The Genome Reduction Excludes the Ribosomal Rescue System in <b><i>Acholeplasmataceae</i></b>

Abstract

The <i>trans</i>-translation process is a ribosomal rescue system for stalled ribosomes processing truncated mRNA. The genes <i>ssrA</i> and <i>smpB</i> fulfil the key functions in most bacteria, but some species have either lost these genes or the function of the ribosomal rescue system is taken over by other genes. To date, the ribosomal rescue system has not been analysed in detail for the <i>Acholeplasmataceae</i>. This family, in the Mollicutes class, comprises the genus <i>Acholeplasma</i> and the provisional taxon “<i>Candidatus</i> Phytoplasma”. Despite their monophyletic origin, the two clades can be separated by traits such as not representing primary pathogens for acholeplasmas versus being phytopathogenic for the majority of phytoplasmas. Both taxa share reduced genomes, but only phytoplasma genomes are characterised by a remarkable level of instability and reduction. Despite the general relevance of the ribosomal rescue system, information is lacking on coding, the genomic context and pseudogenisation of <i>smpB</i> and <i>ssrA</i> and their possible application as a phylogenetic marker. Herein, we provide a comprehensive analysis of the ribosomal rescue system in members of <i>Acholeplasmataceae</i>. The examined <i>Acholeplasmataceae</i> genomes encode a ribosomal rescue system, which depends on tmRNA encoded by <i>ssrA</i> acting in combination with its binding protein SmpB. Conserved gene synteny is evident for <i>smpB</i>, while <i>ssrA</i> shows a less conserved genomic context. Analysis of the tmRNA sequences highlights the variability of proteolysis tag sequences and short conserved sites at the 5′- and 3′-ends. Analyses of <i>smpB</i> provided no hints regarding the coding of pseudogenes, but they did suggest its application as a phylogenetic marker of <i>Acholeplasmataceae</i> – in accordance with 16S rDNA topology. Sequence variability of <i>smpB</i> provides sufficient information for species assignment and phylogenetic analysis.