Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability

Area of Science:

• Molecular Biology
• Genomics
• Evolutionary Biology

Background:

• Chloroplast genomes exhibit distinct codon usage patterns.
• High A+T content in chloroplast genomes generally favors codons ending in A or T.
• The psbA gene is a major translation product in chloroplasts.

Purpose of the Study:

• To investigate codon usage patterns in three sequenced chloroplast genomes: Marchantia, Oryza, and Nicotiana.
• To compare codon usage in the psbA gene with the overall genomic bias.
• To determine if tRNA availability influences codon selection in the psbA gene.

Main Methods:

• Analysis of codon usage in the complete chloroplast genomes of Marchantia, Oryza, and Nicotiana.
• Specific examination of codon bias in the psbA gene across these species and other known psbA sequences.
• Comparison of psbA gene codon usage with the availability of complementary tRNAs within the chloroplast genome.

Main Results:

• Overall chloroplast genomes show a bias towards NNA and NNT codons, correlating with high A+T content.
• The psbA gene deviates from this pattern, favoring NNC over NNT codons for twofold degenerate amino acids.
• This NNC codon preference in psbA aligns with the presence of a single complementary tRNA for that codon.

Conclusions:

• The psbA gene's codon usage is influenced by tRNA availability, deviating from the general chloroplast genomic bias.
• Selection acts on the psbA gene to optimize codon usage according to tRNA abundance, similar to findings in unicellular organisms.
• This suggests a specific evolutionary pressure on the translation of essential chloroplast proteins like psbA.