The lineage-specific base-pair contents in the stem regions of ribosomal RNAs and their influence on the estimation of evolutionary distances

Journal of Molecular Evolution

Volumn 55, Issue 5, 2002, Pages 584-594

  Sugaya, Nobuyoshi ^a   Otsuka, Jinya ^a  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

Archaebacteria; Base composition bias; Base pair change; Divergence time; Eubacteria; Eukaryotes; Evolutionary distance; Phylogeny of organisms; Ribosomal RNAs; Selection

Indexed keywords

RIBOSOME RNA;

ARTICLE; BASE PAIRING; CALCULATION; EUKARYOTE; MOLECULAR EVOLUTION; PROKARYOTE; PROMOTER REGION; SPECIES DIFFERENCE;

ANIMALS; ARCHAEA; BACTERIA; BASE COMPOSITION; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; EUKARYOTA; GIARDIA; MICROSPORIDIA; MYCOPLASMA; PROKARYOTA;

EID: 0036841205     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2354-9     Document Type: Article

References (34)

1. 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
2. Cloud PE Jr (1988) Oasis in space: Earth history from the beginning. W.W. Norton, New York
3. Curtiss WC, Vournakis JN (1984) Quantitation of base substitutions in eukaryotic 5S rRNA: Selection for the maintenance of RNA secondary structure. J Mol Evol 20:351-361
4. De Rijk P, Van de Peer Y, Van den Broeck I, De Wachter R (1995) Evolution according to large ribosomal subunit RNA. J Mol Evol 41:366-375
5. De Rijk P, Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R (2000) The European large subunit ribosomal RNA database. Nucleic Acids Res 28:177-178
6. Dickerson RE (1971) The structures of cytochrome c and the rates of molecular evolution. J Mol Evol 1:26-45
7. Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-477
8. Germot A, Philippe H, Le Guyader H (1997) Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol 87:159-168
9. Ghosh S, Field J, Rogers R, Hickman M, Samuelson J (2000) The Entamoeba histolytica mitochondrion-derived organelle (crypton) contains double-stranded DNA and appears to be bound by a double membrane. Infect Immun 68:4319-4322
10. Hashimoto T, Sánchez LB, Shirakura T, Müller M, Hasegawa M (1998) Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc Natl Acad Sci USA 95:6860-6865
11. Hori H (1976) Molecular evolution of 5S RNA. Mol Gen Genet 145:119-123
12. Hori H, Osawa S (1979) Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc Natl Acad Sci USA 76:381-385
13. Hori H, Osawa S (1986) Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 352 5S RNA species. BioSystems 19:163-172
14. Hori H, Osawa S (1987) Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Mol Biol Evol 4:445-472
15. Horimoto K, Otsuka J, Kunisawa T (1989) Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA. Protein Seq Data Anal 2:93-99
16. 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 86:9355-9359
17. Kumazaki T, Hori H, Osawa S (1983) Phylogeny of protozoa deduced from 5S rRNA sequences. J Mol Evol 19:411-419
18. Lake JA (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc Natl Acad Sci USA 91:1455-1459
19. Mai Z, Ghosh S, Frisardi M, Rosenthal B, Rogers R, Samuelson J (1999) Hsp60 is targeted to a cryptic mitochondrion-drived organelle ("crypton") in the microaerophilic protozoan parasite Entamoeba histolytica. Mol Cell Biol 19:2198-2205
20. Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
21. Otsuka J, Nakano T, Terai G (1997) A theoretical study on the nucleotide changes under a definite functional constraint of forming stable base-pairs in the stem regions of ribosomal RNAs: Its application to the phylogeny of eukaryotes. J Theor Biol 184:171-186
22. Otsuka J, Terai G, Nakano T (1999) Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs. J Mol Evol 48:218-235
23. Otsuka J, Kawai Y, Sugaya N (2001) The influence of selection on the evolutionary distance estimated from the base changes observed between homologous nucleotide sequences. J Theor Biol 213:129-144
24. Peyretaillade E, Broussolle V, Peyret P, Méténier G, Gouy M, Vivarès CP (1998) Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin. Mol Biol Evol 15:683-689
25. Raué HA, Musters W, Rutgers CA, Riet JV, Planta RJ (1990) rRNA: from structure to function. In: Hill WE, Moore PB, Dahlberg A, Schlessinger D, Garret RA, Warner JR (eds) The ribosome: Structure, function, and evolution. American Society for Microbiology, Washington DC, pp 217-235
26. Reimer TO, Barghoorn ES, Margulis L (1979) Primary productivity in an early Archean microbial ecosystem. Precambrian Res 9:93-104
27. Roger AJ, Svärd SG, Tovar J, Clark CG, Smith MW, Gillin FD, Sogin ML (1998) A mitochondrial-like chaperonin 60 gene in Gardia lamblia: Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc Natl Acad Sci USA 95:229-234
28. Saccone C, Lanave C, Pesole G, Preparata G (1990) Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol 183:570-583
29. Saccone C, Gissi C, Lanave C, Pesole G (1995) Molecular classification of living organisms. J Mol Evol 40:273-279
30. Soltys BJ, Gupta RS (1994) Presence and cellular distribution of a 60-kDa protein related to mitochondrial hsp60 in Giardia lamblia. J Parasitol 80:580-590
31. Tovar J, Fischer A, Clark CG (1999) The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol Microbiol 32:1013-1021
32. Van de Peer Y, Baldauf SL, Doolittle WF, Meyer A (2000) An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J Mol Evol 51:565-576
33. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
34. Woese CR, Maniloff J, Zablen LB (1980) Phylogenetic analysis of the mycoplasmas. Proc Natl Acad Sci USA 77:494-498