RDE-1 explained

RDE-1 (RNAi-DEfective 1) is a primary Argonaute protein required for RNA-mediated interference (RNAi) in Caenorhabditis elegans. The rde-1 gene locus was first characterized in C. elegans mutants resistant to RNAi, and is a member of a highly conserved Piwi gene family that includes plant, Drosophila, and vertebrate homologs.[1]

Role in RNAi pathway

Primary siRNA-argonaute complex

Upon uptake into the cell, exogenous trigger dsRNA is bound by RDE-4 and cleaved into 21-25nt primary siRNA by a Dicer complex that includes RDE-1.[2] Primary siRNA binding to RDE-1 then promotes the formation of the RNA-induced silencing complex (RISC). Unlike in other Argonautes characterized in Drosophila[3] and humans,[4] the catalytic RNase H motif in RDE-1 has not been shown to exhibit Slicer activity of the target transcript. Instead, RNase H activity in RDE-1 is primarily facilitates siRNA maturation through cleavage of the passenger strand.[5]

Secondary siRNA-argonaute complex

The primary Argonaute complex recruits an RNA-dependent RNA polymerase (RdRP) to generate secondary siRNAs, triggering an amplification response. Secondary siRNAs are bound by degenerate secondary Argonautes, which are then directly involved in target transcript degradation.[6] However, RDE-1 shows no stable association with the more abundant secondary siRNAs.[7]

Whereas rde-4 deficiency can be rescued by high concentrations of trigger dsRNA,[8] and secondary Argonaute exhibit functional redundancy,[6] there has been no evidence that RNA-mediated silencing can be reinstated in rde-1 deficient mutants. To this extent, RDE-1 appears to have a qualitatively distinct activity in the exogenous RNAi pathway.[7]

Structure

Canonical Argonaute proteins possess three primary domains forming a crescent-shaped base: the PAZ, MID, and PIWI domains. PAZ and MID orient and anchor the double-stranded siRNA by binding to the 3’ and 5’ termini, respectively, leaving the internal nucleotides accessible for base pairing. The PIWI domain folds into an RNase H-like structure, and contains the conserved catalytic triad “DDH” (two aspartate residues, one histidine residue).[9] The crystal structure of RDE-1 has not been formally elucidated, but can be assumed to closely resemble its human homologs.

Passenger strand degradation

Mutation of any residues in the RNase H catalytic triad abolishes Slicer activity in human Argonaute protein Ago2, suggesting that the RNase H domain is directly responsible for target mRNA degradation.[10] However, RDE-1 has not been implicated in mRNA-cleavage activity.

Instead, RDE-1 with mutations in the conserved DDH motif exhibit reduced passenger (sense) strand turnover, suggesting that RNase H activity serves to cleave the passenger strand, leaving the guide (antisense) strand accessible for base-pairing to target mRNA.[5] Further, target silencing can be fully restored in DDH motif mutants by loading single-stranded siRNA, suggesting that a downstream component in the RNAi pathway is responsible for Slicer activity.[5] Thus, RDE-1's RNase H domain facilitates siRNA maturation but is not directly involved in cleaving target mRNA transcripts.

See also

External links

Notes and References

  1. Tabara, H. . Sarkissian, M. . Kelly, W. G. . Fleenor, J. . Grishok, A. . Timmons, L. . Fire, A. . & Mello, C. C. . The rde-1 gene, RNA interference and transposon silencing in C. elegans . Cell . 99 . 2 . 123–32 . Oct 1999 . 10535731 . 10.1016/S0092-8674(00)81644-X . free .
  2. Tabara, H. . Yigit, E. . Siomi, H. . Mello, C. . Mello, C. C. . The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1 and a DExH-box helicase to direct RNAi in C. elegans . Cell . 109 . 7 . 861–871 . Jun 2002 . 12110183 . 10.1016/S0092-8674(02)00793-6. free .
  3. Hammond SM, Bernstein E, Beach D, Hannon GJ . An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells . Nature . 404 . 6775 . 293–296 . Mar 2000 . 10749213 . 10.1038/35005107. 9091863 .
  4. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T . Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs . Mol Cell . 15 . 2 . 185–197 . Jul 2004 . 15260970 . 10.1016/j.molcel.2004.07.007. free .
  5. Steiner, F. A. . Okihara, K. L. . Hoogstrate, S. W. . Sijen, T. . Ketting, R. F. . RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans . Nat Struct Mol Biol . 16 . 2 . 207–11 . Feb 2009 . 19151723 . 10.1038/nsmb.1541. 22909313 .
  6. Boisvert, M.E. . Simard, M.J . RNAi pathway in C. elegans: the argonautes and collaborators . Curr. Top. Microbiol. Immunol. . Current Topics in Microbiology and Immunology . 320 . 21–36 . 2008 . 18268838 . 10.1007/978-3-540-75157-1_2. 978-3-540-75156-4 .
  7. Yigit E, Batista PJ, Bei Y, Pang KM, Chen CC, Tolia NH, Joshua-Tor L, Mitani S, Simard MJ, Mello CC . Analysis of the C. elegans Argonaute Family Reveals that Distinct Argonautes Act Sequentially during RNAi . Cell . 127 . 4 . 747–57 . 2006 . 17110334 . 10.1016/j.cell.2006.09.033. free .
  8. Habig JW, Aruscavage PJ, Bass BL . In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4 . PLOS ONE . 3 . 12 . e4052 . 2008 . 19112503 . 10.1371/journal.pone.0004052 . 2603325. free .
  9. Song, J.J. . Smith, S.K. . Hannon, G.J. . Joshua-Tor, L. . Crystal structure of Argonaute and its implications for RISC slicer activity . Science . 305 . 1434–7 . Sep 2004 . 5689 . 15284453 . 10.1126/science.1102514. 38557910 . free .
  10. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ . Argonaute2 is the catalytic engine of mammalian RNAi . Science . 305 . 1437–41 . Sep 2004. 5689 . 15284456 . 10.1126/science.1102513. 2778088 . free .