Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 50, 2013, Pages 20338-20343

  Monk, Jonathan M ^a   Charusanti, Pep ^b   Aziz, Ramy K ^b,c   Lerman, Joshua A ^d   Premyodhin, Ned ^b   Orth, Jeffrey D ^b,e   Feist, Adam M ^b   Palsson, Bernhard Ø ^b,d  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c CAIRO UNIVERSITY   (Egypt)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e INTREXON CORPORATION   (United States)

Author keywords

Core and pan genome; Mathematical modeling; Systems biology

Indexed keywords

4 HYDROXYPHENYLACETIC ACID; ACETOACETIC ACID; AGMATINE; ALLOSE; ARABINITOL; ARGININE; BUTYRIC ACID; DOPAMINE; FOLIC ACID; LEUCINE; METHIONINE; NICOTINAMIDE; NICOTINIC ACID; PHENETHYLAMINE; RAFFINOSE; RIBITOL; SUCROSE; THIAMINE; TRYPTOPHAN; TYRAMINE; UREA;

ACCURACY; ADAPTATION; ARTICLE; AUXOTROPHY; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOSYNTHESIS; CATABOLISM; COMMENSAL ESCHERICHIA COLI; DNA SEQUENCE; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; GENE POOL; GENE SEQUENCE; GENETIC MODEL; GENOME ANALYSIS; NONHUMAN; NUTRITION; PREDICTION; PRIORITY JOURNAL; SHIGELLA;

EID: 84890290025     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1307797110     Document Type: Article

References (36)

1. Hayashi T, et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8(1):11-22.
2. Perna NT, et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409(6819):529-533.
3. Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67(2):238-276.
4. Touchon M, et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5(1):e1000344.
5. Liao YC, et al. (2011) An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol 193(7):1710-1717.
6. Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT (2011) The evolution of metabolic networks of E. coli. BMC Syst Biol 5:182.
7. Archer CT, et al. (2011) The genome sequence of E. coli W (ATCC 9637): Comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12:9.
8. Yoon SH, et al. (2012) Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol 13(5):R37.
9. Charusanti P, et al. (2011) An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Syst Biol 5:163.
10. Thiele I, et al. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol 5:8.
11. Blattner FR, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-1462.
12. Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97(10):5528-5533.
13. Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4(9):R54.
14. Feist AM, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121.
15. Orth JD, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011. Mol Syst Biol 7:535.
16. McCloskey D, Palsson BO, Feist AM (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 9:661.
17. Feist AM, Palsson BO (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26(6):659-667.
18. Lee SY (2009) Systems Biology and Biotechnology of Escherichia coli (Springer, New York).
19. Pupo GM, Lan R, Reeves PR (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci USA 97(19):10567-10572.
20. DebRoy C, Roberts E, Fratamico PM (2011) Detection of O antigens in Escherichia coli. Anim Health Res Rev 12(2):169-185.
21. Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7(2):129-143.
22. Bliven KA, Maurelli AT (2012) Antivirulence genes: Insights into pathogen evolution through gene loss. Infect Immun 80(12):4061-4070.
23. Erbersdobler HF, Faist V (2001) Metabolic transit of Amadori products. Nahrung 45(3):177-181.
24. Smith EA, Macfarlane GT (1996) Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J Appl Bacteriol 81(3):288-302.
25. Prieto MA, Díaz E, García JL (1996) Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: Engineering a mobile aromatic degradative cluster. J Bacteriol 178(1):111-120.
26. Karch H, Tarr PI, Bielaszewska M (2005) Enterohaemorrhagic Escherichia coli in human medicine. Int J Med Microbiol 295(6-7):405-418.
27. Nakano M, et al. (2001) Association of the urease gene with enterohemorrhagic Escherichia coli strains irrespective of their serogroups. J Clin Microbiol 39(12):4541-4543.
28. Reed JL, et al. (2006) Systems approach to refining genome annotation. Proc Natl Acad Sci USA 103(46):17480-17484.
29. Prunier AL, Schuch R, Fernández RE, Maurelli AT (2007) Genetic structure of the nadA and nadB antivirulence loci in Shigella spp. J Bacteriol 189(17):6482-6486.
30. Zagaglia C, et al. (1991) Virulence plasmids of enteroinvasive Escherichia coli and Shigella flexneri integrate into a specific site on the host chromosome: Integration greatly reduces expression of plasmid-carried virulence genes. Infect Immun 59(3):792-799.
31. Durfee T, et al. (2008) The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse. J Bacteriol 190(7):2597-2606.
32. Jenkins LS, Nunn WD (1987) Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: The ato system. J Bacteriol 169(1):42-52.
33. Bernier-Fébreau C, et al. (2004) Use of deoxyribose by intestinal and extraintestinal pathogenic Escherichia coli strains: A metabolic adaptation involved in competitiveness. Infect Immun 72(10):6151-6156.
34. Díaz E, Ferrández A, Prieto MA, García JL (2001) Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 65(4):523-569.
35. Prunier AL, et al. (2007) nadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity. Microbiology 153(Pt 7):2363-2372.
36. Lee DH, Palsson BO (2010) Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol 76(13):4158-4168.