Minimal Mechanistic Model of SiRNA-dependent Target RNA Slicing by Recombinant Human Argonaute 2 Protein

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2013 Oct 9

PMID 24101500

Citations 33

Authors

Andrea Deerberg

Sarah Willkomm

Tobias Restle

Affiliations

Soon will be listed here.

Abstract

Argonaute (Ago) proteins are the key component of the RNA-induced silencing complex and mediate RNA interference (RNAi) in association with small RNAs. Although overall the mechanism of RNAi is well understood, many molecular details of this complex process are not. Here we report about in-depth steady-state and, in particular, pre-steady-state characterization of siRNA binding, target RNA recognition, sequence-specific cleavage and product release by recombinant human Ago 2 (hAgo2). In combining our biochemical studies with crystal structures of bacterial Ago proteins and of recently released hAgo2, we relate kinetic data to conformational changes along the pathway and propose a comprehensive minimal mechanistic model describing fundamental steps during RNAi. Furthermore, in contrast to the current conception, our hAgo2 preparations are programmable with double-stranded siRNA. Accordingly, the system investigated represents a functional minimal RNA-induced silencing complex.

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References

Hutvagner G, Simard M . Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol. 2007; 9(1):22-32. DOI: 10.1038/nrm2321. View

Song J, Smith S, Hannon G, Joshua-Tor L . Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004; 305(5689):1434-7. DOI: 10.1126/science.1102514. View

Stefani G, Slack F . Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol. 2008; 9(3):219-30. DOI: 10.1038/nrm2347. View

Kim K, Lee Y, Carthew R . Conversion of pre-RISC to holo-RISC by Ago2 during assembly of RNAi complexes. RNA. 2006; 13(1):22-9. PMC: 1705758. DOI: 10.1261/rna.283207. View

Boland A, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O . Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein. Proc Natl Acad Sci U S A. 2011; 108(26):10466-71. PMC: 3127882. DOI: 10.1073/pnas.1103946108. View

Ameres S, Martinez J, Schroeder R . Molecular basis for target RNA recognition and cleavage by human RISC. Cell. 2007; 130(1):101-12. DOI: 10.1016/j.cell.2007.04.037. View

Siomi H, Siomi M . On the road to reading the RNA-interference code. Nature. 2009; 457(7228):396-404. DOI: 10.1038/nature07754. View

Ma J, Ye K, Patel D . Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature. 2004; 429(6989):318-322. PMC: 4700412. DOI: 10.1038/nature02519. View

Wang Y, Sheng G, Juranek S, Tuschl T, Patel D . Structure of the guide-strand-containing argonaute silencing complex. Nature. 2008; 456(7219):209-13. PMC: 4689319. DOI: 10.1038/nature07315. View

10.

Xie X, Lu J, Kulbokas E, Golub T, Mootha V, Lindblad-Toh K . Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005; 434(7031):338-45. PMC: 2923337. DOI: 10.1038/nature03441. View

11.

Frank F, Sonenberg N, Nagar B . Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2. Nature. 2010; 465(7299):818-22. DOI: 10.1038/nature09039. View

12.

Hutvagner G, Zamore P . A microRNA in a multiple-turnover RNAi enzyme complex. Science. 2002; 297(5589):2056-60. DOI: 10.1126/science.1073827. View

13.

Elbashir S, Lendeckel W, Tuschl T . RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 2001; 15(2):188-200. PMC: 312613. DOI: 10.1101/gad.862301. View

14.

Tomari Y, Zamore P . Perspective: machines for RNAi. Genes Dev. 2005; 19(5):517-29. DOI: 10.1101/gad.1284105. View

15.

Song J, Liu J, Tolia N, Schneiderman J, Smith S, Martienssen R . The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol. 2003; 10(12):1026-32. DOI: 10.1038/nsb1016. View

16.

Bernstein E, Caudy A, Hammond S, Hannon G . Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 2001; 409(6818):363-6. DOI: 10.1038/35053110. View

17.

MacRae I, Li F, Zhou K, Cande W, Doudna J . Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harb Symp Quant Biol. 2007; 71:73-80. DOI: 10.1101/sqb.2006.71.042. View

18.

Wee L, Flores-Jasso C, Salomon W, Zamore P . Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell. 2012; 151(5):1055-67. PMC: 3595543. DOI: 10.1016/j.cell.2012.10.036. View

19.

Parker J, Roe S, Barford D . Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 2004; 23(24):4727-37. PMC: 535097. DOI: 10.1038/sj.emboj.7600488. View

20.

Winter J, Diederichs S . Argonaute proteins regulate microRNA stability: Increased microRNA abundance by Argonaute proteins is due to microRNA stabilization. RNA Biol. 2011; 8(6):1149-57. DOI: 10.4161/rna.8.6.17665. View