Deletions, duplications and rearrangements in mycoplasma ribosomal RNA gene sequences

Mycoplasma genomes lack several entire ribosomal RNA gene sets, and the remaining RNA genes lack some nucleotides. Analysis of mycoplasma 5S RNAs utilizing generalized models for prokaryotic 5S RNA secondary structure allows us to specify the molecular locations and identify many of the nucleotides missing from mycoplasma 5S RNAs and to detect the presence of unusual structural features. The most extensive alterations occur in the 5S RNAs from M. mycoides subsp. capri and M. capricolum, which have a similar pattern. Each of these 5S RNAs, as well as the Spiroplasma BC3 5S RNA, has a concentration of deletions in helix V, and they also share several unusual structures. We also noted the occurrence in mycoplasma 5S RNAs of numerous repeated sequences. The genetic process of unequal crossing-over is suggested as the explanation for the repeated sequences observed in mycoplasma RNAs.