Pseudogenization of the chaperonin system in '<i>Candidatus</i> Phytoplasma pruni' revealed by genome sequencing and comparative genomics

GroE is a chaperonin folding system consisting of GroEL (Cpn60, a 60 kDa chaperonin), and the smaller co-chaperonin GroES (Cpn10). Many 'client' proteins require GroE to fold properly, including several that are essential for cell viability. GroE is found in nearly all bacteria and eukaryotes. <i>Mollicutes</i> are the only micro-organisms that lack GroE in almost all cases. Only two clades of <i>Mollicutes</i> have retained the ancestral GroE system, or perhaps reacquired one; these exceptions include the family <i>Acholeplasmataceae</i>, consisting of the genera <i>Acholeplasma</i> and '<i>Candidatus</i> Phytoplasma'. The role of GroEL in these unique <i>Mollicutes</i> is a source of speculation, given how many non-canonical 'moonlighting' roles have been ascribed to this protein. GroEL has been suggested to play a role in pathogenesis in plant and animal pathogenic <i>Mollicutes</i> by binding to host cells and facilitating invasion. However, in one further layer of exception, the phytopathogenic taxon '<i>Candidatus</i> Phytoplasma pruni' (ribosomal group 16SrIII) was reported in 2012 to lack a GroE system. This study confirms the lack of a functional GroE system in 16SrIII by providing two new, high-quality, non-fragmented genome assemblies, as well as a thorough survey of other 16SrIII genomes for genes encoding GroEL/GroES, including those that may not resemble phytoplasma GroEL (i.e. acquired by horizontal gene transfer, HGT). We discuss the implications of a clearly phytopathogenic, invasive group of <i>Mollicutes</i> that nevertheless lacks GroE, in light of the presumed role of GroEL for this species. We determined that multiple genomes of 16SrIII contain short, non-functional <i>groEL</i> pseudogenes, while most of the reported genomes lack any semblance of a GroE system. Examination of the new assemblies allowed us to rule out HGT as a means of GroE acquisition.