HUSSAIN, Sofia M*; LIVINGSTON, Brian T; University of South Florida; University of South Florida: Codon usage frequencies are influenced by concerted evolution and selection in a gene encoding a protein containing imperfect repeats
Codon usage in a protein coding gene is limited by the amino acids required to produce a functional product. Within this constraint, codon usage frequencies are shaped by forces of neutral evolution and selection. When there are a series of repeated elements in the protein coding region, concerted evolution homogenizes the codon usage frequencies. The effect is some codons are found in high frequencies while some are found in low frequencies or absent. Also, if a codon reduces the expression of a protein it may be selected against. Therefore selection can reduce the frequency of certain codons as well.
SM50 is a protein coding gene found in sea urchins containing a series of imperfect repeats that are influenced by concerted evolution. However, we believe concerted evolution alone is not sufficient to explain the lack of certain codons in SM50 in all species examined to date. We propose that an additional force of selection is limiting the usage of certain codons in this gene.
The secondary structure of an mRNA molecule is directly related to the codon usage in the gene being translated. If this secondary structure is too stable, translation may be inhibited. In this way, selection may reduce the usage of codons that produce a mRNA molecule with a highly stable secondary structure. We used a computer program (RNAfold) to calculate the minimum free energy of first real sequences, and then of hypothetical mRNA sequences that contained altered codon usage frequencies. We determined that some of the codons never seen in the real sequences increase the stability of the mRNA secondary structure. Therefore, we propose that selection on translational efficiency may also be influencing codon usage frequencies in the SM50 gene.
