Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

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

Volumn 105, Issue 29, 2008, Pages 10039-10044

  Dagan, Tal ^a   Artzy Randrup, Yael ^b,c   Martin, William ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b TEL AVIV UNIVERSITY   (Israel)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Community structure; Microbial genomes; Molecular phylogeny

Indexed keywords

ARTICLE; COMMUNITY STRUCTURE; EVOLUTION; GENE; GENE TRANSFER; GENOME; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; SPECTROSCOPY;

ARCHAEA; BACTERIA; BACTERIAL PROTEINS; EVOLUTION; GENE REGULATORY NETWORKS; GENE TRANSFER, HORIZONTAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; MODELS, GENETIC; PHYLOGENY; PROKARYOTIC CELLS;

PROKARYOTA;

EID: 48249151749     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0800679105     Document Type: Article

References (49)

1. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711-721.
2. Lang AS, Beatty JT (2007) Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol 15:54-62.
3. Moran NA (2007) Symbiosis as an adaptive process and source of phenotypic complexity. Proc Natl Acad Sci USA 104:8627-8633.
4. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2128.
5. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226-2238.
6. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616-1620.
7. Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309-338.
8. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005) The net of life: Reconstructing the microbial phylogenetic network. Genome Res 15:954-959.
9. Doolittle WF, Bapteste E (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104:2043-2049.
10. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361-375.
11. Ciccarelli FD, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.
12. Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760-766.
13. Alon U (2007) Network motifs: Theory and experimental approaches. Nat Rev Genet 8:450-461.
14. Pal C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372-1375.
15. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42.
16. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254-267.
17. Rezende EL, Lavabre JE, Guimaraes PR, Jordano P, Bascompte J (2007) Non-random coextinctions in phylogenetically structured mutualistic networks. Nature 448:925-928.
18. Proulx SR, Promislow DE, Phillips PC (2005) Network thinking in ecology and evolution. Trends Ecol Evol 20:345-353.
19. Burt RS (1980) Models of network stucture. Annu Rev Sociol 6:79-141.
20. Albert R, Jeong H, Barabási AL (1999) Internet diameter of the world-wide web. Nature 401:130-131.
21. Guimera R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 433:895-900.
22. Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818.
23. Newman MEJ (2006) Finding community structure in networks using the eigenvectors of matrices. Phys Rev E 7 4:036104.
24. Gallos LK, Song C, Havlin S, Makse HA (2007) Scaling theory of transport in complex biological networks. Proc Natl Acad Sci USA 104:7746-7751.
25. Comas I, Moya A, Azad RK, Lawrence JG, Gonzalez-Candelas F (2006) The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process. Mol Biol Evol 23:2049-2057.
26. Boetius A, et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626.
27. McInerney JO, Cotton JA, Pisani D (2008) The prokaryotic tree of life: Past, present. . . and future? Trends Ecol Evol 276:276-281.
28. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332-14337.
29. Huang J, Gogarten JP (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol 8:R99.
30. Ueda K, Beppu T (2007) Lessons from studies of Symbiobacterium thermophilum, a unique syntrophic bacterium. Biosci Biotechnol Biochem 71:1115-1121.
31. Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21:108-110.
32. Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155.
33. Boucher Y, et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37:283-328.
34. Doolittle WF, et al. (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Phil Trans R Soc Lond B 358:39-58.
35. Dagan T, Martin W (2007) Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci USA 104:870-875.
36. Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45:167-256.
37. Artzy-Randrup Y, Stone L (2005) Generating uniformly distributed random networks: The ADD method. Phys Rev E 72:056708.35.
38. Clauset A, Shalizi CR, Newman MEJ (2007) Power-law distributions in empirical data. Physics 0706.1062 E-print.
39. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
40. Susko E, Leigh J, Doolittle WF, Bapteste E (2006) Visualizing and assessing phylogenetic congruence of core gene sets:Acase study of the gamma-proteobacteria. Mol Biol Evol 23:1019-1030.
41. Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12:406-411.
42. 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 8:11-22.
43. Sorek R, et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452.
44. Bapteste E, et al. (2008) Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol 25:83-91.
45. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33-36.
46. Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: 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.
47. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575-1584.
48. Brohée S, van Helden J (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7:488.
49. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) (Department of Genome Sciences, Univ of Washington, Seattle), version 3.6.