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From DNA to Protein

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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

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Related Experiment Video

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Labelling and Visualization of Mitochondrial Genome Expression Products in Baker's Yeast Saccharomyces cerevisiae

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Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection.

Wenli Jia¹, Paul G Higgs

¹Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada.

Molecular Biology and Evolution

|December 1, 2007

Summary

Context-dependent mutation significantly influences codon usage in animal mitochondrial genomes. Evidence for translational selection is minimal, except in specific cases involving unusual mitochondrial transfer RNA wobble bases and genetic code reassignment.

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Area of Science:

Mitochondrial genomics
Molecular evolution
Bioinformatics

Background:

Synonymous codon usage in animal mitochondrial genomes, particularly in mammals and fish, is influenced by base frequencies at degenerate sites.
Context-dependent mutation creates correlations between adjacent bases, leading to consistent patterns of dinucleotide excess and deficit across species.

Purpose of the Study:

To investigate the role of translational selection in shaping codon usage within animal mitochondrial genomes.
To differentiate the effects of translational selection from context-dependent mutation.

Main Methods:

Analysis of synonymous codon frequencies in animal mitochondrial genomes.
Development and application of a method to detect translational accuracy selection while controlling for context-dependent mutation.
Examination of codon usage in conserved versus variable sites within mitochondrial genes.
Investigation of codon usage bias in relation to mitochondrial transfer RNA anticodons and unusual wobble base modifications.

Main Results:

Context-dependent mutation strongly influences base frequencies at 4-fold degenerate sites in mitochondrial genomes.
Little evidence for translational accuracy selection was found in the analyzed mitochondrial genes.
Translational efficiency selection appears weak, with limited observable effects on codon usage across codon families.
Specific instances of codon usage selection were detected in cases involving unusual bases at the tRNA wobble position, linked to mitochondrial genetic code reassignment.

Conclusions:

Context-dependent mutation is a major driver of codon usage patterns in animal mitochondrial genomes.
Translational selection plays a minor role in mitochondrial codon usage, with notable exceptions linked to tRNA modifications and genetic code evolution.