The evolution of modularity in bacterial metabolic networks

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

Volumn 105, Issue 19, 2008, Pages 6976-6981

  Kreimer, Anat ^a   Borenstein, Elhanan ^b,c   Gophna, Uri ^a   Ruppin, Eytan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b STANFORD UNIVERSITY   (United States)

^c SANTA FE INSTITUTE   (United States)

Author keywords

Bacterial evolution; Horizontal gene transfer; Lateral gene transfer; Network modules; Systems biology

Indexed keywords

ARTICLE; BACTERIAL METABOLISM; ENDOSYMBIONT; ENVIRONMENTAL FACTOR; HORIZONTAL GENE TRANSFER; METABOLIC REGULATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; STRAIN DIFFERENCE; SYSTEMS BIOLOGY; TREE OF LIFE; BACTERIUM; EVOLUTION; METABOLISM; PROTEOBACTERIA;

BACTERIA (MICROORGANISMS); HEXAPODA; MAMMALIA;

BACTERIA; EVOLUTION; METABOLIC NETWORKS AND PATHWAYS; PROTEOBACTERIA;

EID: 44349157798     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712149105     Document Type: Article

References (36)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52.
2. Wolf DM, Arkin AP (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6:125-134.
3. Segal E, Shapira M, Regev A, Pe'er D, Botstein D (2003) Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34:166-176.
4. Segal E, Friedman N, Koller D, Regev A (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36:1090-1098.
5. Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci USA 100:1128-1133.
6. Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res, 14:391-397.
7. Campillos M, von Mering C, Jensen LJ, Bork P (2006) Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 16:374-382.
8. Qin H, Lu HHS, Wu WB, Li W-H (2003) Evolution of the yeast protein interaction network. Proc Natl Acad Sci USA 100:12820-12824.
9. Spirin V, Gelfand MS, Mironov AA, Mirny LA (2006) A metabolic network in the evolutionary context: Multiscale structure and modularity. Proc Natl Acad Sci USA 103:8774-8779.
10. Pereira-Leal B, Teichmann SA (2005) Novel specificities emerge by stepwise duplication of functional modules. Genome Res 15:552-559.
11. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Nat Genet 297:1551-1555.
12. J. Zhao, et al. (2007) Modular co-evolution of metabolic networks. BMC Bioinformatics 8:311-322.
13. Wagner GP, Mezey J, Calabretta R (2001) Natural selection and the origin of modules. Modularity: Understanding the Development and Evolution of Complex Natural Systems, eds Callabaut W, Rasskin-Gutman D (MIT Press, Cambridge, MA).
14. Wagner A (2005) Robustness and Evolvability in Living Systems (Princeton Univ Press, Princeton).
15. Wilke CO, Adami C (2003) Evolution of mutational robustness. Mutat Res Front 8:3-11.
16. Lawrence JG, Roth JR (1996) Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860.
17. Rainey PB, Cooper TF (2004) Evolution of bacterial diversity and the origins of modularity. Res Microbiol 155:370-375.
18. Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 102:13773-13778.
19. Kashtan N, Noor E, Alon U (2007) Varying environments can speed up evolution. Proc Natl Acad Sci USA 104:13711-13716.
20. Parter M, Kashtan N, Alon U (2007) Environmental variability and modularity of bacterial metabolic networks. BMC Evol Biol 7:169-195.
21. Ciccarelli FD, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.
22. Achtman M, et al. (1999) Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci USA 96:14043-14048.
23. Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci USA 103:8577-8582.
24. Couturier E, Rocha EPC (2006) Replication-associated gene dosage effects shape the genomesof fast-growing bacteria but only for transcription and translation genes. Mol Microbiol 59:1506-1518.
25. Horowitz NH (1945) On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 31:153-157.
26. Pal C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372-1375.
27. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2128.
28. Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12:406-411.
29. Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760-766.
30. Wellner A, Lurie MN, Gophna U (2007) Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biol 8:R156.
31. Hintze A, Adami C (2008) Evolution of complex modular biological networks. PLoS Comput Biol 4:e23.
32. Ma H, Zeng AP (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19:270-277.
33. Raymond J, Segre D (2006) The effect of oxygen on biochemical networks and the evolution of complex life. Science 311:1764-1767.
34. Kharchenko P, Church GM, Vitkup D (2005) Expression dynamics of a cellular metabolic network. Mol Syst Biol 10.1038/msb4100023.
35. Cormen TH, Leiserson CE, Rivest RL (1990) Introduction to Algorithms. (MIT Press, Cambridge, MA, and McGraw-Hill, New York), First Ed.
36. Fitch W (1971) Towards defining the course of evolution: Minimum change for a specific tree topology. Syst Zool 20:406-416.