Structural analysis of polarizing indels: An emerging consensus on the root of the tree of life

Biology Direct

Volumn 4, Issue , 2009, Pages

  Valas, Ruben E ^a   Bourne, Philip E ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEGIBACTERIA;

BACTERIAL PROTEIN; ELONGATION FACTOR; RIBOSOME PROTEIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CHEMISTRY; EVOLUTION; GENETICS; MOLECULAR GENETICS; MUTATION; PROTEIN QUATERNARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL MODEL;

AMINO ACID SEQUENCE; ARCHAEA; BACTERIA; BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; MUTATION; PEPTIDE ELONGATION FACTORS; PROTEIN STRUCTURE, QUATERNARY; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77949884370     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-4-30     Document Type: Article

References (47)

1. Wong JT, Chen J, Mat WK, Ng SK, Xue H. Polyphasic evidence delineating the root of life and roots of biological domains. Gene 2007, 403(1-2):39-52. 10.1016/j.gene.2007.07.032, 17884304.
2. Martin W, Baross J, Kelley D, Russell MJ. Hydrothermal vents and the origin of life. Nat Rev Microbiol 2008, 6(11):805-814. 10.1038/nrmicro1991, 18820700.
3. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 1989, 86(23):9355-9359. 10.1073/pnas.86.23.9355, 298494, 2531898.
4. Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole RJ, Date T, Oshima T, et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA 1989, 86(17):6661-6665. 10.1073/pnas.86.17.6661, 297905, 2528146.
5. Zhaxybayeva O, Lapierre P, Gogarten JP. Ancient gene duplications and the root(s) of the tree of life. Protoplasma 2005, 227(1):53-64. 10.1007/s00709-005-0135-1, 16389494.
6. Philippe H, Forterre P. The rooting of the universal tree of life is not reliable. J Mol Evol 1999, 49(4):509-523. 10.1007/PL00006573, 10486008.
7. Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006, 1:19. 10.1186/1745-6150-1-19, 1586193, 16834776.
8. Price PB. Microbial life in glacial ice and implications for a cold origin of life. FEMS Microbiol Ecol 2007, 59(2):217-231. 10.1111/j.1574-6941.2006.00234.x, 17328118.
9. Trevors JT, Pollack GH. Hypothesis: the origin of life in a hydrogel environment. Prog Biophys Mol Biol 2005, 89(1):1-8. 10.1016/j.pbiomolbio.2004.07.003, 15826671.
10. Lake JA, Herbold CW, Rivera MC, Servin JA, Skophammer RG. Rooting the tree of life using nonubiquitous genes. Mol Biol Evol 2007, 24(1):130-136. 10.1093/molbev/msl140, 17023560.
11. Servin JA, Herbold CW, Skophammer RG, Lake JA. Evidence excluding the root of the tree of life from the actinobacteria. Mol Biol Evol 2008, 25(1):1-4. 10.1093/molbev/msm249, 18003601.
12. Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA. Evidence that the root of the tree of life is not within the Archaea. Mol Biol Evol 2006, 23(9):1648-1651. 10.1093/molbev/msl046, 16801395.
13. Skophammer RG, Servin JA, Herbold CW, Lake JA. Evidence for a gram-positive, eubacterial root of the tree of life. Mol Biol Evol 2007, 24(8):1761-1768. 10.1093/molbev/msm096, 17513883.
14. Lake JA, Servin JA, Herbold CW, Skophammer RG. Evidence for a new root of the tree of life. Syst Biol 2008, 57(6):835-843. 10.1080/10635150802555933, 19085327.
15. Lake JA, Skophammer RG, Herbold CW, Servin JA. Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci 2009, 364(1527):2177-2185. 10.1098/rstb.2009.0035, 19571238.
16. Liu SV. A Fundamentally New Perspective on the Origin and Evolution of Life. Pioneer 2008, 3:7-17.
17. Doolittle WF, Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 2007, 104(7):2043-2049. 10.1073/pnas.0610699104, 1892968, 17261804.
18. Puigbo P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009, 8(6):59. 10.1186/jbiol159, 19594957, 2737373.
19. Cavalier-Smith T. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 2001, 53(4-5):555-595. 10.1007/s002390010245, 11675615.
20. Martin W, Russell MJ. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci 2003, 358(1429):59-83. discussion 83-55., 10.1098/rstb.2002.1183, 1693102, 12594918.
21. Mulkidjanian AY, Galperin MY, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci 2009, 34(4):206-215. 10.1016/j.tibs.2009.01.005, 19303305, 2752816.
22. Di Giulio M. The evidence that the tree of life is not rooted within the Archaea is unreliable: a reply to Skophammer et al. Gene 2007, 394(1-2):105-106. 10.1016/j.gene.2007.01.024, 17395404.
23. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008, (36 Database):D475-479. 2238992, 17981842.
24. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002, 52(Pt 1):7-76.
25. Valas RE, Bourne PE. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol 2008, 66(5):494-504. 10.1007/s00239-008-9075-7, 18389302.
26. Gupta RS. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62(4):1435-1491. 98952, 9841678.
27. Philippe H, Budin K, Moreira D. Horizontal transfers confuse the prokaryotic phylogeny based on the HSP70 protein family. Mol Microbiol 1999, 31(3):1007-1010. 10.1046/j.1365-2958.1999.01185.x, 10048042.
28. Chang YW, Sun YJ, Wang C, Hsiao CD. Crystal structures of the 70-kDa heat shock proteins in domain disjoining conformation. J Biol Chem 2008, 283(22):15502-15511. 10.1074/jbc.M708992200, 18400763.
29. Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN. CE-MC: a multiple protein structure alignment server. Nucleic Acids Res 2004, (32 Web Server):W100-103. 10.1093/nar/gkh464, 441602, 15215359.
30. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
31. Gupta RS. What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol 1998, 29(3):695-707. 10.1046/j.1365-2958.1998.00978.x, 9723910.
32. Soding J, Remmert M, Biegert A. HHrep: de novo protein repeat detection and the origin of TIM barrels. Nucleic Acids Res 2006, (34 Web Server):W137-142. 10.1093/nar/gkl130, 1538828, 16844977.
33. Norager S, Jensen KF, Bjornberg O, Larsen S. E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases. Structure 2002, 10(9):1211-1223. 10.1016/S0969-2126(02)00831-6, 12220493.
34. Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, et al. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res 2009, (37 Database):D216-223. 10.1093/nar/gkn734, 2686591, 18940865.
35. Rowland P, Norager S, Jensen KF, Larsen S. Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure 2000, 8(12):1227-1238. 10.1016/S0969-2126(00)00530-X, 11188687.
36. Valas RE, Yang S, Bourne PE. Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol 2009, 19(3):329-34. 10.1016/j.sbi.2009.03.011, 19394812.
37. Veeramalai M, Ye Y, Godzik A. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics 2008, 9:358. 10.1186/1471-2105-9-358, 2553092, 18759993.
38. Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, et al. MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res 2007, (35 Database):D298-300. 10.1093/nar/gkl952, 1751549, 17135201.
39. Forterre P. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 2006, 117(1):5-16. 10.1016/j.virusres.2006.01.010, 16476498.
40. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 2002, 297(5578):105-107. 10.1126/science.1072113, 12029065.
41. Forterre P. The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 2002, 5(5):525-532. 10.1016/S1369-5274(02)00360-0, 12354562.
42. Leipe DD, Aravind L, Koonin EV. Did DNA replication evolve twice independently?. Nucleic Acids Res 1999, 27(17):3389-3401. 10.1093/nar/27.17.3389, 148579, 10446225.
43. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. MUSTANG: a multiple structural alignment algorithm. Proteins 2006, 64(3):559-574. 10.1002/prot.20921, 16736488.
44. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004, 25(13):1605-1612. 10.1002/jcc.20084, 15264254.
45. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
46. Zhaxybayeva O, Gogarten J. Horizontal gene transfer, gene histories, and the root of the tree of life. Planetary systems and the origin of life 2007, Cambridge; New York: Cambridge University Press, Pudritz RE, Higgs PG, Stone JR.
47. Glansdorff N, Xu Y, Labedan B. The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 2008, 3:29. 10.1186/1745-6150-3-29, 2478661, 18613974.