Congruence of evidence for a Methanopyrus-proximal root of life based on transfer RNA and aminoacyl-tRNA synthetase genes

Gene

Volumn 360, Issue 2, 2005, Pages 120-130

  Xue, Hong ^a   Ng, Siu Kin ^a   Tong, Ka Lok ^a   Wong, J Tze Fei ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Aminoacyl tRNA synthetases; Root of life; tRNA

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; TRANSFER RNA;

ARCHAEBACTERIUM; ARTICLE; GENETIC ANALYSIS; METHANOPYRUS; NONHUMAN; PHYLOGENETIC TREE ROOT; PRIORITY JOURNAL;

AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; ARCHAEA; EURYARCHAEOTA; PHYLOGENY; RNA, TRANSFER; TRANSCRIPTION, GENETIC;

ARCHAEA; METHANOPYRUS; METHANOPYRUS KANDLERI;

EID: 26844542163     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.06.027     Document Type: Article

References (36)

1. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acid Res. 25 1997 3389 3402
2. A.D. Baxevanis, and B.F.F. Ouelette Bioinformatics 2nd ed 2001 Wiley-Interscience New York 335 340
3. M. Bocchetta, S. Gribaldo, A. Sanangelantoni, and P. Cammarano Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor and RNA polymerase subunit sequences J. Mol. Evol. 50 2000 366 380
4. C. Brochier, S. Gribaldo, Y. Zivanovic, F. Confalonieri, and P. Forterre Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving lineage related to Thermococcales? Genome Biol. 6 2005 R42.1 R42.10
5. J.R. Brown, C.J. Douady, M.J. Italia, W.E. Marshall, and M.J. Stanhope Universal trees based on large combined protein sequence data sets Nat. Genet. 28 2001 281 285
6. P.A. Cejchan LUCA, or just a conserved Archaeon? Gene 333 2004 47 50 comments on Xue et al. (2003)
7. P. De Rijk, Y. Van de Peer, I. Van den Broeck, and R. De Wachter Evolution according to large ribosomal subunit RNA J. Mol. Evol. 41 1995 366 375
8. G. Dirheimer, G. Keith, P. Dumas, and E. Westhof Primary, secondary and tertiary structures of tRNAs D. Soll U RajBhandary tRNAs: Structure, Biosynthesis and Function 1995 ASM Press Washington D.C. 93 126
9. K. Farahi, G.D. Pusch, R. Overbeek, and W.B. Whitman Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method J. Mol. Evol. 58 2004 615 631
10. J. Felsenstein PHYLIP-phylogeny inference package Cladistics 5 1989 164 166
11. J.P. Gogarten, and L. Olendzenski Orthologs, paralogs and genome comparisons Curr. Opin. Genet. Dev. 9 1999 630 636
12. S. Gribaldo, and H. Philippe Ancient phylogenetic relationships Theor. Popul. Biol. 61 2002 391 408
13. H. Huber, M.J. Hohn, R. Rachel, T. Fuchs, V.C. Wimmer, and K.O. Stetter A new phylum of Archaea represented by a nanonized hyperthermophilic symbiont Nature 417 2002 63 67
14. T.H. Jukes, and C.R. Cantor Evolution of protein molecules H.N. Munro Mammalian Protein Metabolism 1969 Academic Press New York 21 123
15. M.A. Kimura A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences J. Mol. Evol. 16 1980 111 120
16. K.S. Makarova, and E.V. Koonin Comparative genomics of archaea: how much have we learned in six years, and what's next? Genome Biol. 4 2003 115.1 115.17
17. C. Marck, and H. Grosjean tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features RNA 8 2002 1189 1232
18. C.L. Nesbo, Y. Boucher, and W.F. Doolittle Defining the core of non-transferable prokaryotic genes: the euryarchaeal core J. Mol. Evol. 53 2001 340 350
19. E. Pennisi Is it time to uproot the tree of life? Science 284 1999 1305 1307
20. H. Philippe, and P. Forterre The rooting of the universal tree of life is not reliable J. Mol. Evol. 49 1999 509 523
21. L. Randau, R. Munch, M.J. Hohn, D. Jahn, and D. Soll Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-havles Nature 433 2005 537 541
22. A. Sauerwald RNA-dependent cysteine biosynthesis in Archaea Science 307 2005 1969 1972
23. R.M. Schwartz, and M.O. Dayhoff Origins of prokaryotes, eukaryotes, mitochondria and chloroplasts Science 199 1978 395 403
24. A.I. Slesarev The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens Proc. Natl. Acad. Sci. U. S. A. 99 2002 4644 4649
25. K. Tamura, and M. Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Mol. Biol. Evol. 10 1993 512 526
26. R.L. Tatusov, E.V. Koonin, and D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
27. S.A. Teichmann, and G. Mitchison Is there a phylogenetic signal in prokaryotic proteins? J. Mol. Evol. 49 1999 98 107
28. K.L. Tong, and J.T. Wong Anticodon and wobble evolution Gene 333 2004 169 177
29. G. Van der Auwera, C.J.B. Hofmann, P. De Rijk, and R. De Wachter The origin of red algae and cryptomonad nucleomorphs: a comparative phylogeny based on small and large subunit rRNA sequences of Palmaria palmata, Gracilaria verrucosa, and the Guillardia theta nucleomorph Mol. Phylogenet. Evol. 10 1998 333 342
30. C.R. Woese, G.J. Olsen, M. Ibba, and D. Soll Aminoacyl-tRNA synthetases, the genetic code and the evolutionary process Microbiol. Mol. Biol. Rev. 64 2000 202 236
31. Y.I. Wolf, I.B. Rogozin, N.V. Grishin, and E.V. Koonin Genome trees and the tree of life Trends Genet. 18 2002 472 479
32. J.T. Wong A coevolution theory of the genetic code Proc. Natl. Acad. Sci. U. S. A. 72 1975 1909 1912
33. J.T. Wong Coevolution theory of the genetic code at age thirty BioEssays 27 2005 416 425
34. J.T. Wong, and H. Xue Self-perfecting evolution of heteropolymer building blocks and sequences as the basis of life G. Palyi C. Zucchi L. Caglioti Fundamentals of Life 2002 Elsevier Paris 473 494
35. H. Xue, K.L. Tong, C. Marck, H. Grosjean, and J.T. Wong Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life Gene 310 2003 59 66
36. A. Zharkikh Estimation of evolutionary distances between nucleotide sequences J. Mol. Evol. 39 1994 315 329