlo
Oyarzabal, Omar A
Backert, Steffen
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Host cell invasion by the foodborne pathogen Campylobacter jejuni is considered as one of the primary reasons of gut tissue damage, however, mechanisms and key factors involved in this process are widely unclear. It was reported that small Rho GTPases, including Cdc42, are activated and play a role during invasion, but the involved signaling cascades remained unknown. Here we utilised knockout cell lines derived from fibronectin-/-, integrin-beta1-/-, focal adhesion kinase (FAK)-/- and Src/Yes/Fyn-/- deficient mice, and wild-type control cells, to investigate C. jejuni-induced mechanisms leading to Cdc42 activation and bacterial uptake.
2016-01-20T15:11:29Z
2016-01-20T15:11:29Z
2011
Article
The signaling pathway of Campylobacter jejuni-induced Cdc42 activation: Role of fibronectin, integrin beta1, tyrosine kinases and guanine exchange factor Vav2. 2011, 9:32 Cell Commun. Signal
1478-811X
22204307
10.1186/1478-811X-9-32
http://hdl.handle.net/10033/594419
Cell communication and signaling : CCS
en
oai:repository.helmholtz-hzi.de:10033/5955512019-08-30T11:36:33Zcom_10033_338554col_10033_621787
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
Meier-Kolthoff, Jan P
Hahnke, Richard L
Petersen, Jörn
Scheuner, Carmen
Michael, Victoria
Fiebig, Anne
Rohde, Christine
Rohde, Manfred
Fartmann, Berthold
Goodwin, Lynne A
Chertkov, Olga
Reddy, Tbk
Pati, Amrita
Ivanova, Natalia N
Markowitz, Victor
Kyrpides, Nikos C
Woyke, Tanja
Göker, Markus
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
2016-02-04T10:30:29Z
2016-02-04T10:30:29Z
2014
Article
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. 2014, 9:2 Stand Genomic Sci
1944-3277
25780495
10.1186/1944-3277-9-2
http://hdl.handle.net/10033/595551
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5955712019-08-30T11:37:00Zcom_10033_338554col_10033_621787
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.
Scheuner, Carmen
Tindall, Brian J
Lu, Megan
Nolan, Matt
Lapidus, Alla
Cheng, Jan-Fang
Goodwin, Lynne
Pitluck, Sam
Huntemann, Marcel
Liolios, Konstantinos
Pagani, Ioanna
Mavromatis, Konstantinos
Ivanova, Natalia
Pati, Amrita
Chen, Amy
Palaniappan, Krishna
Jeffries, Cynthia D
Hauser, Loren
Land, Miriam
Mwirichia, Romano
Rohde, Manfred
Abt, Birte
Detter, John C
Woyke, Tanja
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Göker, Markus
Kyrpides, Nikos C
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
2016-02-04T11:38:14Z
2016-02-04T11:38:14Z
2014
Article
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. 2014, 9:10 Stand Genomic Sci
1944-3277
25780503
10.1186/1944-3277-9-10
http://hdl.handle.net/10033/595571
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/5963752019-08-30T11:36:05Zcom_10033_338554col_10033_338544
How distinct Arp2/3 complex variants regulate actin filament assembly.
Rottner, Klemens
Stradal, Theresia E B
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
The heptameric Arp2/3 complex generates branched actin filament networks that drive lamellipodium protrusion, vesicle trafficking and pathogen motility. Distinct variants of the Arp2/3 complex are now shown to have different roles in tuning actin assembly and disassembly, in concert with the prominent actin regulators cortactin and coronin.
2016-02-16T15:53:36Z
2016-02-16T15:53:36Z
2015-12-23
Article
How distinct Arp2/3 complex variants regulate actin filament assembly. 2015, 18 (1):1-3 Nat. Cell Biol.
1476-4679
26693915
10.1038/ncb3293
http://hdl.handle.net/10033/596375
Nature cell biology
en
oai:repository.helmholtz-hzi.de:10033/5969772019-08-30T11:36:59Zcom_10033_338554col_10033_621787
Nocardiopsis mwathae sp. nov., isolated from the haloalkaline Lake Elmenteita in the African Rift Valley.
Akhwale, Juliah Khayeli
Göker, Markus
Rohde, Manfred
Schumann, Peter
Boga, Hamadi Iddi
Klenk, Hans-Peter
German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
During a screening for novel and biotechnologically useful bacteria in haloalkaline lakes, strain No.156(T) was isolated from a sediment sample from lake Elmenteita in the African Rift Valley and studied by a polyphasic taxonomic approach. The strain was observed to form yellow aerial and substrate mycelia; optimal growth was found to be at 30-35 °C in salt concentrations of 6-9 % (w/v) and at pH 7-9. The DNA G+C content of the novel strain was 71 mol%. Analysis of 16S rRNA sequences indicated that the isolate belongs to the genus Nocardiopsis with sequence similarities below 98 % to the type strains of all other representatives of the genus. Mycolic acids were not detected in whole cell methanolysates. The peptidoglycan was found to contain meso-diaminopimelic acid as the diamino acid with no diagnostic sugars. The main polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol but no diphosphatidylglycerol. The predominant menaquinones were MK-11(H8), MK-11(H6), MK-10(H8) and MK-10(H6). Cellular fatty acids were found to consist of saturated and monounsaturated iso- and anteiso-branched acids with 16-18 C-length, tuberculostearic acid (Me18:0), and straight-chain saturated (16:0, 18:0) acids. These characteristics match those of the genus Nocardiopsis. Based on 16S rRNA gene sequence analysis and phenotypic characteristics, a novel species with the name Nocardiopsis mwathae is proposed. The type strain is No.156(T) (=DSM 46659(T) = CECT 8552(T)). The INSDC accession number for the 16S rRNA gene sequence of strain No.156(T) is KF976731.
2016-02-23T12:51:50Z
2016-02-23T12:51:50Z
2016-01-18
Article
Nocardiopsis mwathae sp. nov., isolated from the haloalkaline Lake Elmenteita in the African Rift Valley. 2016: Antonie Van Leeuwenhoek
1572-9699
26781972
10.1007/s10482-016-0647-z
http://hdl.handle.net/10033/596977
Antonie van Leeuwenhoek
oai:repository.helmholtz-hzi.de:10033/5970862019-08-30T11:31:49Zcom_10033_338554col_10033_621787
Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).
Clum, Alicia
Tindall, Brian J
Sikorski, Johannes
Ivanova, Natalia
Mavrommatis, Konstantinos
Lucas, Susan
Glavina, Tijana
Del Rio
Nolan, Matt
Chen, Feng
Tice, Hope
Pitluck, Sam
Cheng, Jan-Fang
Chertkov, Olga
Brettin, Thomas
Han, Cliff
Detter, John C
Kuske, Cheryl
Bruce, David
Goodwin, Lynne
Ovchinikova, Galina
Pati, Amrita
Mikhailova, Natalia
Chen, Amy
Palaniappan, Krishna
Land, Miriam
Hauser, Loren
Chang, Yun-Juan
Jeffries, Cynthia D
Chain, Patrick
Rohde, Manfred
Göker, Markus
Bristow, Jim
Eisen, Jonathan A
Markowitz, Victor
Hugenholtz, Philip
Kyrpides, Nikos C
Klenk, Hans-Peter
Lapidus, Alla
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
2016-02-24T13:20:06Z
2016-02-24T13:20:06Z
2009
Article
Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). 2009, 1 (3):308-16 Stand Genomic Sci
1944-3277
21304671
10.4056/sigs.51657
http://hdl.handle.net/10033/597086
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/6009352019-08-30T11:32:16Zcom_10033_338554col_10033_621787
The Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus.
Borrero-de Acuña, José Manuel
Rohde, Manfred
Wissing, Josef
Jänsch, Lothar
Schobert, Max
Molinari, Gabriella
Timmis, Kenneth N
Jahn, Martina
Jahn, Dieter
Helmholtz Centre for infection research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.
Oxidative phosphorylation using multiple component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacterium Pseudomonas aeruginosa. During denitrification, nitrate (Nar), nitrite (Nir), nitric-oxide (Nor) and nitrous-oxide (Nos) reductases catalyze the reaction cascade of NO(3-) → NO(2-) → NO → N2O → N2. Genetic experiments suggested that the nitric-oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy co-localization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous-oxide reductase, NosZ, is linked via NosR. The nitrate transporter, NarK2, the nitrate regulatory system, NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins, NosFL, were also found to be attached. A number of proteins associated with energy generation, including electron donating dehydrogenases, the complete ATP synthase, almost all enzymes of the TCA cycle, and the SEC system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane and periplasmic proteins, to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment.
2016-03-08T14:41:35Z
2016-03-08T14:41:35Z
2016-02-22
Article
The Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus. 2016: J. Bacteriol.
1098-5530
26903416
10.1128/JB.00055-16
http://hdl.handle.net/10033/600935
Journal of bacteriology
oai:repository.helmholtz-hzi.de:10033/6043712019-08-30T11:33:05Zcom_10033_338554col_10033_621787
The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales.
Golyshina, Olga V
Lünsdorf, Heinrich
Kublanov, Ilya V
Goldenstein, Nadine I
Hinrichs, Kai-Uwe
Golyshin, Peter N
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Two novel cell-wall-less, acidophilic, mesophilic, organotrophic and facultatively anaerobic archaeal strains were isolated from acidic streamers formed on the surfaces of copper-ore-containing sulfidic deposits in south-west Spain and North Wales, UK. Cells of the strains varied from 0.1 to 2 μm in size and were pleomorphic, with a tendency to form filamentous structures. The optimal pH and temperature for growth for both strains were 1.0-1.2 and 37-40 °C, with the optimal substrates for growth being beef extract (3 g l- 1) for strain S5T and beef extract with tryptone (3 and 1 g l- 1, respectively) for strain PM4. The lipid composition was dominated by intact polar lipids consisting of a glycerol dibiphytanyl glycerol tetraether (GDGT) core attached to predominantly glycosidic polar headgroups. In addition, free GDGT and small relative amounts of intact and core diether lipids were present. Strains S5T and PM4 possessed mainly menaquinones with minor fractions of thermoplasmaquinones. The DNA G+C content was 37.3 mol% in strain S5T and 37.16 mol% for strain PM4. A similarity matrix of 16S rRNA gene sequences (identical for both strains) showed their affiliation to the order Thermoplasmatales, with 73.9-86.3 % identity with sequences from members of the order with validly published names. The average nucleotide identity between genomes of the strains determined in silico was 98.75 %, suggesting, together with the 16S rRNA gene-based phylogenetic analysis, that the strains belong to the same species. A novel family, Cuniculiplasmataceae fam. nov., genus Cuniculiplasma gen. nov. and species Cuniculiplasma divulgatum sp. nov. are proposed based on the phylogenetic, chemotaxonomic analyses and physiological properties of the two isolates, S5T and PM4 ( = JCM 30641 = VKM B-2940). The type strain of Cuniculiplasma divulgatum is S5T ( = JCM 30642T = VKM B-2941T).
2016-04-04T14:00:23Z
2016-04-04T14:00:23Z
2016-01
Article
The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales. 2016, 66 (1):332-40 Int. J. Syst. Evol. Microbiol.
1466-5034
26518885
10.1099/ijsem.0.000725
http://hdl.handle.net/10033/604371
International journal of systematic and evolutionary microbiology
en
info:eu-repo/grantAgreement/EC/FP7/287589
embargoedAccess
oai:repository.helmholtz-hzi.de:10033/6065552019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae.
Foesel, Bärbel U
Mayer, Susanne
Luckner, Manja
Wanner, Gerhard
Rohde, Manfred
Overmann, Jörg
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Three Gram-negative, non-spore-forming, encapsulated bacteria were isolated from a Namibian river-bank soil (strains 277T and 307) and a semiarid savannah soil (strain A2-1cT). 16S rRNA gene sequence analyses placed them within subdivision 1 of the Acidobacteria and revealed 100 % similarity between strains 277T and 307 and 98.2 % similarity between A2-1cT and the former two strains. The closest relatives with validly published names were Telmatobacter bradus, Acidicapsa borealis and Acidicapsa ligni (94.7-95.9 % similarity to the type strains). Cells of all three strains were rod-shaped and motile and divided by binary fission. Ultrastructural analyses revealed a thick cell envelope, resulting mainly from a thick periplasmic space. Colonies of strains 277T and 307 were white to cream and light pink, respectively, while strain A2-1cT displayed a bright pink colour. All three strains were aerobic, chemoheterotrophic mesophiles with a broad temperature range for growth and a moderately acidic pH optimum. Sugars and complex proteinaceous substrates were the preferred carbon and energy sources. A few polysaccharides were degraded. The major quinone in all three strains was MK-8; MK-7 occurred in strain A2-1cT as a minor compound. Major fatty acids were iso-C15 : 0 and iso-C17 : 1ω7c. In addition, iso-C17 : 0 occurred in significant amounts. The DNA G+C contents of strains 277T, 307 and A2-1cT were 59.6, 59.9 and 58.5 mol%, respectively. Based on these characteristics, the three isolates are assigned to two novel species of the novel genus Occallatibacter gen. nov., Occallatibacter riparius sp. nov. [type strain 277T ( = DSM 25168T = LMG 26948T) and reference strain 307 ( = DSM 25169 = LMG 26947)] and Occallatibacter savannae sp. nov. [type strain A2-1cT ( = DSM 25170T = LMG 26946T)]. Together with several other recently described taxa, the novel isolates provide the basis for an emended description of the established family Acidobacteriaceae.
2016-04-22T08:04:23Z
2016-04-22T08:04:23Z
2016-01
Article
Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae. 2016, 66 (1):219-29 Int. J. Syst. Evol. Microbiol.
1466-5034
26486590
10.1099/ijsem.0.000700
http://hdl.handle.net/10033/606555
International journal of systematic and evolutionary microbiology
en
oai:repository.helmholtz-hzi.de:10033/6077392019-08-30T11:26:13Zcom_10033_338554col_10033_338544
Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments.
Thiam, Hawa-Racine
Vargas, Pablo
Carpi, Nicolas
Crespo, Carolina Lage
Raab, Matthew
Terriac, Emmanuel
King, Megan C
Jacobelli, Jordan
Alberts, Arthur S
Stradal, Theresia
Lennon-Dumenil, Ana-Maria
Piel, Matthieu
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Cell migration has two opposite faces: although necessary for physiological processes such as immune responses, it can also have detrimental effects by enabling metastatic cells to invade new organs. In vivo, migration occurs in complex environments and often requires a high cellular deformability, a property limited by the cell nucleus. Here we show that dendritic cells, the sentinels of the immune system, possess a mechanism to pass through micrometric constrictions. This mechanism is based on a rapid Arp2/3-dependent actin nucleation around the nucleus that disrupts the nuclear lamina, the main structure limiting nuclear deformability. The cells' requirement for Arp2/3 to pass through constrictions can be relieved when nuclear stiffness is decreased by suppressing lamin A/C expression. We propose a new role for Arp2/3 in three-dimensional cell migration, allowing fast-moving cells such as leukocytes to rapidly and efficiently migrate through narrow gaps, a process probably important for their function.
2016-05-03T13:57:47Z
2016-05-03T13:57:47Z
2016
Article
Perinuclear Arp2/3-driven actin polymerization enables nuclear deformation to facilitate cell migration through complex environments. 2016, 7:10997 Nat Commun
2041-1723
26975831
10.1038/ncomms10997
http://hdl.handle.net/10033/607739
Nature communications
en
oai:repository.helmholtz-hzi.de:10033/6087872019-08-30T11:31:22Zcom_10033_338554col_10033_621787
Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families
Overmann, Jörg
Foesel, Bärbel U.
Geppert, Alicia
Rohde, Manfred
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
2016-05-10T11:55:33Z
2016-05-10T11:55:33Z
2016-02-01
Article
Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families 2016, 66 (2):652 International Journal of Systematic and Evolutionary Microbiology
1466-5026
1466-5034
10.1099/ijsem.0.000770
http://hdl.handle.net/10033/608787
International Journal of Systematic and Evolutionary Microbiology
http://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000770
oai:repository.helmholtz-hzi.de:10033/6122992019-08-30T11:29:47Zcom_10033_338554col_10033_621787
Planctomycetes do possess a peptidoglycan cell wall.
Jeske, Olga
Schüler, Margarete
Schumann, Peter
Schneider, Alexander
Boedeker, Christian
Jogler, Mareike
Bollschweiler, Daniel
Rohde, Manfred
Mayer, Christoph
Engelhardt, Harald
Spring, Stefan
Jogler, Christian
Helmholtzzentrum für Infektionsforschung 38124 Braunschweig
Most bacteria contain a peptidoglycan (PG) cell wall, which is critical for maintenance of shape and important for cell division. In contrast, Planctomycetes have been proposed to produce a proteinaceous cell wall devoid of PG. The apparent absence of PG has been used as an argument for the putative planctomycetal ancestry of all bacterial lineages. Here we show, employing multiple bioinformatic methods, that planctomycetal genomes encode proteins required for PG synthesis. Furthermore, we biochemically demonstrate the presence of the sugar and the peptide components of PG in Planctomycetes. In addition, light and electron microscopic experiments reveal planctomycetal PG sacculi that are susceptible to lysozyme treatment. Finally, cryo-electron tomography demonstrates that Planctomycetes possess a typical PG cell wall and that their cellular architecture is thus more similar to that of other Gram-negative bacteria. Our findings shed new light on the cellular architecture and cell division of the maverick Planctomycetes.
2016-06-09T10:40:58Z
2016-06-09T10:40:58Z
2015
Article
Planctomycetes do possess a peptidoglycan cell wall. 2015, 6:7116 Nat Commun
2041-1723
25964217
10.1038/ncomms8116
http://hdl.handle.net/10033/612299
Nature communications
en
oai:repository.helmholtz-hzi.de:10033/6156582019-08-30T11:31:23Zcom_10033_338554col_10033_621787
Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.
Ben Hania, Wajdi
Joseph, Manon
Schumann, Peter
Bunk, Boyke
Fiebig, Anne
Spröer, Cathrin
Klenk, Hans-Peter
Fardeau, Marie-Laure
Spring, Stefan
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2(T) had a size of 0.2 - 0.25 × 8-9 μm, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.
2016-07-06T14:10:50Z
2016-07-06T14:10:50Z
2015
Article
Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. 2015, 10:7 Stand Genomic Sci
1944-3277
26203324
10.1186/1944-3277-10-7
http://hdl.handle.net/10033/615658
Standards in genomic sciences
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6156642019-08-30T11:30:32Zcom_10033_338554col_10033_621787
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.
Dogs, Marco
Teshima, Hazuki
Petersen, Jörn
Fiebig, Anne
Chertkov, Olga
Dalingault, Hajnalka
Chen, Amy
Pati, Amrita
Goodwin, Lynne A
Chain, Patrick
Detter, John C
Ivanova, Natalia
Lapidus, Alla
Rohde, M
Gronow, Sabine
Kyrpides, Nikos C
Woyke, Tanja
Simon, Meinhard
Göker, Markus
Klenk, Hans-Peter
Brinkhoff, Thorsten
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
2016-07-07T08:58:50Z
2016-07-07T08:58:50Z
2013-10-16
Article
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. 2013, 9 (1):142-59 Stand Genomic Sci
1944-3277
24501652
10.4056/sigs.4287962
http://hdl.handle.net/10033/615664
Standards in genomic sciences
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6172652021-08-04T14:14:02Zcom_10033_338554col_10033_620574
Loss of cortactin causes endothelial barrier dysfunction via disturbed adrenomedullin secretion and actomyosin contractility.
García Ponce, Alexander
Citalán Madrid, Alí F
Vargas Robles, Hilda
Chánez Paredes, Sandra
Nava, Porfirio
Betanzos, Abigail
Zarbock, Alexander
Rottner, Klemens
Vestweber, Dietmar
Schnoor, Michael
Department for Molecular Biomedicine, Center of Research and Advanced Studies (CINVESTAV-IPN), 07360 Mexico-City, Mexico.
Changes in vascular permeability occur during inflammation and the actin cytoskeleton plays a crucial role in regulating endothelial cell contacts and permeability. We demonstrated recently that the actin-binding protein cortactin regulates vascular permeability via Rap1. However, it is unknown if the actin cytoskeleton contributes to increased vascular permeability without cortactin. As we consistently observed more actin fibres in cortactin-depleted endothelial cells, we hypothesised that cortactin depletion results in increased stress fibre contractility and endothelial barrier destabilisation. Analysing the contractile machinery, we found increased ROCK1 protein levels in cortactin-depleted endothelium. Concomitantly, myosin light chain phosphorylation was increased while cofilin, mDia and ERM were unaffected. Secretion of the barrier-stabilising hormone adrenomedullin, which activates Rap1 and counteracts actomyosin contractility, was reduced in plasma from cortactin-deficient mice and in supernatants of cortactin-depleted endothelium. Importantly, adrenomedullin administration and ROCK1 inhibition reduced actomyosin contractility and rescued the effect on permeability provoked by cortactin deficiency in vitro and in vivo. Our data suggest a new role for cortactin in controlling actomyosin contractility with consequences for endothelial barrier integrity.
2016-07-20T14:29:29Z
2016-07-20T14:29:29Z
2016
Article
Loss of cortactin causes endothelial barrier dysfunction via disturbed adrenomedullin secretion and actomyosin contractility. 2016, 6:29003 Sci Rep
2045-2322
27357373
10.1038/srep29003
http://hdl.handle.net/10033/617265
Scientific reports
en
oai:repository.helmholtz-hzi.de:10033/6176512019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).
Kappler, Ulrike
Davenport, Karen
Beatson, Scott
Lapidus, Alla
Pan, Chongle
Han, Cliff
Montero-Calasanz, Maria Del Carmen
Land, Miriam
Hauser, Loren
Rohde, Manfred
Göker, Markus
Ivanova, Natalia
Woyke, Tanja
Klenk, Hans-Peter
Kyrpides, Nikos C
Helmholtzzentrum für Infektionsforschung, 38124 Braunschweig
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
2016-07-28T12:01:06Z
2016-07-28T12:01:06Z
2016
Article
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). 2016, 11:38 Stand Genomic Sci
1944-3277
27274784
10.1186/s40793-016-0162-x
http://hdl.handle.net/10033/617651
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/6179382019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.
Panschin, Irina
Huang, Sixing
Meier-Kolthoff, Jan P
Tindall, Brian J
Rohde, Manfred
Verbarg, Susanne
Lapidus, Alla
Han, James
Trong, Stephan
Haynes, Matthew
Reddy, T B K
Huntemann, Marcel
Pati, Amrita
Ivanova, Natalia N
Mavromatis, Konstantinos
Markowitz, Victor
Woyke, Tanja
Göker, Markus
Klenk, Hans-Peter
Kyrpides, Nikos C
Hahnke, Richard L
helmholtzzentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig
Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.
2016-08-04T11:43:26Z
2016-08-04T11:43:26Z
2016
Article
Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. 2016, 11:37 Stand Genomic Sci
1944-3277
27274783
10.1186/s40793-016-0163-9
http://hdl.handle.net/10033/617938
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/6184732019-08-30T11:29:17Zcom_10033_338554col_10033_621787
High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).
Tashkandy, Nisreen
Sabban, Sari
Fakieh, Mohammad
Meier-Kolthoff, Jan P
Huang, Sixing
Tindall, Brian J
Rohde, Manfred
Baeshen, Mohammed N
Baeshen, Nabih A
Lapidus, Alla
Copeland, Alex
Pillay, Manoj
Reddy, T B K
Huntemann, Marcel
Pati, Amrita
Ivanova, Natalia
Markowitz, Victor
Woyke, Tanja
Göker, Markus
Klenk, Hans-Peter
Kyrpides, Nikos C
Hahnke, Richard L
Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.
2016-08-17T10:05:31Z
2016-08-17T10:05:31Z
2016
Article
High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T). 2016, 11:42 Stand Genomic Sci
1944-3277
27313837
10.1186/s40793-016-0159-5
http://hdl.handle.net/10033/618473
Standards in genomic sciences
en
oai:repository.helmholtz-hzi.de:10033/6191572019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Streptococcus pyogenes adhesion and colonization.
Brouwer, Stephan
Barnett, Timothy C
Rivera-Hernandez, Tania
Rohde, M
Walker, Mark J
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
Streptococcus pyogenes (group A Streptococcus, GAS) is a human-adapted pathogen responsible for a wide spectrum of disease. GAS can cause relatively mild illnesses, such as strep throat or impetigo, and less frequent but severe life-threatening diseases such as necrotizing fasciitis and streptococcal toxic shock syndrome. GAS is an important public health problem causing significant morbidity and mortality worldwide. The main route of GAS transmission between humans is through close or direct physical contact, and particularly via respiratory droplets. The upper respiratory tract and skin are major reservoirs for GAS infections. The ability of GAS to establish an infection in the new host at these anatomical sites primarily results from two distinct physiological processes, namely bacterial adhesion and colonization. These fundamental aspects of pathogenesis rely upon a variety of GAS virulence factors, which are usually under strict transcriptional regulation. Considerable progress has been made in better understanding these initial infection steps. This review summarizes our current knowledge of the molecular mechanisms of GAS adhesion and colonization.
2016-08-31T14:31:25Z
2016-08-31T14:31:25Z
2016-06-17
Article
Streptococcus pyogenes adhesion and colonization. 2016: FEBS Lett.
1873-3468
27312939
10.1002/1873-3468.12254
http://hdl.handle.net/10033/619157
FEBS letters
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6198382019-08-30T11:29:17Zcom_10033_338554col_10033_621787
A novel protein quality control mechanism contributes to heat shock resistance of worldwide-distributed Pseudomonas aeruginosa clone C strains.
Lee, Changhan
Wigren, Edvard
Trček, Janja
Peters, Verena
Kim, Jihong
Hasni, Muhammad Sharif
Nimtz, Manfred
Lindqvist, Ylva
Park, Chankyu
Curth, Ute
Lünsdorf, Heinrich
Römling, Ute
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
Pseudomonas aeruginosa is a highly successful nosocomial pathogen capable of causing a wide variety of infections with clone C strains most prevalent worldwide. In this study, we initially characterize a molecular mechanism of survival unique to clone C strains. We identified a P. aeruginosa clone C-specific genomic island (PACGI-1) that contains the highly expressed small heat shock protein sHsp20c, the founding member of a novel subclass of class B bacterial small heat shock proteins. sHsp20c and adjacent gene products are involved in resistance against heat shock. Heat stable sHsp20c is unconventionally expressed in stationary phase in a wide temperature range from 20 to 42°C. Purified sHsp20c has characteristic features of small heat shock protein class B as it is monodisperse, forms sphere-like 24-meric oligomers and exhibits significant chaperone activity. As the P. aeruginosa clone C population is significantly more heat shock resistant than genetically unrelated P. aeruginosa strains without sHsp20c, the horizontally acquired shsp20c operon might contribute to the survival of worldwide-distributed clone C strains.
2016-09-05T11:50:09Z
2016-09-05T11:50:09Z
2015-11
Article
A novel protein quality control mechanism contributes to heat shock resistance of worldwide-distributed Pseudomonas aeruginosa clone C strains. 2015, 17 (11):4511-26 Environ. Microbiol.
1462-2920
26014207
10.1111/1462-2920.12915
http://hdl.handle.net/10033/619838
Environmental microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6198552019-08-30T11:33:29Zcom_10033_338554col_10033_621787
Protein homeostasis-more than resisting a hot bath.
Lee, Changhan
Wigren, Edvard
Lünsdorf, Heinrich
Römling, Ute
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
Maintenance of protein homeostasis is essential for survival of all organisms. In bacteria, the protein quality control system has a broad physiological impact beyond heat shock resistance, being involved in virulence, antibiotic resistance, as well as protection against environmental stresses. Its contribution to rejuvenation and growth arrest suggests interference with protein quality control to be a novel antimicrobial strategy. Remarkably, a protein quality control module originating from environmental strains has been found to be horizontally transferred to predominant clonal groups of bacteria providing exquisite thermotolerance to recently emerged global pathogens suggesting that novel features related to protein homeostasis contribute to the transition to new environments.
2016-09-05T11:55:06Z
2016-09-05T11:55:06Z
2016-04
Article
Protein homeostasis-more than resisting a hot bath. 2016, 30:147-54 Curr. Opin. Microbiol.
1879-0364
26974352
10.1016/j.mib.2016.02.006
http://hdl.handle.net/10033/619855
Current opinion in microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6200292019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Characterization of Five Zoonotic Streptococcus suis Strains from Germany, Including One Isolate from a Recent Fatal Case of Streptococcal Toxic Shock-Like Syndrome in a Hunter.
Eisenberg, Tobias
Hudemann, Christoph
Hossain, Hamid M
Hewer, Angela
Tello, Khodr
Bandorski, Dirk
Rohde, M
Valentin-Weigand, Peter
Baums, Christoph Georg
Infectious Diseases, College of Veterinary Medicine, University Leipzig, Leipzig.
A Streptococcus suis isolate from a German hunter with streptococcal toxic shock-like syndrome (STSLS) and four additional zoonotic isolates were genotyped as mrp(+) epf* (variant 1890) sly(+) cps2(+). All five zoonotic German strains were characterized by high multiplication in human blood samples ex vivo, but induction of only low levels of proinflammatory cytokines compared to a Chinese STSLS strain.
2016-09-09T10:36:34Z
2016-09-09T10:36:34Z
2015-12
Article
Characterization of Five Zoonotic Streptococcus suis Strains from Germany, Including One Isolate from a Recent Fatal Case of Streptococcal Toxic Shock-Like Syndrome in a Hunter. 2015, 53 (12):3912-5 J. Clin. Microbiol.
1098-660X
26424844
10.1128/JCM.02578-15
http://hdl.handle.net/10033/620029
Journal of clinical microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6205172019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae.
Kuipers, Kirsten
Gallay, Clement
Martínek, Václav
Rohde, M
Martínková, Markéta
van der Beek, Samantha L
Jong, Wouter S P
Venselaar, Hanka
Zomer, Aldert
Bootsma, Hester
Veening, Jan-Willem
de Jonge, Marien I
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig.
Proteins belonging to the DHH family, a member of the phosphoesterase superfamily, are produced by most bacterial species. While some of these proteins are well studied in Bacillus subtilis and Escherichia coli, their functions in Streptococcus pneumoniae remain unclear. Recently, the highly conserved DHH subfamily 1 protein PapP (SP1298) has been reported to play an important role in virulence. Here, we provide a plausible explanation for the attenuated virulence of the papP mutant. Recombinant PapP specifically hydrolyzed nucleotides 3'-phosphoadenosine-5'-phosphate (pAp) and 5'-phosphoadenylyl-(3'->5')-adenosine (pApA). Deletion of papP, potentially leading to pAp/pApA accumulation, resulted in morphological defects and mis-localization of several cell division proteins. Incubation with both polar solvent and detergent led to robust killing of the papP mutant, indicating that membrane integrity is strongly affected. This is in line with previous studies showing that pAp inhibits the ACP synthase, an essential enzyme involved in lipid precursor production. Remarkably, partial inactivation of the lipid biosynthesis pathway, by inhibition of FabF or depletion of FabH, phenocopied the papP mutant. We conclude that pAp and pApA phosphatase activity of PapP is required for maintenance of membrane lipid homeostasis providing an explanation how inactivation of this protein may attenuate pneumococcal virulence.
2016-09-19T10:42:13Z
2016-09-19T10:42:13Z
2016-07
Article
Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. 2016, 101 (1):12-26 Mol. Microbiol.
1365-2958
26691161
10.1111/mmi.13312
http://hdl.handle.net/10033/620517
Molecular microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6205582019-08-30T11:27:16Zcom_10033_620533com_10033_620652com_10033_338554col_10033_621787col_10033_620534col_10033_620675
Coprinuslactone protects the edible mushroom Coprinus comatus against biofilm infections by blocking both quorum-sensing and MurA.
de Carvalho, Maira P
Gulotta, Giuseppe
do Amaral, Matheus W
Lünsdorf, Heinrich
Sasse, Florenz
Abraham, Wolf-Rainer
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Pathogens embedded in biofilms are involved in many infections and are very difficult to treat with antibiotics because of higher resistance compared to planktonic cells. Therefore, new approaches for their control are urgently needed. One way to search for biofilm dispersing compounds is to look at defense strategies of organisms exposed to wet environments, which makes them prone to biofilm infections. It is reasonable to assume that mushrooms have developed mechanisms to control biofilms on their sporocarps (fruiting bodies). A preliminary screening for biofilms on sporocarps revealed several species with few or no bacteria on their sporocarps. From the edible mushroom Coprinus comatus where no bacteria on the sporocarp could be detected (3R,4S)-2-methylene-3,4-dihydroxypentanoic acid 1,4-lactone, named coprinuslactone, was isolated. Coprinuslactone interfered with quorum-sensing and dispersed biofilms of Pseudomonas aeruginosa, where it also reduced the formation of the pathogenicity factors pyocyanin and rhamnolipid B. Coprinuslactone also damaged Staphylococcus aureus cells in biofilms at subtoxic concentrations. Furthermore, it inhibited UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), essential for bacterial cell wall synthesis. These two modes of action ensure the inhibition of a broad spectrum of pathogens on the fruiting body but may also be useful for future clinical applications. This article is protected by copyright. All rights reserved.
2016-10-20T07:47:09Z
2016-10-20T07:47:09Z
2016-10-03
Article
Coprinuslactone protects the edible mushroom Coprinus comatus against biofilm infections by blocking both quorum-sensing and MurA. 2016 Environ. Microbiol.
1462-2920
27696655
10.1111/1462-2920.13560
http://hdl.handle.net/10033/620558
Environmental microbiology
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6205872019-08-30T11:26:13Zcom_10033_338554col_10033_621787
Lysozyme and bilirubin bind to ACE and regulate its conformation and shedding.
Danilov, Sergei M
Lünsdorf, Heinrich
Akinbi, Henry T
Nesterovitch, Andrew B
Epshtein, Yuliya
Letsiou, Eleftheria
Kryukova, Olga V
Piegeler, Tobias
Golukhova, Elena Z
Schwartz, David E
Dull, Randal O
Minshall, Richard D
Kost, Olga A
Garcia, Joe G N
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Angiotensin I-converting enzyme (ACE) hydrolyzes numerous peptides and is a critical participant in blood pressure regulation and vascular remodeling. Elevated tissue ACE levels are associated with increased risk for cardiovascular and respiratory disorders. Blood ACE concentrations are determined by proteolytic cleavage of ACE from the endothelial cell surface, a process that remains incompletely understood. In this study, we identified a novel ACE gene mutation (Arg532Trp substitution in the N domain of somatic ACE) that increases blood ACE activity 7-fold and interrogated the mechanism by which this mutation significantly increases blood ACE levels. We hypothesized that this ACE mutation disrupts the binding site for blood components which may stabilize ACE conformation and diminish ACE shedding. We identified the ACE-binding protein in the blood as lysozyme and also a Low Molecular Weight (LMW) ACE effector, bilirubin, which act in concert to regulate ACE conformation and thereby influence ACE shedding. These results provide mechanistic insight into the elevated blood level of ACE observed in patients on ACE inhibitor therapy and elevated blood lysozyme and ACE levels in sarcoidosis patients.
2016-11-18T10:20:16Z
2016-11-18T10:20:16Z
2016-10-13
Article
Lysozyme and bilirubin bind to ACE and regulate its conformation and shedding. 2016, 6:34913 Sci Rep
2045-2322
27734897
10.1038/srep34913
http://hdl.handle.net/10033/620587
Scientific reports
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6207282019-08-30T11:27:46Zcom_10033_338554col_10033_621787
Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments.
Golyshina, Olga V
Kublanov, Ilya V
Tran, Hai
Korzhenkov, Alexei A
Lünsdorf, Heinrich
Nechitaylo, Taras Y
Gavrilov, Sergey N
Toshchakov, Stepan V
Golyshin, Peter N
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions.
2017-01-18T15:23:34Z
2017-01-18T15:23:34Z
2016-12-14
Article
Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments. 2016, 6:39034 Sci Rep
2045-2322
27966672
10.1038/srep39034
http://hdl.handle.net/10033/620728
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6208892019-08-30T11:29:47Zcom_10033_338554col_10033_620574
Coordination by Cdc42 of Actin, Contractility, and Adhesion for Melanoblast Movement in Mouse Skin.
Woodham, Emma F
Paul, Nikki R
Tyrrell, Benjamin
Spence, Heather J
Swaminathan, Karthic
Scribner, Michelle R
Giampazolias, Evangelos
Hedley, Ann
Clark, William
Kage, Frieda
Marston, Daniel J
Hahn, Klaus M
Tait, Stephen W G
Larue, Lionel
Brakebusch, Cord H
Insall, Robert H
Machesky, Laura M
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The individual molecular pathways downstream of Cdc42, Rac, and Rho GTPases are well documented, but we know surprisingly little about how these pathways are coordinated when cells move in a complex environment in vivo. In the developing embryo, melanoblasts originating from the neural crest must traverse the dermis to reach the epidermis of the skin and hair follicles. We previously established that Rac1 signals via Scar/WAVE and Arp2/3 to effect pseudopod extension and migration of melanoblasts in skin. Here we show that RhoA is redundant in the melanocyte lineage but that Cdc42 coordinates multiple motility systems independent of Rac1. Similar to Rac1 knockouts, Cdc42 null mice displayed a severe loss of pigmentation, and melanoblasts showed cell-cycle progression, migration, and cytokinesis defects. However, unlike Rac1 knockouts, Cdc42 null melanoblasts were elongated and displayed large, bulky pseudopods with dynamic actin bursts. Despite assuming an elongated shape usually associated with fast mesenchymal motility, Cdc42 knockout melanoblasts migrated slowly and inefficiently in the epidermis, with nearly static pseudopods. Although much of the basic actin machinery was intact, Cdc42 null cells lacked the ability to polarize their Golgi and coordinate motility systems for efficient movement. Loss of Cdc42 de-coupled three main systems: actin assembly via the formin FMNL2 and Arp2/3, active myosin-II localization, and integrin-based adhesion dynamics.
2017-04-07T08:25:19Z
2017-04-07T08:25:19Z
2017-03-06
Article
Coordination by Cdc42 of Actin, Contractility, and Adhesion for Melanoblast Movement in Mouse Skin. 2017, 27 (5):624-637 Curr. Biol.
1879-0445
28238662
10.1016/j.cub.2017.01.033
http://hdl.handle.net/10033/620889
Current biology : CB
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6208932019-08-30T11:37:23Zcom_10033_338554col_10033_338544col_10033_620574
FMNL formins boost lamellipodial force generation.
Kage, Frieda
Winterhoff, Moritz
Dimchev, Vanessa
Mueller, Jan
Thalheim, Tobias
Freise, Anika
Brühmann, Stefan
Kollasser, Jana
Block, Jennifer
Dimchev, Georgi
Geyer, Matthias
Schnittler, Hans-Joachim
Brakebusch, Cord
Stradal, Theresia E B
Carlier, Marie-France
Sixt, Michael
Käs, Josef
Faix, Jan
Rottner, Klemens
Helmholtz Centre for infection research, Inhoffenstr.7, 38124 Braunschweig, Germany.
Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.
2017-04-07T14:44:37Z
2017-04-07T14:44:37Z
2017-03-22
Article
FMNL formins boost lamellipodial force generation. 2017, 8:14832 Nat Commun
2041-1723
28327544
10.1038/ncomms14832
http://hdl.handle.net/10033/620893
Nature communications
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6209312019-08-30T11:29:47Zcom_10033_338554col_10033_621787
High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.
Nouioui, Imen
Göker, Markus
Carro, Lorena
Montero-Calasanz, Maria Del Carmen
Rohde, M
Woyke, Tanja
Kyrpides, Nikos C
Klenk, Hans-Peter
Helmholtz Centre for infection research, Inhoffenstr. 7., 38124 Braunschweig, Germany.
Nakamurella lactea DLS-10(T), isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10(T) and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10(T) presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.
2017-05-31T14:19:13Z
2017-05-31T14:19:13Z
2017
Article
High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea. 2017, 12:4 Stand Genomic Sci
28074122
10.1186/s40793-016-0216-0
http://hdl.handle.net/10033/620931
Standards in genomic sciences
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6209352019-08-30T11:27:16Zcom_10033_338554col_10033_621050
The murine cytomegalovirus M35 protein antagonizes type I IFN induction downstream of pattern recognition receptors by targeting NF-κB mediated transcription.
Chan, Baca
Gonçalves Magalhães, Vladimir
Lemmermann, Niels A W
Juranić Lisnić, Vanda
Stempel, Markus
Bussey, Kendra A
Reimer, Elisa
Podlech, Jürgen
Lienenklaus, Stefan
Reddehase, Matthias J
Jonjić, Stipan
Brinkmann, Melanie M
Helmholtz Centre for infection research, Inhoffenstr. 7., 38124 Braunschweig, Germany.
The type I interferon (IFN) response is imperative for the establishment of the early antiviral immune response. Here we report the identification of the first type I IFN antagonist encoded by murine cytomegalovirus (MCMV) that shuts down signaling following pattern recognition receptor (PRR) sensing. Screening of an MCMV open reading frame (ORF) library identified M35 as a novel and strong negative modulator of IFNβ promoter induction following activation of both RNA and DNA cytoplasmic PRR. Additionally, M35 inhibits the proinflammatory cytokine response downstream of Toll-like receptors (TLR). Using a series of luciferase-based reporters with specific transcription factor binding sites, we determined that M35 targets NF-κB-, but not IRF-mediated, transcription. Expression of M35 upon retroviral transduction of immortalized bone marrow-derived macrophages (iBMDM) led to reduced IFNβ transcription and secretion upon activation of stimulator of IFN genes (STING)-dependent signaling. On the other hand, M35 does not antagonize interferon-stimulated gene (ISG) 56 promoter induction or ISG transcription upon exogenous stimulation of the type I IFN receptor (IFNAR). M35 is present in the viral particle and, upon MCMV infection of fibroblasts, is immediately shuttled to the nucleus where it exerts its immunomodulatory effects. Deletion of M35 from the MCMV genome and hence from the viral particle resulted in elevated type I IFN transcription and secretion in vitro and in vivo. In the absence of M35, lower viral titers are observed during acute infection of the host, and productive infection in the salivary glands was not detected. In conclusion, the M35 protein is released by MCMV immediately upon infection in order to deftly inhibit the antiviral type I IFN response by targeting NF-κB-mediated transcription. The identification of this novel viral protein reinforces the importance of timely countermeasures in the complex relationship between virus and host.
2017-06-08T14:38:25Z
2017-06-08T14:38:25Z
2017-05
Article
The murine cytomegalovirus M35 protein antagonizes type I IFN induction downstream of pattern recognition receptors by targeting NF-κB mediated transcription. 2017, 13 (5):e1006382 PLoS Pathog.
1553-7374
28542326
10.1371/journal.ppat.1006382
http://hdl.handle.net/10033/620935
PLoS pathogens
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6209782019-08-30T11:36:05Zcom_10033_128109com_10033_620644com_10033_338554col_10033_621787col_10033_128110col_10033_620646
Yersinia pseudotuberculosis supports Th17 differentiation and limits de novo regulatory T cell induction by directly interfering with T cell receptor signaling.
Pasztoi, Maria
Bonifacius, Agnes
Pezoldt, Joern
Kulkarni, Devesha
Niemz, Jana
Yang, Juhao
Teich, René
Hajek, Janina
Pisano, Fabio
Rohde, Manfred
Dersch, Petra
Huehn, Jochen
Helmholtz Centre for infection research, Inhoffenstr.7, 38124 Braunschweig, Germany.
Adaptive immunity critically contributes to control acute infection with enteropathogenic Yersinia pseudotuberculosis; however, the role of CD4(+) T cell subsets in establishing infection and allowing pathogen persistence remains elusive. Here, we assessed the modulatory capacity of Y. pseudotuberculosis on CD4(+) T cell differentiation. Using in vivo assays, we report that infection with Y. pseudotuberculosis resulted in enhanced priming of IL-17-producing T cells (Th17 cells), whereas induction of Foxp3(+) regulatory T cells (Tregs) was severely disrupted in gut-draining mesenteric lymph nodes (mLNs), in line with altered frequencies of tolerogenic and proinflammatory dendritic cell (DC) subsets within mLNs. Additionally, by using a DC-free in vitro system, we could demonstrate that Y. pseudotuberculosis can directly modulate T cell receptor (TCR) downstream signaling within naïve CD4(+) T cells and Tregs via injection of effector molecules through the type III secretion system, thereby affecting their functional properties. Importantly, modulation of naïve CD4(+) T cells by Y. pseudotuberculosis resulted in an enhanced Th17 differentiation and decreased induction of Foxp3(+) Tregs in vitro. These findings shed light to the adjustment of the Th17-Treg axis in response to acute Y. pseudotuberculosis infection and highlight the direct modulation of CD4(+) T cell subsets by altering their TCR downstream signaling.
2017-06-23T14:41:00Z
2017-06-23T14:41:00Z
2017-04-04
Article
Yersinia pseudotuberculosis supports Th17 differentiation and limits de novo regulatory T cell induction by directly interfering with T cell receptor signaling. 2017 Cell. Mol. Life Sci.
1420-9071
28378044
10.1007/s00018-017-2516-y
http://hdl.handle.net/10033/620978
Cellular and molecular life sciences : CMLS
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6209842019-08-30T11:31:23Zcom_10033_311624com_10033_6839com_10033_620626com_10033_311308com_10033_338554col_10033_621787col_10033_311625col_10033_620721col_10033_620629
Degradable magnesium implant-associated infections by bacterial biofilms induce robust localized and systemic inflammatory reactions in a mouse model.
Rahim, Muhammad Imran
Babbar, Anshu
Lienenklaus, Stefan
Pils, Marina
Rohde, M
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Biomaterial-associated Pseudomonas aeruginosa biofilm infections constitute cascade of host immune reactions ultimately leading towards implant failure. Due to lack of relevant in vivo biofilm models, majority of the studies report host immune responses against free living or planktonic bacteria while bacteria in clinical situations live more frequently as biofilm communities than as single cells. Present study investigated host immune responses against biomaterial-associated P. aeruginosa biofilms in a clinically relevant mouse model. Previously, we reported metallic magnesium, a prospective biodegradable implant, to be permissive for bacterial biofilms in vivo even though it exhibits antibacterial properties in vitro. Therefore, magnesium was employed as biomaterial to investigate in vivo biofilm formation and associated host immune responses by using two P. aeruginosa strains and two mouse strains. P. aeruginosa formed biofilms on subcutaneously implanted magnesium discs. Non-invasive in vivo imaging indicated transient inflammatory responses at control sites whereas robust prolonged interferon-β (IFN-β) expression was observed from biofilms in a transgenic animal reporter. Further, immunohistology and electron microscopic results showed that bacterial biofilms were located in two dimensions immediately on the implant surface and at a short distance in the adjacent tissue. These biofilms were surrounded by inflammatory cells (mainly polymorphonuclear cells) as compared to controls. Interestingly, even though the number of live bacteria in various organs remained below detectable levels, splenomegaly indicated systemic inflammatory processes. Overall, these findings confirmed the resistance of biofilm infections in vivo to potentially antibacterial properties of magnesium degradation products. In vivo imaging and histology indicated the induction of both, local and systemic host inflammatory responses against P. aeruginosa biofilms. Even though the innate host immune defenses could not eliminate the local infection for up to two weeks, there was no apparent systemic bacteremia and all animals investigated survived the infection.
2017-06-28T13:41:37Z
2017-06-28T13:41:37Z
2017-06-01
Article
Degradable magnesium implant-associated infections by bacterial biofilms induce robust localized and systemic inflammatory reactions in a mouse model. 2017 Biomed Mater
1748-605X
28569671
10.1088/1748-605X/aa7667
http://hdl.handle.net/10033/620984
Biomedical materials (Bristol, England)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210152019-08-30T11:28:23Zcom_10033_338554col_10033_621050
The Mouse Cytomegalovirus Gene m42 Targets Surface Expression of the Protein Tyrosine Phosphatase CD45 in Infected Macrophages.
Thiel, Nadine
Keyser, Kirsten A
Lemmermann, Niels A W
Oduro, Jennifer D
Wagner, Karen
Elsner, Carina
Halenius, Anne
Lenac Roviš, Tihana
Brinkmann, Melanie M
Jonjić, Stipan
Cicin-Sain, Luka
Messerle, Martin
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The receptor-like protein tyrosine phosphatase CD45 is expressed on the surface of cells of hematopoietic origin and has a pivotal role for the function of these cells in the immune response. Here we report that following infection of macrophages with mouse cytomegalovirus (MCMV) the cell surface expression of CD45 is drastically diminished. Screening of a set of MCMV deletion mutants allowed us to identify the viral gene m42 of being responsible for CD45 down-modulation. Moreover, expression of m42 independent of viral infection upon retroviral transduction of the RAW264.7 macrophage cell line led to comparable regulation of CD45 expression. In immunocompetent mice infected with an m42 deletion mutant lower viral titers were observed in all tissues examined when compared to wildtype MCMV, indicating an important role of m42 for viral replication in vivo. The m42 gene product was identified as an 18 kDa protein expressed with early kinetics and is predicted to be a tail-anchored membrane protein. Tracking of surface-resident CD45 molecules revealed that m42 induces internalization and degradation of CD45. The observation that the amounts of the E3 ubiquitin ligases Itch and Nedd4 were diminished in cells expressing m42 and that disruption of a PY motif in the N-terminal part of m42 resulted in loss of function, suggest that m42 acts as an activator or adaptor for these Nedd4-like ubiquitin ligases, which mark CD45 for lysosomal degradation. In conclusion, the down-modulation of CD45 expression in MCMV-infected myeloid cells represents a novel pathway of virus-host interaction.
2017-07-20T11:29:58Z
2017-07-20T11:29:58Z
2016-12
Article
The Mouse Cytomegalovirus Gene m42 Targets Surface Expression of the Protein Tyrosine Phosphatase CD45 in Infected Macrophages. 2016, 12 (12):e1006057 PLoS Pathog.
1553-7374
27926943
10.1371/journal.ppat.1006057
http://hdl.handle.net/10033/621015
PLoS pathogens
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210202019-08-30T11:31:23Zcom_10033_338554col_10033_621787
Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion.
Laass, Sebastian
Kleist, Sarah
Bill, Nelli
Drüppel, Katharina
Kossmehl, Sebastian
Wöhlbrand, Lars
Rabus, Ralf
Klein, Johannes
Rohde, Manfred
Bartsch, Annekathrin
Wittmann, Christoph
Schmidt-Hohagen, Kerstin
Tielen, Petra
Jahn, Dieter
Schomburg, Dietmar
Helmholtz-Zentrum für Infektionsforschung, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Metabolic flexibility is the key to the ecological success of the marine Roseobacter clade bacteria. We investigated the metabolic adaptation and the underlying changes in gene expression of Dinoroseobacter shibae DFL12(T) to anoxic life by a combination of metabolome, proteome, and transcriptome analyses. Time-resolved studies during continuous oxygen depletion were performed in a chemostat using nitrate as the terminal electron acceptor. Formation of the denitrification machinery was found enhanced on the transcriptional and proteome level, indicating that D. shibae DFL12(T) established nitrate respiration to compensate for the depletion of the electron acceptor oxygen. In parallel, arginine fermentation was induced. During the transition state, growth and ATP concentration were found to be reduced, as reflected by a decrease of A578 values and viable cell counts. In parallel, the central metabolism, including gluconeogenesis, protein biosynthesis, and purine/pyrimidine synthesis was found transiently reduced in agreement with the decreased demand for cellular building blocks. Surprisingly, an accumulation of poly-3-hydroxybutanoate was observed during prolonged incubation under anoxic conditions. One possible explanation is the storage of accumulated metabolites and the regeneration of NADP(+) from NADPH during poly-3-hydroxybutanoate synthesis (NADPH sink). Although D. shibae DFL12(T) was cultivated in the dark, biosynthesis of bacteriochlorophyll was increased, possibly to prepare for additional energy generation via aerobic anoxygenic photophosphorylation. Overall, oxygen depletion led to a metabolic crisis with partly blocked pathways and the accumulation of metabolites. In response, major energy-consuming processes were reduced until the alternative respiratory denitrification machinery was operative.
2017-07-25T14:37:36Z
2017-07-25T14:37:36Z
2014-05-09
Article
Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. 2014, 289 (19):13219-31 J. Biol. Chem.
1083-351X
24648520
10.1074/jbc.M113.545004
http://hdl.handle.net/10033/621020
The Journal of biological chemistry
en
oai:repository.helmholtz-hzi.de:10033/6210742019-08-30T11:32:17Zcom_10033_338554col_10033_621787
Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4.
Rast, Patrick
Glöckner, Ines
Boedeker, Christian
Jeske, Olga
Wiegand, Sandra
Reinhardt, Richard
Schumann, Peter
Rohde, M
Spring, Stefan
Glöckner, Frank O
Jogler, Christian
Jogler, Mareike
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The cell wall of free-living bacteria consists of peptidoglycan (PG) and is critical for maintenance of shape as dissolved solutes cause osmotic pressure and challenge cell integrity. Surprisingly, the subdivision 4 of the phylum Verrucomicrobia appears to be exceptional in this respect. Organisms of this subdivision are described to be devoid of muramic or diaminopimelic acid (DAP), usually found as components of PG in bacterial cell walls. Here we describe three novel bacterial strains from a freshwater lake, IG15(T), IG16b(T), and IG31(T), belonging to a new genus in the subdivision 4 of Verrucomicrobia which we found to possess PG as part of their cell walls. Biochemical analysis revealed the presence of DAP not only in these novel strains, but also in Opitutus terrae PB90-1(T), the closest described relative of strains IG15(T), IG16b(T), and IG31(T). Furthermore, we found that nearly all genes necessary for peptidoglycan synthesis are present in genomes of subdivision 4 members, as well as in the complete genome sequence of strain IG16b(T). In addition, we isolated and visualized PG-sacculi for strain IG16b(T). Thus, our results challenge the concept of peptidoglycan-less free-living bacteria. Our polyphasic taxonomy approach places the novel strains in a new genus within the family Opitutaceae, for which the name Lacunisphaera gen. nov. is proposed. Strain designations for IG15(T), IG16b(T) and IG31(T) are Lacunisphaera parvula sp. nov. (=DSM 26814 = LMG 29468), L. limnophila sp. nov. (=DSM 26815 = LMG 29469) and L. anatis sp. nov. (=DSM 103142 = LMG 29578) respectively, with L. limnophila IG16b(T) being the type species of the genus.
2017-08-23T14:23:59Z
2017-08-23T14:23:59Z
2017
Article
Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4. 2017, 8:202 Front Microbiol
1664-302X
28243229
10.3389/fmicb.2017.00202
http://hdl.handle.net/10033/621074
Frontiers in microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210802019-08-30T11:26:13Zcom_10033_338554com_10033_620591col_10033_621050col_10033_620599
A highly conserved redox-active Mx(2)CWx(6)R motif regulates Zap70 stability and activity.
Thurm, Christoph
Poltorak, Mateusz P
Reimer, Elisa
Brinkmann, Melanie M
Leichert, Lars
Schraven, Burkhart
Simeoni, Luca
Helmholtz Centre of infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
ζ-associated protein of 70 kDa (Zap70) is crucial for T-cell receptor (TCR) signaling. Loss of Zap70 in both humans and mice results in severe immunodeficiency. On the other hand, the expression of Zap70 in B-cell malignancies correlates with the severity of the disease. Because of its role in immune-related disorders, Zap70 has become a therapeutic target for the treatment of human diseases. It is well-established that the activity/expression of Zap70 is regulated by post-translational modifications of crucial amino acids including the phosphorylation of tyrosines and the ubiquitination of lysines. Here, we have investigated whether also oxidation of cysteine residues regulates Zap70 functions. We have identified C575 as a major sulfenylation site of Zap70. A C575A substitution results in protein instability, reduced activity, and increased dependency on the Hsp90/Cdc37 chaperone system. Indeed, Cdc37 overexpression reconstituted partially the expression but fully the function of Zap70C575A. C575 lies within a Mx(2)CWx(6)R motif which is highly conserved among almost all human tyrosine kinases. Mutation of any of the conserved amino acids, but not of a non-conserved residue preceding the cysteine, also results in Zap70 instability. Collectively, we have identified a new redox-active motif which is crucial for the regulation of Zap70 stability/activity. We believe that this motif has the potential to become a novel target for the development of therapeutic tools to modulate the expression/activity of kinases.
2017-08-30T11:18:03Z
2017-08-30T11:18:03Z
2017-05-09
Article
A highly conserved redox-active Mx(2)CWx(6)R motif regulates Zap70 stability and activity. 2017, 8 (19):30805-30816 Oncotarget
1949-2553
28415650
10.18632/oncotarget.16486
http://hdl.handle.net/10033/621080
Oncotarget
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211032019-08-30T11:29:17Zcom_10033_338554col_10033_621787
Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella.
Abraham, Wolf-Rainer
de Carvalho, Maira Peres
da Costa Neves, Thais Souto Paula
Memoria, Marina Torquato
Tartuci, Iago Toledo
Vancanneyt, Marc
Smit, John
Rohde, M
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr.7,38124 Braunschweig, Germany.
Two Gram-negative, heterotrophic, aerobic, prosthecated, marine bacteria, designated strains MCS23T and MCS27T, were isolated from seawater samples. NaCl was required for growth. The major polar lipid detected in strain MCS27T was phosphatidylglycerol, whereas those detected in MCS23T were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and 1,2-diacyl-3-α-d-glucuronopyranosyl-sn-glycerol taurineamide. The most abundant cellular fatty acids were C18 : 1ω7 and C16 : 0, hydroxyl-fatty acids were 3-OH C12 : 0 in both strains and 3-OH C11 : 0 in MCS23T. Strains MCS23T and MCS27T had DNA G+C contents of 57.0 and 55.0 mol%, respectively. The two strains shared 99.3 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Henriciella were 99.4-97.8 % but DNA-DNA hybridizations were 53 % or lower. Besides their 16S rRNA gene sequences, the novel strains can be differentiated from other species of the genus Henriciella by cell morphology, lipid and fatty acid patterns and enzyme activities. The data obtained led to the identification of two novel species, for which the names Henriciella barbarensis sp. nov. (type strain MCS23T=LMG 28705T=CCUG 66934T) and Henriciella algicola sp. nov. (type strain MCS27T=LMG 29152T=CCUG 67844T) are proposed. As these two novel species are the first prosthecate species in the genus Henriciella, an emended genus description is also provided.
2017-09-11T13:02:46Z
2017-09-11T13:02:46Z
2017-08
Article
Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella. 2017, 67 (8):2804-2810 Int. J. Syst. Evol. Microbiol.
1466-5034
28820095
10.1099/ijsem.0.002024
http://hdl.handle.net/10033/621103
International journal of systematic and evolutionary microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211042019-08-30T11:33:30Zcom_10033_620644com_10033_338554col_10033_621787col_10033_621787col_10033_620647
The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment.
Gottschick, Cornelia
Deng, Zhi-Luo
Vital, Marius
Masur, Clarissa
Abels, Christoph
Pieper, Dietmar H
Wagner-Döbler, Irene
Helmholtz Centre for infection researchGmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The urinary microbiota is similarly complex as the vaginal and penile microbiota, yet its role as a reservoir for pathogens and for recurrent polymicrobial biofilm diseases like bacterial vaginosis (BV) is not clear.
2017-09-12T08:48:46Z
2017-09-12T08:48:46Z
2017-08-14
Article
The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment. 2017, 5 (1):99 Microbiome
2049-2618
28807017
10.1186/s40168-017-0305-3
http://hdl.handle.net/10033/621104
Microbiome
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211132019-08-30T11:34:22Zcom_10033_128109com_10033_338554col_10033_621787col_10033_128110
Mesenteric lymph node stromal cell-derived extracellular vesicles contribute to peripheral de novo induction of Foxp3(+) regulatory T cells.
Pasztoi, Maria
Pezoldt, Joern
Beckstette, Michael
Lipps, Christoph
Wirth, Dagmar
Rohde, M
Paloczi, Krisztina
Buzas, Edit Iren
Huehn, Jochen
Helmholtz Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Intestinal regulatory T cells (Tregs) are fundamental in peripheral tolerance toward commensals and food-borne antigens. Accordingly, gut-draining mesenteric lymph nodes (mLNs) represent a site of efficient peripheral de novo Treg induction when compared to skin-draining peripheral LNs (pLNs), and we had recently shown that LN stromal cells substantially contribute to this process. Here, we aimed to unravel the underlying molecular mechanisms and generated immortalized fibroblastic reticular cell lines (iFRCs) from mLNs and pLNs, allowing unlimited investigation of this rare stromal cell subset. In line with our previous findings, mLN-iFRCs showed a higher Treg-inducing capacity when compared to pLN-iFRCs. RNA-seq analysis focusing on secreted molecules revealed a more tolerogenic phenotype of mLN- as compared to pLN-iFRCs. Remarkably, mLN-iFRCs produced substantial numbers of microvesicles (MVs) that carried elevated levels of TGF-β when compared to pLN-iFRC-derived MVs, and these novel players of intercellular communication were shown to be responsible for the tolerogenic properties of mLN-iFRCs. Thus, stromal cells originating from mLNs contribute to peripheral tolerance by fostering de novo Treg induction using TGF-β-carrying MVs. This finding provides novel insights into the subcellular/molecular mechanisms of de novo Treg induction and might serve as promising tool for future therapeutic applications to treat inflammatory disorders.
2017-09-19T13:06:36Z
2017-09-19T13:06:36Z
2017-08-18
Article
Mesenteric lymph node stromal cell-derived extracellular vesicles contribute to peripheral de novo induction of Foxp3(+) regulatory T cells. 2017 Eur. J. Immunol.
1521-4141
28833065
10.1002/eji.201746960
http://hdl.handle.net/10033/621113
European journal of immunology
en
info:eu-repo/grantAgreement/EC/H2020/656319
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
oai:repository.helmholtz-hzi.de:10033/6211222019-12-03T01:57:49Zcom_10033_338554col_10033_338544col_10033_620574
FMNL2 and -3 regulate Golgi architecture and anterograde transport downstream of Cdc42.
Kage, Frieda
Steffen, Anika
Ellinger, Adolf
Ranftler, Carmen
Gehre, Christian
Brakebusch, Cord
Pavelka, Margit
Stradal, Theresia
Rottner, Klemens
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.
The Rho-family small GTPase Cdc42 localizes at plasma membrane and Golgi complex and aside from protrusion and migration operates in vesicle trafficking, endo- and exocytosis as well as establishment and/or maintenance of cell polarity. The formin family members FMNL2 and -3 are actin assembly factors established to regulate cell edge protrusion during migration and invasion. Here we report these formins to additionally accumulate and function at the Golgi apparatus. As opposed to lamellipodia, Golgi targeting of these proteins required both their N-terminal myristoylation and the interaction with Cdc42. Moreover, Golgi association of FMNL2 or -3 induced a phalloidin-detectable actin meshwork around the Golgi. Importantly, functional interference with FMNL2/3 formins by RNAi or CRISPR/Cas9-mediated gene deletion invariably induced Golgi fragmentation in different cell lines. Furthermore, absence of these proteins led to enlargement of endosomes as well as defective maturation and/or sorting into late endosomes and lysosomes. In line with Cdc42 - recently established to regulate anterograde transport through the Golgi by cargo sorting and carrier formation - FMNL2/3 depletion also affected anterograde trafficking of VSV-G from the Golgi to the plasma membrane. Our data thus link FMNL2/3 formins to actin assembly-dependent functions of Cdc42 in anterograde transport through the Golgi apparatus.
2017-09-26T12:48:35Z
2017-09-26T12:48:35Z
2017-08-29
Article
FMNL2 and -3 regulate Golgi architecture and anterograde transport downstream of Cdc42. 2017, 7 (1):9791 Sci Rep
2045-2322
28852060
10.1038/s41598-017-09952-1
http://hdl.handle.net/10033/621122
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211352019-08-30T11:33:57Zcom_10033_620644com_10033_338554com_10033_620533col_10033_621891col_10033_621787col_10033_620647
Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis.
Gottschick, Cornelia
Deng, Zhi-Luo
Vital, Marius
Masur, Clarissa
Abels, Christoph
Pieper, Dietmar H
Rohde, Manfred
Mendling, Werner
Wagner-Döbler, Irene
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like preterm labor. BV is characterized by a high recurrence rate for which biofilms frequently found on vaginal epithelial cells may be a reason.
2017-10-12T08:37:35Z
2017-10-12T08:37:35Z
2017-09-13
Article
Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis. 2017, 5 (1):119 Microbiome
2049-2618
28903767
10.1186/s40168-017-0326-y
http://hdl.handle.net/10033/621135
Microbiome
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211382019-08-30T11:36:32Zcom_10033_338554col_10033_621787
Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales.
Hahn, Martin W
Schmidt, Johanna
Koll, Ulrike
Rohde, M
Verbarg, Susanne
Pitt, Alexandra
Nakai, Ryosuke
Naganuma, Takeshi
Lang, Elke
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria. Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia. These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia, that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales. We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.
2017-10-16T12:54:50Z
2017-10-16T12:54:50Z
2017-08
Article
Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. 2017, 67 (8):2555-2568 Int. J. Syst. Evol. Microbiol.
1466-5034
28771119
10.1099/ijsem.0.001965
http://hdl.handle.net/10033/621138
International journal of systematic and evolutionary microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211492019-08-30T11:34:43Zcom_10033_620636com_10033_620644com_10033_338554col_10033_621787col_10033_620665col_10033_620650
Engineered Salmonella enterica serovar Typhimurium overcomes limitations of anti-bacterial immunity in bacteria-mediated tumor therapy
Felgner, Sebastian
Kocijancic, Dino
Frahm, Michael
Heise, Ulrike
Rohde, Manfred
Zimmermann, Kurt
Falk, Christine
Erhardt, Marc
Weiss, Siegfried
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Mouse-Pathology Service Unit, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Symbio Gruppe GmbH & Co KG, Herborn, Lower Saxony, Germany
Institute of Transplant Immunology, Medical School Hannover, Hannover, Hessia, Germany
Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
2017-11-01T12:17:44Z
2017-11-01T12:17:44Z
2017-09-29
Article
Engineered Salmonella enterica serovar Typhimurium overcomes limitations of anti-bacterial immunity in bacteria-mediated tumor therapy 2017:e1382791 OncoImmunology
2162-402X
10.1080/2162402X.2017.1382791
http://hdl.handle.net/10033/621149
OncoImmunology
https://www.tandfonline.com/doi/full/10.1080/2162402X.2017.1382791
http://creativecommons.org/licenses/by-nc-sa/4.0/
rdf///com_10033_338554/100