Loss of genes related to Nucleotide Excision Repair (NER) and implications for reductive genome evolution in symbionts of deep-sea vesicomyid clams.

Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution(RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair(NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades(5 cladeI and 7 cladeII symbionts). While uvrA, uvrDp and mfd were conserved in all symbionts, uvrB and uvrC were degraded in all cladeI symbionts but were apparently intact in cladeII symbionts. UvrD was disrupted in two cladeII symbionts. Among the intact genes in Ca. Vesicomyosocius okutanii ( cladeI), expressions of uvrD and mfd were detected by reverse transcription-polymerase chain reaction (RT-PCR), but those of uvrA and uvrDp were not. In contrast, all intact genes were expressed in the symbiont of Calyptogena pacifica ( cladeII). To assess how gene losses affect RGE (question 2), genetic distancesof the examined genes in symbionts from Bathymodiolusseptemdierum were shown to be larger in cladeI than cladeII symbionts. In addition, these genes had lower guanine+cytosine ( GC) contentand higher repeat sequencedensities in cladeI than measured in cladeII. Our results suggest that NER genes are currently being lost from the extant lineages of vesicomyid clam symbionts. The loss of NER genes and mutY in these symbionts is likely to promote increases in genetic distanceand repeat sequencedensity as well as reduced GC contentin genomic genes, and may have facilitated reductive evolution of the genome.