title: Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways.
abstract: In plants, animals, and fungi, members of the Dicer family of RNase III-related enzymes process double-stranded RNA (dsRNA) to initiate small-RNA-mediated gene-silencing mechanisms. To learn how C. elegans Dicer, DCR-1, functions in multiple distinct silencing mechanisms, we used a mass-spectrometry-based proteomics approach to identify DCR-1-interacting proteins. We then generated and characterized deletion alleles for the corresponding genes. The interactors are required for production of three species of small RNA, including (1) small interfering RNAs (siRNAs), derived from exogenous dsRNA triggers (exo-siRNAs); (2) siRNAs derived from endogenous triggers (endo-siRNAs); and (3) developmental regulatory microRNAs (miRNAs). One interactor, the conserved RNA-phosphatase homolog PIR-1, is required for the processing of a putative amplified DCR-1 substrate. Interactors required for endo-siRNA production include ERI-1 and RRF-3, whose loss of function enhances RNAi. Our findings provide a first glimpse at the complex biochemical niche of Dicer and suggest that competition exists between DCR-1-mediated small-RNA pathways.
authors.affiliation: Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Duchaine
authors.forename: James A
authors.initials: JA
authors.lastname: Wohlschlegel
authors.forename: Scott
authors.initials: S
authors.lastname: Kennedy
authors.forename: Yanxia
authors.initials: Y
authors.lastname: Bei
authors.forename: Darryl
authors.initials: D
authors.lastname: Conte
authors.forename: Kaming
authors.initials: K
authors.lastname: Pang
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Brownell
authors.forename: Sandra
authors.initials: S
authors.lastname: Harding
authors.forename: Shohei
authors.initials: S
authors.lastname: Mitani
authors.forename: Gary
authors.initials: G
authors.lastname: Ruvkun
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.forename: Craig C
authors.initials: CC
authors.lastname: Mello
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001667:Binding, Competitive; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004722:Endoribonucleases / Q000235:genetics* / Q000378:metabolism; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism; D017353:Gene Deletion; D013058:Mass Spectrometry; D035683:MicroRNAs / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D015394:Molecular Structure; D040901:Proteomics; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000378:metabolism; D043244:Ribonuclease III; D016415:Sequence Alignment; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D029742:Caenorhabditis elegans Proteins; D004268:DNA-Binding Proteins; D035683:MicroRNAs; D034741:RNA, Small Interfering; D012324:RNA-Dependent RNA Polymerase; C472756:RNA-directed RNA polymerase RRF-3, C elegans; C482202:ERI-1 protein, C elegans; D004722:Endoribonucleases; D005095:Exoribonucleases; C118116:dcr-1 protein, C elegans; D043244:Ribonuclease III