The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery

Journal of Molecular Evolution

Volumn 47, Issue 5, 1998, Pages 508-516

  Gribaldo, Simonetta ^a   Cammarano, Piero ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Gene duplication; Last universal common ancestor; Phylogeny; Signal recognition particle (SRP); SRP receptor; Tree of life

Indexed keywords

DOCKING PROTEIN; GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATE; SIGNAL RECOGNITION PARTICLE;

AMINO ACID SEQUENCE; ARTICLE; GENE DUPLICATION; GENE EXPRESSION REGULATION; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; NONHUMAN; PHYLOGENY; PROTEIN TARGETING; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; SPECIES DIFFERENTIATION; TAXONOMY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ARCHAEA; BACTERIA; FUNGI; GENE DUPLICATION; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0031735878     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006407     Document Type: Article

References (30)

1. Adachi J (1995) Modeling of molecular evolution and maximum likelihood inference of molecular phylogeny, PhD dissertation. Graduate University for Advanced Studies
2. Adachi J, Hasegawa M (1992) MOLPHY: Programs for molecular phylogenetics. I. PROTML: Maximum likelihood inference of protein phylogeny. Computer Science Monographs, No. 27. Institute of Statistical Mathematics, Tokyo, Vol 1
3. Ævarsson A (1995) Structure based sequence alignment of elongation factors Tu and G with related GTPases involved in translation. J Mol Evol 41:1096-1104
4. Althoff S, Selinger D, Wise JA (1994) Molecular evolution of SRP cycle components: Functional implications. Nucleic Acids Res 22: 1933-1947
5. Altschul SF, Gish G, Miller W, Myers E, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
6. Baldauf SL, Palmer JD, Doolittle WF (1996) The root of the universal tree and the origin of eucaryotes based on elongation factor phylogeny. Proc Natl Acad Sci USA 93:7749-7754
7. Bernstein HD, Poritz MA, Strub K, Hoben PJ, Brenner S, Walter P (1989) Model for signal sequence recognition from the amino acid sequence of 54 K subunit of signal recognition particle. Nature 340:482-486
8. Brown JR, Doolittle WF (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92:2441-2445
9. Brown JR, Doolittle WF (1997) Archaea and the Prokaryote-to-Eucaryote transition. Microbiol Mol Biol Rev 61:456-502
10. Cammarano P, Creti R, Sanangelantoni AM, Palm P (1998) Splitting the Archaea? A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of sequence positions. J Mol Evol (in press)
11. Deveraux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis program for the VAX. Nucleic Acids Res 12: 387-395
12. Felsenstein J (1989) Phylip - phylogeny inference package. Cladistics 5:164-166
13. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle
14. Forterre P, Benachenou-Lahfa N, Confalonieri F, Duguet M, Elie C, Labedan B (1993) The nature of the last universal ancestor and the root of the tree of life, still open questions. Byosystems 28:15-32
15. +-ATPase: Implications for the origin of eucaryotes. Proc Natl Acad Sci USA 86:6661-6665
16. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919
17. Hilario E, Gogarten JP (1993) Horizontal gene transfer of ATPase genes - the tree of life becomes the net of life. BioSystems 31:111-119
18. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86:9335-9359
19. Lawson FS, Charlebois RL, Dillon JAR (1996) Phylogenetic analysis of carbamoyl-phosphate genes: Evolution involving multiple gene duplications, gene fusions, and insertions and deletions of surrounding sequences. Mol Biol Evol 13:970-977
20. Kaine BP, Merkel UL (1989) Isolation and characterization of the 7S RNA gene from Methanococcus voltae. J Bacteriol 171:4261-4266
21. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea. J Mol Evol 29:170-179
22. Kishino H, Myiata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 30:151-160
23. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparisons. Proc Natl Acad Sci USA 85:2444-2448
24. Pohlschröder M, Prinz WA, Hartmann E, Beckwith J (1997) Protein translocation in the three domains of life: Variations of a theme. Cell 91:563-566
25. Poritz MA, Bernstein HD, Strub K, Zopf D, Wilkhelm H, Walter P (1990) An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle. Science 250:1111-1117
26. Romisch K, Webb J, Herz J, Prehn S, Frank R, Vingron M, Dobberstein B (1989) Homology of 54 K protein of signal recognition particle docking protein and two E. coli proteins with putative GTP binding domains. Nature 340:478-482
27. Strimmer K, Von Haeseler A (1996) Quartet puzzling: A quartet maximum likelihood method tor reconstructing tree topologies. Mol Biol Evol 13:964-969
28. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
29. Wadell PJ (1995) Statistical methods of phylogenetic analysis: Including Hadamard conjugations, LogDet transforms, and maximum likelihood, PhD dissertation, Massey University, Palmezston, North New Zealand
30. Walter P, Johnson AE (1994) Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu Rev Cell Biol 10:87-119