水稻Dicer-like蛋白研究进展

doi:10.3969/j.issn.1674-7968.2025.10.014

Abstract
Figure/Table
References
Related Citation (15)

Download: PDF (4377 KB) HTML (1 KB)
Export: BibTeX | EndNote (RIS)

Abstract Dicer-like (DCL) protein is a key enzyme in the RNA interference (RNAi) pathway, responsible for processing double-strand RNA (dsRNA) or precursor miRNA (pre-miRNA) into small interfering RNA (siRNA) or mature miRNA, thereby guiding mRNA degradation or gene expression inhibition. The rice (Oryza sativa) genome encodes 8 DCL proteins (OsDCLs) that exhibit distinct substrate specificity, small RNA (sRNA) product length, and biological functions. This review summarized the research progress on the functional diversification and mechanisms of OsDCLs in the processing of different types of sRNAs, their specialized roles in regulating growth, development, and important agronomic traits, as well as the regulatory mechanisms of their own activities. Moreover, the potential role of OsDCL-mediated RNA silencing pathways in the formation of rice heterosis was analyzed and the application value of OsDCLs in breeding and variety improvement was discussed. In-depth investigation of the OsDCL family would contribute to a comprehensive understanding of the roles of RNA silencing pathways in rice and other cereal crops. This review provides theoretical foundations and technical support for elucidating the mechanisms underlying heterosis formation and creating new germplasm with superior agronomic traits.

Key words： Rice DCL (Dicer-like) Small RNA (sRNA) RNA silencing Structure Functional differentiation Substrate recognition

Received: 13 November 2024

ZTFLH:

S-1

Corresponding Authors: **xiaolinli@163.com

About author:: * These authors contributed equally to this study

	Service

	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	NIAN Wei
	ZHANG Jin-Wen
	YANG You-Qiong
	DENG Wei
	GUAN Jun-Jiao
	LI Xiao-Lin

Cite this article:

NIAN Wei,ZHANG Jin-Wen,YANG You-Qiong, et al. Advances in Research on Rice (Oryza sativa) Dicer-like Proteins[J]. 农业生物技术学报, 2025, 33(10): 2257-2271.

URL:

https://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2025.10.014 OR https://journal05.magtech.org.cn/Jwk_ny/EN/Y2025/V33/I10/2257

[1] 年伟, 杨友琼, 张锦文, 等. 2024. 非生物胁迫下水稻miRNA作用之研究现状与展望[J]. 分子植物育种: 1-27. https://link.cnki.net/urlid/46.1068.S.20240301.1631.008.
(Nian W, Yang Y Q, Zhang J W, et al. 2024. Current status and prospects of studies on the role of rice miRNAs under abiotic stress[J]. Molecular Plant Breeding, 1-27.)
[2] 赵梓钧, 吴如会, 王硕, 等. 2023. 水稻PDL2的突变导致小穗外稃退化[J]. 中国农业科学, 56(7): 1248-1259.
(Zhao Z J, Wu R H, Wang S, et al.2023. Mutation of PDL2 gene causes degeneration of lemma in the spikelet of rice[J]. Scientia Agricultura Sinica, 56(7): 1248-1259.)
[3] Alarcón C R, Lee H, Goodarzi H, et al.2015. N6-methyladenosine marks primary microRNAs for processing[J]. Nature, 519(7544): 482-485.
[4] Anderson S J, Kramer M C, Gosai S J, et al.2018. N6- methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis[J]. Cell Reports, 25(5): 1146-1157.
[5] Bai Z T, Chen J F, Liao Y, et al.2016. The impact and origin of copy number variations in the Oryza species[J]. BMC Genomics, 17(1): 261.
[6] Bao N, Lye K W, Barton M K.2004. MicroRNA binding sites in Arabidopsis class Ⅲ HD-ZIP mRNAs are required for methylation of the template chromosome[J]. Developmental Cell, 7(5): 653-662.
[7] Bélanger S, Zhan J P, Meyers B C.2023. Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants[J]. Plant Physiology, 192(2): 1183-1203.
[8] Bernstein E, Caudy A A, Hammond S M, et al.2001. Role for a bidentate ribonuclease in the initiation step of RNA interference[J]. Nature, 409(6818): 363-366.
[9] Bhat S S, Bielewicz D, Gulanicz T, et al.2020. mRNA adenosine methylase (MTA) deposits m⁶A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences of the USA, 117(35): 21785-21795.
[10] Bodi Z, Zhong S L, Mehra S, et al.2012. Adenosine methylation in Arabidopsis mRNA is associated with the 3' end and reduced levels cause developmental defects[J]. Frontiers in Plant Science, 3(48): 1-15.
[11] Borges F, Martienssen R A.2015. The expanding world of small RNAs in plants[J]. Nature Reviews Molecular Cell Biology, 16(12): 727-741.
[12] Brocard M, Ruggieri A, Locker N.2017. m⁶A RNA methylation, a new hallmark in virus-host interactions[J]. Journal of General Virology, 98(9): 2207-2214.
[13] Carmell M A, Hannon G J.2004. RNaseⅢ enzymes and the initiation of gene silencing[J]. Nature Structural & Molecular Biology, 11(3): 214-218.
[14] Chen S R, Liu W, Naganuma M, et al.2022. Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain[J]. Nucleic Acids Research, 50(8): 4669-4684.
[15] Duan H C, Wei L H, Zhang C, et al.2017. ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition[J]. The Plant Cell, 29(12): 2995-3011.
[16] Fan Y R, Yang J Y, Mathioni S M, et al.2016. PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice[J]. Proceedings of the National Academy of Sciences of the USA, 113(52): 15144-15149.
[17] Fu C Y, Ma C, Zhu M S, et al.2023. Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice[J]. The Plant Journal, 115(1): 139-154.
[18] Hiraguri A, Itoh R, Kondo N, et al.2005. Specific interactions between Dicer-like proteins and HYL1/DRB- family dsRNA-binding proteins in Arabidopsis thaliana[J]. Plant Molecular Biology, 57(2): 173-188.
[19] Ho T, Rusholme Pilcher R L, Edwards M-L, et al.2008. Evidence for GC preference by monocot Dicer-like proteins[J]. Biochemical and Biophysical Research Communications, 368(2): 433-437.
[20] Huang J, Li Z Y, Zhao D Z.2016. Deregulation of the OsmiR160 target gene OsARF18 causes growth and developmental defects with an alteration of auxin signaling in rice[J]. Scientific Reports, 6(1): 29938.
[21] Huang J, Wang R Q, Dai X B, et al.2019. A microRNA biogenesis-like pathway for producing phased small interfering RNA from a long non-coding RNA in rice[J]. Journal of Experimental Botany, 70(6): 1767-1774.
[22] Iwata Y, Takahashi M, Fedoroff N V, et al.2013. Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing[J]. Nucleic Acids Research, 41(19): 9129-9140.
[23] Jiang P F, Lian B, Liu C Z, et al.2020. 21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells[J]. Nature Communications, 11(1): 5191.
[24] Kapoor M, Arora R, Lama T, et al.2008. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice[J]. Bmc Genomics, 9(1): 451.
[25] Kim V N.2005. MicroRNA biogenesis: Coordinated cropping and dicing[J]. Nature Reviews Molecular Cell Biology, 6(5): 376-385.
[26] Komiya R, Ohyanagi H, Niihama M, et al.2014. Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs[J]. The Plant Journal, 78(3): 385-397.
[27] Kurihara Y, Takashi Y, Watanabe Y.2006. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis[J]. RNA, 12(2): 206-212.
[28] Kurihara Y, Watanabe Y.2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions[J]. Proceedings of the National Academy of Sciences of the USA, 101(34): 12753-12758.
[29] Li X P, Ma X C, Wang H, et al.2020. Osa-miR162a fine-tunes rice resistance to Magnaporthe oryzae and yield[J]. Rice, 13(1): 38.
[30] Liao P F, Ouyang J X, Zhang J J, et al.2019. OsDCL3b affects grain yield and quality in rice[J]. Plant Molecular Biology, 99(3): 193-204.
[31] Liu B, Chen Z Y, Song X W, et al.2007. Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development[J]. The Plant Cell, 19(9): 2705-2718.
[32] Liu B, Li P C, Li X, et al.2005. Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice[J]. Plant Physiology, 139(1): 296-305.
[33] Liu Y L, Teng C, Xia R, et al.2020. PhasiRNAs in plants: Their biogenesis, genic sources, and roles in stress responses, development, and reproduction[J]. The Plant Cell, 32(10): 3059-3080.
[34] MacRae I J, Zhou K H, Li F, et al.2006. Structural basis for double-stranded RNA processing by Dicer[J]. Science, 311(5758): 195-198.
[35] Margis R, Fusaro A F, Smith N A, et al.2006. The evolution and diversification of Dicers in plants[J]. FEBS Letters, 580(10): 2442-2450.
[36] Matzke M A, Mosher R A.2014. RNA-directed DNA methylation: An epigenetic pathway of increasing complexity[J]. Nature Reviews Genetics, 15(6): 394-408.
[37] Meijer A, Atighi M R, Demeestere K, et al.2023. Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses[J]. Plant Physiology, 193(3): 2071-2085.
[38] Meyer K D, Jaffrey S R.2017. Rethinking m⁶A readers, writers, and erasers[J]. Annual Review of Cell and Developmental Biology, 33: 319-342.
[39] Nagano H, Fukudome A, Hiraguri A, et al.2013. Distinct substrate specificities of Arabidopsis DCL3 and DCL4[J]. Nucleic Acids Research, 42(3): 1845-1856.
[40] Nigam D, Latourrette K, Garcia-Ruiz H.2020. Mutations in virus-derived small RNAs[J]. Scientific Reports, 10(1): 9540.
[41] Niu D D, Zhang X, Song X O, et al.2018. Deep sequencing uncovers rice long siRNAs and its involvement in immunity against Rhizoctonia solani[J]. Phytopathology, 108(1): 60-69.
[42] Ou-Yang F Q, Luo Q J, Zhang Y, et al.2013. Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice[J]. Functional & Integrative Genomics, 13(2): 207-216.
[43] Peng X J, Yu C, Li S B, et al.2011. Cloning and expressing an OsDCL3b gene from Oryza sativa indica[C]. 2011 International Conference on Remote Sensing, Environment and Transportation Engineering, Nanjing, pp. 8108-8111.
[44] Qiao L L, Zheng L Y, Sheng C, et al.2020. Rice siR109944 suppresses plant immunity to sheath blight and impacts multiple agronomic traits by affecting auxin homeostasis[J]. The Plant Journal, 102(5): 948-964.
[45] Qin H N, Chen F D, Huan X L, et al.2010. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction[J]. RNA, 16(3): 474-481.
[46] Raghuram B, Sheikh A H, Rustagi Y, et al.2014. MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis[J]. The FEBS Journal, 282(3): 521-536.
[47] Reshetnyak G, Jacobs J M, Auguy F, et al.2021. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection[J]. Scientific Reports, 11(1): 24141.
[48] Rogers R, Chen X M.2013. Biogenesis, turnover, and mode of action of plant microRNAs[J]. The Plant Cell, 25(7): 2383-2399.
[49] Secco D, Wang C, Shou H X, et al.2015. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements[J]. Elife, 4: e09343.
[50] Shen J Q, Liu J H, Xie K B, et al.2017. Translational repression by a miniature inverted-repeat transposable element in the 3' untranslated region[J]. Nature Communications, 8(1).
[51] Song X W, Li P C, Zhai J X, et al.2012a. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis[J]. The Plant Journal, 69(3): 462-474.
[52] Song X W, Li Y, Cao X F, et al.2019. MicroRNAs and their regulatory roles in plant-environment interactions[J]. Annual Review of Plant Biology, 70(1): 489-525.
[53] Song X W, Wang D K, Ma L J, et al.2012b. Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development[J]. The Plant Journal, 71(3): 378-389.
[54] Sun S, Zhu J M, Guo R Z, et al.2021. DNA methylation is involved in acclimation to iron-deficiency in rice (Oryza sativa)[J]. The Plant Journal, 107(3): 727-739.
[55] Ueno Y, Yoshida R, Kishi-Kaboshi M, et al.2015. Abiotic stresses antagonize the rice defence pathway through the tyrosine-dephosphorylation of OsMPK6[J]. PLOS Pathogens, 11(10): e1005231.
[56] Urayama S, Moriyama H, Aoki N, et al.2009. Knock-down of OsDCL2 in rice negatively affects maintenance of the endogenous dsRNA Virus, Oryza sativa endornavirus[J]. Plant and Cell Physiology, 51(1): 58-67.
[57] Voinnet O.2009. Origin, biogenesis, and activity of plant microRNAs[J]. Cell, 136(4): 669-687.
[58] Wang Q, Xue Y, Zhang L X, et al.2021. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation[J]. Science, 374(6571): 1152-1157.
[59] Wang T, You L, Li R, et al.2016. Cloning, identification, and expression analysis of a Dicer-Like gene family from Solanum lycopersicum[J]. Biologia Plantarum, 60(3): 410-418.
[60] Wang Y, Qiao R, Wei C H, et al.2019. Rice dwarf virus small RNA profiles in rice and leafhopper reveal distinct patterns in cross-kingdom hosts[J]. Viruses, 11(9): 847.
[61] Wei L Y, Gu L F, Song X W, et al.2014. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice[J]. Proceedings of the National Academy of Sciences of the USA, 111(10): 3877-3882.
[62] Wei X B, Ke H H, Wen A J, et al.2021. Structural basis of microRNA processing by Dicer-like 1[J]. Nature Plants, 7(10): 1389-1396.
[63] Williams G D, Gokhale N S, Horner S M.2019. Regulation of viral infection by the RNA modification N6-methyladenosine[J]. Annual Review of Virology, 6: 235-253.
[64] Wu J G, Yang Z R, Wang Y, et al.2015. Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA[J]. Elife, 4: e05733.
[65] Wu L, Zhang Q Q, Zhou H Y, et al.2009. Rice microRNA effector complexes and targets[J]. The Plant Cell, 21(11): 3421-3435.
[66] Wu L, Zhou H Y, Zhang Q Q, et al.2010. DNA methylation mediated by a microRNA pathway[J]. Molecular Cell, 38(3): 465-475.
[67] Xu D L, Zhou G H.2017. Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation[J]. Virology Journal, 14(1): 27.
[68] Yan F, Zhang H M, Adams M J, et al.2010. Characterization of siRNAs derived from Rice stripe virus in infected rice plants by deep sequencing[J]. Archives of Virology, 155(6): 935-940.
[69] Yan Y S, Zhang Y M, Yang K, et al.2011. Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice[J]. The Plant Journal, 65(5): 820-828.
[70] Yang Y, Zhong J, Ouyang Y D, et al.2013. The integrative expression and co-expression analysis of the AGO gene family in rice[J]. Gene, 528(2): 221-235.
[71] Yang Z R, Li Y.2018. Dissection of RNAi-based antiviral immunity in plants[J]. Current Opinion in Virology, 32: 88-99.
[72] Yin S, Chen Y D, Chen Y C, et al.2023. Genome-wide profiling of rice Double-stranded RNA-Binding Protein 1-associated RNAs by targeted RNA editing[J]. Plant Physiology, 192(2): 805-820.
[73] Yu Y, Jia T R, Chen X M2017. The 'how' and 'where' of plant microRNA[J]. New Phytologist, 216(4): 1002-1017.
[74] Yuan Z D, Pan J H, Chen C P, et al.2022. DRB2 modulates leaf rolling by regulating accumulation of microRNAs related to leaf development in rice[J]. International Journal of Molecular Sciences, 23(19): 11147.
[75] Zhang D D, Liu M X, Tang M Z, et al.2015. Repression of microRNA biogenesis by silencing of OsDCL1 activates the basal resistance to Magnaporthe oryzae in rice[J]. Plant Science, 237: 24-32.
[76] Zhang F, Zhang Y C, Liao J Y, et al.2019. The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice[J]. PLOS Genetics, 15(5): e1008120.
[77] Zhang H D, Kolb F A, Jaskiewicz L, et al.2004. Single processing center models for human Dicer and bacterial RNase Ⅲ[J]. Cell, 118(1): 57-68.
[78] Zhang K, Zhuang X J, Dong Z Z, et al.2021. The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses[J]. Genome Biology, 22(1): 189.
[79] Zhang Y C, Lei M Q, Zhou Y F, et al.2020. Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice[J]. Nature Communications, 11(1): 6031.
[80] Zhang Z Y, Li J H, Li F, et al.2017. OsMAPK3 phosphorylates OsbHLH002/OsICE1 and inhibits its ubiquitination to activate OsTPP1 and enhances rice chilling tolerance[J]. Developmental Cell, 43(6): 731-743.
[81] Zheng L J, Zhang C, Shi C N, et al.2017. Rice stripe virus NS3 protein regulates primary miRNA processing through association with the miRNA biogenesis factor OsDRB1 and facilitates virus infection in rice[J]. PLOS Pathogens, 13(10): e1006662.