TY - JOUR
T1 - Ecology and molecular targets of hypermutation in the global microbiome
AU - Roux, Simon
AU - Paul, Blair G.
AU - Bagby, Sarah C.
AU - Nayfach, Stephen
AU - Allen, Michelle A.
AU - Attwood, Graeme
AU - Cavicchioli, Ricardo
AU - Chistoserdova, Ludmila
AU - Gruninger, Robert J.
AU - Hallam, Steven J.
AU - Hernandez, Maria E.
AU - Hess, Matthias
AU - Liu, Wen Tso
AU - McAllister, Tim A.
AU - O’Malley, Michelle A.
AU - Peng, Xuefeng
AU - Rich, Virginia I.
AU - Saleska, Scott R.
AU - Eloe-Fadrosh, Emiley A.
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.
AB - Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.
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U2 - 10.1038/s41467-021-23402-7
DO - 10.1038/s41467-021-23402-7
M3 - Article
C2 - 34031405
AN - SCOPUS:85106571392
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 3076
ER -