The role of lateral gene transfer in the evolutionary diversification and adaptation of haloarchaea

Comparative genomics has revealed that prokaryotic genomes are mosaic in nature; distinct genomic regions have incongruent evolutionary histories as a result of frequent and promiscuous gene exchange. Studies of pathogenic bacteria indicate lateral gene transfer (LGT) can lead to rapid adaptation through the acquisition of novel gene function and that gene exchange via homologous recombination often overwhelms mutation as a source of within- species sequence divergence. To contribute to a unified model of prokaryotic genome evolution, this study proposes to explore the nature of gene exchange within a single archaeal group, the haloarchaea. We have previously identified genes exhibiting incongruent histories characteristic of lateral gene transfer by orthologous gene replacement in this group. To investigate the frequency and process of LGT we will systematically compare the evolutionary histories of five conserved proteins and the 16S rRNA gene within haloarchaeal groups of increasing taxonomic rank. In addition, we will investigate the mechanisms and barriers to gene exchange in haloarchaea by an experimental genetics approach focused on the function of the archaeal DNA mismatch repair (MMR) system. In eukaryotes and bacteria, MMR reduces the spontaneous mutation rate and MMR deficiency is linked to cancer in humans and increased pathogenesis in bacteria. MMR is also a potent inhibitor of recombination and therefore a barrier to inter-species gene transfer. Genetic analysis of MMR in archaea will provide valuable insight into the modulation of spontaneous mutation and gene exchange by this DNA repair pathway.