The identification of oppA gene homologues as part of the oligopeptide transport system in mycoplasmas

• An approach for identification and annotation of oppA gene homologues is proposed.
• All mycoplasmas, except hemoplasmas contain one or more opp operons.
• An oppA gene homologue could be identified as part of all opp operons.
• Phylogenetic analysis of Opp proteins allow grouping of operons into three types.
• OppAs of each type have characteristic motifs.

The lack of an annotated oppA gene as part of many oligopeptide permease (opp) operons has questioned the necessity of the oligopeptide-binding domain (OppA) as a part of the Opp transport system in mycoplasmas. This study investigated the occurrence of an oppA gene as part of the oppBCDF operon in 42 mycoplasma genomes. Except for hemoplasma, all mycoplasmas were found to possess one or more copies of the oppBCDF operon and with the help of similarity searches their oppA genes could be identified. Phylogenetic analysis of the combined OppABCDF amino acid sequences allowed them to be grouped into three types. Each type has a unique set of conserved motifs, which are likely to reflect substrate preference and adaption strategies. Our approach allowed the identification of oppA gene homologues for all mycoplasma opp operons and thereby provides a method for re-evaluating the current annotation of oppA genes in mycoplasma genomes.