Molecular Evolution in Large Genetic Networks: Does Connectivity Equal Constraint?

Journal of Molecular Evolution

Volumn 58, Issue 2, 2004, Pages 203-211

  Hahn, Matthew W ^a   Conant, Gavin C ^b   Wagner, Andreas ^b  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Genetic network; Mutational robustness; Power law; Selective constraint

Indexed keywords

FUNGAL PROTEIN;

ARTICLE; BACTERIAL METABOLISM; CELL CYCLE; CORRELATION ANALYSIS; ESCHERICHIA COLI; EVOLUTIONARY RATE; GENETIC TRANSCRIPTION; MOLECULAR EVOLUTION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

ENERGY METABOLISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; POINT MUTATION; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SELECTION (GENETICS); TWO-HYBRID SYSTEM TECHNIQUES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0842290925     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2544-0     Document Type: Article

References (48)

1. Akashi H (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11:660-666
2. Albert R, Jeong H, Barabasi A-L (2000) Error and attack tolerance of complex networks. Nature 406:378-382
3. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
4. Barabasi A-L, Albert R (1999) Emergence of scaling in random networks. Science 286:509-512
5. Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283:381-387
6. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462
7. Conant GC, Wagner A (2002) GenomeHistory: A software tool and its application to fully sequenced genomes. Nucleic Acids Res 30:3378-3386
8. Dykhuizen DE, Hartl DL (1983) Functional effects of PGI allozymes in Escherichia coli. Genetics 105:1-18
9. Edwards JS, Palsson BO (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274:17410-17416
10. Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5533
11. Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:495-512
12. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296:750-752
13. Fraser HB, Wall DP, Hirsh AE (2003) A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol 3:11
14. Gavin AC, Bosche M, Krause R, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147
15. The Gene Ontology Consortium (2000) Gene Ontology: Tool for the unification of biology. Nature Genet 25:25-29
16. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:563-567
17. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725-736
18. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52
19. Ho Y, Gruhler A, Heilbut A, Bader GD, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
20. Hurst LD, Smith NGC (1999) Do essential genes evolve slowly? Curr Biol 9:747-750
21. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574
22. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi A-L (2000) The large-scale organization of metabolic networks. Nature 407:651-654
23. Jeong H, Mason SP, Barabasi A-L, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42
24. Jordan IK, Wolf YI, Koonin EV (2003a) No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly. BMC Evol Biol 3:1
25. Jordan IK, Wolf YI, Koonin EV (2003b) Correction: No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly. BMC Evol Biol 3:5
26. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
27. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275-276
28. Kumar S, Subramanian S (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci USA 99:803-808
29. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
30. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155
31. Mewes HW, Heumann K, Kaps A, Mayer K, Pfeiffer F, Stocker S, Frishman D (1999) MIPS: A database for genomes and protein sequences. Nucleic Acids Res 27:44-48
32. Morowitz HJ (1992) Beginnings of cellular life. Yale University Press, New Haven, CT
33. Rausher MD, Miller RE, Tiffin P (1999) Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. Mol Biol Evol 16:266-274
34. Ross-Macdonald P, Coelho PSR, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L, Heldtman M, Nelson FK, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder GS, Snyder M (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413-418
35. Smith V, Chou KN, Lashkari D, Botstein D, Brown PO (1996) Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274:2069-2074
36. Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV (1996) Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol 6:279-291
37. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
38. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang MJ, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627
39. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-403
40. Wagner A (2000) Mutational robustness in genetic networks of yeast. Nature Genet 24:355-361
41. Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few duplicate genes. Mol Biol Evol 18:1283-1292
42. Wagner A (2002) Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res 12:309-315
43. Wagner A, Fell D (2001) The small world inside large metabolic networks. Proc Roy Soc Lond Ser B 280:1803-1810
44. Watts DJ (1999) Small worlds. Princeton University Press, Princeton, NJ
45. Watts DJ, Strogatz SH (1998) Collective dynamics of small-world networks. Nature 393:440-442
46. Williams EJB, Hurst LD (2000) The proteins of linked genes evolve at similar rates. Nature 407:900-903
47. Winzeler EA, Shoemaker DD, Astromoff A, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion ad parallel analysis. Science 285:901-906
48. Wood V, Gwilliam R, Rajandream MA, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880