Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Blair G. Paul, Sarah C. Bagby, Elizabeth Czornyj, Diego Arambula, Sumit Handa, Alexander Sczyrba, Partho Ghosh, Jeff F. Miller and David L. Valentine ()
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Blair G. Paul: Marine Science Institute, University of California
Sarah C. Bagby: Marine Science Institute, University of California
Elizabeth Czornyj: Immunology and Molecular Genetics, University of California
Diego Arambula: Immunology and Molecular Genetics, University of California
Sumit Handa: University of California San Diego
Alexander Sczyrba: Center for Biotechnology and Faculty of Technology, Bielefeld University
Partho Ghosh: University of California San Diego
Jeff F. Miller: Immunology and Molecular Genetics, University of California
David L. Valentine: Marine Science Institute, University of California

Nature Communications, 2015, vol. 6, issue 1, 1-8

Abstract: Abstract In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >1018 protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.

Date: 2015
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DOI: 10.1038/ncomms7585

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