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PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097. eCollection 2017.

DNA recognition by an RNA-guided bacterial Argonaute.

Doxzen KW1, Doudna JA1,2,3,4,5,6,7.

Author information

1
Biophysics Graduate Group, University of California, Berkeley, California, United States of America.
2
Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America.
3
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
4
Center for RNA Systems Biology, University of California, Berkeley, California, United States of America.
5
Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America.
6
Innovative Genomics Institute, University of California, Berkeley, California, United States of America.
7
Department of Chemistry, University of California, Berkeley, California, United States of America.

Abstract

Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.

PMID:
28520746
PMCID:
PMC5435312
DOI:
10.1371/journal.pone.0177097
[Indexed for MEDLINE]
Free PMC Article

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