Draft:DCL4
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DCL4 (an abbreviation of Dicer-like 4) is a gene in plants that encodes the DCL4 protein, a ribonuclease III enzyme involved in the processing of double-stranded RNA (dsRNA) into 21-nucleotide small interfering RNAs (siRNAs). DCL4 is one of four Dicer family proteins typically encoded in eudicot genomes.[1] DCL4 plays a central role in post-transcriptional gene silencing pathways, particularly in the biogenesis of trans-acting siRNAs (ta-siRNAs) and phased siRNAs (phasiRNAs).[2][3][4] The gene was first identified in Arabidopsis due to the mutant phenotype and the role of ta-siRNAs in vegetative phase change in Arabidopsis.[2][3][4] DCL4 functions together with the double-stranded RNA (dsRNA) binding protein DRB4 to process substrate double-stranded RNA.[5] Although DCL4 is homologous to the metazoan Dicer protein, its biological functions are specialized within plant small RNA pathways and are distinct from those of DCL1, which primarily mediates microRNA (miRNA) maturation. DCL4 activity is also a key component of antiviral defense in plants, where it processes viral dsRNA into siRNAs that guide RNA silencing responses.[6]
Function
[edit]In plants, dsRNA precursors are processed by distinct Dicer-like enzymes that generate small interfering RNAs of characteristic lengths. DCL4 primarily produces 21-nucleotide siRNAs.[7] A subset of endogenous siRNAs known as ta-siRNAs generated by DCL4 functions analogously to microRNAs by regulating gene expression at distant genomic loci.[2][3][4] Formation of ta-siRNAs is initiated by microRNA-mediated cleavage of noncoding TAS transcripts, followed by RNA-dependent RNA polymerase 6 (RDR6)–dependent synthesis of dsRNA, which serves as the substrate for DCL4 processing.[2][3][4]
DCL4 is the principal Dicer-like enzyme responsible for the phased processing of TAS3 transcripts into 21-nucleotide trans-acting siRNAs. Following miR390-guided cleavage of the TAS3 long noncoding RNA and conversion of the cleavage products into double-stranded RNA by RNA-dependent RNA polymerase 6 (RDR6), DCL4 generates regularly phased siRNAs that regulate AUXIN RESPONSE FACTOR (ARF) genes.[8]
In rice (Oryza sativa), DCL4 plays an essential role in small RNA–mediated regulation of plant development. Genetic disruption or knockdown of OsDCL4 results in pleiotropic developmental defects, including abnormalities in vegetative growth and severe alterations in spikelet identity, indicating a broad requirement for DCL4-dependent siRNA pathways during monocot development.[9] These phenotypes differ markedly from those observed in Arabidopsis dcl4 mutants,[4] suggesting that DCL4-mediated silencing has expanded or diverged functions in grasses. Molecular analyses show that OsDCL4 is the primary enzyme responsible for generating 21-nucleotide siRNAs from both endogenous loci and inverted-repeat substrates, including trans-acting siRNAs derived from TAS transcripts, linking its biochemical activity directly to developmental regulation in rice.[9]
DCL4 is also a central component of the pathway that produces 21-nucleotide phased small interfering RNAs, including reproductive phasiRNAs, across the angiosperms.[7][10] In rice, large numbers of phased siRNA loci are initiated by miRNA-directed cleavage and subsequently processed by OsDCL4 into regularly spaced 21-nucleotide products.[9] These phased siRNAs are highly enriched in male reproductive tissues, particularly developing anthers, and represent one of the most abundant classes of DCL4-dependent small RNAs in monocots.[11]
Evolutionary history
[edit]DCL4 arose early in the evolution of land plants as a specialized paralog within the plant Dicer-like (DCL) gene family.[12] Phylogenetic analyses indicate that DCL4 emerged through gene duplication following the divergence of plants from other eukaryotic lineages, with clear orthologs present in bryophytes and vascular plants but absent from algae and non-plant eukaryotes.[13][12] This diversification accompanied the expansion of RNA-dependent RNA polymerase–based silencing pathways in plants, enabling the production of 21-nucleotide small interfering RNAs from dsRNA substrates.[14] Over evolutionary time, DCL4 became functionally specialized for phased and trans-acting siRNA biogenesis and antiviral defense, roles that distinguish it from other plant DCL paralogs such as DCL1 and DCL3.[13] Comparative genomic analyses show that TAS3 is conserved across all major land plant lineages, including bryophytes, indicating that the DCL4-dependent TAS3 pathway arose early during terrestrial plant evolution.[15][12] This exceptional conservation makes TAS3 one of the oldest known plant long noncoding RNAs and therefore DCL4 is a core component of an ancient regulatory circuit linking small RNAs to developmental patterning.[14]
Category:Wikipedia Student Program Category:Ribonucleases Category:Plant proteins Category:Plant genes Category:RNA interference
- ^ Margis, Rogerio; Fusaro, Adriana F.; Smith, Neil A.; Curtin, Shaun J.; Watson, John M.; Finnegan, E. Jean; Waterhouse, Peter M. (2006-05-01). "The evolution and diversification of Dicers in plants". FEBS Letters. 580 (10): 2442–2450. Bibcode:2006FEBSL.580.2442M. doi:10.1016/j.febslet.2006.03.072. ISSN 0014-5793. PMID 16638569.
- ^ a b c d Gasciolli, Virginie; Mallory, Allison C.; Bartel, David P.; Vaucheret, Hervé (2005-08-01). "Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs". Current Biology. 15 (16): 1494–1500. Bibcode:2005CBio...15.1494G. doi:10.1016/j.cub.2005.07.024. PMID 16040244.
- ^ a b c d Xie, Zhixin; Allen, Edwards; Wilken, April; Carrington, James C. (2005-09-06). "DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana". Proceedings of the National Academy of Sciences. 102 (36): 12984–12989. Bibcode:2005PNAS..10212984X. doi:10.1073/pnas.0506426102. ISSN 0027-8424. PMC 1200315. PMID 16129836.
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- ^ a b Song, Xianwei; Li, Pingchuan; Zhai, Jixian; Zhou, Ming; Ma, Lijia; Liu, Bin; Jeong, Dong-Hoon; Nakano, Mayumi; Cao, Shouyun; Liu, Chunyan; Chu, Chengcai; Wang, Xiu-Jie; Green, Pamela J.; Meyers, Blake C.; Cao, Xiaofeng (2011-10-04). "Roles of DCL4 and DCL3b in rice phased small RNA biogenesis". The Plant Journal. 69 (3): 462–474. doi:10.1111/j.1365-313X.2011.04805.x. ISSN 0960-7412. PMID 21973320.
- ^ Montgomery, Taiowa A.; Howell, Miya D.; Cuperus, Josh T.; Li, Dawei; Hansen, Jesse E.; Alexander, Amanda L.; Chapman, Elisabeth J.; Fahlgren, Noah; Allen, Edwards; Carrington, James C. (2008-04-01). "Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation". Cell. 133 (1): 128–141. doi:10.1016/j.cell.2008.02.033. PMID 18342362.
- ^ a b c Liu, Bin; Chen, Zhiyu; Song, Xianwei; Liu, Chunyan; Cui, Xia; Zhao, Xianfeng; Fang, Jun; Xu, Wenying; Zhang, Huiyong; Wang, Xiujie; Chu, Chengcai; Deng, Xingwang; Xue, Yongbiao; Cao, Xiaofeng (2007-10-29). "Oryza sativa Dicer-like4 Reveals a Key Role for Small Interfering RNA Silencing in Plant Development". The Plant Cell. 19 (9): 2705–2718. Bibcode:2007PlanC..19.2705L. doi:10.1105/tpc.107.052209. ISSN 1532-298X. PMC 2048709. PMID 17905898.
- ^ Pokhrel, Suresh; Huang, Kun; Bélanger, Sébastien; Zhan, Junpeng; Caplan, Jeffrey L.; Kramer, Elena M.; Meyers, Blake C. (2021-08-16). "Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants". Nature Communications. 12 (1) 4941. Bibcode:2021NatCo..12.4941P. doi:10.1038/s41467-021-25128-y. ISSN 2041-1723. PMC 8368212. PMID 34400639.
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