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PMID: 19187762 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein.

Molecular cell ·Vol. 33 ·No. 2 ·2009-01-30 ·Pages 204-14

Parker JS, Parizotto EA, Wang M, Roe SM, Barford D

Abstract

Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. Over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. Enhancement is achieved through a reduced entropy penalty for the interaction. In contrast, interactions 3' of the seed are inhibited. We quantified mismatched target recognition inside and outside the seed, revealing amplified discrimination at the third position in the seed mediated by the PIWI/MID domain. Thus, association of the guide strand with the PIWI/MID domain generates an enhanced affinity anchor site over the seed that can promote fidelity in target recognition and stabilize and guide the assembly of the active silencing complex.

MeSH Terms
Archaeal Proteins/chemistry,metabolism Archaeoglobus fulgidus/metabolism Binding Sites Entropy Models, Biological Models, Molecular Protein Conformation Protein Structure, Tertiary RNA Interference/physiology RNA, Archaeal/genetics,metabolism RNA, Guide/genetics,metabolism
Chemicals
Archaeal Proteins RNA, Archaeal RNA, Guide
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Parker James S
Institute of Cancer Research, Chester Beatty Laboratories, London, UK. james.parker@bioch.ox.ac.uk
Parizotto Eneida A
Wang Muhan
Roe S Mark
Barford David
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Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-4164
DOI
10.1016/j.molcel.2008.12.012
Email
james.parker@bioch.ox.ac.uk
Published
2009-01-30
Pages
204-14
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC2642989
Subset
IM
Grants
Medical Research Council · G0600097 · United Kingdom
Wellcome Trust · United Kingdom
Cancer Research UK · United Kingdom
Databases
PDB
2W42
External Links
PubMed source DOI: 10.1016/j.molcel.2008.12.012 PMC Full Text View journal details
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