Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life

Frontiers in Ecology and Evolution

Volumn 2, Issue NOV, 2014, Pages

  Cheng, Shu ^a   Karkar, Slim ^a,b   Bapteste, Eric ^b   Yee, Nathan ^a   Falkowski, Paul ^a   Bhattacharya, Debashish ^a  

^a RUTGERS UNIVERSITY   (United States)

^b CNRS   (France)

Author keywords

Conductance; Great Oxygenation Event; Microbial evolution; Redox enzymes; Respiratory lifestyles; Sequence similarity network analysis

Indexed keywords

EID: 84976213044     PISSN: None     EISSN: 2296701X     Source Type: Journal    
DOI: 10.3389/fevo.2014.00072     Document Type: Article

References (46)

1. Atkinson, H. J., Morris, J. H., Ferrin, T. E., and Babbitt, P. C. (2009). Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE 4:e4345. doi: 10.1371/journal.pone.0004345
2. Bapteste, E., Lopez, P., Bouchard, F., Baquero, F., McInerney, J. O., and Burian, R. M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc. Natl. Acad. Sci. U.S.A. 109, 18266-18272. doi: 10.1073/pnas.1206541109
3. Bapteste, E., van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., et al. (2013). Networks: expanding evolutionary thinking. Trends Genet. 29, 439-441. doi: 10.1016/j.tig.2013.05.007
4. Beaudet, D., Terrat, Y., Halary, S., de la Providencia, I. E., and Hijri, M. (2013). Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes. Genome Biol. Evol. 5, 1628-1643. doi: 10.1093/gbe/evt120
5. Beauregard-Racine, J., Bicep, C., Schliep, K., Lopez, P., Lapointe, F.-J., and Bapteste, E. (2011). Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol. Dir. 6:39. doi: 10.1186/1745-6150-6-39
6. Blondel, V., Guillaume, J.-L., Lambiotte, R., and Lefebvre, E. (2008). Fast unfolding of communities in large networks. J. Stat. Mech. 2008:P10008. doi: 10.1088/1742-5468/2008/10/P10008
7. Bolten, E., Schliep, A., Schneckener, S., Schomburg, D., and Schrader, R. (2001). Clustering protein sequences-structure prediction by transitive homology. Bioinformatics 17, 935-941. doi: 10.1093/bioinformatics/17.10.935
8. Brocchieri, L., and Karlin, S. (2005). Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 33, 3390-3400. doi: 10.1093/nar/gki615
9. Camoglu, O., Can, T., and Singh, A. K. (2006). Integrating multi-attribute similarity networks for robust representation of the protein space. Bioinformatics 22, 1585-1592. doi: 10.1093/bioinformatics/btl130
10. Ciccarelli, F. D., Doerks, T., Von Mering, C., Creevey, C. J., Snel, B., and Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287. doi: 10.1126/science.1123061
11. Collins, L. J., Poole, A. M., and Penny, D. (2003). Using ancestral sequences to uncover potential gene homologues. Appl. Bioinform. 2, S85-S95
12. Dagan, T., Artzy-Randrup, Y., and Martin, W. (2008). Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. U.S.A. 105, 10039-10044. doi: 10.1073/pnas.0800679105
13. David, L. A., and Alm, E. J. (2011). Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469, 93-96. doi: 10.1038/nature09649
14. Doolittle, W. F. (2009). The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them. Phil. Trans. R. Soc. Lond. B Biol. Sci. 364, 2221-2228. doi: 10.1098/rstb.2009.0032
15. Dupont, C. L., Yang, S., Palenik, B., and Bourne, P. E. (2006). Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc. Natl. Acad. Sci. U.S.A. 103, 17822-17827. doi: 10.1073/pnas.0605798103
16. Dupont, C. L., Butcher, A., Valas, R. E., Bourne, P. E., and Caetano-Anollés, G. (2010). History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc. Natl. Acad. Sci. U.S.A. 107, 10567-10572. doi: 10.1073/pnas.0912491107
17. Falkowski, P. G., Fenchel, T., and Delong, E. F. (2008). The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034-1039. doi: 10.1126/science.1153213
18. Frickey, T., and Lupas, A. (2004). CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20, 3702-3704. doi: 10.1093/bioinformatics/bth444
19. Godfrey, L. V., and Falkowski, P. G. (2009). The cycling and redox state of nitrogen in the Archaean ocean. Nat. Geosci. 2, 725-729. doi: 10.1038/ngeo633
20. Haft, D. H., Selengut, J. D., and White, O. (2003). The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371-373. doi: 10.1093/nar/gkg128
21. Haggerty, L. S., Jachiet, P. A., Hanage, W. P., Fitzpatrick, D. A., Lopez, P., O'Connell, M. J., et al. (2014). A pluralistic account of homology: adapting the models to the data. Mol. Biol. Evol. 31, 501-516. doi: 10.1093/molbev/mst228
22. Halary, S., Leigh, J. W., Cheaib, B., Lopez, P., and Bapteste, E. (2010). Network analyses structure genetic diversity in independent genetic worlds. Proc. Natl. Acad. Sci. U.S.A. 107, 127-132. doi: 10.1073/pnas.0908978107
23. Halary, S., McInerney, J. O., Lopez, P., and Bapteste, E. (2013). EGN: a wizard for construction of gene and genome similarity networks. BMC Evol. Biol. 13:146. doi: 10.1186/1471-2148-13-146
24. Heimann, A., Johnson, C. M., Beard, B. L., Valley, J. W., Roden, E. E., Spicuzza, M. J., et al. (2010). Fe, C, and O isotope compositions of banded iron formation carbonates demonstrate a major role for dissimilatory iron reduction in ~2.5Ga marine environments. Earth Planet. Sci. Lett. 294, 8-18. doi: 10.1016/j.epsl.2010.02.015
25. Jachiet, P. A., Colson, P., Lopez, P., and Bapteste, E. (2014). Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol. Evol. 6, 2195-2205. doi: 10.1093/gbe/evu168
26. Jiang, Y. Y., Kong, D. X., Qin, T., Li, X., Caetano-Anolles, G., and Zhang, H. Y. (2012). The impact of oxygen on metabolic evolution: a chemoinformatic investigation. PLoS Comp. Biol. 8:e1002426. doi: 10.1371/journal.pcbi.1002426
27. Johnson, C. M., Beard, B. L., Klein, C., Beukes, N. J., and Roden, E. E. (2008). Iron isotopes constrain biologic and abiologic processes in banded iron formation genesis. Geochim. Cosmochim. Acta 72, 151-169. doi: 10.1016/j.gca.2007.10.013
28. Kim, K. M., Qin, T., Jiang, Y. Y., Chen, L. L., Xiong, M., Caetano-Anollés, D., et al. (2012). Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure 20, 67-76. doi: 10.1016/j.str.2011.11.003
29. Kim, J. D., Senn, S., Harel, A., Jelen, B. I., and Falkowski, P. G. (2013). Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases. Phil. Trans. R. Soc. Lond. B Biol. Sci. 368, e20120257. doi: 10.1098/rstb.2012.0257
30. Korona, R. (2011). Gene dispensability. Curr. Opin. Biotechnol. 22, 547-551. doi: 10.1016/j.copbio.2011.04.017
31. Lapierre, P., and Gogarten, J. P. (2009). Estimating the size of the bacterial pan-genome. Trends Genet. 25, 107-110. doi: 10.1016/j.tig.2008.12.004
32. Leskovec, J., Lang, K. J., Dasgupta, A., and Mahoney, M. W. (2008). "Statistical properties of community structure in large social and information networks". in Proceedings of the 17th International World Wide Web Conference (New York, NY: ACM), 695-704
33. Marchler-Bauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., Deweese-Scott, C., et al. (2011). CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39, D225-D229. doi: 10.1093/nar/gkq1189
34. Matsui, M., Tomita, M., and Kanai, A. (2013). Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. Genome Biol. Evol. 5, 267-282. doi: 10.1093/gbe/evt004
35. Rappoport, N., Linial, N., and Linial, M. (2013). ProtoNet: charting the expanding universe of protein sequences. Nat. Biotechnol. 31, 290-292. doi: 10.1038/nbt.2553
36. Raymond, J., and Segre, D. (2006). The effect of oxygen on biochemical networks and the evolution of complex life. Science 311, 1764-1767. doi: 10.1126/science.1118439
37. Sasson, O., Vaaknin, A., Fleischer, H., Portugaly, E., Bilu, Y., Linial, N., et al. (2003). ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res. 31, 348-352. doi: 10.1093/nar/gkg096
38. Shen, Y., Buick, R., and Canfield, D. E. (2001). Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410, 77-81. doi: 10.1038/35065071
39. Slesarev, A. I., Mezhevaya, K. V., Makarova, K. S., Polushin, N. N., Shcherbinina, O. V., Shakhova, V. V., et al. (2002). The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. U.S.A. 99, 4644-4649. doi: 10.1073/pnas.032671499
40. Sober, E., and Steel, M. (2002). Testing the hypothesis of common ancestry. J. Theor. Biol. 218, 395-408. doi: 10.1016/S0022-5193(02)93086-9
41. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997). A genomic perspective on protein families. Science 278, 631-637
42. Tian, W., and Skolnick, J. (2003). How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol. 333, 863-882. doi: 10.1016/j.jmb.2003.08.057
43. Wagner, M., Roger, A. J., Flax, J. L., Brusseau, G. A., and Stahl, D. A. (1998). Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol. 180, 2975-2982
44. Wylie, K. M., Truty, R. M., Sharpton, T. J., Mihindukulasuriya, K. A., Zhou, Y., Gao, H., et al. (2012). Novel bacterial taxa in the human microbiome. PLoS ONE 7:e35294. doi: 10.1371/journal.pone.0035294
45. Yona, G., Linial, N., and Linial, M. (2000). ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res. 28, 49-55. doi: 10.1093/nar/28.1.49
46. Zhang, S. B., Zhou, S. Y., He, J. G., and Lai, J. H. (2011). Phylogeny inference based on spectral graph clustering. J. Comput. Biol. 18, 627-637. doi: 10.1089/cmb.2009.0028