2024-03-28T21:26:26Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/85122019-08-30T11:35:10Zcom_10033_620533col_10033_621891
Monitoring Key Reactions in Degradation of Chloroaromatics by In Situ 1H Nuclear Magnetic Resonance: Solution Structures of Metabolites Formed from cis-Dienelactone
Pieper, Dietmar H.
Pollmann, Katrin
Nikodem, Patricia
Gonzalez, Bernardo
Wray, Victor
2007-02-19T09:27:43Z
2002-03
2007-02-19T09:27:43Z
2002-03
Journal of Bacteriology 2002 184(5):1466-1470
0021-9193
1098-5530
11844781
10.1128/JB.184.5.1466-1470.2002
http://hdl.handle.net/10033/8512
134862
en_US
Copyright © 2002, American Society for Microbiology.
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/85132019-08-30T11:34:46Zcom_10033_620533col_10033_621891
Importance of Different tfd Genes for Degradation of Chloroaromatics by Ralstonia eutropha JMP134†
Plumeier, Iris
Pérez-Pantoja, Danilo
Heim, Sabina
González, Bernardo
Pieper, Dietmar H.
2007-02-19T09:28:40Z
2002-08
2007-02-19T09:28:40Z
2002-08
Journal of Bacteriology 2002 184(15):4054-4064
0021-9193
1098-5530
12107121
10.1128/JB.184.15.4054-4064.2002
http://hdl.handle.net/10033/8513
135226
en_US
Copyright © 2002, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/85142019-08-30T11:35:11Zcom_10033_620533col_10033_621891
Metabolism of Dichloromethylcatechols as Central Intermediates in the Degradation of Dichlorotoluenes by Ralstonia sp. Strain PS12
Pollmann, Katrin
Kaschabek, Stefan
Wray, Victor
Reineke, Walter
Pieper, Dietmar H.
2007-02-19T09:29:29Z
2002-10
2007-02-19T09:29:29Z
2002-10
Journal of Bacteriology 2002 184(19):5261-5274
0021-9193
1098-5530
12218011
10.1128/JB.184.19.5261-5274.2002
http://hdl.handle.net/10033/8514
135362
en_US
Copyright © 2002, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/85242019-08-30T11:35:11Zcom_10033_620533col_10033_621891
Efficient Turnover of Chlorocatechols Is Essential for Growth of Ralstonia eutropha JMP134(pJP4) in 3-Chlorobenzoic Acid
Pérez-Pantoja, D.
Ledger, T.
Pieper, D. H.
González, B.
2007-02-19T10:18:58Z
2003-03
2007-02-19T10:18:58Z
2003-03
Journal of Bacteriology 2003 185(5):1534-1542
0021-9193
1098-5530
12591870
10.1128/JB.185.5.1534-1542.2003
http://hdl.handle.net/10033/8524
148064
en_US
Copyright © 2003, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/85332019-08-30T11:35:11Zcom_10033_620533col_10033_621891
Substrate Specificity and Expression of Three 2,3-Dihydroxybiphenyl 1,2-Dioxygenases from Rhodococcus globerulus Strain P6
McKay, David B.
Prucha, Matthias
Reineke, Walter
Timmis, Kenneth N.
Pieper, Dietmar H.
2007-02-19T10:38:50Z
2003-05
2007-02-19T10:38:50Z
2003-05
Journal of Bacteriology 2003 185(9):2944-2951
0021-9193
1098-5530
12700274
10.1128/JB.185.9.2944-2951.2003
http://hdl.handle.net/10033/8533
154411
en_US
Copyright © 2003, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/86372019-08-30T11:35:12Zcom_10033_620533col_10033_621891
Heterologous expression of biphenyl dioxygenase-encoding genes from a gram-positive broad-spectrum polychlorinated biphenyl degrader and characterization of chlorobiphenyl oxidation by the gene products.
McKay, D B
Seeger, M
Zielinski, M
Hofer, Bernd
Timmis, K N
2007-02-20T13:33:19Z
1997-03
2007-02-20T13:33:19Z
1997-03
Journal of Bacteriology 1997 179(6):1924-1930
0021-9193
1098-5530
9068637
http://hdl.handle.net/10033/8637
178915
en_US
oai:repository.helmholtz-hzi.de:10033/86232019-08-30T11:34:43Zcom_10033_620533col_10033_621891
New Bacterial Pathway for 4- and 5-Chlorosalicylate Degradation via 4-Chlorocatechol and Maleylacetate in Pseudomonas sp. Strain MT1
Nikodem, Patricia
Hecht, Volker
Schlömann, Michael
Pieper, Dietmar H.
2007-02-20T13:22:19Z
2003-12
2007-02-20T13:22:19Z
2003-12
Journal of Bacteriology 2003 185(23):6790-6800
0021-9193
1098-5530
14617643
10.1128/JB.185.23.6790-6800.2003
http://hdl.handle.net/10033/8623
262710
en_US
Copyright © 2003, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/86582019-08-30T11:36:05Zcom_10033_620533col_10033_621891
The sensitivity of DNA cleavage by SnoI to methylation by M.EcoK.
Hofer, Bernd
Kühlein, B
Images
2007-02-20T14:31:53Z
1989-10-11
2007-02-20T14:31:53Z
1989-10-11
Nucleic Acids Research 1989 17(19):8009
0305-1048
1362-4962
2798148
http://hdl.handle.net/10033/8658
334927
en_US
oai:repository.helmholtz-hzi.de:10033/86982019-08-30T11:35:10Zcom_10033_620533col_10033_621891
Chloromethylmuconolactones as Critical Metabolites in the Degradation of Chloromethylcatechols: Recalcitrance of 2-Chlorotoluene
Pollmann, Katrin
Wray, Victor
Pieper, Dietmar H.
2007-02-21T08:37:48Z
2005-04
2007-02-21T08:37:48Z
2005-04
Journal of Bacteriology 2005 187(7):2332-2340
0021-9193
1098-5530
15774876
10.1128/JB.187.7.2332-2340.2005
http://hdl.handle.net/10033/8698
1065237
en_US
Copyright © 2005, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/87732019-08-30T11:35:11Zcom_10033_620533col_10033_621891
Assessment of Toluene/Biphenyl Dioxygenase Gene Diversity in Benzene-Polluted Soils: Links between Benzene Biodegradation and Genes Similar to Those Encoding Isopropylbenzene Dioxygenases†
Witzig, Robert
Junca, Howard
Hecht, Hans-Jürgen
Pieper, Dietmar H.
2007-02-22T15:22:22Z
2006-05
2007-02-22T15:22:22Z
2006-05
Applied and Environmental Microbiology 2006 72(5):3504-3514
0099-2240
1098-5336
16672497
10.1128/AEM.72.5.3504-3514.2006
http://hdl.handle.net/10033/8773
1472391
en_US
Copyright © 2006, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/123552019-08-30T11:36:05Zcom_10033_620533col_10033_621891
Chlorophenol hydroxylases encoded by plasmid pJP4 differentially contribute to chlorophenoxyacetic acid degradation.
Ledger, T
Pieper, D H
González, B
Phenoxyalkanoic compounds are used worldwide as herbicides. Cupriavidus necator JMP134(pJP4) catabolizes 2,4-dichlorophenoxyacetate (2,4-D) and 4-chloro-2-methylphenoxyacetate (MCPA), using tfd functions carried on plasmid pJP4. TfdA cleaves the ether bonds of these herbicides to produce 2,4-dichlorophenol (2,4-DCP) and 4-chloro-2-methylphenol (MCP), respectively. These intermediates can be degraded by two chlorophenol hydroxylases encoded by the tfdB(I) and tfdB(II) genes to produce the respective chlorocatechols. We studied the specific contribution of each of the TfdB enzymes to the 2,4-D/MCPA degradation pathway. To accomplish this, the tfdB(I) and tfdB(II) genes were independently inactivated, and growth on each chlorophenoxyacetate and total chlorophenol hydroxylase activity were measured for the mutant strains. The phenotype of these mutants shows that both TfdB enzymes are used for growth on 2,4-D or MCPA but that TfdB(I) contributes to a significantly higher extent than TfdB(II). Both enzymes showed similar specificity profiles, with 2,4-DCP, MCP, and 4-chlorophenol being the best substrates. An accumulation of chlorophenol was found to inhibit chlorophenoxyacetate degradation, and inactivation of the tfdB genes enhanced the toxic effect of 2,4-DCP on C. necator cells. Furthermore, increased chlorophenol production by overexpression of TfdA also had a negative effect on 2,4-D degradation by C. necator JMP134 and by a different host, Burkholderia xenovorans LB400, harboring plasmid pJP4. The results of this work indicate that codification and expression of the two tfdB genes in pJP4 are important to avoid toxic accumulations of chlorophenols during phenoxyacetic acid degradation and that a balance between chlorophenol-producing and chlorophenol-consuming reactions is necessary for growth on these compounds.
2007-06-19T09:08:58Z
2007-06-19T09:08:58Z
2006-04-01
Article
Appl. Environ. Microbiol. 2006, 72(4):2783-92
0099-2240
16597983
10.1128/AEM.72.4.2783-2792.2006
http://hdl.handle.net/10033/12355
en
oai:repository.helmholtz-hzi.de:10033/124252019-08-30T11:35:39Zcom_10033_620533col_10033_621891
Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries.
Junca, Howard
Pieper, Dietmar H
Developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures and to monitor their dynamics under in situ conditions. However, there has been a distinct lack of emphasis on monitoring the functional diversity in the environment. Genes encoding catechol 2,3-dioxygenases (C23O), as key enzymes of various aerobic aromatic degradation pathways, were used as functional targets to assess the catabolic gene diversity in differentially BTEX contaminated environments by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP). Site specific PCR-SSCP fingerprints were obtained, showing that gene diversity experienced shifts correlated to temporal changes and levels of contamination. PCR-SSCP enabled the recovery of predominant gene polymorphs, and results closely matched with the information retrieved from random sequencing of PCR-DNA clone libraries. A new method for isolating strains capable of growing on BTEX compounds was developed to diminish preselection or enrichment bias and to assess the function of predominant gene polymorphs. C23O abundance in isolates correlated with the levels of BTEX pollution in the soil samples analysed. Isolates harbouring C23O genes, identical to the gene polymorph predominant in all contaminated sites analysed, showed an unexpected benzene but not toluene mineralizing phenotype whereas isolates harbouring a C23O gene variant differing by a single point mutation and observed in highly polluted sites only, were capable, among some other isolates, to mineralize benzene and toluene, indicating a catabolically determined sharing of carbon sources on-site. The PCR-SSCP technique is thus a powerful tool for assessing the diversity of functional genes and the identification of predominant gene polymorphs in environmental samples as a prerequisite to understand the functioning of microbial communities.
2007-06-25T12:03:09Z
2007-06-25T12:03:09Z
2004-02-01
Article
Environ. Microbiol. 2004, 6(2):95-110
1462-2912
14756875
http://hdl.handle.net/10033/12425
en
oai:repository.helmholtz-hzi.de:10033/175322019-08-30T11:36:05Zcom_10033_620533col_10033_621891
4-sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2.
Halak, Sad
Basta, Tamara
Bürger, Sibylle
Contzen, Matthias
Wray, Victor
Pieper, Dietmar Helmut
Stolz, Andreas
Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany.
The 4-carboxymethylen-4-sulfo-but-2-en-olide (4-sulfomuconolactone) hydrolases from Hydrogenophaga intermedia strain S1 and Agrobacterium radiobacter strain S2 are part of a modified protocatechuate pathway responsible for the degradation of 4-sulfocatechol. In both strains, the hydrolase-encoding genes occur downstream of those encoding the enzymes that catalyze the lactonization of 3-sulfomuconate. The deduced amino acid sequences of the 4-sulfomuconolactone hydrolases demonstrated the highest degree of sequence identity to 2-pyrone-4,6-dicarboxylate hydrolases, which take part in the meta cleavage pathway of protocatechuate. The 4-sulfomuconolactone hydrolases did not convert 2-pyrone-4,6-dicarboxylate, and the 2-pyrone-4,6-dicarboxylate hydrolase from Sphingomonas paucimobilis SYK-6 did not convert 4-sulfomuconolactone. Nevertheless, the presence of highly conserved histidine residues in the 4-sulfomuconolactone and the 2-pyrone-4,6-dicarboxylate hydrolases and some further sequence similarities suggested that both enzymes belong to the metallo-dependent hydrolases (the "amidohydrolase superfamily"). The 4-sulfomuconolactone hydrolases were heterologously expressed as His-tagged enzyme variants. Gel filtration experiments suggested that the enzymes are present as monomers in solution, with molecular weights of approximately 33,000 to 35,000. 4-Sulfomuconolactone was converted by sulfomuconolactone hydrolases to stoichiometric amounts of maleylacetate and sulfite. The 4-sulfomuconolactone hydrolases from both strains showed pH optima at pH 7 to 7.5 and rather similar catalytic constant (k(cat)/K(M))values. The suggested 4-sulfocatechol pathway from 4-sulfocatechol to maleylacetate was confirmed by in situ nuclear magnetic resonance analysis using the recombinantly expressed enzymes.
2008-02-05T14:03:31Z
2008-02-05T14:03:31Z
2007-10
Article
4-sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. 2007, 189 (19):6998-7006 J. Bacteriol.
0021-9193
17660282
10.1128/JB.00611-07
http://hdl.handle.net/10033/17532
Journal of bacteriology
en
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17660282
oai:repository.helmholtz-hzi.de:10033/187332019-08-30T11:35:39Zcom_10033_620533col_10033_621891
Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls.
Cámara, Beatriz
Seeger, Michael
González, Myriam
Standfuss-Gabisch, Christine
Kahl, Silke
Hofer, Bernd
Laboratorio de Microbiología Molecular y Biotechnología Ambiental, Departamento de Química and Millennium Nucleus of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Téchnica Federico Santa María, Valparaíso, Chile.
Recently, a sequence-based approach has been developed for the fast isolation and characterization of class II aryl-hydroxylating dioxygenase activities (S. Kahl and B. Hofer, Microbiology 149:1475-1481, 2003). It comprises the PCR amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bphA gene cluster of Burkholderia xenovorans LB400. One of the resulting chimeric enzymes, harboring the core segment of a dioxygenase from Pseudomonas sp. strain B4-Magdeburg, has now been characterized with respect to the oxidation of chlorobiphenyls (CBs). Its substrate and product specificities differed favorably from those of the parental dioxygenase of strain LB400. The hybrid possessed a higher regiospecificity and yielded less unproductive dioxygenations at meta and para carbons. It attacked ortho-, meta-, and para-chlorinated rings with comparable efficiencies. It gave significantly higher yields in ortho,meta-dioxygenation of recalcitrant congeners containing a doubly ortho-chlorinated ring. While the parental enzyme yielded mainly unproductive meta, para dioxygenation of 2,5,4'-CB, the hybrid predominantly converted this congener into an ortho,meta-dioxygenated product. The subsequent enzymes of the LB400 catabolic pathway were able to transform most of the metabolites formed by the novel dioxygenase, indicating that the substrate ranges of these biocatalysts are not adapted to that of their initial pathway enzyme. Some of the catabolites, however, were identified as problematic for further degradation. Our results demonstrate that the outlined approach can successfully be applied to obtain novel dioxygenase specificities that favorably complement or supplement known ones.
2008-02-20T14:27:26Z
2008-02-20T14:27:26Z
2007-04
Article
Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. 2007, 73 (8):2682-9 Appl. Environ. Microbiol.
0099-2240
17322323
10.1128/AEM.02523-06
http://hdl.handle.net/10033/18733
Applied and environmental microbiology
en
oai:repository.helmholtz-hzi.de:10033/191952019-08-30T11:34:43Zcom_10033_620533col_10033_621891
Eight Americas: a new definition for "Americas"?
Junca, Howard
2008-02-26T14:07:20Z
2008-02-26T14:07:20Z
2007-01
Article
Eight Americas: a new definition for "Americas"? 2007, 4 (1):e42 PLoS Med.
1549-1676
17411316
10.1371/journal.pmed.0040042
http://hdl.handle.net/10033/19195
PLoS medicine
en
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17411316
oai:repository.helmholtz-hzi.de:10033/887532019-08-30T11:34:48Zcom_10033_620533col_10033_621891
Novel metal-binding site of Pseudomonas reinekei MT1 trans-dienelactone hydrolase.
Marín, Macarena
Pieper, Dietmar H
Division of Microbial Pathogenesis, HZI - Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Pseudomonasreinekei MT1 is capable of growing on 4- and 5-chlorosalicylate as the sole carbon source involving a pathway with trans-dienelactone hydrolase as the key enzyme. This enzyme transforms 4-chloromuconolactone to maleylacetate and thereby avoids the spontaneous formation of toxic protoanemonin. trans-Dienelactone hydrolase is a Zn(2+)-dependent hydrolase where activity can be modulated by the exchange of Zn(2+) by Mn(2+) in at least two of the three metal-binding sites. Site directed variants of conserved residues of the Q(101)XXXQ(105)XD(107)XXXH(111) motif and of H281 and E294 exhibit a two order of magnitude decrease in activity and a strong decrease in metal-binding capability. As none of the variants exhibited a change in secondary structure, the analyzed amino acid residues can be assumed to be involved in metal binding, forming a novel trinuclear metal-binding motif.
2010-01-05T13:12:47Z
2010-01-05T13:12:47Z
2009-12-25
Article
Novel metal-binding site of Pseudomonas reinekei MT1 trans-dienelactone hydrolase. 2009, 390 (4):1345-8 Biochem. Biophys. Res. Commun.
1090-2104
19895788
10.1016/j.bbrc.2009.10.151
http://hdl.handle.net/10033/88753
Biochemical and biophysical research communications
en
oai:repository.helmholtz-hzi.de:10033/887552019-08-30T11:36:05Zcom_10033_620533col_10033_621891
Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome.
Kunze, Markus
Zerlin, Kay F
Retzlaff, Alexander
Pohl, Jens O
Schmidt, Eberhard
Janssen, Dick B
Vilchez-Vargas, Ramiro
Pieper, Dietmar H
Reineke, Walter
Bergische Universität Wuppertal, Chemical Microbiology, D-42097 Wuppertal, Germany.
Pseudomonas putida GJ31 has been reported to grow on chlorobenzene using a meta-cleavage pathway with chlorocatechol 2,3-dioxygenase (CbzE) as a key enzyme. The CbzE-encoding gene was found to be localized on the 180 kb plasmid pKW1 in a cbzTEXGS cluster, which is flanked by transposases and encodes only a partial (chloro)catechol meta-cleavage pathway comprising ferredoxin reductase, chlorocatechol 2,3-dioxygenase, an unknown protein, 2-hydroxymuconic semialdehyde dehydrogenase and glutathione S-transferase. Downstream of cbzTEXGS are located cbzJ, encoding a novel type of 2-hydroxypent-2,4-dienoate hydratase, and a transposon region highly similar to Tn5501. Upstream of cbzTEXGS, traNEOFG transfer genes were found. The search for gene clusters possibly completing the (chloro)catechol metabolic pathway of GJ31 revealed the presence of two additional catabolic gene clusters on pKW1. The mhpRBCDFETP cluster encodes enzymes for the dissimilation of 2,3-dihydroxyphenylpropionate in a novel arrangement characterized by the absence of a gene encoding 3-(3-hydroxyphenyl)propionate monooxygenase and the presence of a GntR-type regulator, whereas the nahINLOMKJ cluster encodes part of the naphthalene metabolic pathway. Transcription studies supported their possible involvement in chlorobenzene degradation. The upper pathway cluster, comprising genes encoding a chlorobenzene dioxygenase and a chlorobenzene dihydrodiol dehydrogenase, was localized on the chromosome. A high level of transcription in response to chlorobenzene revealed it to be crucial for chlorobenzene degradation. The chlorobenzene degradation pathway in strain GJ31 is thus a mosaic encoded by four gene clusters.
2010-01-05T13:36:37Z
2010-01-05T13:36:37Z
2009-12
Article
Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome. 2009, 155 (Pt 12):4069-83 Microbiology (Reading, Engl.)
1465-2080
19744988
10.1099/mic.0.032110-0
http://hdl.handle.net/10033/88755
Microbiology (Reading, England)
en
oai:repository.helmholtz-hzi.de:10033/1399622019-08-30T11:33:57Zcom_10033_620533col_10033_620538
The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate.
Lu, Xin
Sun, Jibin
Nimtz, Manfred
Wissing, Josef
Zeng, An-Ping
Rinas, Ursula
Helmholtz Center for Infection Research, Inhoffenstr, Braunschweig, Germany.
The filamentous fungus Aspergillus niger is well-known as a producer of primary metabolites and extracellular proteins. For example, glucoamylase is the most efficiently secreted protein of Aspergillus niger, thus the homologous glucoamylase (glaA) promoter as well as the glaA signal sequence are widely used for heterologous protein production. Xylose is known to strongly repress glaA expression while maltose is a potent inducer of glaA promoter controlled genes. For a more profound understanding of A. niger physiology, a comprehensive analysis of the intra- and extracellular proteome of Aspergillus niger AB1.13 growing on defined medium with xylose or maltose as carbon substrate was carried out using 2-D gel electrophoresis/Maldi-ToF and nano-HPLC MS/MS.
2011-08-17T13:57:00Z
2011-08-17T13:57:00Z
2010
Article
The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. 2010, 9:23 Microb. Cell Fact.
1475-2859
20406453
10.1186/1475-2859-9-23
http://hdl.handle.net/10033/139962
Microbial cell factories
en
oai:repository.helmholtz-hzi.de:10033/1456122019-08-30T11:36:05Zcom_10033_620533col_10033_621891
Characterization of bacterial communities exposed to Cr(III) and Pb(II) in submerged fixed-bed biofilms for groundwater treatment.
Vílchez, R
Gómez-Silván, C
Purswani, J
González-López, J
Rodelas, B
Grupo de Microbiología Ambiental (Environmental Microbiology Research Group), Instituto del Agua y Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, 18071, Granada, Spain.
Two pilot-scale submerged-bed microbial biofilms were set up for the removal of Cr(III) and Pb(II) from groundwater, and the biological activities and structure of the bacterial communities developed in the presence of the heavy metals were analyzed. Artesian groundwater was polluted with Cr(III) or Pb(II) (15 mg/l) and amended with sucrose (250 mg/l) as carbon source. While Pb(II) was over 99% removed from groundwater during long-term operation (130 days), the efficiency of the removal of Cr(III) significantly decreased in time (95-73% after 60 days). Cr(III)-amended biofilms displayed significant lower sucrose consumption, ATP cell contents and alkaline phosphatase activity, compared to biofilms formed in the presence of Pb(II), while analysis of exopolymers demonstrated significant differences in their composition (content of carbohydrates and acetyl groups) in response to each heavy metal. According to transmission electron microscopy (TEM) and electron-dispersive X-ray analysis (EDX), Cr(III) bioaccumulated in the exopolymeric matrix without entering bacterial cells, while Pb(II) was detected both extra and intracellularly, associated to P and Si. Temperature-gradient gel electrophoresis (TGGE) profiling based on partial amplification of 16S rRNA genes was used to analyze the differences in the structure of the biofilm bacterial communities developed under exposure to each heavy metal. Prevalent populations in the biofilms were further identified by reamplification and sequencing of isolated TGGE bands. 75% of the sequences in the Pb(II) biofilter were evolutively close to the Rhodobacterales, while in the Cr(III) biofilter 43% of the sequences were found affiliated to the Rhizobiales and Sphingomonadales, and 57% to Betaproteobacteria.
2011-10-18T09:10:45Z
2011-10-18T09:10:45Z
2011-06
Article
Characterization of bacterial communities exposed to Cr(III) and Pb(II) in submerged fixed-bed biofilms for groundwater treatment. 2011, 20 (4):779-92 Ecotoxicology
1573-3017
21400090
10.1007/s10646-011-0629-x
http://hdl.handle.net/10033/145612
Ecotoxicology (London, England)
en
oai:repository.helmholtz-hzi.de:10033/1903392019-08-30T11:33:28Zcom_10033_620533col_10033_620538
Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid
Koutinas, Michalis
Kiparissides, Alexandros
Lam, Ming-Chi
Silva-Rocha, Rafael
Godinho, Miguel
de Lorenzo, Victor
Martins dos Santos, Vitor A.P.
Pistikopoulos, Efstratios N.
Mantalaris, Athanasios
Helmholtz Center for Infection Research (HZI), 38124 Braunschweig, Germany.
2011-11-22T15:39:44Z
2011-11-22T15:39:44Z
2011-11-22T15:39:44Z
Article
Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid 2011, 55 (2):108 Biochemical Engineering Journal
1369703X
10.1016/j.bej.2011.03.012
http://hdl.handle.net/10033/190339
Biochemical Engineering Journal
null
http://linkinghub.elsevier.com/retrieve/pii/S1369703X11000829
oai:repository.helmholtz-hzi.de:10033/2162972019-08-30T11:33:57Zcom_10033_620533col_10033_620538
A viability assay for Candida albicans based on the electron transfer mediator 2,6-dichlorophenolindophenol.
Hassan, Rabeay Y A
Bilitewski, Ursula
Biological Systems Analysis Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
Candida albicans is an opportunistic fungal pathogen with comparably high respiratory activity. Thus, we established a viability test based on 2,6-dichlorophenolindophenol (DCIP), a membrane-permeable electron transfer agent. NADH dehydrogenases catalyze the reduction of DCIP by NADH, and the enzymatic activity can be determined either electrochemically via oxidation reactions of DCIP or photometrically. Among the specific respiratory chain inhibitors, only the complex I inhibitor rotenone decreased the DCIP signal from C. albicans, leaving residual activity of approximately 30%. Thus, the DCIP-reducing activity of C. albicans was largely dependent on complex I activity. C. albicans is closely related to the complex I-negative yeast Saccharomyces cerevisiae, which had previously been used in DCIP viability assays. Via comparative studies, in which we included the pathogenic complex I-negative yeast Candida glabrata, we could define assay conditions that allow a distinction of complex I-negative and -positive organisms. Basal levels of DCIP turnover by S.cerevisiae and C. glabrata were only 30% of those obtained from C. albicans but could be increased to the C. albicans level by adding glucose. No significant increases were observed with galactose. DCIP reduction rates from C. albicans were not further increased by any carbon source.
2012-03-22T14:02:04Z
2012-03-22T14:02:04Z
2011-12-01
Article
A viability assay for Candida albicans based on the electron transfer mediator 2,6-dichlorophenolindophenol. 2011, 419 (1):26-32 Anal. Biochem.
1096-0309
21864496
10.1016/j.ab.2011.07.025
http://hdl.handle.net/10033/216297
Analytical biochemistry
en
Archived with thanks to Analytical biochemistry
oai:repository.helmholtz-hzi.de:10033/2333312019-08-30T11:36:05Zcom_10033_620533col_10033_621891
Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales.
Pérez-Pantoja, Danilo
Donoso, Raúl
Agulló, Loreine
Córdova, Macarena
Seeger, Michael
Pieper, Dietmar H
González, Bernardo
Center for Advanced Studies in Ecology and Biodiversity, Millennium Nucleus in Plant Functional Genomics, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago, Chile.
The relevance of the β-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring-cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring-cleavage, catechol ortho ring-cleavage, homogentisate ring-cleavage and phenylacetyl-CoA ring-cleavage pathways found in at least 60% of genomes analysed. In general, a genus-specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus-specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
2012-07-12T09:51:32Z
2012-07-12T09:51:32Z
2012-05
Article
Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. 2012, 14 (5):1091-117 Environ. Microbiol.
1462-2920
22026719
10.1111/j.1462-2920.2011.02613.x
http://hdl.handle.net/10033/233331
Environmental microbiology
en
Archived with thanks to Environmental microbiology
oai:repository.helmholtz-hzi.de:10033/2451852019-08-30T11:36:04Zcom_10033_620533col_10033_621891
Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen.
Ferrer, Manuel
Ghazi, Azam
Beloqui, Ana
Vieites, José María
López-Cortés, Nieves
Marín-Navarro, Julia
Nechitaylo, Taras Y
Guazzaroni, María-Eugenia
Polaina, Julio
Waliczek, Agnes
Chernikova, Tatyana N
Reva, Oleg N
Golyshina, Olga V
Golyshin, Peter N
CSIC, Institute of Catalysis, Madrid, Spain. mferrer@icp.csic.es
Microbial communities from cow rumen are known for their ability to degrade diverse plant polymers at high rates. In this work, we identified 15 hydrolases through an activity-centred metagenome analysis of a fibre-adherent microbial community from dairy cow rumen. Among them, 7 glycosyl hydrolases (GHs) and 1 feruloyl esterase were successfully cloned, expressed, purified and characterised. The most striking result was a protein of GH family 43 (GHF43), hereinafter designated as R_09-02, which had characteristics very distinct from the other proteins in this family with mono-functional β-xylosidase, α-xylanase, α-L-arabinase and α-L-arabinofuranosidase activities. R_09-02 is the first multifunctional enzyme to exhibit β-1,4 xylosidase, α-1,5 arabinofur(pyr)anosidase, β-1,4 lactase, α-1,6 raffinase, α-1,6 stachyase, β-galactosidase and α-1,4 glucosidase activities. The R_09-02 protein appears to originate from the chromosome of a member of Clostridia, a class of phylum Firmicutes, members of which are highly abundant in ruminal environment. The evolution of R_09-02 is suggested to be driven from the xylose- and arabinose-specific activities, typical for GHF43 members, toward a broader specificity to the glucose- and galactose-containing components of lignocellulose. The apparent capability of enzymes from the GHF43 family to utilise xylose-, arabinose-, glucose- and galactose-containing oligosaccharides has thus far been neglected by, or could not be predicted from, genome and metagenome sequencing data analyses. Taking into account the abundance of GHF43-encoding gene sequences in the rumen (up to 7% of all GH-genes) and the multifunctional phenotype herein described, our findings suggest that the ecological role of this GH family in the digestion of ligno-cellulosic matter should be significantly reconsidered.
2012-09-20T10:49:09Z
2012-09-20T10:49:09Z
2012
Article
Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen. 2012, 7 (6):e38134 PLoS ONE
1932-6203
22761666
10.1371/journal.pone.0038134
http://hdl.handle.net/10033/245185
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/2524932019-08-30T11:36:04Zcom_10033_620533col_10033_621891
Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway.
Marín, Macarena
Plumeier, Iris
Pieper, Dietmar H
Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Braunschweig, Germany.
2,3-Dihydroxybenzoate is the precursor in the biosynthesis of several siderophores and an important plant secondary metabolite that, in bacteria, can be degraded via meta-cleavage of the aromatic ring. The dhb cluster of Pseudomonas reinekei MT1 encodes a chimeric meta-cleavage pathway involved in the catabolism of 2,3-dihydroxybenzoate. While the first two enzymes, DhbA and DhbB, are phylogenetically related to those involved in 2,3-dihydroxy-p-cumate degradation, the subsequent steps are catalyzed by enzymes related to those involved in catechol degradation (DhbCDEFGH). Characterization of kinetic properties of DhbA extradiol dioxygenase identified 2,3-dihydroxybenzoate as the preferred substrate. Deletion of the encoding gene impedes growth of P. reinekei MT1 on 2,3-dihydroxybenzoate. DhbA catalyzes 3,4-dioxygenation with 2-hydroxy-3-carboxymuconate as the product, which is then decarboxylated by DhbB to 2-hydroxymuconic semialdehyde. This compound is then subject to dehydrogenation and further degraded to citrate cycle intermediates. Transcriptional analysis revealed genes of the dhB gene cluster to be highly expressed during growth with 2,3-dihydroxybenzoate, whereas a downstream-localized gene encoding 2-hydroxymuconic semialdehyde hydrolase, dispensable for 2,3-dihydroxybenzoate metabolism but crucial for 2,3-dihydroxy-p-cumate degradation, was only marginally expressed. This is the first report describing a gene cluster encoding enzymes for the degradation of 2,3-dihydroxybenzoate.
2012-11-16T14:58:01Z
2012-11-16T14:58:01Z
2012-08
Article
Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. 2012, 194 (15):3851-60 J. Bacteriol.
1098-5530
22609919
10.1128/JB.00430-12
http://hdl.handle.net/10033/252493
Journal of bacteriology
en
Archived with thanks to Journal of bacteriology
oai:repository.helmholtz-hzi.de:10033/2697162019-08-30T11:32:41Zcom_10033_620533col_10033_620538
The fungicide fludioxonil antagonizes fluconazole activity in the human fungal pathogen Candida albicans.
Buschart, Anna
Burakowska, Anna
Bilitewski, Ursula
Biological Systems Analysis, Helmholtz Centre for Infection Research, Braunschweig, Germany.
The fungicide fludioxonil is widely used in agriculture. Residua of this fungicide are occasionally detected in fruits and can therefore be ingested by humans. The human fungal pathogen Candida albicans expresses the target of fludioxonil, Nik1p, a type III histidine kinase involved in stress response. Inhibition of yeast and hyphae growth was hardly observable after treatment of C. albicans SC5314 with fludioxonil. As a side effect, however, we observed a concentration-dependent induction of the expression of the genes CDR1 and CDR2, encoding ATP-binding cassette (ABC) transporters. This was independent of the presence of the target of fludioxonil as induction was also observed in a Δnik1 deletion mutant. Deletion of the CDR1 gene aggravated the inhibition of germ tube formation by fludioxonil, indicating that, in the wild-type, the fungicide was discharged from the cell by Cdr1p. Cdr1p is also known as a resistance factor of C. albicans against the commonly used antimycotic fluconazole. Thus, the effect of concurrent exposure to fludioxonil and known cargoes of ABC transporters on their extrusion and the growth of C. albicans was examined. Pre-incubation with fludioxonil decreased the export rate of rhodamine 6G. The resistance to fluconazole was increased by fludioxonil, independently of Nik1p. Therefore, exposure of C. albicans to fludioxonil may lead to increased resistance to fluconazole treatment.
2013-02-18T15:19:02Z
2013-02-18T15:19:02Z
2012-12
Article
The fungicide fludioxonil antagonizes fluconazole activity in the human fungal pathogen Candida albicans. 2012, 61 (Pt 12):1696-703 J. Med. Microbiol.
1473-5644
22918865
10.1099/jmm.0.050963-0
http://hdl.handle.net/10033/269716
Journal of medical microbiology
en
Archived with thanks to Journal of medical microbiology
oai:repository.helmholtz-hzi.de:10033/2699402019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.
Guazzaroni, María-Eugenia
Herbst, Florian-Alexander
Lores, Iván
Tamames, Javier
Peláez, Ana Isabel
López-Cortés, Nieves
Alcaide, María
Del Pozo, Mercedes V
Vieites, José María
von Bergen, Martin
Gallego, José Luis R
Bargiela, Rafael
López-López, Arantxa
Pieper, Dietmar H
Rosselló-Móra, Ramón
Sánchez, Jesús
Seifert, Jana
Ferrer, Manuel
Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain.
Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.
2013-02-21T14:02:20Z
2013-02-21T14:02:20Z
2013-01
Article
Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation. 2013, 7 (1):122-36 ISME J
1751-7370
22832345
10.1038/ismej.2012.82
http://hdl.handle.net/10033/269940
The ISME journal
en
Archived with thanks to The ISME journal
oai:repository.helmholtz-hzi.de:10033/2757132019-08-30T11:35:12Zcom_10033_620533col_10033_621891
From the test tube to the environment - and back.
de Lorenzo, Victor
Pieper, Dietmar
Ramos, Juan L
CSIC- Centro Nacional de Biotecnologia, Madrid, Spain.
2013-03-22T14:07:24Z
2013-03-22T14:07:24Z
2013-01
Article
From the test tube to the environment - and back. 2013, 15 (1):6-11 Environ. Microbiol.
1462-2920
23286645
10.1111/j.1462-2920.2012.02896.x
http://hdl.handle.net/10033/275713
Environmental microbiology
en
Archived with thanks to Environmental microbiology
oai:repository.helmholtz-hzi.de:10033/2837732019-08-30T11:36:05Zcom_10033_620533col_10033_620538
Involvement of the mitogen activated protein kinase Hog1p in the response of Candida albicans to iron availability.
Kaba, Hani Ej
Nimtz, Manfred
Müller, Peter P
Bilitewski, Ursula
ABSTRACT: BACKGROUND: Iron is an essential nutrient for almost all organisms, and generating iron limiting conditions for pathogens is one of the host defense strategies against microbial infections. Excess of iron can be toxic; therefore, iron uptake is tightly controlled. The high affinity iron uptake system of the opportunistic pathogenic yeast Candida albicans has been shown to be essential for virulence. Several transcription factors and regulators of iron uptake genes were identified, but the knowledge of signaling pathways is still limited. Gene expression profiling of the Deltahog1 deletion mutant indicated an involvement of the mitogen activated protein (MAP) kinase Hog1p. However, the function of Hog1p in the response of C. albicans to iron availability was not studied in detail. Thus, we analyzed phenotypic and molecular responses of C. albicans to different iron concentrations particularly with respect to the activity of the Hog1p MAP kinase module. RESULTS: We observed flocculation of yeast cells, when the iron ion concentration was equal to or higher than 5 muM. This phenotype was dependent on the MAP kinase Hog1p and the corresponding MAP kinase kinase Pbs2p. Moreover, high extracellular iron ion concentrations led to hyper-phosphorylation of Hog1p. We determined lower amounts of multicopper ferroxidase (MCFO) proteins and lower ferric reductase activity, when the iron ion concentration in the medium was increased. This effect was also observed for the Deltahog1 mutant. However, the amounts of MCFO proteins and the cell surface ferric reductase activity were increased in the Deltahog1 in comparison to wild type cells. This effect was independent of iron availability in growth media. CONCLUSIONS: In C. albicans, the MAP kinase Hog1p is part of the network regulating the response of the organism to iron availability. Hog1p was transiently phosphorylated under high iron concentrations and was essential for a flocculent phenotype. Furthermore, deletion of HOG1 led to increased levels of components of the reductive iron uptake system in comparison to the wild-type, independent of iron concentrations in the media. However, the additional induction of this system by low iron concentrations was independent of HOG1.
2013-04-24T12:06:10Z
2013-04-24T12:06:10Z
2013-01-24
Article
Involvement of the mitogen activated protein kinase Hog1p in the response of Candida albicans to iron availability. 2013, 13 (1):16 BMC Microbiol.
1471-2180
23347662
10.1186/1471-2180-13-16
http://hdl.handle.net/10033/283773
BMC microbiology
Archived with thanks to BMC microbiology
oai:repository.helmholtz-hzi.de:10033/2930062019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.
de Lima-Morales, Daiana
Chaves-Moreno, Diego
Jarek, Michael
Vilchez-Vargas, Ramiro
Jauregui, Ruy
Pieper, Dietmar H
Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany;
Pseudomonas veronii strain 1YdBTEX2 was isolated from a benzene-contaminated site. Here we report the draft genome sequence of 1YdBTEX2 and its genes associated with aromatic metabolism. The broad catabolic potential of this strain is consistent with the environment from which it was isolated.
2013-05-29T10:39:54Z
2013-05-29T10:39:54Z
2013
Article
Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2. 2013, 1 (3): Genome Announc
2169-8287
23682152
10.1128/genomeA.00258-13
http://hdl.handle.net/10033/293006
Genome announcements
en
Archived with thanks to Genome announcements
oai:repository.helmholtz-hzi.de:10033/2954842019-08-30T11:33:57Zcom_10033_620533col_10033_620538
Direct electrochemical determination of Candida albicans activity.
Hassan, Rabeay Y A
Bilitewski, Ursula
Helmholtz Centre for Infection Research, Working Group BiSA, Inhoffenstr. 7, 38124 Braunschweig, Germany; Microanalysis Lab, Applied Organic Chemistry Department, National Research Centre (NRC), Eltahrir Street, 12311-Dokki, Cairo, Egypt. Electronic address: rabeayy@yhaoo.com.
Despite advances made in the field, rapid detection methods for the human pathogen Candida albicans are still missing. In this regard, bio-electrochemical systems including electrochemical sensors and biosensors satisfy the increasing demand for rapid, reliable, and direct microbial analyses. In this study, the bioelectrochemical characteristics of C. albicans were investigated for use in an analytical system that determines the viability of the organisms. The electrochemical responses of viable and non-viable cells of C. albicans and Saccharomyces cerevisiae were monitored. Cyclic voltammograms (CV) showed an irreversible oxidation peak at about 750mV that accounts for viable cells. The peak current increased at viable cell numbers ranging from 3×10(5) to 1.6×10(7)cells/ml, indicating that the amount of viable cells can be accurately quantified. To elucidate the underlying electron transfer processes, the influence of electron transfer chain (ETC) - inhibitors on the electrochemical behavior of the two organisms were investigated. Inhibition of the function of classical respiratory chain (CRC) led to a decrease in the electrochemical response, whereas the oxidation current increased when the alternative oxidase (AOX) pathway was blocked by salicylhydroxamic acid (SHA). Blocking the AOX pathway improved the electrochemical performance, suggesting an involvement in the CRC, with cytochrome c oxidase (COX) as a relevant protein complex. Mutants, in which components of COX were deleted, showed a lower electro-activity than the wild-type strain. Particularly, deletion of subunit COX5a almost completely abolished the electrochemical signal. We believe that this work can be utilized for the development of early detection assays and opens the door for new technological developments in the field of C. albicans.
2013-07-08T13:36:57Z
2013-07-08T13:36:57Z
2013-05-15
Article
Direct electrochemical determination of Candida albicans activity. 2013, 49C:192-198 Biosens Bioelectron
1873-4235
23747360
10.1016/j.bios.2013.05.015
http://hdl.handle.net/10033/295484
Biosensors & bioelectronics
Archived with thanks to Biosensors & bioelectronics
oai:repository.helmholtz-hzi.de:10033/2974772019-08-30T11:34:22Zcom_10033_620533col_10033_620538
Identification of inhibitors of yeast-to-hyphae transition in Candida albicans by a reporter screening assay.
Heintz-Buschart, Anna
Eickhoff, Holger
Hohn, Erwin
Bilitewski, Ursula
Department of Biological Systems Analysis, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Candida albicans is one of the most common opportunistic fungal pathogens, causing life-threatening disease in immunocompromised patients. As it is not primarily a pathogen, but can exist in a commensal state, we aimed at the identification of new anti-infective compounds which do not eradicate the fungus, but primarily disable a virulence determinant. The yeast–hyphae-dimorphism of C. albicans is considered a major contributor to fungal disease, as mutants locked into either yeast or hyphal state have been shown to be less virulent in the mouse-model. We devised a high-throughput screening procedure which allows us to find inhibitors of the induction of hyphae. Hyphae-formation was induced by nitrogen starvation at 37 °C and neutral pH in a reporter strain, which couples promoter activity of the hyphae-specific HWP1 to β-galactosidase expression. In a pilot screening of 720 novel synthetic compounds, we identified substances which inhibited the outgrowth of germ tubes. They belonged to chemical classes not yet known for antimycotic properties, namely methyl aryl-oxazoline carboxylates, dihydrobenzo[d]isoxazolones and thiazolo[4,5-e]benzoisoxazoles. In conclusion we developed a novel screening assay, which addresses the morphological switch from the yeast form of C. albicans to its hyphal form and identified novel chemical structures with activity against C. albicans.
2013-08-07T14:04:32Z
2013-08-07T14:04:32Z
2013-03-10
Article
Identification of inhibitors of yeast-to-hyphae transition in Candida albicans by a reporter screening assay. 2013, 164 (1):137-42 J. Biotechnol.
1873-4863
23262131
10.1016/j.jbiotec.2012.12.004
http://hdl.handle.net/10033/297477
Journal of biotechnology
en
Archived with thanks to Journal of biotechnology
oai:repository.helmholtz-hzi.de:10033/3050742019-08-30T11:30:32Zcom_10033_620533col_10033_620538
Deletion of the HAMP domains from the histidine kinase CaNik1p of Candida albicans or treatment with fungicides activates the MAP kinase Hog1p in S. cerevisiae transformants.
El-Mowafy, Mohammed
Bahgat, Mahmoud M
Bilitewski, Ursula
Microorganisms use two-component signal transduction (TCST) systems to regulate the response of the organism to changes of environmental conditions. Such systems are absent from mammalian cells and are thus of interest as drug targets. Fungal TCST systems are usually composed of a hybrid histidine kinase, comprising the histidine kinase (HisKA) domain and a receiver domain, a histidine phosphotransfer protein and a response regulator. Among the 11 groups of fungal histidine kinases, group III histidine kinases are of particular relevance as they are essential for the activity of different groups of fungicides. A characteristic feature is the N-terminal amino acid repeat domain comprising multiple HAMP domains, of which the function is still largely unknown. In Candida albicans, a fungal human pathogen, three histidine kinases were identified, of which CaNik1p is a group III histidine kinase. Heterologous expression of this protein in Sacchromyces cerevisiae conferred susceptibility to different fungicides. Fungicide activity was associated with phosphorylation of the mitogen activated protein kinase Hog1p.
2013-11-07T12:05:13Z
2013-11-07T12:05:13Z
2013-09-17
Article
Deletion of the HAMP domains from the histidine kinase CaNik1p of Candida albicans or treatment with fungicides activates the MAP kinase Hog1p in S. cerevisiae transformants. 2013, 13 (1):209 BMC Microbiol.
1471-2180
24044701
10.1186/1471-2180-13-209
http://hdl.handle.net/10033/305074
BMC microbiology
Archived with thanks to BMC microbiology
oai:repository.helmholtz-hzi.de:10033/3229312019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Factors that cause trimethoprim resistance in Streptococcus pyogenes.
Bergmann, René
van der Linden, Mark
Chhatwal, Gursharan S
Nitsche-Schmitz, D Patric
The use of trimethoprim in treatment of Streptococcus pyogenes infections has long been discouraged because it has been widely believed that this pathogen is resistant to this antibiotic. To gain more insight into the extent and molecular basis of trimethoprim resistance in S. pyogenes, we tested isolates from India and Germany and sought the factors that conferred the resistance. Resistant isolates were identified in tests for trimethoprim or trimethoprim-sulfamethoxazole (SXT) susceptibility. Resistant isolates were screened for the known horizontally transferable trimethoprim-insensitive dihydrofolate reductase (dfr) genes dfrG, dfrF, dfrA, dfrD, and dfrK. The nucleotide sequence of the intrinsic dfr gene was determined for resistant isolates lacking the horizontally transferable genes. Based on tentative criteria, 69 out of 268 isolates (25.7%) from India were resistant to trimethoprim. Occurring in 42 of the 69 resistant isolates (60.9%), dfrF appeared more frequently than dfrG (23 isolates; 33.3%) in India. The dfrF gene was also present in a collection of SXT-resistant isolates from Germany, in which it was the only detected trimethoprim resistance factor. The dfrF gene caused resistance in 4 out of 5 trimethoprim-resistant isolates from the German collection. An amino acid substitution in the intrinsic dihydrofolate reductase known from trimethoprim-resistant Streptococcus pneumoniae conferred resistance to S. pyogenes isolates of emm type 102.2, which lacked other aforementioned dfr genes. Trimethoprim may be more useful in treatment of S. pyogenes infections than previously thought. However, the factors described herein may lead to the rapid development and spread of resistance of S. pyogenes to this antibiotic agent.
2014-07-15T13:59:12Z
2014-07-15T13:59:12Z
2014-04
Article
Factors that cause trimethoprim resistance in Streptococcus pyogenes. 2014, 58 (4):2281-8 Antimicrob. Agents Chemother.
1098-6596
24492367
10.1128/AAC.02282-13
http://hdl.handle.net/10033/322931
Antimicrobial agents and chemotherapy
en
Archived with thanks to Antimicrobial agents and chemotherapy
oai:repository.helmholtz-hzi.de:10033/3347592019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing.
Camarinha-Silva, Amélia
Jáuregui, Ruy
Chaves-Moreno, Diego
Oxley, Andrew P A
Schaumburg, Frieder
Becker, Karsten
Wos-Oxley, Melissa L
Pieper, Dietmar H
Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
The anterior nares are an important reservoir for opportunistic pathogens and commensal microorganisms. A barcoded Illumina paired-end sequencing method targeting the 16S ribosomal RNA V1-2 hypervariable region was developed to compare the bacterial diversity of the anterior nares across distinct human populations (volunteers from Germany vs a Babongo Pygmy tribe, Africa). Of the 251 phylotypes detected, 231 could be classified to the genus level and 109 to the species level, including the unambiguous identification of the ubiquitous Staphylococcus aureus and Moraxella catarrhalis. The global bacterial community of both adult populations revealed that they shared 85% of the phylotypes, suggesting that our global bacterial communities have likely been with us for thousands of years. Of the 34 phylotypes unique to the non-westernized population, most were related to members within the suborder Micrococcineae. There was an even more overwelming distinction between children and adults of the same population, suggesting a progression of a childhood community of high-diversity comprising species of Moraxellaceae and Streptococcaceae to an adult community of lower diversity comprising species of Propionibacteriaceae, Clostridiales Incertae Sedis XI, Corynebacteriaceae and Staphylococcaceae. Thus, age was a stronger factor for accounting for differing bacterial assemblages than the origin of the human population sampled.
2014-11-12T11:07:41Z
2014-11-12T11:07:41Z
2014-09
Article
Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing. 2014, 16 (9):2939-52 Environ. Microbiol.
1462-2920
24354520
10.1111/1462-2920.12362
http://hdl.handle.net/10033/334759
Environmental microbiology
en
oai:repository.helmholtz-hzi.de:10033/3388702019-08-30T11:36:04Zcom_10033_620533col_10033_621891
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.
Duarte, Márcia
Jauregui, Ruy
Vilchez-Vargas, Ramiro
Junca, Howard
Pieper, Dietmar H
Research group Microbial interactions and processes (MINP). Helmholtz Centre for infection research, Inhoffenstr. 7, D38124 Braunschweig, Germany.
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de.
2015-01-26T15:10:42Z
2015-01-26T15:10:42Z
2014
Article
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. 2014, 2014: Database (Oxford)
1758-0463
25468931
10.1093/database/bau118
http://hdl.handle.net/10033/338870
Database : the journal of biological databases and curation
en
oai:repository.helmholtz-hzi.de:10033/3386592019-08-30T11:36:33Zcom_10033_620533col_10033_621891
Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.
Kerckhof, Frederiek-Maarten
Courtens, Emilie N P
Geirnaert, Annelies
Hoefman, Sven
Ho, Adrian
Vilchez-Vargas, Ramiro
Pieper, Dietmar H
Jauregui, Ruy
Vlaeminck, Siegfried E
Van de Wiele, Tom
Vandamme, Peter
Heylen, Kim
Boon, Nico
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.
2015-01-22T10:20:31Z
2015-01-22T10:20:31Z
2014
Article
Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. 2014, 9 (6):e99517 PLoS ONE
1932-6203
24937032
10.1371/journal.pone.0099517
http://hdl.handle.net/10033/338659
PloS one
en
oai:repository.helmholtz-hzi.de:10033/3386212019-08-30T11:26:13Zcom_10033_620533col_10033_620534
Influence of fenofibrate treatment on triacylglycerides, diacylglycerides and fatty acids in fructose fed rats.
Kopf, Thomas
Schaefer, Hans-Ludwig
Troetzmueller, Martin
Koefeler, Harald
Broenstrup, Mark
Konovalova, Tatiana
Schmitz, Gerd
Fenofibrate (FF) lowers plasma triglycerides via PPARα activation. Here, we analyzed lipidomic changes upon FF treatment of fructose fed rats. Three groups with 6 animals each were defined as control, fructose-fed and fructose-fed/FF treated. Male Wistar Unilever Rats were subjected to 10% fructose-feeding for 20 days. On day 14, fenofibrate treatment (100 mg/kg p.o.) was initiated and maintained for 7 days. Lipid species in serum were analyzed using mass spectrometry (ESI-MS/MS; LC-FT-MS, GC-MS) on days 0, 14 and 20 in all three groups. In addition, lipid levels in liver and intestine were determined. Short-chain TAGs increased in serum and liver upon fructose-feeding, while almost all TAG-species decreased under FF treatment. Long-chain unsaturated DAG-levels (36:1, 36:2, 36:4, 38:3, 38:4, 38:5) increased upon FF treatment in rat liver and decreased in rat serum. FAs, especially short-chain FAs (12:0, 14:0, 16:0) increased during fructose-challenge. VLDL secretion increased upon fructose-feeding and together with FA-levels decreased to control levels during FF treatment. Fructose challenge of de novo fatty acid synthesis through fatty acid synthase (FAS) may enhance the release of FAs ≤ 16:0 chain length, a process reversed by FF-mediated PPARα-activation.
2015-01-22T11:57:04Z
2015-01-22T11:57:04Z
2014
Article
Influence of fenofibrate treatment on triacylglycerides, diacylglycerides and fatty acids in fructose fed rats. 2014, 9 (9):e106849 PLoS ONE
1932-6203
25198467
10.1371/journal.pone.0106849
http://hdl.handle.net/10033/338621
PloS one
en
oai:repository.helmholtz-hzi.de:10033/3386662019-08-30T11:35:12Zcom_10033_620533col_10033_621891
The sensitivity of DNA cleavage by SpeI and ApaLI to methylation by M.EcoK.
Hofer, Bernd
Helmholtz Centre for infection reseatrch, Inhoofenstr. 7, D-38124 Braunschweig, Germany.
2015-01-22T14:01:54Z
2015-01-22T14:01:54Z
1988-06-10
Article
The sensitivity of DNA cleavage by SpeI and ApaLI to methylation by M.EcoK. 1988, 16 (11):5206 Nucleic Acids Res.
0305-1048
2838811
http://hdl.handle.net/10033/338666
Nucleic acids research
en
oai:repository.helmholtz-hzi.de:10033/3443782019-08-30T11:26:13Zcom_10033_620533col_10033_620534
Antiviral drug discovery: broad-spectrum drugs from nature.
Martinez, J P
Sasse, F
Brönstrup, M
Diez, J
Meyerhans, A
Helmholtz Centre for infection research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany.
Covering: up to April 2014. The development of drugs with broad-spectrum antiviral activities is a long pursued goal in drug discovery. It has been shown that blocking co-opted host-factors abrogates the replication of many viruses, yet the development of such host-targeting drugs has been met with scepticism mainly due to toxicity issues and poor translation to in vivo models. With the advent of new and more powerful screening assays and prediction tools, the idea of a drug that can efficiently treat a wide range of viral infections by blocking specific host functions has re-bloomed. Here we critically review the state-of-the-art in broad-spectrum antiviral drug discovery. We discuss putative targets and treatment strategies, with particular focus on natural products as promising starting points for antiviral lead development.
2015-02-11T15:58:06Z
2015-02-11T15:58:06Z
2015-01
Article
Antiviral drug discovery: broad-spectrum drugs from nature. 2015, 32 (1):29-48 Nat Prod Rep
1460-4752
25315648
10.1039/c4np00085d
http://hdl.handle.net/10033/344378
Natural product reports
en
oai:repository.helmholtz-hzi.de:10033/3445842019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Genome sequences of Alicycliphilus denitrificans strains BC and K601T.
Oosterkamp, Margreet J
Veuskens, Teun
Plugge, Caroline M
Langenhoff, Alette A M
Gerritse, Jan
van Berkel, Willem J H
Pieper, Dietmar H
Junca, Howard
Goodwin, Lynne A
Daligault, Hajnalka E
Bruce, David C
Detter, John C
Tapia, Roxanne
Han, Cliff S
Land, Miriam L
Hauser, Loren J
Smidt, Hauke
Stams, Alfons J M
Alicycliphilus denitrificans strain BC and A. denitrificans strain K601(T) degrade cyclic hydrocarbons. These strains have been isolated from a mixture of wastewater treatment plant material and benzene-polluted soil and from a wastewater treatment plant, respectively, suggesting their role in bioremediation of soil and water. Although the strains are phylogenetically closely related, there are some clear physiological differences. The hydrocarbon cyclohexanol, for example, can be degraded by strain K601(T) but not by strain BC. Furthermore, both strains can use nitrate and oxygen as an electron acceptor, but only strain BC can use chlorate as electron acceptor. To better understand the nitrate and chlorate reduction mechanisms coupled to the oxidation of cyclic compounds, the genomes of A. denitrificans strains BC and K601(T) were sequenced. Here, we report the complete genome sequences of A. denitrificans strains BC and K601(T).
2015-02-19T10:17:22Z
2015-02-19T10:17:22Z
2011-09
Article
Genome sequences of Alicycliphilus denitrificans strains BC and K601T. 2011, 193 (18):5028-9 J. Bacteriol.
1098-5530
21742888
10.1128/JB.00365-11
http://hdl.handle.net/10033/344584
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/3445862019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Gulosibacter molinativorax ON4T molinate hydrolase, a novel cobalt-dependent amidohydrolase.
Duarte, Márcia
Ferreira-da-Silva, Frederico
Lünsdorf, Heinrich
Junca, Howard
Gales, Luís
Pieper, Dietmar H
Nunes, Olga C
A new pathway of molinate mineralization has recently been described. Among the five members of the mixed culture able to promote such a process, Gulosibacter molinativorax ON4(T) has been observed to promote the initial breakdown of the herbicide into ethanethiol and azepane-1-carboxylate. In the current study, the gene encoding the enzyme responsible for molinate hydrolysis was identified and heterologously expressed, and the resultant active protein was purified and characterized. Nucleotide sequence analysis revealed that the gene encodes a 465-amino-acid protein of the metal-dependent hydrolase A subfamily of the amidohydrolase superfamily with a predicted molecular mass of 50.9 kDa. Molinate hydrolase shares the highest amino acid sequence identity (48 to 50%) with phenylurea hydrolases of Arthrobacter globiformis and Mycobacterium brisbanense. However, in contrast to previously described members of the metal-dependent hydrolase A subfamily, molinate hydrolase contains cobalt as the only active-site metal.
2015-02-19T12:16:43Z
2015-02-19T12:16:43Z
2011-10
Article
Gulosibacter molinativorax ON4T molinate hydrolase, a novel cobalt-dependent amidohydrolase. 2011, 193 (20):5810-6 J. Bacteriol.
1098-5530
21840982
10.1128/JB.05054-11
http://hdl.handle.net/10033/344586
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/3464652019-08-30T11:37:00Zcom_10033_620533col_10033_620534
Phenotypic plasticity in a willow leaf beetle depends on host plant species: release and recognition of beetle odors.
Austel, Nadine
Reinecke, Andreas
Björkman, Christer
Hilker, Monika
Meiners, Torsten
Helmholtz-Centre for Infection Research, Inhoffen-Str. 7, Department of Chemical Biology, 38124 Braunschweig, Germany.
Aggregation behavior of herbivorous insects is mediated by a wide range of biotic and abiotic factors. It has been suggested that aggregation behavior of the blue willow leaf beetle Phratora vulgatissima is mediated by both host plant odor and by odor released by the beetles. Previous studies show that the beetles respond to plant odors according to their prior host plant experiences. Here, we analyzed the effect of the host plant species on odor released and perceived by adult P. vulgatissima. The major difference between the odor of beetles feeding on salicin-rich and salicin-poor host plants was the presence of salicylaldehyde in the odor of the former, where both males and females released this compound. Electrophysiological studies showed that the intensity of responses to single components of odor released by beetles was sex specific and dependent on the host plant species with which the beetles were fed. Finally, behavioral studies revealed that males feeding on salicin-rich willows were attracted by salicylaldehyde, whereas females did not respond behaviorally to this compound, despite showing clear antennal responses to it. Finally, the ecological relevance of the influence of a host plant species on the plasticity of beetle odor chemistry, perception, and behavior is discussed.
2015-03-10T12:49:06Z
2015-03-10T12:49:06Z
2015-02
Article
Phenotypic plasticity in a willow leaf beetle depends on host plant species: release and recognition of beetle odors. 2015, 40 (2):109-24 Chem. Senses
1464-3553
25537016
10.1093/chemse/bju065
http://hdl.handle.net/10033/346465
Chemical senses
en
oai:repository.helmholtz-hzi.de:10033/3642602019-08-30T11:34:48Zcom_10033_620533col_10033_620534
Cytotoxic and antivascular 1-methyl-4-(3-fluoro-4-methoxyphenyl)-5-(halophenyl)-imidazoles.
Biersack, Bernhard
Muthukumar, Yazh
Schobert, Rainer
Sasse, Florenz
A series of 1-methyl-4,5-diphenylimidazoles 6 with various patterns of m-halogen substitution at the 5-phenyl ring were tested for cytotoxicity in cancer and nonmalignant cell lines and for their capacity to prevent tube formation in HUVEC cultures. Unlike the monofluoro and difluoro derivatives 6a and 6e, the monobromo and diiodo analogs 6c and 6h were strongly cytotoxic and inhibited the polymerization of tubulin and the tube formation by HUVEC. The dibromo derivative 6g displayed a unique selectivity for KB-3-1 cervix and PC-3 prostate cancer cells. It also inhibited the tube formation by HUVEC and the polymerization of tubulin which is indicative of its potential antiangiogenic activity in solid tumors.
2015-04-09T11:20:36Z
2015-04-09T11:20:36Z
2011-11-01
Article
Cytotoxic and antivascular 1-methyl-4-(3-fluoro-4-methoxyphenyl)-5-(halophenyl)-imidazoles. 2011, 21 (21):6270-3 Bioorg. Med. Chem. Lett.
1464-3405
21963303
10.1016/j.bmcl.2011.09.005
http://hdl.handle.net/10033/364260
Bioorganic & medicinal chemistry letters
en
oai:repository.helmholtz-hzi.de:10033/5554202019-08-30T11:36:32Zcom_10033_620533col_10033_621891
Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1.
Marín, Macarena
Pérez-Pantoja, Danilo
Donoso, Raul
Wray, Victor
González, Bernardo
Pieper, Dietmar H
Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.
2015-05-21T11:09:09Z
2015-05-21T11:09:09Z
2010-03
Article
Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1. 2010, 192 (6):1543-52 J. Bacteriol.
1098-5530
20061479
10.1128/JB.01208-09
http://hdl.handle.net/10033/555420
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/5564662019-08-30T11:37:00Zcom_10033_620533col_10033_621891
Draft Genome Sequence of Rhodococcus sp. Strain 311R.
Ehsani, Elham
Jauregui, Ruy
Geffers, Robert
Jareck, Michael
Boon, Nico
Pieper, Dietmar H
Vilchez-Vargas, Ramiro
Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated from a site contaminated with alkanes and aromatic compounds. Strain 311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the closest related bacteria.
2015-06-05T14:18:54Z
2015-06-05T14:18:54Z
2015
Article
Draft Genome Sequence of Rhodococcus sp. Strain 311R. 2015, 3 (3): Genome Announc
2169-8287
25999565
10.1128/genomeA.00378-15
http://hdl.handle.net/10033/556466
Genome announcements
en
oai:repository.helmholtz-hzi.de:10033/5587402019-08-30T11:37:00Zcom_10033_620533col_10033_621891
Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134.
Pérez-Pantoja, Danilo
Leiva-Novoa, Pablo
Donoso, Raúl A
Little, Cedric
Godoy, Margarita
Pieper, Dietmar H
González, Bernardo
Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
2015-07-01T14:52:33Z
2015-07-01T14:52:33Z
2015-06-15
Article
Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. 2015, 81 (12):3914-24 Appl. Environ. Microbiol.
1098-5336
25795675
10.1128/AEM.04207-14
http://hdl.handle.net/10033/558740
Applied and environmental microbiology
en
oai:repository.helmholtz-hzi.de:10033/6210542018-06-13T02:46:39Zcom_10033_620533col_10033_620538
Virus-like particle production with yeast: ultrastructural and immunocytochemical insights into Pichia pastoris producing high levels of the Hepatitis B surface antigen
Lünsdorf, Heinrich
Gurramkonda, Chandrasekhar
Adnan, Ahmad
Khanna, Navin
Rinas, Ursula
Abstract Background A protective immune response against Hepatitis B infection can be obtained through the administration of a single viral polypeptide, the Hepatitis B surface antigen (HBsAg). Thus, the Hepatitis B vaccine is generated through the utilization of recombinant DNA technology, preferentially by using yeast-based expression systems. However, the polypeptide needs to assemble into spherical particles, so-called virus-like particles (VLPs), to elicit the required protective immune response. So far, no clear evidence has been presented showing whether HBsAg assembles in vivo inside the yeast cell into VLPs or later in vitro during down-stream processing and purification. Results High level production of HBsAg was carried out with recombinant Pichia pastoris using the methanol inducible AOX1 expression system. The recombinant vaccine was isolated in form of VLPs after several down-stream steps from detergent-treated cell lysates. Search for the intracellular localization of the antigen using electron microscopic studies in combination with immunogold labeling revealed the presence of HBsAg in an extended endoplasmic reticulum where it was found to assemble into defined multi-layered, lamellar structures. The distance between two layers was determined as ~6 nm indicating that these lamellas represent monolayers of well-ordered HBsAg subunits. We did not find any evidence for the presence of VLPs within the endoplasmic reticulum or other parts of the yeast cell. Conclusions It is concluded that high level production and intrinsic slow HBsAg VLP assembly kinetics are leading to retention and accumulation of the antigen in the endoplasmic reticulum where it assembles at least partly into defined lamellar structures. Further transport of HBsAg to the Golgi apparatus is impaired thus leading to secretory pathway disfunction and the formation of an extended endoplasmic reticulum which bulges into irregular cloud-shaped formations. As VLPs were not found within the cells it is concluded that the VLP assembly process must take place during down-stream processing after detergent-mediated disassembly of HBsAg lamellas and subsequent reassembly of HBsAg into spherical VLPs.
2017-08-14T10:15:19Z
2017-08-14T10:15:19Z
2011-06-26
2015-09-04T08:22:20Z
Journal Article
Microbial Cell Factories. 2011 Jun 26;10(1):48
http://dx.doi.org/10.1186/1475-2859-10-48
http://hdl.handle.net/10033/621054
en
Lünsdorf et al; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6206822019-08-30T11:35:39Zcom_10033_620533col_10033_621891
Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties
Masoudi-Nejad, Ali
Movahedi, Sara
Jáuregui, Ruy
Abstract Background Due to its overarching role in genome function, sequence-dependent DNA curvature continues to attract great attention. The DNA double helix is not a rigid cylinder, but presents both curvature and flexibility in different regions, depending on the sequence. More in depth knowledge of the various orders of complexity of genomic DNA structure has allowed the design of sophisticated bioinformatics tools for its analysis and manipulation, which, in turn, have yielded a better understanding of the genome itself. Curved DNA is involved in many biologically important processes, such as transcription initiation and termination, recombination, DNA replication, and nucleosome positioning. CpG islands and tandem repeats also play significant roles in the dynamics and evolution of genomes. Results In this study, we analyzed the relationship between these three structural features within rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genomes. A genome-scale prediction of curvature distribution in rice and Arabidopsis indicated that most of the chromosomes of both genomes have maximal chromosomal DNA curvature adjacent to the centromeric region. By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value. Further analysis of CpG islands shows a clear interdependence between curvature value, repeat frequencies and CpG islands. Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency. A statistical evaluation demonstrates the significance and non-randomness of these features. Conclusions This study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.
2017-01-06T10:23:54Z
2017-01-06T10:23:54Z
2011-05-06
2015-09-04T08:23:33Z
Journal Article
BMC Genomics. 2011 May 06;12(1):214
http://dx.doi.org/10.1186/1471-2164-12-214
http://hdl.handle.net/10033/620682
en
Masoudi-Nejad et al; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6208452018-06-13T00:05:03Zcom_10033_620533col_10033_620534
Myxobacteria: natural pharmaceutical factories
Diez, Juana
Martinez, Javier P
Mestres, Jordi
Sasse, Florenz
Frank, Ronald
Meyerhans, Andreas
Helmholtz Centre for infection research, Ihoffenstr. 7, 38124 Braunschweig, Germany.
Abstract Myxobacteria are amongst the top producers of natural products. The diversity and unique structural properties of their secondary metabolites is what make these social microbes highly attractive for drug discovery. Screening of products derived from these bacteria has revealed a puzzling amount of hits against infectious and non-infectious human diseases. Preying mainly on other bacteria and fungi, why would these ancient hunters manufacture compounds beneficial for us? The answer may be the targeting of shared processes and structural features conserved throughout evolution.
2017-03-06T11:42:08Z
2017-03-06T11:42:08Z
2012-04-30
2015-09-04T08:25:28Z
Article
Microbial Cell Factories. 2012 Apr 30;11(1):52
http://dx.doi.org/10.1186/1475-2859-11-52
http://hdl.handle.net/10033/620845
en
Diez et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6207842019-08-30T11:26:12Zcom_10033_620533col_10033_620538
Deletion of the HAMP domains from the histidine kinase CaNik1p of Candida albicans or treatment with fungicides activates the MAP kinase Hog1p in S. cerevisiae transformants
El-Mowafy, Mohammed
Bahgat, Mahmoud M
Bilitewski, Ursula
Abstract Background Microorganisms use two-component signal transduction (TCST) systems to regulate the response of the organism to changes of environmental conditions. Such systems are absent from mammalian cells and are thus of interest as drug targets. Fungal TCST systems are usually composed of a hybrid histidine kinase, comprising the histidine kinase (HisKA) domain and a receiver domain, a histidine phosphotransfer protein and a response regulator. Among the 11 groups of fungal histidine kinases, group III histidine kinases are of particular relevance as they are essential for the activity of different groups of fungicides. A characteristic feature is the N-terminal amino acid repeat domain comprising multiple HAMP domains, of which the function is still largely unknown. In Candida albicans, a fungal human pathogen, three histidine kinases were identified, of which CaNik1p is a group III histidine kinase. Heterologous expression of this protein in Sacchromyces cerevisiae conferred susceptibility to different fungicides. Fungicide activity was associated with phosphorylation of the mitogen activated protein kinase Hog1p. Results We have constructed mutated versions of CaNik1p, from which either all HAMP domains were deleted (CaNik1pΔHAMP) or in which the histidine kinase or the receiver domains were not-functional. Expression of CaNIK1ΔHAMP in S. cerevisiae led to severe growth inhibition. Normal growth could be restored by either replacing the phosphate-accepting histidine residue in CaNik1pΔHAMP or by expressing CaNIK1ΔHAMP in S. cerevisiae mutants, in which single genes encoding several components of the HOG pathway were deleted. Expression of proteins with non-functional histidine kinase or receiver domains resulted in complete loss of susceptibility to antifungals, such as fludioxonil. Conditions leading to growth inhibition of transformants also led to phosphorylation of the MAP kinase Hog1p. Conclusion Our results show that functional histidine kinase and receiver domains of CaNik1p were essential for antifungal susceptibility and for activation of the Hog1p. Moreover, for the first time we show that deletion of all HAMP domains from CaNik1p led to activation of Hog1p without an external stimulus. This phenotype was similar to the effects obtained upon treatment with fungicides, as in both cases growth inhibition correlated with Hog1p activation and was dependent on the functionality of the conserved phosphate-accepting histidine residue.
2017-01-27T11:38:20Z
2017-01-27T11:38:20Z
2013-09-17
2015-09-04T08:26:59Z
Journal Article
BMC Microbiology. 2013 Sep 17;13(1):209
http://dx.doi.org/10.1186/1471-2180-13-209
http://hdl.handle.net/10033/620784
en
El-Mowafy et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6207812018-06-12T18:07:03Zcom_10033_620533col_10033_620534
Elevated expression of VEGFR-3 in lymphatic endothelial cells from lymphangiomas
Norgall, Susanne
Papoutsi, Maria
Rössler, Jochen
Schweigerer, Lothar
Wilting, Jörg
Weich, Herbert A
Abstract Background Lymphangiomas are neoplasias of childhood. Their etiology is unknown and a causal therapy does not exist. The recent discovery of highly specific markers for lymphatic endothelial cells (LECs) has permitted their isolation and characterization, but expression levels and stability of molecular markers on LECs from healthy and lymphangioma tissues have not been studied yet. We addressed this problem by profiling LECs from normal dermis and two children suffering from lymphangioma, and also compared them with blood endothelial cells (BECs) from umbilical vein, aorta and myometrial microvessels. Methods Lymphangioma tissue samples were obtained from two young patients suffering from lymphangioma in the axillary and upper arm region. Initially isolated with anti-CD31 (PECAM-1) antibodies, the cells were separated by FACS sorting and magnetic beads using anti-podoplanin and/or LYVE-1 antibodies. Characterization was performed by FACS analysis, immunofluorescence staining, ELISA and micro-array gene analysis. Results LECs from foreskin and lymphangioma had an almost identical pattern of lymphendothelial markers such as podoplanin, Prox1, reelin, cMaf and integrin-α1 and -α9. However, LYVE-1 was down-regulated and VEGFR-2 and R-3 were up-regulated in lymphangiomas. Prox1 was constantly expressed in LECs but not in any of the BECs. Conclusion LECs from different sources express slightly variable molecular markers, but can always be distinguished from BECs by their Prox1 expression. High levels of VEGFR-3 and -2 seem to contribute to the etiology of lymphangiomas.
2017-01-27T11:33:16Z
2017-01-27T11:33:16Z
2007-06-21
2015-09-04T08:27:25Z
Journal Article
BMC Cancer. 2007 Jun 21;7(1):105
http://dx.doi.org/10.1186/1471-2407-7-105
http://hdl.handle.net/10033/620781
en
Norgall et al.
oai:repository.helmholtz-hzi.de:10033/6207632019-08-30T11:28:23Zcom_10033_620533col_10033_620534
The full-ORF clone resource of the German cDNA Consortium
Bechtel, Stephanie
Rosenfelder, Heiko
Duda, Anny
Peter Schmidt, Christian
Ernst, Ute
Wellenreuther, Ruth
Mehrle, Alexander
Schuster, Claudia
Bahr, Andre
Blöcker, Helmut
Heubner, Dagmar
Hoerlein, Andreas
Michel, Guenter
Wedler, Holger
Köhrer, Karl
Ottenwälder, Birgit
Poustka, Annemarie
Wiemann, Stefan
Schupp, Ingo
Abstract Background With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ORF clones thus needs to be extended. In combination with a unique and versatile cloning system, these will provide the tools for genome-wide systematic functional analyses, to achieve a deeper insight into complex biological processes. Results Here we describe the generation of a full-ORF clone resource of human genes applying the Gateway cloning technology (Invitrogen). A pipeline for efficient cloning and sequencing was developed and a sample tracking database was implemented to streamline the clone production process targeting more than 2,200 different ORFs. In addition, a robust cloning strategy was established, permitting the simultaneous generation of two clone variants that contain a particular ORF with as well as without a stop codon by the implementation of only one additional working step into the cloning procedure. Up to 92 % of the targeted ORFs were successfully amplified by PCR and more than 93 % of the amplicons successfully cloned. Conclusion The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.
2017-01-27T09:22:08Z
2017-01-27T09:22:08Z
2007-10-31
2015-09-04T08:28:36Z
Journal Article
BMC Genomics. 2007 Oct 31;8(1):399
http://dx.doi.org/10.1186/1471-2164-8-399
http://hdl.handle.net/10033/620763
en
Bechtel et al.
oai:repository.helmholtz-hzi.de:10033/6207622018-06-12T22:36:04Zcom_10033_620533col_10033_620534
Mouse lung contains endothelial progenitors with high capacity to form blood and lymphatic vessels
Schniedermann, Judith
Rennecke, Moritz
Buttler, Kerstin
Richter, Georg
Städtler, Anna-Maria
Norgall, Susanne
Badar, Muhammad
Barleon, Bernhard
May, Tobias
Wilting, Jörg
Weich, Herbert A
Abstract Background Postnatal endothelial progenitor cells (EPCs) have been successfully isolated from whole bone marrow, blood and the walls of conduit vessels. They can, therefore, be classified into circulating and resident progenitor cells. The differentiation capacity of resident lung endothelial progenitor cells from mouse has not been evaluated. Results In an attempt to isolate differentiated mature endothelial cells from mouse lung we found that the lung contains EPCs with a high vasculogenic capacity and capability of de novo vasculogenesis for blood and lymph vessels. Mouse lung microvascular endothelial cells (MLMVECs) were isolated by selection of CD31+ cells. Whereas the majority of the CD31+ cells did not divide, some scattered cells started to proliferate giving rise to large colonies (> 3000 cells/colony). These highly dividing cells possess the capacity to integrate into various types of vessels including blood and lymph vessels unveiling the existence of local microvascular endothelial progenitor cells (LMEPCs) in adult mouse lung. EPCs could be amplified > passage 30 and still expressed panendothelial markers as well as the progenitor cell antigens, but not antigens for immune cells and hematopoietic stem cells. A high percentage of these cells are also positive for Lyve1, Prox1, podoplanin and VEGFR-3 indicating that a considerabe fraction of the cells are committed to develop lymphatic endothelium. Clonogenic highly proliferating cells from limiting dilution assays were also bipotent. Combined in vitro and in vivo spheroid and matrigel assays revealed that these EPCs exhibit vasculogenic capacity by forming functional blood and lymph vessels. Conclusion The lung contains large numbers of EPCs that display commitment for both types of vessels, suggesting that lung blood and lymphatic endothelial cells are derived from a single progenitor cell.
2017-01-27T09:21:04Z
2017-01-27T09:21:04Z
2010-07-01
2015-09-04T08:28:40Z
Journal Article
BMC Cell Biology. 2010 Jul 01;11(1):50
http://dx.doi.org/10.1186/1471-2121-11-50
http://hdl.handle.net/10033/620762
en
Schniedermann et al.
oai:repository.helmholtz-hzi.de:10033/6207022019-08-30T11:37:00Zcom_10033_620533col_10033_620534
Identification of myxobacteria-derived HIV inhibitors by a high-throughput two-step infectivity assay
Martinez, Javier P
Hinkelmann, Bettina
Fleta-Soriano, Eric
Steinmetz, Heinrich
Jansen, Rolf
Diez, Juana
Frank, Ronald
Sasse, Florenz
Meyerhans, Andreas
Abstract Background Drug-resistance and therapy failure due to drug-drug interactions are the main challenges in current treatment against Human Immunodeficiency Virus (HIV) infection. As such, there is a continuous need for the development of new and more potent anti-HIV drugs. Here we established a high-throughput screen based on the highly permissive TZM-bl cell line to identify novel HIV inhibitors. The assay allows discriminating compounds acting on early and/or late steps of the HIV replication cycle. Results The platform was used to screen a unique library of secondary metabolites derived from myxobacteria. Several hits with good anti-HIV profiles were identified. Five of the initial hits were tested for their antiviral potency. Four myxobacterial compounds, sulfangolid C, soraphen F, epothilon D and spirangien B, showed EC50 values in the nM range with SI > 15. Interestingly, we found a high amount of overlapping hits compared with a previous screen for Hepatitis C Virus (HCV) using the same library. Conclusion The unique structures and mode-of-actions of these natural compounds make myxobacteria an attractive source of chemicals for the development of broad-spectrum antivirals. Further biological and structural studies of our initial hits might help recognize smaller drug-like derivatives that in turn could be synthesized and further optimized.
2017-01-16T15:27:00Z
2017-01-16T15:27:00Z
2013-09-24
2015-09-04T08:30:47Z
Journal Article
Microbial Cell Factories. 2013 Sep 24;12(1):85
http://dx.doi.org/10.1186/1475-2859-12-85
http://hdl.handle.net/10033/620702
en
Martinez et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/6206842019-08-30T11:35:39Zcom_10033_620533col_10033_620534
The myxobacterial metabolite ratjadone A inhibits HIV infection by blocking the Rev/CRM1-mediated nuclear export pathway
Fleta-Soriano, Eric
Martinez, Javier P
Hinkelmann, Bettina
Gerth, Klaus
Washausen, Peter
Diez, Juana
Frank, Ronald
Sasse, Florenz
Meyerhans, Andreas
Abstract Background The nuclear export of unspliced and partially spliced HIV-1 mRNA is mediated by the recognition of a leucine-rich nuclear export signal (NES) in the HIV Rev protein by the host protein CRM1/Exportin1. This makes the CRM1-Rev complex an attractive target for the development of new antiviral drugs. Here we tested the anti-HIV efficacy of ratjadone A, a CRM1 inhibitor derived from myxobacteria. Results Ratjadone A inhibits HIV infection in vitro in a dose-dependent manner with EC50 values at the nanomolar range. The inhibitory effect of ratjadone A occurs around 12 hours post-infection and is specific for the Rev/CRM1-mediated nuclear export pathway. By using a drug affinity responsive target stability (DARTS) assay we could demonstrate that ratjadone A interferes with the formation of the CRM1-Rev-NES complex by binding to CRM1 but not to Rev. Conclusion Ratjadone A exhibits strong anti-HIV activity but low selectivity due to toxic effects. Although this limits its potential use as a therapeutic drug, further studies with derivatives of ratjadones might help to overcome these difficulties in the future.
2017-01-06T10:25:34Z
2017-01-06T10:25:34Z
2014-01-29
2015-09-04T08:31:31Z
Journal Article
Microbial Cell Factories. 2014 Jan 29;13(1):17
http://dx.doi.org/10.1186/1475-2859-13-17
http://hdl.handle.net/10033/620684
en
Fleta-Soriano et al.; licensee BioMed Central Ltd.
oai:repository.helmholtz-hzi.de:10033/5775292019-08-30T11:34:48Zcom_10033_620533col_10033_620534
Soraphen A: A broad-spectrum antiviral natural product with potent anti-hepatitis C virus activity.
Koutsoudakis, George
Romero-Brey, Inés
Berger, Carola
Pérez-Vilaró, Gemma
Monteiro Perin, Paula
Vondran, Florian Wolfgang Rudolf
Kalesse, Markus
Harmrolfs, Kirsten
Müller, Rolf
Martinez, Javier P
Pietschmann, Thomas
Bartenschlager, Ralf
Brönstrup, Mark
Meyerhans, Andreas
Díez, Juana
TWINCORE, Centre for Experimental and Clinical Infection Research, Feodor-Lynen Str. 7, 30625, Hannover, Germany.
Soraphen A (SorA) is a myxobacterial metabolite that inhibits the acetyl-CoA carboxylase, a key enzyme in lipid biosynthesis. We have previously identified SorA to efficiently inhibit the human immunodeficiency virus (HIV). The aim of the present study was to evaluate the capacity of SorA and analogues to inhibit hepatitis C virus (HCV) infection.
2015-09-18T09:08:09Z
2015-09-18T09:08:09Z
2015-06-10
Article
Soraphen A: A broad-spectrum antiviral natural product with potent anti-hepatitis C virus activity. 2015: J. Hepatol.
1600-0641
26070407
10.1016/j.jhep.2015.06.002
http://hdl.handle.net/10033/577529
Journal of hepatology
oai:repository.helmholtz-hzi.de:10033/5794922019-08-30T11:32:41Zcom_10033_620533col_10033_620534
High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae.
Sergeev, Galina
Roy, Sambit
Jarek, Michael
Zapolskii, Viktor
Kaufmann, Dieter E
Nandy, Ranjan K
Tegge, Werner
Pathogenic serotypes of Vibrio cholerae cause the life-threatening diarrheal disease cholera. The increasing development of bacterial resistances against the known antibiotics necessitates the search for new antimicrobial compounds and targets for this pathogen.
2015-10-08T09:45:39Z
2015-10-08T09:45:39Z
2014
Article
High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae. 2014, 14:49 BMC Microbiol.
1471-2180
24568688
10.1186/1471-2180-14-49
http://hdl.handle.net/10033/579492
BMC microbiology
en
oai:repository.helmholtz-hzi.de:10033/5794992019-08-30T11:36:59Zcom_10033_620533col_10033_621891
Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.
Jiménez, Diego Javier
Chaves-Moreno, Diego
van Elsas, Jan Dirk
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, "profiling" of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.
2015-10-08T14:42:22Z
2015-10-08T14:42:22Z
2015
Article
Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw. 2015, 5:13845 Sci Rep
2045-2322
26343383
10.1038/srep13845
http://hdl.handle.net/10033/579499
Scientific reports
en
oai:repository.helmholtz-hzi.de:10033/5810772019-08-30T11:24:31Zcom_10033_620533col_10033_621891
Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers.
Kümmel, Steffen
Herbst, Florian-Alexander
Bahr, Arne
Duarte, Márcia
Pieper, Dietmar H
Jehmlich, Nico
Seifert, Jana
von Bergen, Martin
Bombach, Petra
Richnow, Hans H
Vogt, Carsten
UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, Leipzig, Germany.
Polycyclic aromatic hydrocarbons (PAH) are widespread and persistent environmental contaminants, especially in oxygen-free environments. The occurrence of anaerobic PAH-degrading bacteria and their underlying metabolic pathways are rarely known. In this study, PAH degraders were enriched in laboratory microcosms under sulfate-reducing conditions using groundwater and sediment samples from four PAH-contaminated aquifers. Five enrichment cultures were obtained showing sulfate-dependent naphthalene degradation. Mineralization of naphthalene was demonstrated by the formation of sulfide concomitant with the depletion of naphthalene and the development of (13)C-labeled CO2 from [(13)C6]-naphthalene. 16S rRNA gene and metaproteome analyses revealed that organisms related to Desulfobacterium str. N47 were the main naphthalene degraders in four enrichment cultures. Protein sequences highly similar to enzymes of the naphthalene degradation pathway of N47 were identified, suggesting that naphthalene was activated by a carboxylase, and that the central metabolite 2-naphthoyl-CoA was further reduced by two reductases. The data indicate an importance of members of the family Desulfobacteraceae for naphthalene degradation under sulfate-reducing conditions in freshwater environments.
2015-10-26T10:21:23Z
2015-10-26T10:21:23Z
2015-03
Article
Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers. 2015, 91 (3): FEMS Microbiol. Ecol.
1574-6941
25764566
10.1093/femsec/fiv006
http://hdl.handle.net/10033/581077
FEMS microbiology ecology
en
oai:repository.helmholtz-hzi.de:10033/5811202019-08-30T11:35:14Zcom_10033_620533col_10033_621891
Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway.
Martínez-Lavanchy, P M
Chen, Z
Lünsmann, V
Marin-Cevada, V
Vilchez-Vargas, Ramiro
Pieper, D H
Reiche, N
Kappelmeyer, U
Imparato, V
Junca, Howard
Nijenhuis, I
Müller, J A
Kuschk, P
Heipieper, H J
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.
2015-10-26T15:09:15Z
2015-10-26T15:09:15Z
2015-09-15
Article
Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway. 2015, 81 (18):6241-52 Appl. Environ. Microbiol.
1098-5336
26150458
10.1128/AEM.01822-15
http://hdl.handle.net/10033/581120
Applied and environmental microbiology
en
info:eu-repo/grantAgreement/EC/FP7/211684
openAccess
oai:repository.helmholtz-hzi.de:10033/5823992019-08-30T11:35:08Zcom_10033_620533col_10033_621891
Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
Burbach, Katharina
Seifert, Jana
Pieper, Dietmar H.
Camarinha-Silva, Amélia
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Institute of Animal Science; University of Hohenheim; Stuttgart Germany
Institute of Animal Science; University of Hohenheim; Stuttgart Germany
Microbial Interactions and Processes Research Group; Helmholtz Centre for Infection Research; Braunschweig Germany
Institute of Animal Science; University of Hohenheim; Stuttgart Germany
2015-11-19T12:37:32Z
2015-11-19T12:37:32Z
2015-11
Article
Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions 2015:n/a MicrobiologyOpen
20458827
26541370
10.1002/mbo3.312
http://hdl.handle.net/10033/582399
MicrobiologyOpen
http://doi.wiley.com/10.1002/mbo3.312
oai:repository.helmholtz-hzi.de:10033/5933152019-08-30T11:35:13Zcom_10033_620533col_10033_621891
Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains.
Chaves-Moreno, Diego
Wos-Oxley, Melissa L
Jáuregui, Ruy
Medina, Eva
Oxley, Andrew P A
Pieper, Dietmar H
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Understanding the behaviour of opportunistic pathogens such as Staphylococcus aureus in their natural human niche holds great medical interest. With the development of sensitive molecular methods and deep-sequencing technology, it is now possible to robustly assess the global transcriptome of bacterial species in their human habitat. However, as the genomes of the colonizing strains are often not available compiling the pan-genome for the species of interest may provide an effective method to reliably and rapidly compile the transcriptome of a bacterial species. The pan-genome of S. aureus and its associated core and accessory components were compiled based on 25 genomes and comprises a total of 65,557 proteins clustering into 4,198 Orthologous Groups (OGs). The generated gene catalogue was used to assign RNAseq-derived sequence reads to S. aureus in a variety of in vitro and in vivo samples. In all cases, the number of reads that could be assigned to S. aureus was greater using the OG database than using a reference genome. Growth of two S. aureus strains in synthetic nasal medium confirmed that both strains experienced strong iron starvation. Traits such as purine metabolism appeared to be more affected in a typical nasal colonizer than in a strain representative of the S. aureus USA300 lineage. Mapping sequencing reads from a metatranscriptome generated from the human anterior nares allowed the identification of genes highly expressed by S. aureus in vivo. The OG database generated in this study represents a useful tool to obtain a snapshot of the functional attributes of S. aureus under different in vitro and in vivo conditions. The approach proved to be advantageous to assign sequencing reads to bacterial strains when RNAseq data is derived from samples where strain information and/or the corresponding genome/s are unavailable.
2016-01-12T09:23:42Z
2016-01-12T09:23:42Z
2015
Article
Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains. 2015, 10 (12):e0145861 PLoS ONE
1932-6203
26717500
10.1371/journal.pone.0145861
http://hdl.handle.net/10033/593315
PloS one
en
oai:repository.helmholtz-hzi.de:10033/5933882019-08-30T11:35:11Zcom_10033_620533col_10033_621891
Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes
Lopez-Fernandez, Margarita
Cherkouk, Andrea
Vilchez Vargas, Ramiro
Jauregui, Ruy
Pieper, Dietmar
Boon, Nico
Sanchez-Castro, Ivan
Merroun, Mohamed L.
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
2016-01-14T10:04:45Z
2016-01-14T10:04:45Z
2015-05-30
Article
Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes 2015, 70 (4):922 Microbial Ecology
0095-3628
26024740
10.1007/s00248-015-0630-7
http://hdl.handle.net/10033/593388
Microbial Ecology
http://link.springer.com/10.1007/s00248-015-0630-7
oai:repository.helmholtz-hzi.de:10033/5954332019-08-30T11:33:57Zcom_10033_620533col_10033_620534
Myxobacteria: natural pharmaceutical factories.
Diez, Juana
Martinez, Javier P
Mestres, Jordi
Sasse, Florenz
Frank, Ronald
Meyerhans, Andreas
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Myxobacteria are amongst the top producers of natural products. The diversity and unique structural properties of their secondary metabolites is what make these social microbes highly attractive for drug discovery. Screening of products derived from these bacteria has revealed a puzzling amount of hits against infectious and non-infectious human diseases. Preying mainly on other bacteria and fungi, why would these ancient hunters manufacture compounds beneficial for us? The answer may be the targeting of shared processes and structural features conserved throughout evolution.
2016-02-02T12:37:58Z
2016-02-02T12:37:58Z
2012
Article
Myxobacteria: natural pharmaceutical factories. 2012, 11:52 Microb. Cell Fact.
1475-2859
22545867
10.1186/1475-2859-11-52
http://hdl.handle.net/10033/595433
Microbial cell factories
en
eu-repo/grantAgreement/EC/FP7/261466
openAccess
oai:repository.helmholtz-hzi.de:10033/5955142019-08-30T11:35:13Zcom_10033_620533col_10033_621891
Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems.
Grunert, Oliver
Hernandez-Sanabria, Emma
Vilchez-Vargas, Ramiro
Jauregui, Ruy
Pieper, Dietmar H
Perneel, Maaike
Van Labeke, Marie-Christine
Reheul, Dirk
Boon, Nico
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.
2016-02-03T09:12:37Z
2016-02-03T09:12:37Z
2016
Article
Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems. 2016, 6:18837 Sci Rep
2045-2322
26728128
10.1038/srep18837
http://hdl.handle.net/10033/595514
Scientific reports
en
oai:repository.helmholtz-hzi.de:10033/5959162019-08-30T11:28:23Zcom_10033_620533col_10033_620534
Integration of CD45-positive leukocytes into newly forming lymphatics of adult mice.
Buttler, K
Lohrberg, M
Gross, G
Weich, H A
Wilting, J
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The embryonic origin of lymphatic endothelial cells (LECs) has been a matter of controversy since more than a century. However, recent studies in mice have supported the concept that embryonic lymphangiogenesis is a complex process consisting of growth of lymphatics from specific venous segments as well as the integration of lymphangioblasts into the lymphatic networks. Similarly, the mechanisms of adult lymphangiogenesis are poorly understood and have rarely been studied. We have recently shown that endothelial progenitor cells isolated from the lung of adult mice have the capacity to form both blood vessels and lymphatics when grafted with Matrigel plugs into the skin of syngeneic mice. Here, we followed up on these experiments and studied the behavior of host leukocytes during lymphangiogenesis in the Matrigel plugs. We observed a striking co-localization of CD45(+) leukocytes with the developing lymphatics. Numerous CD45(+) cells expressed the LEC marker podoplanin and were obviously integrated into the lining of lymphatic capillaries. This indicates that, similar to inflammation-induced lymphangiogenesis in man, circulating CD45(+) cells of adult mice are capable of initiating lymphangiogenesis and of adopting a lymphvasculogenic cellular differentiation program. The data are discussed in the context of embryonic and inflammation-induced lymphangiogenesis.
2016-02-09T09:28:37Z
2016-02-09T09:28:37Z
2016-01-09
Article
Integration of CD45-positive leukocytes into newly forming lymphatics of adult mice. 2016: Histochem. Cell Biol.
1432-119X
26748643
10.1007/s00418-015-1399-y
http://hdl.handle.net/10033/595916
Histochemistry and cell biology
oai:repository.helmholtz-hzi.de:10033/5962642019-08-30T11:31:49Zcom_10033_620533col_10033_621891
Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters.
de Lima-Morales, Daiana
Chaves-Moreno, Diego
Wos-Oxley, Melissa L
Jáuregui, Ruy
Vilchez-Vargas, Ramiro
Pieper, Dietmar H
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR.
2016-02-15T13:58:40Z
2016-02-15T13:58:40Z
2015
Article
Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters. 2015, 82 (1):167-73 Appl. Environ. Microbiol.
1098-5336
26475106
10.1128/AEM.03026-15
http://hdl.handle.net/10033/596264
Applied and environmental microbiology
en
oai:repository.helmholtz-hzi.de:10033/5969272019-08-30T11:31:49Zcom_10033_620533col_10033_621891
Linking microbial community and catabolic gene structures during the adaptation of three contaminated soils under continuous long term pollutant stress.
Lima-Morales, Daiana
Jáuregui, Ruy
Camarinha-Silva, Amelia
Geffers, Robert
Pieper, Dietmar H
Vilchez Vargas, Ramiro
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes for a period of 3 months. Different to the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in-situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes were increasing in relative abundance, indicating their superior fitness to pollution stress. Commonalities, but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes were increasing in relative abundance in SUI microcosms after short-term stress with benzene, where catabolic gene surveys indicated metabolic routes enriched. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the metabolic net, indicating that a highly adapted community has been enriched, which had to adapt its gene pool to meet novel challenges.
2016-02-22T14:39:38Z
2016-02-22T14:39:38Z
2016-02-05
Article
Linking microbial community and catabolic gene structures during the adaptation of three contaminated soils under continuous long term pollutant stress. 2016: Appl. Environ. Microbiol.
1098-5336
26850298
10.1128/AEM.03482-15
http://hdl.handle.net/10033/596927
Applied and environmental microbiology
oai:repository.helmholtz-hzi.de:10033/5992592019-11-21T13:17:44Zcom_10033_620533col_10033_620538col_10033_620538
Regulation of Candida albicans Interaction with Macrophages through the Activation of HOG Pathway by Genistein
Cui, Shuna
Hassan, Rabeay
Heintz-Buschart, Anna
Bilitewski, Ursula
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
2016-02-25T15:46:22Z
2016-02-25T15:46:22Z
2016-01-28
Article
Regulation of Candida albicans Interaction with Macrophages through the Activation of HOG Pathway by Genistein 2016, 21 (2):162 Molecules
1420-3049
26828477
10.3390/molecules21020162
http://hdl.handle.net/10033/599259
Molecules
http://www.mdpi.com/1420-3049/21/2/162
oai:repository.helmholtz-hzi.de:10033/6011392019-08-30T11:31:49Zcom_10033_620533col_10033_621891
Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene.
Verstraelen, Hans
Vilchez-Vargas, Ramiro
Desimpel, Fabian
Jauregui, Ruy
Vankeirsbilck, Nele
Weyers, Steven
Verhelst, Rita
De Sutter, Petra
Pieper, Dietmar H
Van De Wiele, Tom
Helmholtz Centre for infection research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.
Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar inasmuch B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.
2016-03-10T13:25:15Z
2016-03-10T13:25:15Z
2016
Article
Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene. 2016, 4:e1602 PeerJ
2167-8359
26823997
10.7717/peerj.1602
http://hdl.handle.net/10033/601139
PeerJ
en
oai:repository.helmholtz-hzi.de:10033/6021932019-08-30T11:31:49Zcom_10033_620533col_10033_621891
RiMINI - the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial.
Schulz, Christian
Schütte, Kerstin
Kropf, Siegfried
Schmitt, Friedhelm C
Vasapolli, Riccardo
Kliegis, Leon M
Riegger, Antonia
Malfertheiner, Peter
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Hepatic encephalopathy (HE) is a clinically significant complication of liver cirrhosis impacting on the patients' quality of life. Minimal hepatic encephalopathy (MHE) is diagnosed by psychometric tests, found in up to 80 % of patients with liver cirrhosis and carries a high risk of progression to overt HE. Continuous therapy with rifaximin in combination with lactulose significantly reduces the risk of overt HE, recurrence of HE and HE-related hospitalizations in randomized, double-blind, placebo-controlled clinical trials. Rifaximin is approved for the therapy of overt HE in Germany. Treatment with lactulose has been shown to improve cognitive functions in patients with liver cirrhosis. Data from prospective clinical trials comparing the efficacy of rifaximin alone against a combination of rifaximin and lactulose in the treatment of MHE are scarce. Changes in the microbiome of the upper and lower gastrointestinal tract as a result of therapy with rifaximin have not yet been addressed in clinical studies.
2016-03-18T10:48:42Z
2016-03-18T10:48:42Z
2016
Article
RiMINI - the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial. 2016, 17 (1):111 Trials
1745-6215
26926775
10.1186/s13063-016-1205-8
http://hdl.handle.net/10033/602193
Trials
en
oai:repository.helmholtz-hzi.de:10033/6082422019-08-30T11:33:30Zcom_10033_620533col_10033_621891
Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.
Courtens, Emilie N P
Vandekerckhove, Tom
Prat, Delphine
Vilchez Vargas, Ramiro
Vital, Marius
Pieper, Dietmar H
Meerbergen, Ken
Lievens, Bart
Boon, Nico
Vlaeminck, Siegfried E
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process.
2016-05-04T14:33:11Z
2016-05-04T14:33:11Z
2016-04-01
Article
Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers. 2016, 92:94-103 Water Res.
1879-2448
26841233
10.1016/j.watres.2016.01.022
http://hdl.handle.net/10033/608242
Water research
en
oai:repository.helmholtz-hzi.de:10033/6113972019-08-30T11:24:31Zcom_10033_620533col_10033_621891
Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a Colombian Caribbean Aquaculture Outbreak.
Gálvez, Eric J C
Carrillo-Castro, Katerine
Zárate, Lina
Güiza, Linda
Pieper, Dietmar H
García-Bonilla, Erika
Salazar, Marcela
Junca, Howard
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a self-limited outbreak of high mortalities in commercial Litopenaeus vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report its draft genome and three novel extrachromosomal elements that it harbors.
2016-06-01T13:17:04Z
2016-06-01T13:17:04Z
2016
Article
Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a Colombian Caribbean Aquaculture Outbreak. 2016, 4 (3): Genome Announc
2169-8287
27174263
10.1128/genomeA.00321-16
http://hdl.handle.net/10033/611397
Genome announcements
en
oai:repository.helmholtz-hzi.de:10033/6119812019-08-30T11:33:05Zcom_10033_620533col_10033_621891
High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables.
Meerburg, Francis A
Vlaeminck, Siegfried E
Roume, Hugo
Seuntjens, Dries
Pieper, Dietmar H
Jauregui, Ruy
Vilchez Vargas, Ramiro
Boon, Nico
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.
2016-06-07T12:45:42Z
2016-06-07T12:45:42Z
2016-05-07
Article
High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables. 2016, 100:137-145 Water Res.
1879-2448
27183209
10.1016/j.watres.2016.04.076
http://hdl.handle.net/10033/611981
Water research
oai:repository.helmholtz-hzi.de:10033/6133292019-08-30T11:33:26Zcom_10033_620533col_10033_620534
Reinvestigation of the Nitration of Trichloroethene - Subsequent Reactions of the Products and Evaluation of Their Antimicrobial and Antifungal Activity
Zapol'skii, Viktor A.
Namyslo, Jan C.
Sergeev, Galina
Brönstrup, Mark
Gjikaj, Mimoza
Kaufmann, Dieter E.
2016-06-16T10:52:26Z
2016-06-16T10:52:26Z
2015-12
Article
Reinvestigation of the Nitration of Trichloroethene - Subsequent Reactions of the Products and Evaluation of Their Antimicrobial and Antifungal Activity 2015, 2015 (35):7763 European Journal of Organic Chemistry
1434193X
10.1002/ejoc.201501066
http://hdl.handle.net/10033/613329
European Journal of Organic Chemistry
http://doi.wiley.com/10.1002/ejoc.201501066
oai:repository.helmholtz-hzi.de:10033/6154642019-08-30T11:26:13Zcom_10033_620533col_10033_620534
What Makes Umbilical Cord Tissue-Derived Mesenchymal Stromal Cells Superior Immunomodulators When Compared to Bone Marrow Derived Mesenchymal Stromal Cells?
Bárcia, R N
Santos, J M
Filipe, M
Teixeira, M
Martins, J P
Almeida, J
Água-Doce, A
Almeida, S C P
Varela, A
Pohl, S
Dittmar, K E J
Calado, S
Simões, S I
Gaspar, M M
Cruz, M E M
Lindenmaier, W
Graça, L
Cruz, H
Cruz, P E
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
MSCs derived from the umbilical cord tissue, termed UCX, were investigated for their immunomodulatory properties and compared to bone marrow-derived MSCs (BM-MSCs), the gold-standard in immunotherapy. Immunogenicity and immunosuppression were assessed by mixed lymphocyte reactions, suppression of lymphocyte proliferation and induction of regulatory T cells. Results showed that UCX were less immunogenic and showed higher immunosuppression activity than BM-MSCs. Further, UCX did not need prior activation or priming to exert their immunomodulatory effects. This was further corroborated in vivo in a model of acute inflammation. To elucidate the potency differences observed between UCX and BM-MSCs, gene expression related to immune modulation was analysed in both cell types. Several gene expression profile differences were found between UCX and BM-MSCs, namely decreased expression of HLA-DRA, HO-1, IGFBP1, 4 and 6, ILR1, IL6R and PTGES and increased expression of CD200, CD273, CD274, IL1B, IL-8, LIF and TGFB2. The latter were confirmed at the protein expression level. Overall, these results show that UCX seem to be naturally more potent immunosuppressors and less immunogenic than BM-MSCs. We propose that these differences may be due to increased levels of immunomodulatory surface proteins such as CD200, CD273, CD274 and cytokines such as IL1β, IL-8, LIF and TGFβ2.
2016-07-04T13:23:51Z
2016-07-04T13:23:51Z
2015
Article
What Makes Umbilical Cord Tissue-Derived Mesenchymal Stromal Cells Superior Immunomodulators When Compared to Bone Marrow Derived Mesenchymal Stromal Cells? 2015, 2015:583984 Stem Cells Int
1687-966X
26064137
10.1155/2015/583984
http://hdl.handle.net/10033/615464
Stem cells international
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6156602019-08-30T11:31:23Zcom_10033_620533col_10033_621891
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease.
Vital, Marius
Harkema, Jack R
Rizzo, Mike
Tiedje, James
Brandenberger, Christina
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
The gut microbiota plays an important role in the development of asthma. With advanced age the microbiome and the immune system are changing and, currently, little is known about how these two factors contribute to the development of allergic asthma in the elderly. In this study we investigated the associations between the intestinal microbiome and allergic airway disease in young and old mice that were sensitized and challenged with house dust mite (HDM). After challenge, the animals were sacrificed, blood serum was collected for cytokine analysis, and the lungs were processed for histopathology. Fecal pellets were excised from the colon and subjected to 16S rRNA analysis. The microbial community structure changed with age and allergy development, where alterations in fecal communities from young to old mice resembled those after HDM challenge. Allergic mice had induced serum levels of IL-17A and old mice developed a greater allergic airway response compared to young mice. This study demonstrates that the intestinal bacterial community structure differs with age, possibly contributing to the exaggerated pulmonary inflammatory response in old mice. Furthermore, our results show that the composition of the gut microbiota changes with pulmonary allergy, indicating bidirectional gut-lung communications.
2016-07-06T14:44:58Z
2016-07-06T14:44:58Z
2015
Article
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. 2015, 2015:892568 J Immunol Res
2314-7156
26090504
10.1155/2015/892568
http://hdl.handle.net/10033/615660
Journal of immunology research
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6178812019-08-30T11:25:11Zcom_10033_620533col_10033_621891
Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME.
Yakimov, Michail M
Crisafi, Francesca
Messina, Enzo
Smedile, Francesco
Lopatina, Anna
Denaro, Renata
Pieper, Dietmar H
Golyshin, Peter N
Giuliano, Laura
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities.
2016-08-03T13:29:16Z
2016-08-03T13:29:16Z
2016-08
Article
Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME. 2016, 8 (4):508-19 Environ Microbiol Rep
1758-2229
27345842
10.1111/1758-2229.12424
http://hdl.handle.net/10033/617881
Environmental microbiology reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6186722019-08-30T11:30:32Zcom_10033_620533col_10033_620534
Evaluation of the inflammatory potential of implant materials in a mouse model by bioluminescent imaging of intravenously injected bone marrow cells.
Rais, Bushra
Köster, Mario
Rahim, Muhammad Imran
Pils, Marina
Seitz, Jan-Marten
Hauser, Hansjörg
Wirth, Dagmar
Mueller, Peter P
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
To evaluate the inflammatory potential of implants a bioluminescent imaging assay was developed using luciferase-expressing bone marrow cells that were injected into the blood circulation of wild-type mice. After subcutaneous implantation of titanium discs as an example for a clinically established biocompatible material, the luminosity was modest. Similarly, low luminosity signals were generated by pure magnesium implants that were used to represent metallic alloys that are presently under investigation as novel degradable implant materials. Increased luminosity was observed in response to degradable polymeric PLGA implants. Surgical wounds induced a basic luminescent response even in the absence of an implant. However, the material-independent response to injury could be minimized using injectable microparticle suspensions. In parallel with the resorption of biodegradable microparticles, the signal induced by PLGA declined faster when compared to non-degradable polystyrene suspensions. By using an interferon type I inducible Mx2 promoter construct to drive luciferase gene expression, the highest luminosity was observed in response to bacteria, indicating that the system could also be employed to monitor implant infections. Overall, labeled bone marrow cells yielded specific, well-defined localized signals that correlated with the inflammatory responses to implants. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2149-2158, 2016.
2016-08-23T13:59:38Z
2016-08-23T13:59:38Z
2016-09
Article
Evaluation of the inflammatory potential of implant materials in a mouse model by bioluminescent imaging of intravenously injected bone marrow cells. 2016, 104 (9):2149-58 J Biomed Mater Res A
1552-4965
27102724
10.1002/jbm.a.35758
http://hdl.handle.net/10033/618672
Journal of biomedical materials research. Part A
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6187302019-08-30T11:33:57Zcom_10033_620533col_10033_620534
Screening and characterization of molecules that modulate the biological activity of IFNs-I.
Bürgi, Milagros
Zapol'skii, Viktor A
Hinkelmann, Bettina
Köster, Mario
Kaufmann, Dieter E
Sasse, Florenz
Hauser, Hansjörg
Etcheverrigaray, Marina
Kratje, Ricardo
Bollati-Fogolín, Mariela
Oggero, Marcos
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
Type I Interferons (IFNs-I) are species-specific glycoproteins which play an important role as primary defence against viral infections and that can also modulate the adaptive immune system. In some autoimmune diseases, interferons (IFNs) are over-produced. IFNs are widely used as biopharmaceuticals for a variety of cancer indications, chronic viral diseases, and for their immuno-modulatory action in patients with multiple sclerosis; therefore, increasing their therapeutic efficiency and decreasing their side effects is of high clinical value. In this sense, it is interesting to find molecules that can modulate the activity of IFNs. In order to achieve that, it was necessary to establish a simple, fast and robust assay to analyze numerous compounds simultaneously. We developed four reporter gene assays (RGAs) to identify IFN activity modulator compounds by using WISH-Mx2/EGFP, HeLa-Mx2/EGFP, A549-Mx2/EGFP, and HEp2-Mx2/EGFP reporter cell lines (RCLs). All of them present a Z' factor higher than 0.7. By using these RGAs, natural and synthetic compounds were analyzed simultaneously. A total of 442 compounds were studied by the Low Throughput Screening (LTS) assay using the four RCLs to discriminate between their inhibitory or enhancing effects on IFN activity. Some of them were characterized and 15 leads were identified. Finally, one promising candidate with enhancing effect on IFN-α/-β activity and five compounds with inhibitory effect were described.
2016-08-24T11:08:33Z
2016-08-24T11:08:33Z
2016-09-10
Article
Screening and characterization of molecules that modulate the biological activity of IFNs-I. 2016, 233:6-16 J. Biotechnol.
1873-4863
27346232
10.1016/j.jbiotec.2016.06.021
http://hdl.handle.net/10033/618730
Journal of biotechnology
en
http://creativecommons.org/licenses/by-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6191012019-08-30T11:26:42Zcom_10033_620533col_10033_621891
The culturome of the human nose habitats reveals individual bacterial fingerprint patterns.
Kaspar, Ursula
Kriegeskorte, André
Schubert, Tanja
Peters, Georg
Rudack, Claudia
Pieper, Dietmar H
Wos-Oxley, Melissa
Becker, Karsten
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The complex anatomy of the human nose might offer distinct microbial niches. Microbiota composition may affect nose inflammatory diseases and Staphylococcus aureus carriage. Considering different nasal cavity locations, microbial colonization was analysed across individuals exhibiting chronic nasal inflammatory diseases (n = 18) and those without local inflammation signs (n = 16). Samples were collected systematically during surgery and examined by an extensive culture-based approach and, for a subset, by 16S rRNA gene community profiling. Cultivation yielded 141 taxa with members of Staphylococcus, Corynebacterium and Propionibacterium as most common isolates comprising the nasal core culturome together with Finegoldia magna. Staphylococcus aureus was most frequently found in association with Staphylococcus epidermidis and Propionibacterium acnes, and the posterior vestibules were redefined as S. aureus' principle habitat. Culturome analysis revealed host-specific bacterial 'fingerprints' irrespective of host-driven factors or intranasal sites. Comparisons between cultivable and molecular fingerprints demonstrated that only a small fraction of phylotypes (6.2%) was correlated. While the total number of different phylotypes was higher in the molecular dataset, the total number of identifications down to the species level was higher in the culturomic approach. To determine host-specific microbiomes, the advantages of molecular approaches should be combined with the resolution and reliability of species identification by culturomic analyses.
2016-08-31T10:02:35Z
2016-08-31T10:02:35Z
2016-07
Article
The culturome of the human nose habitats reveals individual bacterial fingerprint patterns. 2016, 18 (7):2130-42 Environ. Microbiol.
1462-2920
25923378
10.1111/1462-2920.12891
http://hdl.handle.net/10033/619101
Environmental microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6191272019-08-30T11:27:16Zcom_10033_620533col_10033_621891
Exploring the bacterial assemblages along the human nasal passage.
Wos-Oxley, Melissa L
Chaves-Moreno, Diego
Jáuregui, Ruy
Oxley, Andrew P A
Kaspar, Ursula
Plumeier, Iris
Kahl, Silke
Rudack, Claudia
Becker, Karsten
Pieper, Dietmar H
Helmholtz Centre for infection research, Inhoffenstr. 7,38124 Braunschweig, Germany.
The human nasal passage, from the anterior nares through the nasal vestibule to the nasal cavities, is an important habitat for opportunistic pathogens and commensals alike. This work sampled four different anatomical regions within the human nasal passage across a large cohort of individuals (n = 79) comprising individuals suffering from chronic nasal inflammation clinically known as chronic rhinosinusitis (CRS) and individuals not suffering from inflammation (CRS-free). While individuals had their own unique bacterial fingerprint that was consistent across the anatomical regions, these bacterial fingerprints formed into distinct delineated groups comprising core bacterial members, which were consistent across all four swabbed anatomical regions irrespective of health status. The most significant observed pattern was the difference between the global bacterial profiles of swabbed and tissue biopsy samples from the same individuals, being also consistent across different anatomical regions. Importantly, no statistically significant differences could be observed concerning the global bacterial communities, any of the bacterial species or the range of diversity indices used to compare between CRS and CRS-free individuals, and between two CRS phenotypes (without nasal polyps and with nasal polyps). Thus, the role of bacteria in the pathogenesis of sinusitis remains uncertain.
2016-08-31T13:10:44Z
2016-08-31T13:10:44Z
2016-07
Article
Exploring the bacterial assemblages along the human nasal passage. 2016, 18 (7):2259-71 Environ. Microbiol.
1462-2920
27207744
10.1111/1462-2920.13378
http://hdl.handle.net/10033/619127
Environmental microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6200762019-08-30T11:26:13Zcom_10033_620533col_10033_621891
Draft Genome Sequence of Aeromonas sp. Strain EERV15.
Ehsani, Elham
Barrantes, Israel
Vandermaesen, Johanna
Geffers, Robert
Jarek, Michael
Boon, Nico
Springael, Dirk
Pieper, Dietmar H
Vilchez Vargas, Ramiro
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated from sand filter. The organism most closely related to Aeromonas sp. EERV15 is Aeromonas veronii B565, with an average 83% amino acid sequence similarity of putatively encoded protein open reading frames.
2016-09-13T09:22:58Z
2016-09-13T09:22:58Z
2016
Article
Draft Genome Sequence of Aeromonas sp. Strain EERV15. 2016, 4 (4): Genome Announc
2169-8287
27540061
10.1128/genomeA.00811-16
http://hdl.handle.net/10033/620076
Genome announcements
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6205472019-08-30T11:35:39Zcom_10033_620533col_10033_621891
Exploring the transcriptome of Staphylococcus aureus in its natural niche.
Chaves-Moreno, Diego
Wos-Oxley, Melissa L
Jáuregui, Ruy
Medina, Eva
Oxley, Andrew Pa
Pieper, Dietmar H
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Staphylococcus aureus is an important human pathogen and commensal, where the human nose is the predominant reservoir. To better understand its behavior in this environmental niche, RNA was extracted from the anterior nares of three documented S. aureus carriers and the metatranscriptome analyzed by RNAseq. In addition, the in vivo transcriptomes were compared to previously published transcriptomes of two in vitro grown S. aureus strains. None of the in vitro conditions, even growth in medium resembling the anterior nares environment, mimicked in vivo conditions. Survival in the nose was strongly controlled by the limitation of iron and evident by the expression of iron acquisition systems. S. aureus populations in different individuals clearly experience different environmental stresses, which they attempt to overcome by the expression of compatible solute biosynthetic pathways, changes in their cell wall composition and synthesis of general stress proteins. Moreover, the expression of adhesins was also important for colonization of the anterior nares. However, different S. aureus strains also showed different in vivo behavior. The assessment of general in vivo expression patterns and commonalities between different S. aureus strains will in the future result in new knowledge based strategies for controlling colonization.
2016-10-12T09:43:41Z
2016-10-12T09:43:41Z
2016
Article
Exploring the transcriptome of Staphylococcus aureus in its natural niche. 2016, 6:33174 Sci Rep
2045-2322
27641137
10.1038/srep33174
http://hdl.handle.net/10033/620547
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6205552019-08-30T11:26:13Zcom_10033_620533col_10033_620534
New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development.
Klahn, Philipp
Brönstrup, Mark
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The development of bacterial resistance against current antibiotic drugs necessitates a continuous renewal of the arsenal of efficacious drugs. This imperative has not been met by the output of antibiotic research and development of the past decades for various reasons, including the declining efforts of large pharma companies in this area. Moreover, the majority of novel antibiotics are chemical derivatives of existing structures that represent mostly step innovations, implying that the available chemical space may be exhausted. This review negates this impression by showcasing recent achievements in lead finding and optimization of antibiotics that have novel or unexplored chemical structures. Not surprisingly, many of the novel structural templates like teixobactins, lysocin, griselimycin, or the albicidin/cystobactamid pair were discovered from natural sources. Additional compounds were obtained from the screening of synthetic libraries and chemical synthesis, including the gyrase-inhibiting NTBI's and spiropyrimidinetrione, the tarocin and targocil inhibitors of wall teichoic acid synthesis, or the boronates and diazabicyclo[3.2.1]octane as novel β-lactamase inhibitors. A motif that is common to most clinically validated antibiotics is that they address hotspots in complex biosynthetic machineries, whose functioning is essential for the bacterial cell. Therefore, an introduction to the biological targets-cell wall synthesis, topoisomerases, the DNA sliding clamp, and membrane-bound electron transport-is given for each of the leads presented here.
2016-10-19T08:26:52Z
2016-10-19T08:26:52Z
2016-10-05
Article
New Structural Templates for Clinically Validated and Novel Targets in Antimicrobial Drug Research and Development. 2016: Curr. Top. Microbiol. Immunol.
0070-217X
27704270
10.1007/82_2016_501
http://hdl.handle.net/10033/620555
Current topics in microbiology and immunology
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:10033/6205652019-08-30T11:37:00Zcom_10033_620533col_10033_621891
Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T.
Puente-Sánchez, Fernando
Pieper, Dietmar H
Arce-Rodríguez, Alejandro
Helmholtz Centre for infection research, Inf´hoffenstr. 7, 38124 Braunschweig, Germany.
The type strain of Tessaracoccus lapidicaptus was isolated from the deep subsurface of the Iberian Pyrite Belt (southwest Spain). Here, we report its draft genome, consisting of 27 contigs with a ~3.1-Mb genome size. The annotation revealed 2,905 coding DNA sequences, 45 tRNA genes, and three rRNA genes.
2016-10-27T13:00:26Z
2016-10-27T13:00:26Z
2016-09-29
Article
Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T. 2016, 4 (5) Genome Announc
27688325
10.1128/genomeA.01078-16
http://hdl.handle.net/10033/620565
Genome announcements
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6206162019-08-30T11:33:54Zcom_10033_620533col_10033_621891
Fecal Microbiota Transfer in Patients With Chronic Antibiotic-Refractory Pouchitis.
Stallmach, Andreas
Lange, Kathleen
Buening, Juergen
Sina, Christian
Vital, Marius
Pieper, Dietmar H
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
2016-12-02T08:32:19Z
2016-12-02T08:32:19Z
2016-03
Other
Fecal Microbiota Transfer in Patients With Chronic Antibiotic-Refractory Pouchitis. 2016, 111 (3):441-3 Am. J. Gastroenterol.
1572-0241
27018122
10.1038/ajg.2015.436
http://hdl.handle.net/10033/620616
The American journal of gastroenterology
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6206422019-08-30T11:27:16Zcom_10033_620533col_10033_621891
Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.
De Vrieze, Jo
Regueiro, Leticia
Props, Ruben
Vilchez Vargas, Ramiro
Jáuregui, Ruy
Pieper, Dietmar H
Lema, Juan M
Carballa, Marta
HelmholtzCentre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.
2016-12-07T14:51:03Z
2016-12-07T14:51:03Z
2016
Article
Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion. 2016, 9:244 Biotechnol Biofuels
27843490
10.1186/s13068-016-0652-5
http://hdl.handle.net/10033/620642
Biotechnology for biofuels
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6206772019-08-30T11:27:46Zcom_10033_620533col_10033_620534
An aryl dioxygenase shows remarkable double dioxygenation capacity for diverse bis-aryl compounds, provided they are carbocyclic.
Overwin, Heike
González, Myriam
Méndez, Valentina
Seeger, Michael
Wray, Victor
Hofer, Bernd
Hel,holtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The bacterial dioxygenation of mono- or polycyclic aromatic compounds is an intensely studied field. However, only in a few cases has the repeated dioxygenation of a substrate possessing more than a single aromatic ring been described. We previously characterized the aryl-hydroxylating dioxygenase BphA-B4h, an artificial hybrid of the dioxygenases of the biphenyl degraders Burkholderia xenovorans LB400 and Pseudomonas sp. strain B4-Magdeburg, which contains the active site of the latter enzyme, as an exceptionally powerful biocatalyst. We now show that this dioxygenase possesses a remarkable capacity for the double dioxygenation of various bicyclic aromatic compounds, provided that they are carbocyclic. Two groups of biphenyl analogues were examined: series A compounds containing one heterocyclic aromatic ring and series B compounds containing two homocyclic aromatic rings. Whereas all of the seven partially heterocyclic biphenyl analogues were solely dioxygenated in the homocyclic ring, four of the six carbocyclic bis-aryls were converted into ortho,meta-hydroxylated bis-dihydrodiols. Potential reasons for failure of heterocyclic dioxygenations are discussed. The obtained bis-dihydrodiols may, as we also show here, be enzymatically re-aromatized to yield the corresponding tetraphenols. This opens a way to a range of new polyphenolic products, a class of compounds known to exert multiple biological activities. Several of the obtained compounds are novel molecules.
2017-01-02T13:03:55Z
2017-01-02T13:03:55Z
2016-09
Article
An aryl dioxygenase shows remarkable double dioxygenation capacity for diverse bis-aryl compounds, provided they are carbocyclic. 2016, 100 (18):8053-61 Appl. Microbiol. Biotechnol.
1432-0614
27147529
10.1007/s00253-016-7570-0
http://hdl.handle.net/10033/620677
Applied microbiology and biotechnology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6206802019-08-30T11:36:32Zcom_10033_620533col_10033_621891
The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection.
Schulz, Christian
Schütte, Kerstin
Koch, Nadine
Vilchez-Vargas, Ramiro
Wos-Oxley, Melissa L
Oxley, Andrew P A
Vital, Marius
Malfertheiner, Peter
Pieper, Dietmar H
Hel,holtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Patients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.
2017-01-05T16:22:12Z
2017-01-05T16:22:12Z
2016-12-05
Article
The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection. 2016 Gut
1468-3288
27920199
10.1136/gutjnl-2016-312904
http://hdl.handle.net/10033/620680
Gut
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6207342019-08-30T11:36:05Zcom_10033_620533col_10033_620534
Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing.
Spadaccini, Roberta
Reidt, Ulrich
Dybkov, Olexandr
Will, Cindy
Frank, Ronald
Stier, Gunter
Corsini, Lorenzo
Wahl, Markus C
Lührmann, Reinhard
Sattler, Michael
European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
The p14 subunit of the essential splicing factor 3b (SF3b) can be cross-linked to the branch-point adenosine of pre-mRNA introns within the spliceosome. p14 stably interacts with the SF3b subunit SF3b155, which also binds the 65-kDa subunit of U2 auxiliary splicing factor (U2AF65). We combined biochemical and NMR techniques to study the conformation of p14 either alone or complexed with SF3b155 fragments, as well as an interaction network involving p14, SF3b155, U2AF65, and U2 snRNA/pre-mRNA. p14 comprises a canonical RNA recognition motif (RRM) with an additional C-terminal helix (alphaC) and a beta hairpin insertion. SF3b155 binds to the beta-sheet surface of p14, thereby occupying the canonical RNA-binding site of the p14 RRM. The minimal region of SF3b155 interacting with p14 (i.e., residues 381-424) consists of four alpha-helices, which are partially preformed in isolation. Helices alpha2 and alpha3 (residues 401-415) constitute the core p14-binding epitope. Regions of SF3b155 binding to p14 and U2AF65 are nonoverlapping. This allows for a simultaneous interaction of SF3b155 with both proteins, which may support the stable association of U2 snRNP with the pre-mRNA. p14-RNA interactions are modulated by SF3b155 and the RNA-binding site of the p14-SF3b155 complex involves the noncanonical beta hairpin insertion of the p14 RRM, consistent with the beta-sheet surface being occupied by the helical SF3b155 peptide and p14 helix alphaC. Our data suggest that p14 lacks inherent specificity for recognizing the branch point, but that some specificity may be achieved by scaffolding interactions involving other components of SF3b.
2017-01-20T11:50:35Z
2017-01-20T11:50:35Z
2006-03
Article
Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing. 2006, 12 (3):410-25 RNA
1355-8382
16495236
10.1261/rna.2271406
http://hdl.handle.net/10033/620734
RNA (New York, N.Y.)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6207352019-08-30T11:28:23Zcom_10033_620533col_10033_620534
Immunization of pigs to prevent disease in humans: construction and protective efficacy of a Salmonella enterica serovar Typhimurium live negative-marker vaccine.
Selke, Martin
Meens, Jochen
Springer, Sven
Frank, Ronald
Gerlach, Gerald-F
nstitute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany.
Zoonotic infections caused by Salmonella enterica serovar Typhimurium pose a constant threat to consumer health, with the pig being a particularly major source of multidrug-resistant isolates. Vaccination, as a promising approach to reduce colonization and shedding, has been scarcely used, as it interferes with current control programs relying on serology as a means of herd classification. In order to overcome this problem, we set out to develop a negative-marker vaccine allowing the differentiation of infected from vaccinated animals (DIVA). Applying an immunoproteomic approach with two-dimensional gel electrophoresis, Western blot, and quadrupole time-of-flight tandem mass spectrometry, we identified the OmpD protein as a suitable negative marker. Using allelic exchange, we generated an isogenic mutant of the licensed live vaccine strain Salmoporc and showed that virulence of Salmoporc and that of the mutant strain, SalmoporcDeltaompD, were indistinguishable in BALB/c mice. In a pig infection experiment including two oral immunizations with SalmoporcDeltaompD and challenge with a multiresistant S. enterica serovar Typhimurium DT104 clinical isolate, we confirmed the protective efficacy of SalmoporcDeltaompD in pigs, showing a significant reduction of both clinical symptoms and colonization of lymph nodes and intestinal tract. OmpD immunogenic epitopes were determined by peptide spot array analyses. Upon testing of several 9-mer peptides, each including an immunogenic epitope, one peptide (positions F(100) to Y(108)) that facilitated the detection of infected animals independent of their vaccination status (DIVA function) was identified. The approach described overcomes the problems currently limiting the use of bacterial live vaccines and holds considerable potential for future developments in the field.
2017-01-20T12:15:59Z
2017-01-20T12:15:59Z
2007-05
Article
Immunization of pigs to prevent disease in humans: construction and protective efficacy of a Salmonella enterica serovar Typhimurium live negative-marker vaccine. 2007, 75 (5):2476-83 Infect. Immun.
0019-9567
17296750
10.1128/IAI.01908-06
http://hdl.handle.net/10033/620735
Infection and immunity
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6207392019-08-30T11:28:23Zcom_10033_620533col_10033_620534
EU-OPENSCREEN-chemical tools for the study of plant biology and resistance mechanisms.
Meiners, Torsten
Stechmann, Bahne
Frank, Ronald
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
EU-OPENSCREEN is an academic research infrastructure initiative in Europe for enabling researchers in all life sciences to take advantage of chemical biology approaches to their projects. In a collaborative effort of national networks in 16 European countries, EU-OPENSCREEN will develop novel chemical compounds with external users to address questions in, among other fields, systems and network biology (directed and selective perturbation of signalling pathways), structural biology (compound-target interactions at atomic resolution), pharmacology (early drug discovery and toxicology) and plant biology (response of wild or crop plants to environmental and agricultural substances). EU-OPENSCREEN supports all stages of a tool development project, including assay adaptation, high-throughput screening and chemical optimisation of the 'hit' compounds. All tool compounds and data will be made available to the scientific community. EU-OPENSCREEN integrates high-capacity screening platforms throughout Europe, which share a rationally selected compound collection comprising up to 300,000 (commercial and proprietary compounds collected from European chemists). By testing systematically this chemical collection in hundreds of assays originating from very different biological themes, the screening process generates enormous amounts of information about the biological activities of the substances and thereby steadily enriches our understanding of how and where they act.
2017-01-23T14:08:52Z
2017-01-23T14:08:52Z
2014-10
Article
EU-OPENSCREEN-chemical tools for the study of plant biology and resistance mechanisms. 2014, 7 (4):113-8 J Chem Biol
1864-6158
25320643
10.1007/s12154-014-0118-9
http://hdl.handle.net/10033/620739
Journal of chemical biology
en
oai:repository.helmholtz-hzi.de:10033/6207402019-08-30T11:28:23Zcom_10033_620533col_10033_620534
Multiple antibody targets on herpes B glycoproteins B and D identified by screening sera of infected rhesus macaques with peptide microarrays.
Hotop, Sven-Kevin
Abd El Wahed, Ahmed
Beutling, Ulrike
Jentsch, Dieter
Motzkus, Dirk
Frank, Ronald
Hunsmann, Gerhard
Stahl-Hennig, Christiane
Fritz, Hans-Joachim
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Herpes B virus (or Herpesvirus simiae or Macacine herpesvirus 1) is endemic in many populations of macaques, both in the wild and in captivity. The virus elicits only mild clinical symptoms (if any) in monkeys, but can be transmitted by various routes, most commonly via bites, to humans where it causes viral encephalitis with a high mortality rate. Hence, herpes B constitutes a considerable occupational hazard for animal caretakers, veterinarians and laboratory personnel. Efforts are therefore being made to reduce the risk of zoonotic infection and to improve prognosis after accidental exposure. Among the measures envisaged are serological surveillance of monkey colonies and specific diagnosis of herpes B zoonosis against a background of antibodies recognizing the closely related human herpes simplex virus (HSV). 422 pentadecapeptides covering, in an overlapping fashion, the entire amino acid sequences of herpes B proteins gB and gD were synthesized and immobilized on glass slides. Antibodies present in monkey sera that bind to subsets of the peptide collection were detected by microserological techniques. With 42 different rhesus macaque sera, 114 individual responses to 18 different antibody target regions (ATRs) were recorded, 17 of which had not been described earlier. This finding may pave the way for a peptide-based, herpes B specific serological diagnostic test.
2017-01-23T14:19:39Z
2017-01-23T14:19:39Z
2014
Article
Multiple antibody targets on herpes B glycoproteins B and D identified by screening sera of infected rhesus macaques with peptide microarrays. 2014, 9 (1):e86857 PLoS ONE
1932-6203
24497986
10.1371/journal.pone.0086857
http://hdl.handle.net/10033/620740
PloS one
en
oai:repository.helmholtz-hzi.de:10033/6207412019-08-30T11:31:49Zcom_10033_620533col_10033_620534
Peptide-mediated interference with influenza A virus polymerase.
Ghanem, Alexander
Mayer, Daniel
Chase, Geoffrey
Tegge, Werner
Frank, Ronald
Kochs, Georg
García-Sastre, Adolfo
Schwemmle, Martin
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The assembly of the polymerase complex of influenza A virus from the three viral polymerase subunits PB1, PB2, and PA is required for viral RNA synthesis. We show that peptides which specifically bind to the protein-protein interaction domains in the subunits responsible for complex formation interfere with polymerase complex assembly and inhibit viral replication. Specifically, we provide evidence that a 25-amino-acid peptide corresponding to the PA-binding domain of PB1 blocks the polymerase activity of influenza A virus and inhibits viral spread. Targeting polymerase subunit interactions therefore provides a novel strategy to develop antiviral compounds against influenza A virus or other viruses.
2017-01-24T10:25:18Z
2017-01-24T10:25:18Z
2007-07
Article
Peptide-mediated interference with influenza A virus polymerase. 2007, 81 (14):7801-4 J. Virol.
0022-538X
17494067
10.1128/JVI.00724-07
http://hdl.handle.net/10033/620741
Journal of virology
en
oai:repository.helmholtz-hzi.de:10033/6207452019-08-30T11:27:46Zcom_10033_620533col_10033_620534
The interaction of the gammaherpesvirus 68 orf73 protein with cellular BET proteins affects the activation of cell cycle promoters.
Ottinger, Matthias
Pliquet, Daniel
Christalla, Thomas
Frank, Ronald
Stewart, James P
Schulz, Thomas F
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Infection of mice with murine gammaherpesvirus 68 (MHV-68) provides a valuable animal model for gamma-2 herpesvirus (rhadinovirus) infection and pathogenesis. The MHV-68 orf73 protein has been shown to be required for the establishment of viral latency in vivo. This study describes a novel transcriptional activation function of the MHV-68 orf73 protein and identifies the cellular bromodomain containing BET proteins Brd2/RING3, Brd3/ORFX, and BRD4 as interaction partners for the MHV-68 orf73 protein. BET protein members are known to interact with acetylated histones, and Brd2 and Brd4 have been implicated in fundamental cellular processes, including cell cycle regulation and transcriptional regulation. Using MHV-68 orf73 peptide array assays, we identified Brd2 and Brd4 interaction sites in the orf73 protein. Mutation of one binding site led to a loss of the interaction with Brd2/4 but not the retinoblastoma protein Rb, to impaired chromatin association, and to a decreased ability to activate the BET-responsive cyclin D1, D2, and E promoters. The results therefore pinpoint the binding site for Brd2/4 in a rhadinoviral orf73 protein and suggest that the recruitment of a member of the BET protein family allows the MHV-68 orf73 protein to activate the promoters of G(1)/S cyclins. These findings point to parallels between the transcriptional activator functions of rhadinoviral orf73 proteins and papillomavirus E2 proteins.
2017-01-24T15:02:03Z
2017-01-24T15:02:03Z
2009-05
Article
The interaction of the gammaherpesvirus 68 orf73 protein with cellular BET proteins affects the activation of cell cycle promoters. 2009, 83 (9):4423-34 J. Virol.
1098-5514
19244327
10.1128/JVI.02274-08
http://hdl.handle.net/10033/620745
Journal of virology
en
oai:repository.helmholtz-hzi.de:10033/6207462019-08-30T11:28:23Zcom_10033_620533col_10033_620534
Identification of high-affinity PB1-derived peptides with enhanced affinity to the PA protein of influenza A virus polymerase.
Wunderlich, Kerstin
Juozapaitis, Mindaugas
Ranadheera, Charlene
Kessler, Ulrich
Martin, Arnold
Eisel, Jessica
Beutling, Ulrike
Frank, Ronald
Schwemmle, Martin
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The influenza A virus polymerase complex, consisting of the subunits PB1, PB2, and PA, represents a promising target for the development of new antiviral drugs. We have previously demonstrated the feasibility of targeting the protein-protein interaction domain between PA and PB1 using peptides derived from the extreme N terminus of PB1 (amino acids [aa] 1 to 15), comprising the PA-binding domain of PB1. To increase the binding affinity of these peptides, we performed a systematic structure-affinity relationship analysis. Alanine and aspartic acid scans revealed that almost all amino acids in the core binding region (aa 5 to 11) are indispensable for PA binding. Using a library of immobilized peptides representing all possible single amino acid substitutions, we were able to identify amino acid positions outside the core PA-binding region (aa 1, 3, 12, 14, and 15) that are variable and can be replaced by affinity-enhancing residues. Surface plasmon resonance binding studies revealed that combination of several affinity-enhancing mutations led to an additive effect. Thus, the feasibility to enhance the PA-binding affinity presents an intriguing possibility to increase antiviral activity of the PB1-derived peptide and one step forward in the development of an antiviral drug against influenza A viruses.
2017-01-24T15:13:42Z
2017-01-24T15:13:42Z
2011-02
Article
Identification of high-affinity PB1-derived peptides with enhanced affinity to the PA protein of influenza A virus polymerase. 2011, 55 (2):696-702 Antimicrob. Agents Chemother.
1098-6596
21135188
10.1128/AAC.01419-10
http://hdl.handle.net/10033/620746
Antimicrobial agents and chemotherapy
en
oai:repository.helmholtz-hzi.de:10033/6207482019-08-30T11:34:22Zcom_10033_620533col_10033_620534
Archazolid and apicularen: novel specific V-ATPase inhibitors.
Huss, Markus
Sasse, Florenz
Kunze, Brigitte
Jansen, Rolf
Steinmetz, Heinrich
Ingenhorst, Gudrun
Zeeck, Axel
Wieczorek, Helmut
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
V-ATPases constitute a ubiquitous family of heteromultimeric, proton translocating proteins. According to their localization in a multitude of eukaryotic membranes, they energize many different transport processes. Since their malfunction is correlated with various diseases in humans, the elucidation of the properties of this enzyme for the development of selective inhibitors and drugs is one of the challenges in V-ATPase research.
2017-01-26T09:43:29Z
2017-01-26T09:43:29Z
2005-08-04
Article
Archazolid and apicularen: novel specific V-ATPase inhibitors. 2005, 6:13 BMC Biochem.
1471-2091
16080788
10.1186/1471-2091-6-13
http://hdl.handle.net/10033/620748
BMC biochemistry
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6207492019-08-30T11:34:22Zcom_10033_620533col_10033_620534
Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level.
Dalby, Andrew R
Emam, Ibrahim
Franke, Raimo
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC) can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that sub-classes were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC.
2017-01-26T10:33:25Z
2017-01-26T10:33:25Z
2012
Article
Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level. 2012, 7 (11):e50253 PLoS ONE
1932-6203
23209689
10.1371/journal.pone.0050253
http://hdl.handle.net/10033/620749
PloS one
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
rdf///com_10033_620533/100