Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes.
BACKGROUND
Animal mitochondrial genomes typically encode one tRNA for each synonymous codon family, so that each tRNA anticodon essentially has to wobble to recognize two or four synonymous codons. Several factors have been hypothesized to determine the nucleotide at the wobble site of a tRNA anticodon in mitochondrial genomes, such as the codon-anticodon adaptation hypothesis, the wobble versatility hypothesis, the translation initiation and elongation conflict hypothesis, and the wobble cost hypothesis.


RESULTS
In this study, we analyzed codon usage and tRNA anticodon wobble sites of 29 marine bivalve mitochondrial genomes to evaluate features of the wobble nucleotides in tRNA anticodons. The strand-specific mutation bias favors G and T on the H strand in all the 29 marine bivalve mitochondrial genomes. A bias favoring G and T is also visible in the third codon positions of protein-coding genes and the wobble sites of anticodons, rejecting that codon usage bias drives the wobble sites of tRNA anticodons or tRNA anticodon bias drives the evolution of codon usage. Almost all codon families (98.9%) from marine bivalve mitogenomes support the wobble versatility hypothesis. There are a few interesting exceptions involving tRNA(Trp) with an anticodon CCA fixed in Pectinoida species, tRNA(Ser) with a GCU anticodon fixed in Mytiloida mitogenomes, and the uniform anticodon CAU of tRNA(Met) translating the AUR codon family.


CONCLUSIONS
These results demonstrate that most of the nucleotides at the wobble sites of tRNA anticodons in marine bivalve mitogenomes are determined by wobble versatility. Other factors such as the translation initiation and elongation conflict, and the cost of wobble translation may contribute to the determination of the wobble nucleotide in tRNA anticodons. The finding presented here provides valuable insights into the previous hypotheses of the wobble nucleotide in tRNA anticodons by adding some new evidence.
Fisheries College, Ocean University of China, Qingdao, Shandong, China.
Hong
H
Yu
Qi
Q
Li
D000818:Animals; D000926:Anticodon / Q000235:genetics*; D049872:Bivalvia / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D020125:Mutation, Missense; D009711:Nucleotides / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics*
D000926:Anticodon; D009711:Nucleotides; D012343:RNA, Transfer
Mol Biol Evol. 2000 Apr;17(4):540-52
10742046
PLoS Genet. 2007 Jan 12;3(1):e13
17222063
PLoS One. 2007 Feb 21;2(2):e227
17311091
BMC Evol Biol. 2008 Jul 19;8:211
18638409
Gene. 2004 May 26;333:169-77
15177692
Nucleic Acids Res. 2004 Jan 09;32(1):223-38
14715921
Science. 2010 Jan 15;327(5963):301
20075246
Bioinformatics. 2004 Nov 22;20(17):3252-5
15180927
Heredity (Edinb). 2008 Oct;101(4):301-20
18612321
BMC Evol Biol. 2010 Feb 18;10:50
20167078
Biochim Biophys Acta. 1998 Jul 30;1399(1):78-82
9714749
Proc Natl Acad Sci U S A. 1980 Jun;77(6):3167-70
6997870
Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8751-6
16731622
Mol Phylogenet Evol. 2006 May;39(2):323-34
16359875
J Hered. 2001 Jul-Aug;92(4):371-3
11535656
Nucleic Acids Res. 1999 Nov 1;27(21):4291-7
10518623
J Mol Evol. 1995 Sep;41(3):353-8
7563121
DNA Res. 2007 Oct 31;14(5):201-6
17974594
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
9023104
Genetics. 1991 Nov;129(3):897-907
1752426
Mol Biol Evol. 2008 Jul;25(7):1253-6
18397919
Microbiol Rev. 1992 Mar;56(1):229-64
1579111
J Mol Evol. 2008 May;66(5):484-93
18401633
Gene. 1999 Sep 30;238(1):195-209
10570997
Nucleic Acids Res. 1999 Jun 15;27(12):2554-9
10352185
Nature. 1987 Feb 19-25;325(6106):728-30
2434856
Gene. 2007 Sep 1;399(1):11-9
17587513
Mol Biol Evol. 2001 Sep;18(9):1734-44
11504853
Biochemistry. 1994 Mar 1;33(8):2234-9
7509636
Mol Phylogenet Evol. 2008 Sep;48(3):850-7
18621550
J Mol Evol. 2001 Oct-Nov;53(4-5):314-26
11675591
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
J Biol Chem. 1994 Sep 9;269(36):22902-6
8077242
Nucleic Acids Symp Ser. 1997;(37):197-8
9586067
Mol Phylogenet Evol. 2009 Jan;50(1):117-28
18992830
Gene. 2005 Jan 17;345(1):13-20
15716092
J Biol Chem. 1998 Feb 6;273(6):3363-8
9452455
PLoS Biol. 2006 May;4(5):e127
16620150