Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways
Biochemistry & Molecular Pharmacology
Graduate School of Biomedical Sciences; Program in Molecular Medicine
Medical Subject Headings
Amino Acid Sequence; Animals; Binding, Competitive; Caenorhabditis elegans; Caenorhabditis elegans Proteins; DNA-Binding Proteins; Endoribonucleases; Exoribonucleases; Gene Deletion; Mass Spectrometry; MicroRNAs; Models, Biological; Molecular Sequence Data; Molecular Structure; Proteomics; RNA Interference; RNA Replicase; RNA, Small Interfering; Sequence Alignment; Signal Transduction
Life Sciences | Medicine and Health Sciences
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.
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Citation: Cell. 2006 Jan 27;124(2):343-54. Link to article on publisher's site
Duchaine, Thomas F.; Wohlschlegel, James A.; Kennedy, Scott; Bei, Yanxia; Conte, Darryl; Pang, Ka Ming; Brownell, Daniel R.; Harding, Sandra; Mitani, Shohei; Ruvkun, Gary; Yates, John R.; and Mello, Craig C., "Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways" (2006). GSBS Student Publications. 330.