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PMID: 21244678 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

BMC systems biology ·Vol. 5 ·2011-01-18 ·Pages 8

Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D

Abstract

Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem. Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches. Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.

MeSH Terms
Anti-Bacterial Agents/metabolism,pharmacology Cooperative Behavior Databases, Factual Genes, Bacterial/genetics Humans Metabolic Networks and Pathways Models, Biological Salmonella typhimurium/drug effects,genetics,metabolism Systems Biology
Chemicals
Anti-Bacterial Agents
Authors & Affiliations
27 authors, click to expand affiliations / ORCID
Thiele Ines
Center for Systems Biology, University of Iceland, Reykjavik, Iceland.
Hyduke Daniel R
Steeb Benjamin
Fankam Guy
Allen Douglas K
Bazzani Susanna
Charusanti Pep
Chen Feng-Chi
Fleming Ronan M T
Hsiung Chao A
De Keersmaecker Sigrid C J
Liao Yu-Chieh
Marchal Kathleen
Mo Monica L
Özdemir Emre
Raghunathan Anu
Reed Jennifer L
Shin Sook-il
Sigurbjörnsdóttir Sara
Steinmann Jonas
Sudarsan Suresh
Swainston Neil
Thijs Inge M
Zengler Karsten
Palsson Bernhard O
Adkins Joshua N
Bumann Dirk
References (43)
43 references, click to expand
  1. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters.
    FEMS Microbiol Lett. 2006 Apr;257(2):278-84 PMID: 16553864
  2. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D511-4 PMID: 17202167
  3. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
    Nat Biotechnol. 2008 Oct;26(10):1155-60 PMID: 18846089
  4. Optimization based automated curation of metabolic reconstructions.
    BMC Bioinformatics. 2007 Jun 20;8:212 PMID: 17584497
  5. Virulence of antibiotic-resistant Salmonella typhimurium.
    Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3949-53 PMID: 9520473
  6. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
    PLoS Comput Biol. 2009 Mar;5(3):e1000312 PMID: 19282977
  7. Salmonella: a model for bacterial pathogenesis.
    Annu Rev Med. 2001;52:259-74 PMID: 11160778
  8. Two-dimensional annotation of genomes.
    Nat Biotechnol. 2004 Oct;22(10):1218-9 PMID: 15470454
  9. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.
    BMC Syst Biol. 2007 Jun 08;1:26 PMID: 17555602
  10. Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis.
    J Biol Chem. 2008 Feb 22;283(8):5148-57 PMID: 18070885
  11. Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain.
    J Biol Chem. 2009 Oct 23;284(43):29480-8 PMID: 19690172
  12. Reconstruction of biochemical networks in microorganisms.
    Nat Rev Microbiol. 2009 Feb;7(2):129-43 PMID: 19116616
  13. Robust Salmonella metabolism limits possibilities for new antimicrobials.
    Nature. 2006 Mar 16;440(7082):303-7 PMID: 16541065
  14. Lack of development of new antimicrobial drugs: a potential serious threat to public health.
    Lancet Infect Dis. 2005 Feb;5(2):115-9 PMID: 15680781
  15. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.
    Nature. 2001 Oct 25;413(6858):852-6 PMID: 11677609
  16. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
    Nat Protoc. 2011 Aug 04;6(9):1290-307 PMID: 21886097
  17. A protocol for generating a high-quality genome-scale metabolic reconstruction.
    Nat Protoc. 2010 Jan;5(1):93-121 PMID: 20057383
  18. Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli.
    Proc Natl Acad Sci U S A. 2007 May 15;104(20):8484-9 PMID: 17494765
  19. Global reconstruction of the human metabolic network based on genomic and bibliomic data.
    Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82 PMID: 17267599
  20. Towards genome-scale signalling network reconstructions.
    Nat Rev Genet. 2010 Apr;11(4):297-307 PMID: 20177425
  21. Multi-target therapeutics: when the whole is greater than the sum of the parts.
    Drug Discov Today. 2007 Jan;12(1-2):34-42 PMID: 17198971
  22. Towards multidimensional genome annotation.
    Nat Rev Genet. 2006 Feb;7(2):130-41 PMID: 16418748
  23. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
    Biophys J. 2010 May 19;98(10):2072-81 PMID: 20483314
  24. Reconstruction annotation jamborees: a community approach to systems biology.
    Mol Syst Biol. 2010 Apr 13;6:361 PMID: 20393581
  25. Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.
    Biophys Chem. 2009 Dec;145(2-3):47-56 PMID: 19783351
  26. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
    Mol Syst Biol. 2007;3:121 PMID: 17593909
  27. Gut inflammation provides a respiratory electron acceptor for Salmonella.
    Nature. 2010 Sep 23;467(7314):426-9 PMID: 20864996
  28. Genome-scale gene/reaction essentiality and synthetic lethality analysis.
    Mol Syst Biol. 2009;5:301 PMID: 19690570
  29. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism.
    Genome Biol. 2007;8(5):R89 PMID: 17521419
  30. The Edinburgh human metabolic network reconstruction and its functional analysis.
    Mol Syst Biol. 2007;3:135 PMID: 17882155
  31. Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2.
    J Bacteriol. 1969 Oct;100(1):215-9 PMID: 4898986
  32. Functional states of the genome-scale Escherichia coli transcriptional regulatory system.
    PLoS Comput Biol. 2009 Jun;5(6):e1000403 PMID: 19503608
  33. Identification of potential pathway mediation targets in Toll-like receptor signaling.
    PLoS Comput Biol. 2009 Feb;5(2):e1000292 PMID: 19229310
  34. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
    Nat Biotechnol. 2008 Jun;26(6):659-67 PMID: 18536691
  35. Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages.
    J Biol Chem. 2006 Sep 29;281(39):29131-40 PMID: 16893888
  36. KEGG for linking genomes to life and the environment.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4 PMID: 18077471
  37. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
    Genome Biol. 2003;4(9):R54 PMID: 12952533
  38. Growth control in the Salmonella-containing vacuole.
    Curr Opin Microbiol. 2008 Feb;11(1):46-52 PMID: 18282735
  39. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions.
    PLoS Comput Biol. 2009 Mar;5(3):e1000308 PMID: 19282964
  40. Applications of genome-scale metabolic reconstructions.
    Mol Syst Biol. 2009;5:320 PMID: 19888215
  41. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.
    BMC Syst Biol. 2009 Apr 08;3:38 PMID: 19356237
  42. Amino acid metabolism of Salmonellae.
    J Bacteriol. 1961 Jan;81:126-9 PMID: 13688128
  43. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.
    PLoS Comput Biol. 2009 Feb;5(2):e1000285 PMID: 19214212
Article Info
Journal
BMC systems biology
Abbr.
BMC Syst Biol
ISSN
1752-0509
DOI
10.1186/1752-0509-5-8
Published
2011-01-18
Epub
2011-00-18
Pages
8
Language
English
Region
England
NLM ID
101301827
PMCID
PMC3032673
Subset
IM
Grants
NIAID NIH HHS · Y1-AI-8401-01 · United States
External Links
PubMed source DOI: 10.1186/1752-0509-5-8 PMC Full Text View journal details
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