The role of cellular objectives and selective pressures in metabolic pathway evolution

Current Opinion in Biotechnology

Volumn 22, Issue 4, 2011, Pages 595-600

  Nam, Hojung ^a   Conrad, Tom M ^b   Lewis, Nathan E ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-MOLECULAR; EXPERIMENTAL LABORATORY; EXTREME CONDITIONS; METABOLIC NETWORK; METABOLIC PATHWAYS; MICROBIAL EVOLUTION; MOLECULAR LEVELS; NEW SPECIES; NUTRIENT AVAILABILITY; SELECTIVE PRESSURE; TIME-SCALES;

GENES;

METABOLISM;

ETHYLENE GLYCOL; PROPYLENE GLYCOL;

BACTERIAL GENOME; EVOLUTION; GENE EXPRESSION; MICROBIAL METABOLISM; MICROORGANISM; MOLECULAR INTERACTION; NONHUMAN; NUTRIENT AVAILABILITY; PHENOTYPE; PRIORITY JOURNAL; REVIEW;

BACTERIA; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; METABOLIC NETWORKS AND PATHWAYS; PHENOTYPE;

EID: 79960963439     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.03.006     Document Type: Review

References (38)

1. Whitaker J.W., Letunic I., McConkey G.A., Westhead D.R. metaTIGER: a metabolic evolution resource. Nucleic Acids Res 2009, 37:D531-D538.
2. Mithani A., Hein J., Preston G.M. Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in pseudomonas. Mol Biol Evol 2011, 28:483-499.
3. Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
4. Seshasayee A.S., Fraser G.M., Babu M.M., Luscombe N.M. Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 2009, 19:79-91.
5. Noor E., Eden E., Milo R., Alon U. Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell 2010, 39:809-820.
6. Pal C., Papp B., Lercher M.J., Csermely P., Oliver S.G., Hurst L.D. Chance and necessity in the evolution of minimal metabolic networks. Nature 2006, 440:667-670.
7. Borenstein E., Kupiec M., Feldman M.W., Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci USA 2008, 105:14482-14487.
8. Maslov S., Krishna S., Pang T.Y., Sneppen K. Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci USA 2009, 106:9743-9748.
9. Pace N.R. Origin of life-facing up to the physical setting. Cell 1991, 65:531-533.
10. Huang S.L., Wu L.C., Liang H.K., Pan K.T., Horng J.T., Ko M.T. PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics 2004, 20:276-278.
11. Takemoto K., Nacher J.C., Akutsu T. Correlation between structure and temperature in prokaryotic metabolic networks. BMC Bioinform 2007, 8:303.
12. Takemoto K., Akutsu T. Origin of structural difference in metabolic networks with respect to temperature. BMC Syst Biol 2008, 2:82.
13. Edwards J.S., Ibarra R.U., Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001, 19:125-130.
14. Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
15. Teusink B., Wiersma A., Jacobs L., Notebaart R.A., Smid E.J. Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol 2009, 5:e1000410.
16. Fong S.S., Palsson B.O. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004, 36:1056-1058.
17. Lewis N.E., Hixson K.K., Conrad T.M., Lerman J.A., Charusanti P., Polpitiya A.D., Adkins J.N., Schramm G., Purvine S.O., Lopez-Ferrer D., et al. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 2010, 6:390.
18. Dekel E., Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436:588-592.
19. Herring C.D., Raghunathan A., Honisch C., Patel T., Applebee M.K., Joyce A.R., Albert T.J., Blattner F.R., van den Boom D., Cantor C.R., Palsson B.O. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 2006, 38:1406-1412.
20. Conrad T.M., Joyce A.R., Applebee M.K., Barrett C.L., Xie B., Gao Y., Palsson B.O. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 2009, 10:R118.
21. Charusanti P., Conrad T.M., Knight E.M., Venkataraman K., Fong N.L., Xie B., Gao Y., Palsson B.O. Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet 2010, 6:e1001186.
22. Conrad T.M., Frazier M., Joyce A.R., Cho B.K., Knight E.M., Lewis N.E., Landick R., Palsson B.O. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci USA 2010, 107:20500-20505.
23. Blount Z.D., Borland C.Z., Lenski R.E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 2008, 105:7899-7906.
24. Lee D.H., Palsson B.O. Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol 2010, 76:4158-4168.
25. Boronat A., Caballero E., Aguilar J. Experimental evolution of a metabolic pathway for ethylene glycol utilization by Escherichia coli. J Bacteriol 1983, 153:134-139.
26. Hochhauser S.J., Weiss B. Escherichia coli mutants deficient in deoxyuridine triphosphatase. J Bacteriol 1978, 134:157-166.
27. Atsumi S., Wu T.Y., Machado I.M., Huang W.C., Chen P.Y., Pellegrini M., Liao J.C. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol 2010, 6:449.
28. Gonzalez R., Tao H., Purvis J.E., York S.W., Shanmugam K.T., Ingram L.O. Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol Prog 2003, 19:612-623.
29. Goodarzi H., Bennett B.D., Amini S., Reaves M.L., Hottes A.K., Rabinowitz J.D., Tavazoie S. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol 2010, 6:378.
30. Veeravalli K., Boyd D., Iverson B.L., Beckwith J., Georgiou G. Laboratory evolution of glutathione biosynthesis reveals natural compensatory pathways. Nat Chem Biol 2011, 7:101-105.
31. Masip L., Veeravalli K., Georgiou G. The many faces of glutathione in bacteria. Antioxid Redox Signal 2006, 8:753-762.
32. Horowitz N.H. On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 1945, 31:153-157.
33. Jensen R.A. Enzyme recruitment in evolution of new function. Annu Rev Microbiol 1976, 30:409-425.
34. Kim J., Kershner J.P., Novikov Y., Shoemaker R.K., Copley S.D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol Syst Biol 2010, 6:436.
35. Soo V.W., Hanson-Manful P., Patrick W.M. From the cover: artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc Natl Acad Sci USA 2011, 108:1484-1489.
36. Fisher M.A., McKinley K.L., Bradley L.H., Viola S.R., Hecht M.H. De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth. PLoS One 2011, 6:e15364.
37. Babic A., Lindner A.B., Vulic M., Stewart E.J., Radman M. Direct visualization of horizontal gene transfer. Science 2008, 319:1533-1536.
38. Zhang Y., Thiele I., Weekes D., Li Z., Jaroszewski L., Ginalski K., Deacon A.M., Wooley J., Lesley S.A., Wilson I.A., et al. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 2009, 325:1544-1549.