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PMID: 20057383 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

A protocol for generating a high-quality genome-scale metabolic reconstruction.

Nature protocols ·Vol. 5 ·No. 1 ·2010-01-00 ·Pages 93-121

Thiele I, Palsson BØ

Abstract

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

MeSH Terms
Biomass Computer Simulation Gene Expression Profiling Gene Expression Regulation Genome Metabolome/genetics Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Thiele Ines
Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Palsson Bernhard Ø
References (87)
87 references, click to expand
  1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  2. Optimization based automated curation of metabolic reconstructions.
    BMC Bioinformatics. 2007 Jun 20;8:212 PMID: 17584497
  3. Optimization-based framework for inferring and testing hypothesized metabolic objective functions.
    Biotechnol Bioeng. 2003 Jun 20;82(6):670-7 PMID: 12673766
  4. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.
    J Biol Chem. 2006 Dec 29;281(52):40041-8 PMID: 17062565
  5. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.
    Biophys J. 2004 Jul;87(1):37-46 PMID: 15240442
  6. Bayesian-based selection of metabolic objective functions.
    Bioinformatics. 2007 Feb 1;23(3):351-7 PMID: 17150997
  7. Group contribution method for thermodynamic analysis of complex metabolic networks.
    Biophys J. 2008 Aug;95(3):1487-99 PMID: 18645197
  8. Integrating high-throughput and computational data elucidates bacterial networks.
    Nature. 2004 May 6;429(6987):92-6 PMID: 15129285
  9. Matrix formalism to describe functional states of transcriptional regulatory systems.
    PLoS Comput Biol. 2006 Aug 11;2(8):e101 PMID: 16895435
  10. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
    Nucleic Acids Res. 2005 Oct 07;33(17):5691-702 PMID: 16214803
  11. Reconstruction of biochemical networks in microorganisms.
    Nat Rev Microbiol. 2009 Feb;7(2):129-43 PMID: 19116616
  12. Annotation of bacterial and archaeal genomes: improving accuracy and consistency.
    Chem Rev. 2007 Aug;107(8):3431-47 PMID: 17658903
  13. Global analysis of protein localization in budding yeast.
    Nature. 2003 Oct 16;425(6959):686-91 PMID: 14562095
  14. Global organization of metabolic fluxes in the bacterium Escherichia coli.
    Nature. 2004 Feb 26;427(6977):839-43 PMID: 14985762
  15. Multidimensional annotation of the Escherichia coli K-12 genome.
    Nucleic Acids Res. 2007;35(22):7577-90 PMID: 17940092
  16. Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
    BMC Syst Biol. 2009 Mar 25;3:37 PMID: 19321003
  17. 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
  18. Is maximization of molar yield in metabolic networks favoured by evolution?
    J Theor Biol. 2008 Jun 7;252(3):497-504 PMID: 18249414
  19. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
    PLoS Comput Biol. 2008 Oct;4(10):e1000210 PMID: 18974823
  20. The number of ribosomal RNA genes in Mycoplasma capricolum.
    Mol Gen Genet. 1981;182(3):502-4 PMID: 6272066
  21. Enhancement of the chemical semantic web through the use of InChI identifiers.
    Org Biomol Chem. 2005 May 21;3(10):1832-4 PMID: 15889163
  22. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism.
    Genome Res. 2005 Jun;15(6):820-9 PMID: 15930493
  23. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12 PMID: 17170002
  24. The COG database: an updated version includes eukaryotes.
    BMC Bioinformatics. 2003 Sep 11;4:41 PMID: 12969510
  25. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.
    J Biol Chem. 2005 Mar 25;280(12):11683-95 PMID: 15572364
  26. Locating proteins in the cell using TargetP, SignalP and related tools.
    Nat Protoc. 2007;2(4):953-71 PMID: 17446895
  27. The EcoCyc Database.
    Nucleic Acids Res. 2002 Jan 1;30(1):56-8 PMID: 11752253
  28. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D511-4 PMID: 17202167
  29. Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum.
    J Biol Chem. 1985 Jan 25;260(2):899-906 PMID: 2981849
  30. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks.
    Eur J Biochem. 2004 Jul;271(14):2905-22 PMID: 15233787
  31. Rapid screening method for quantitation of bacterial cell lipids from whole cells.
    J Microbiol Methods. 2003 Nov;55(2):411-8 PMID: 14529962
  32. Towards multidimensional genome annotation.
    Nat Rev Genet. 2006 Feb;7(2):130-41 PMID: 16418748
  33. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  34. 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
  35. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.
    Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19103-8 PMID: 16357206
  36. Predicting subcellular localization of proteins using machine-learned classifiers.
    Bioinformatics. 2004 Mar 1;20(4):547-56 PMID: 14990451
  37. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
    J Theor Biol. 2000 Apr 7;203(3):229-48 PMID: 10716907
  38. 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
  39. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
    Nat Protoc. 2007;2(3):727-38 PMID: 17406635
  40. Mycobacterial cell wall: structure and role in natural resistance to antibiotics.
    FEMS Microbiol Lett. 1994 Oct 15;123(1-2):11-8 PMID: 7988876
  41. Systems approach to refining genome annotation.
    Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17480-4 PMID: 17088549
  42. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D274-9 PMID: 17135193
  43. Predicting biological system objectives de novo from internal state measurements.
    BMC Bioinformatics. 2008 Jan 24;9:43 PMID: 18218092
  44. Systematic assignment of thermodynamic constraints in metabolic network models.
    BMC Bioinformatics. 2006 Nov 23;7:512 PMID: 17123434
  45. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
    BMC Syst Biol. 2008 Sep 16;2:79 PMID: 18793442
  46. Metabolic network analysis integrated with transcript verification for sequenced genomes.
    Nat Methods. 2009 Aug;6(8):589-92 PMID: 19597503
  47. Genome-scale microbial in silico models: the constraints-based approach.
    Trends Biotechnol. 2003 Apr;21(4):162-9 PMID: 12679064
  48. Correcting ligands, metabolites, and pathways.
    BMC Bioinformatics. 2006 Nov 28;7:517 PMID: 17132165
  49. 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
  50. Genome annotation: from sequence to biology.
    Nat Rev Genet. 2001 Jul;2(7):493-503 PMID: 11433356
  51. Internet-based tools for communication and collaboration in chemistry.
    Drug Discov Today. 2008 Jun;13(11-12):502-6 PMID: 18549976
  52. Chance and necessity in the evolution of minimal metabolic networks.
    Nature. 2006 Mar 30;440(7084):667-70 PMID: 16572170
  53. Functional states of the genome-scale Escherichia coli transcriptional regulatory system.
    PLoS Comput Biol. 2009 Jun;5(6):e1000403 PMID: 19503608
  54. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
    Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13134-9 PMID: 14578455
  55. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21 PMID: 18045790
  56. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
    Mol Syst Biol. 2006;2:2006.0004 PMID: 16738551
  57. Identification of potential pathway mediation targets in Toll-like receptor signaling.
    PLoS Comput Biol. 2009 Feb;5(2):e1000292 PMID: 19229310
  58. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
    Nat Biotechnol. 2008 Jun;26(6):659-67 PMID: 18536691
  59. Regulatory on/off minimization of metabolic flux changes after genetic perturbations.
    Proc Natl Acad Sci U S A. 2005 May 24;102(21):7695-700 PMID: 15897462
  60. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.
    Mol Syst Biol. 2008;4:177 PMID: 18364711
  61. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
    J Theor Biol. 1992 Feb 21;154(4):421-54 PMID: 1593896
  62. The RAST Server: rapid annotations using subsystems technology.
    BMC Genomics. 2008 Feb 08;9:75 PMID: 18261238
  63. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.
    Biophys J. 2006 Jun 1;90(11):3919-28 PMID: 16533855
  64. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.
    J Biol Chem. 2007 Sep 28;282(39):28791-28799 PMID: 17573341
  65. The Pathway Tools software.
    Bioinformatics. 2002;18 Suppl 1:S225-32 PMID: 12169551
  66. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.
    J Bacteriol. 2008 Apr;190(8):2790-803 PMID: 18192387
  67. 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
  68. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
    J Bacteriol. 2005 Aug;187(16):5818-30 PMID: 16077130
  69. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D293-5 PMID: 14681416
  70. A revised annotation and comparative analysis of Helicobacter pylori genomes.
    Nucleic Acids Res. 2003 Mar 15;31(6):1704-14 PMID: 12626712
  71. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.
    Bioinformatics. 2005 Mar 1;21(5):617-23 PMID: 15501914
  72. Accelerating the reconstruction of genome-scale metabolic networks.
    BMC Bioinformatics. 2006 Jun 13;7:296 PMID: 16772023
  73. Analysis of optimality in natural and perturbed metabolic networks.
    Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):15112-7 PMID: 12415116
  74. The European Bioinformatics Institute's data resources: towards systems biology.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D46-53 PMID: 15608238
  75. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis.
    Bioinformatics. 2003 Nov 1;19(16):2144-6 PMID: 14594721
  76. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
    Bioinformatics. 2003 Jan 22;19(2):261-9 PMID: 12538248
  77. KEGG for linking genomes to life and the environment.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4 PMID: 18077471
  78. Structural and functional analysis of cellular networks with CellNetAnalyzer.
    BMC Syst Biol. 2007 Jan 08;1:2 PMID: 17408509
  79. Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima.
    J Biol Chem. 2003 Feb 28;278(9):7540-52 PMID: 12475972
  80. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.
    PLoS Comput Biol. 2009 Feb;5(2):e1000285 PMID: 19214212
  81. metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.
    Nucleic Acids Res. 2005 Mar 03;33(4):1399-409 PMID: 15745999
  82. Large-scale analysis of the yeast genome by transposon tagging and gene disruption.
    Nature. 1999 Nov 25;402(6760):413-8 PMID: 10586881
  83. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
    Genome Res. 2004 Sep;14(9):1797-805 PMID: 15342562
  84. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.
    Mol Syst Biol. 2007;3:119 PMID: 17625511
  85. Ribosomal genes in Escherichia coli.
    Annu Rev Genet. 1986;20:297-326 PMID: 2434021
  86. Genome-scale models of bacterial metabolism: reconstruction and applications.
    FEMS Microbiol Rev. 2009 Jan;33(1):164-90 PMID: 19067749
  87. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.
    Biotechnol Bioeng. 2000-2001;71(4):286-306 PMID: 11291038
Article Info
Journal
Nature protocols
Abbr.
Nat Protoc
ISSN
1750-2799
DOI
10.1038/nprot.2009.203
Published
2010-01-00
Epub
2010-00-07
Pages
93-121
Language
English
Region
England
NLM ID
101284307
PMCID
PMC3125167
Subset
IM
Grants
NIGMS NIH HHS · R01 GM057089 · United States
NIGMS NIH HHS · R01 GM057089-12 · United States
External Links
PubMed source DOI: 10.1038/nprot.2009.203 PMC Full Text View journal details
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