Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways.
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.
Duchaine
Thomas F
TF
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.
Wohlschlegel
James A
JA
Kennedy
Scott
S
Bei
Yanxia
Y
Conte
Darryl
D
Pang
Kaming
K
Brownell
Daniel R
DR
Harding
Sandra
S
Mitani
Shohei
S
Ruvkun
Gary
G
Yates
John R
JR
Mello
Craig C
CC
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*
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