2024-03-29T07:08:31Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/481582019-08-30T11:30:32Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Puchałka, Jacek
author
Oberhardt, Matthew A
author
Godinho, Miguel
author
Bielecka, Agata
author
Regenhardt, Daniela
author
Timmis, Kenneth N
author
Papin, Jason A
author
Martins dos Santos, Vítor A P
department
Synthetic and Systems Biology Group, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.
2009-01-28T13:53:44Z
2008-10
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. 2008, 4 (10):e1000210 PLoS Comput. Biol.
1553-7358
18974823
10.1371/journal.pcbi.1000210
http://hdl.handle.net/10033/48158
PLoS computational biology
A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures, high-throughput phenotyping data, (13)C-measurement of internal flux distributions, and specifically generated knock-out mutants. Auxotrophy was correctly predicted in 75% of the cases. These systematic analyses revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence. Finally, we drew on the model to devise metabolic engineering strategies to improve production of polyhydroxyalkanoates, a class of biotechnologically useful compounds whose synthesis is not coupled to cell survival. The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to capitalize on its vast biotechnological potential.
en
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
Article
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URL
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oai:repository.helmholtz-hzi.de:10033/483352019-08-30T11:24:31Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Oberhardt, Matthew A
author
Puchałka, Jacek
author
Fryer, Kimberly E
author
Martins dos Santos, Vítor A P
author
Papin, Jason A
department
Department of Biomedical Engineering, University of Virginia Health System, Box 800759, Charlottesville, VA 22908, USA.
2009-02-02T15:11:37Z
2008-04
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. 2008, 190 (8):2790-803 J. Bacteriol.
1098-5530
18192387
10.1128/JB.01583-07
http://hdl.handle.net/10033/48335
Journal of bacteriology
Pseudomonas aeruginosa is a major life-threatening opportunistic pathogen that commonly infects immunocompromised patients. This bacterium owes its success as a pathogen largely to its metabolic versatility and flexibility. A thorough understanding of P. aeruginosa's metabolism is thus pivotal for the design of effective intervention strategies. Here we aim to provide, through systems analysis, a basis for the characterization of the genome-scale properties of this pathogen's versatile metabolic network. To this end, we reconstructed a genome-scale metabolic network of Pseudomonas aeruginosa PAO1. This reconstruction accounts for 1,056 genes (19% of the genome), 1,030 proteins, and 883 reactions. Flux balance analysis was used to identify key features of P. aeruginosa metabolism, such as growth yield, under defined conditions and with defined knowledge gaps within the network. BIOLOG substrate oxidation data were used in model expansion, and a genome-scale transposon knockout set was compared against in silico knockout predictions to validate the model. Ultimately, this genome-scale model provides a basic modeling framework with which to explore the metabolism of P. aeruginosa in the context of its environmental and genetic constraints, thereby contributing to a more thorough understanding of the genotype-phenotype relationships in this resourceful and dangerous pathogen.
en
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.
Article
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URL
https://hzi.openrepository.com/bitstream/10033/48335/1/Oberhardt%20et%20al_final.pdf
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oai:repository.helmholtz-hzi.de:10033/3029852019-08-30T11:37:00Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Wodke, Judith A H
author
Puchałka, Jacek
author
Lluch-Senar, Maria
author
Marcos, Josep
author
Yus, Eva
author
Godinho, Miguel
author
Gutiérrez-Gallego, Ricardo
author
dos Santos, Vitor A P Martins
author
Serrano, Luis
author
Klipp, Edda
author
Maier, Tobias
department
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain.
2013-10-08T13:50:36Z
2013
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. 2013, 9:653 Mol. Syst. Biol.
1744-4292
23549481
10.1038/msb.2013.6
http://hdl.handle.net/10033/302985
Molecular systems biology
Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.
en
Archived with thanks to Molecular systems biology
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.
Article
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URL
https://hzi.openrepository.com/bitstream/10033/302985/1/Wodke%20et%20al_final.pdf
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oai:repository.helmholtz-hzi.de:10033/3173862019-08-30T11:30:58Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Barbier, Mariette
author
Damron, F Heath
author
Bielecki, Piotr
author
Suárez-Diez, María
author
Puchałka, Jacek
author
Albertí, Sebastian
author
Dos Santos, Vitor Martins
author
Goldberg, Joanna B
department
Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
2014-05-23T12:40:54Z
2014
From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. 2014, 9 (2):e89941 PLoS ONE
1932-6203
24587139
10.1371/journal.pone.0089941
http://hdl.handle.net/10033/317386
PloS one
Pseudomonas aeruginosa is a highly versatile opportunistic pathogen capable of colonizing multiple ecological niches. This bacterium is responsible for a wide range of both acute and chronic infections in a variety of hosts. The success of this microorganism relies on its ability to adapt to environmental changes and re-program its regulatory and metabolic networks. The study of P. aeruginosa adaptation to temperature is crucial to understanding the pathogenesis upon infection of its mammalian host. We examined the effects of growth temperature on the transcriptome of the P. aeruginosa PAO1. Microarray analysis of PAO1 grown in Lysogeny broth at mid-exponential phase at 22°C and 37°C revealed that temperature changes are responsible for the differential transcriptional regulation of 6.4% of the genome. Major alterations were observed in bacterial metabolism, replication, and nutrient acquisition. Quorum-sensing and exoproteins secreted by type I, II, and III secretion systems, involved in the adaptation of P. aeruginosa to the mammalian host during infection, were up-regulated at 37°C compared to 22°C. Genes encoding arginine degradation enzymes were highly up-regulated at 22°C, together with the genes involved in the synthesis of pyoverdine. However, genes involved in pyochelin biosynthesis were up-regulated at 37°C. We observed that the changes in expression of P. aeruginosa siderophores correlated to an overall increase in Fe²⁺ extracellular concentration at 37°C and a peak in Fe³⁺ extracellular concentration at 22°C. This suggests a distinct change in iron acquisition strategies when the bacterium switches from the external environment to the host. Our work identifies global changes in bacterial metabolism and nutrient acquisition induced by growth at different temperatures. Overall, this study identifies factors that are regulated in genome-wide adaptation processes and discusses how this life-threatening pathogen responds to temperature.
en
Archived with thanks to PloS one
From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C.
Article
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oai:repository.helmholtz-hzi.de:10033/3243472019-08-30T11:36:04Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Fang, Kechi
author
Zhao, Hansheng
author
Sun, Changyue
author
Lam, Carolyn M C
author
Chang, Suhua
author
Zhang, Kunlin
author
Panda, Gurudutta
author
Godinho, Miguel
author
Martins dos Santos, Vítor A P
author
Wang, Jing
2014-08-07T13:05:02Z
2011
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. 2011, 5:83 BMC Syst Biol
1752-0509
21609491
10.1186/1752-0509-5-83
http://hdl.handle.net/10033/324347
BMC systems biology
Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets.
en
Archived with thanks to BMC systems biology
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction.
Article
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oai:repository.helmholtz-hzi.de:10033/3390362019-08-30T11:36:32Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Porcar, Manuel
author
Danchin, Antoine
author
de Lorenzo, Victor
author
Dos Santos, Vitor A
author
Krasnogor, Natalio
author
Rasmussen, Steen
author
Moya, Andrés
2015-01-29T12:40:39Z
2011-06
The ten grand challenges of synthetic life. 2011, 5 (1-2):1-9 Syst Synth Biol
1872-5333
21949672
10.1007/s11693-011-9084-5
http://hdl.handle.net/10033/339036
Systems and synthetic biology
The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life in the lab.
en
The ten grand challenges of synthetic life.
Article
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URL
https://hzi.openrepository.com/bitstream/10033/339036/1/porcar%20et%20al_final.pdf
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URL
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oai:repository.helmholtz-hzi.de:10033/6206832019-08-30T11:35:39Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Fang, Kechi
author
Zhao, Hansheng
author
Sun, Changyue
author
Lam, Carolyn M C
author
Chang, Suhua
author
Zhang, Kunlin
author
Panda, Gurudutta
author
Godinho, Miguel
author
Martins dos Santos, Vítor A P
author
Wang, Jing
2017-01-06T10:24:53Z
2011-05-25
BMC Systems Biology. 2011 May 25;5(1):83
http://dx.doi.org/10.1186/1752-0509-5-83
Abstract Background Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. Results We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. Conclusions As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.
en
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Journal Article
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oai:repository.helmholtz-hzi.de:10033/5831652019-08-30T11:36:05Zcom_10033_48156com_10033_6832col_10033_48157
Helmholtz Zentrum für Infektionsforschung Repository
author
Varga, John J
author
Barbier, Mariette
author
Mulet, Xavier
author
Bielecki, Piotr
author
Bartell, Jennifer A
author
Owings, Joshua P
author
Martinez-Ramos, Inmaculada
author
Hittle, Lauren E
author
Davis, Michael R
author
Damron, F Heath
author
Liechti, George W
author
Puchałka, Jacek
author
Dos Santos, Vitor A P Martins
author
Ernst, Robert K
author
Papin, Jason A
author
Albertí, Sebastian
author
Oliver, Antonio
author
Goldberg, Joanna B
department
HZI-Helmholtzzentrum für Infektionsforschung
2015-12-03T10:36:44Z
2015
Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. 2015, 16 (1):883 BMC Genomics
1471-2164
26519161
10.1186/s12864-015-2069-0
http://hdl.handle.net/10033/583165
BMC genomics
Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized.
en
Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains.
Article
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