A bacterial Argonaute with noncanonical guide RNA specificity

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4057-62. doi: 10.1073/pnas.1524385113. Epub 2016 Mar 30.


Eukaryotic Argonaute proteins induce gene silencing by small RNA-guided recognition and cleavage of mRNA targets. Although structural similarities between human and prokaryotic Argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that Argonautes encoded within CRISPR-cas [clustered regularly interspaced short palindromic repeats (CRISPR)-associated] bacterial immunity operons have divergent activities. We show here that the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) protein cleaves single-stranded target sequences using 5'-hydroxylated guide RNAs rather than the 5'-phosphorylated guides used by all known Argonautes. The 2.0-Å resolution crystal structure of an MpAgo-RNA complex reveals a guide strand binding site comprising residues that block 5' phosphate interactions. Using structure-based sequence alignment, we were able to identify other putative MpAgo-like proteins, all of which are encoded within CRISPR-cas loci. Taken together, our data suggest the evolution of an Argonaute subclass with noncanonical specificity for a 5'-hydroxylated guide.

Keywords: Argonaute; RNA interference; small noncoding RNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Argonaute Proteins / chemistry
  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Genes, Bacterial
  • Models, Molecular
  • RNA, Guide, CRISPR-Cas Systems / metabolism*


  • Argonaute Proteins
  • Bacterial Proteins
  • RNA, Guide, CRISPR-Cas Systems

Associated data

  • PDB/5I4A