title: Targeted diversity generation by intraterrestrial archaea and archaeal viruses.
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 >10(18) 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.
authors: Marine Science Institute, University of California, Santa Barbara, California 93106, USA.
authors: Blair G
authors: BG
authors: Paul
authors: Marine Science Institute, University of California, Santa Barbara, California 93106, USA.
authors: Sarah C
authors: SC
authors: Bagby
authors: Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA.
authors: Elizabeth
authors: E
authors: Czornyj
authors: Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA.
authors: Diego
authors: D
authors: Arambula
authors: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
authors: Sumit
authors: S
authors: Handa
authors: 1] Center for Biotechnology and Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany [2] DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors: Alexander
authors: 0000000244053847
authors: A
authors: Sczyrba
authors: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
authors: Partho
authors: P
authors: Ghosh
authors: 1] Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA [2] Molecular Biology Institute, University of California, Los Angeles, California 90095, USA [3] California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
authors: Jeff F
authors: JF
authors: Miller
authors: 1] Marine Science Institute, University of California, Santa Barbara, California 93106, USA [2] Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106 USA.
authors: David L
authors: DL
authors: Valentine
mesh_terms: D001105:Archaea / Q000821:virology; D019843:Archaeal Proteins / Q000235:genetics*; D023641:Archaeal Viruses / Q000235:genetics*; D001483:Base Sequence; D014644:Genetic Variation; D054892:Metagenome / Q000235:genetics*; D008969:Molecular Sequence Data; D059645:Mutation Rate; D046588:Nanoarchaeota / Q000235:genetics* / Q000821:virology; D018626:Retroelements
chemical_list: D019843:Archaeal Proteins; D018626:Retroelements