| Structural highlights
Function
[DCL4_ARATH] Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the biogenesis of trans-acting small interfering RNAs (ta-siRNAs, derived from the TAS1, TAS2 or TAS3 endogenous transcripts) by cleaving small dsRNAs into 21-24 nucleotide ta-siRNAs. Functions with the dsRNA-binding protein DRB4 in ta-siRNAs processing. Acts in the RDR6/SGS3/DCL4/AGO7 ta-siRNA pathway involved in leaf developmental timing. Plays a role in transitive silencing of transgenes by processing secondary siRNAs. This pathway, which requires DCL2 and RDR6, amplifies silencing by using the target RNA as substrate to generate secondary siRNAs, providing an efficient mechanism for long-distance silencing. Required for the production of the 30-40 nucleotide bacterial-induced long siRNAs (lsiRNA). May participate with DCL3 in the production of 24 nucleotide repeat-associated siRNAs (ra-siRNAs) which derive from heterochromatin and DNA repeats such as transposons. Plays an important role in antiviral RNA silencing. Involved in the production of viral siRNAs derived from the cucumber mosaic virus (CMV), turnip crinkle virus (TCV) and tobacco rattle virus (TRV). Targeted by the viral silencing suppressor (VSR) protein 2b of the cucumber mosaic virus (CMV) that inactivates DCL4 function in RNA silencing. Does not seem to be involved in microRNAs (miRNAs) processing.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.
Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction.,Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA RNA. 2010 Mar;16(3):474-81. Epub 2010 Jan 27. PMID:20106953[12]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Xie Z, Allen E, Wilken A, Carrington JC. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12984-9. Epub 2005 Aug 29. PMID:16129836 doi:http://dx.doi.org/10.1073/pnas.0506426102
- ↑ Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol. 2005 Aug 23;15(16):1494-500. PMID:16040244 doi:http://dx.doi.org/S0960-9822(05)00765-7
- ↑ Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 2005 Sep 15;19(18):2164-75. Epub 2005 Aug 30. PMID:16131612 doi:http://dx.doi.org/10.1101/gad.1352605
- ↑ Dunoyer P, Himber C, Voinnet O. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet. 2005 Dec;37(12):1356-60. Epub 2005 Nov 6. PMID:16273107 doi:http://dx.doi.org/10.1038/ng1675
- ↑ Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouche N, Gasciolli V, Vaucheret H. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol. 2006 May 9;16(9):927-32. PMID:16682354 doi:http://dx.doi.org/10.1016/j.cub.2006.03.035
- ↑ Bouche N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 2006 Jul 26;25(14):3347-56. Epub 2006 Jun 29. PMID:16810317 doi:http://dx.doi.org/10.1038/sj.emboj.7601217
- ↑ Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev. 2007 Dec 1;21(23):3123-34. Epub 2007 Nov 14. PMID:18003861 doi:http://dx.doi.org/10.1101/gad.1595107
- ↑ Diaz-Pendon JA, Li F, Li WX, Ding SW. Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell. 2007 Jun;19(6):2053-63. Epub 2007 Jun 22. PMID:17586651 doi:http://dx.doi.org/10.1105/tpc.106.047449
- ↑ Moissiard G, Parizotto EA, Himber C, Voinnet O. Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA. 2007 Aug;13(8):1268-78. Epub 2007 Jun 25. PMID:17592042 doi:http://dx.doi.org/10.1261/rna.541307
- ↑ Donaire L, Barajas D, Martinez-Garcia B, Martinez-Priego L, Pagan I, Llave C. Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs. J Virol. 2008 Jun;82(11):5167-77. doi: 10.1128/JVI.00272-08. Epub 2008 Mar 19. PMID:18353962 doi:http://dx.doi.org/10.1128/JVI.00272-08
- ↑ Qu F, Ye X, Morris TJ. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14732-7. doi:, 10.1073/pnas.0805760105. Epub 2008 Sep 17. PMID:18799732 doi:http://dx.doi.org/10.1073/pnas.0805760105
- ↑ Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. RNA. 2010 Mar;16(3):474-81. Epub 2010 Jan 27. PMID:20106953 doi:10.1261/rna.1965310
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