Thermal adaptation of the small subunit ribosomal RNA gene: A comparative study

Journal of Molecular Evolution

Volumn 63, Issue 1, 2006, Pages 120-126

  Wang, Huai Chun ^a,b   Xia, Xuhua ^b   Hickey, Donal ^c  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

^c Gina Cody School of Engineering and Computer Science   (Canada)

Author keywords

GC content; Optimal growth temperature; Phylogenetic independent contrast; Secondary structure; Small subunit ribosomal RNA

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GROWTH; BACTERIUM; COLD BLOODED VERTEBRATE; COMPARATIVE STUDY; CORRELATION COEFFICIENT; EUKARYOTE; GC RICH SEQUENCE; GENE; NONHUMAN; PHYLOGENY; RNA SEQUENCE; RNA STRUCTURE; SMALL SUBUNIT RIBOSOMAL RNA GENE; TEMPERATURE; TEMPERATURE ACCLIMATIZATION; THERMOPHILIC BACTERIUM; VERTEBRATE; WARM BLOODED VERTEBRATE;

ACCLIMATIZATION; ANIMALS; BASE COMPOSITION; GENES, ARCHAEAL; GENES, BACTERIAL; GENES, RRNA; HEAT; PHYLOGENY; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; SEQUENCE ALIGNMENT; TEMPERATURE; VERTEBRATES;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; VERTEBRATA;

EID: 33745626786     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0255-4     Document Type: Article

References (17)

1. Bernardi G (2000) The compositional evolution of vertebrate genomes. Gene 259:31-43
2. Brochier C, Forterre P, Gribaldo S (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries:tackling the Methanopyrus kandleri paradox. Genome Biol 5(3):R17
3. Dalgaard JZ, Garrett RA (1993) Archaeal hyperthermophile genes. In: Kates M, Kushner DJ, Matheson AT (eds) The biochemistry of Archaea (Archaebacteria). Elsevier, Amsterdam, p 535
4. Felsenstein J (1985) Phylogeny and the comparative method. Am Nat 125:1-15
5. Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48:284-290
6. Galagan JE, Nusbaum C, Roy A, et al. (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12:532-542
7. Galtier N, Lobry JR (1997) Relationships between genomic GC content, RNA secondary structures and optimal growth temperature in prokaryotes. J Mol Evol 44:632-636
8. Gutell RR, Cannone JJ, Shang Z, Du Y, Serra MJ (2000) A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol 304:335-354
9. Harvey PH, Pagel MD (1991) The comparative method in evolutionary biology. Oxford University Press, Oxford
10. Hasegawa M, Hashimoto T (1993) Ribosomal RNA trees misleading? Nature 361:23
11. Hurst LD, Merchant AR (2001) High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc R Soc Lond B 268:493-497
12. Nakashima H, Fukuchi S, Nishikawa K (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem 133:507-513
13. Singer GAC, Hickey DA (2003) Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317:39-47
14. Van de Peer Y, De Rijk P, Wuyts J, Winkelmans T, De Wachter R (2000) The European small subunit ribosomal RNA database. Nucleic Acids Res. 28:175-176
15. Wang H-C (2005) The effects of nucleotide bias on genome evolution. PhD thesis. University of Ottawa, Ottawa
16. Wang H-C, Hickey DA (2002) Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res 30:2501-2507
17. Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R (2002) The European database on small subunit ribosomal RNA. Nucleic Acids Res 30:183-185