期刊
NATURE MICROBIOLOGY
卷 2, 期 6, 页码 -出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nmicrobiol.2017.45
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资金
- National Science Foundation [OCE-1046144]
- National Institutes of Health [R01 AI096838]
- US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231, DE-SC0004918]
- US DOE Joint Genome Institute, a DOE Office of Science User Facility [DE-AC02-05CH11231]
- DOE
- Center for Dark Energy Biosphere Investigations (C-DEBI)
- long-term EMBO fellowship
- Directorate For Geosciences [1046144] Funding Source: National Science Foundation
- Division Of Ocean Sciences [1046144] Funding Source: National Science Foundation
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life(1-5). The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability(6-8), are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have definedmonophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.
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