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Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes.

ABSTRACT: 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. PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.

SUBMITTER: Yu H

PROVIDER: S-EPMC3022732 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes.

Yu Hong H Li Qi Q

PloS one 20110118 1

<h4>Background</h4>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 wobbl ...[more]

PMID: 21267462

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Project description:Abstract Taking advantage of the unique system of doubly uniparental inheritance (DUI) of mitochondria, we developed a reliable molecular method to sex individuals of the marine bivalve Macoma balthica rubra. In species with DUI (~100 known bivalves), both sexes transmit their mitochondria: males bear both a male‐ and female‐type mitogenome, while females bear only the female type. Male and female mitotypes are sufficiently divergent to reliably PCR‐amplify them specifically. Loop‐mediated isothermal amplification (LAMP) is a precise, economical and portable alternative to PCR for molecular sexing and we demonstrate its application in this context. We used 154 individuals sampled along the Atlantic coast of France and sexed microscopically by gonad examination to test for the congruence among gamete type, PCR sexing and LAMP sexing. We show an exact match among the sexing results from these three methods using the male and female mt‐cox1 genes. DUI can be disrupted in inter‐specific hybrids, causing unexpected distribution of mitogenomes, such as homoplasmic males or heteroplasmic females. To our knowledge, DUI disruption at the intra‐specific scale has never been tested. We applied our sexing protocol to control for unexpected heteroplasmy caused by hybridization between divergent genetic lineages and found no evidence of disruption in the mode of mitochondrial inheritance in M. balthica rubra. We propose LAMP as a useful tool to accelerate eco‐evolutionary studies of DUI. It offers the opportunity to investigate the potential role of, previously unaccounted‐for, sex‐specific patterns such as sexual selection or sex‐specific dispersal bias in the evolution of free‐spawning benthic species. Our paper reports testing on the evolutionary stability of sex‐link mitochondrial heteroplasmy in males of the gonochoric bivalve Macomabalthicarubra, and the practical use of this stability to sex individuals molecularly, using loop‐mediated isothermal DNA amplification.

Dataset Information

Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes.

Publications

Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes.

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