Abstract
microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that an RNA-binding protein MOS2 binds to pri-miRNAs and is involved in efficient processing of pri-miRNAs. MOS2 does not interact with HYL1, SE, and DCL1 and is not localized in D-bodies. Interestingly, in the absence of MOS2, the recruitment of pri-miRNAs by HYL1 is greatly reduced and the localization of HYL1 in D-bodies is compromised. These data suggest that MOS2 promotes pri-miRNA processing through facilitating the recruitment of pri-miRNAs by the Dicing complexes.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
Accession codes
References
Carthew RW, Sontheimer EJ . Origins and mechanisms of miRNAs and siRNAs. Cell 2009; 136:642–655.
Kim VN . MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005; 6:376–385.
Kurihara Y, Watanabe Y . Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA. 2004; 101:12753–12758.
Kurihara Y, Takashi Y, Watanabe Y . The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 2006; 12:206–212.
Park W, Li J, Song R, Messing J, Chen X . CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 2002; 12:1484–1495.
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP . MicroRNAs in plants. Genes Dev 2002; 16:1616–1626.
Laubinger S, Sachsenberg T, Zeller G, et al. Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci USA 2008; 105: 8795–8800.
Kim S, Yang JY, Xu J, Jang IC, Prigge MJ, Chua NH . Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol 2008; 49:1634–1644.
Gregory BD, O'Malley RC, Lister R, et al. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 2008; 14:854–866.
Yu B, Bi L, Zheng B, et al. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA. 2008; 105:10073–10078.
Han MH, Goud S, Song L, Fedoroff N . The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci USA 2004; 101:1093–1098.
Vazquez F, Gasciolli V, Crete P, Vaucheret H . The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol 2004; 14:346–351.
Grigg SP, Canales C, Hay A, Tsiantis M . SERRATE coordinates shoot meristem function and leaf axial patterning in Arabidopsis. Nature 2005; 437:1022–1026.
Lobbes D, Rallapalli G, Schmidt DD, Martin C, Clarke J . SERRATE: a new player on the plant microRNA scene. EMBO Rep 2006; 7:1052–1058.
Song L, Han MH, Lesicka J, Fedoroff N . Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body. Proc Natl Acad Sci USA 2007; 104:5437–5442.
Fang Y, Spector DL . Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol 2007; 17:818–823.
Dong Z, Han MH, Fedoroff N . The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci USA 2008; 105:9970–9975.
Manavella PA, Hagmann J, Ott F, et al. Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 2012; 151:859–870.
Li J, Yang Z, Yu B, Liu J, Chen X . Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 2005; 15:1501–1507.
Yu B, Yang Z, Li J, et al. Methylation as a crucial step in plant microRNA biogenesis. Science 2005; 307:932–935.
Mi S, Cai T, Hu Y, et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 2008; 133:116–127.
Qi Y, Denli AM, Hannon GJ . Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 2005; 19:421–428.
Baumberger N, Baulcombe DC . Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA. 2005; 102:11928–11933.
Vaucheret H, Vazquez F, Crete P, Bartel DP . The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 2004; 18:1187–1197.
Iki T, Yoshikawa M, Meshi T, Ishikawa M . Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J 2011; 31:267–278.
Iki T, Yoshikawa M, Nishikiori M, et al. In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Mol Cell 2010; 39:282–291.
Smith MR, Willmann MR, Wu G, et al. Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proc Natl Acad Sci USA 2009; 106:5424–5429.
Wang W, Ye R, Xin Y et al. An importin β protein negatively regulates microRNA activity in Arabidopsis. Plant Cell 2011; 23:3565–3576.
Voinnet O . Origin, biogenesis, and activity of plant microRNAs. Cell 2009; 136:669–687.
Wu L, Zhou H, Zhang Q, et al. DNA methylation mediated by a microRNA pathway. Mol Cell 2010; 38:465–475.
Zhang Y, Cheng YT, Bi D, Palma K, Li X . MOS2, a protein containing G-patch and KOW motifs, is essential for innate immunity in Arabidopsis thaliana. Curr Biol 2005; 15:1936–1942.
Baulcombe D . RNA silencing in plants. Nature 2004; 431:356–363.
Morel JB, Godon C, Mourrain P, et al. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 2002; 14:629–639.
Allen RS, Li J, Stahle MI, Dubroué A, Gubler F, Millar AA . Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc Natl Acad Sci USA. 2007; 104:16371–16376.
Dugas DV, Bartel B . Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol Biol 2008; 67:403–417.
Yang L, Liu Z, Lu F, Dong A, Huang H . SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 2006; 47:841–850.
Hiraguri A, Itoh R, Kondo N, et al. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol Biol 2005; 57:173–188.
Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA . Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure 2010; 18:594–605.
Navarro L, Dunoyer P, Jay F, et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006; 312:436–439.
Li Y, Zhang Q, Zhang J, Wu L, Qi Y, Zhou JM . Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol 2010; 152:2222–2231.
Fukudome A, Kanaya A, Egami M, et al. Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4. RNA 2011; 17:750–760.
Nakazawa Y, Hiraguri A, Moriyama H, Fukuhara T . The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway. Plant Mol Biol 2007; 63:777–785.
Adenot X, Elmayan T, Lauressergues D, et al. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol 2006; 16:927–932.
Ren G, Xie M, Dou Y, Zhang S, Zhang C, Yu B . Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci USA. 2012; 109:12817–12821.
Aksaas AK, Larsen AC, Rogne M, Rosendal K, Kvissel AK, Skålhegg BS . G-patch domain and KOW motifs-containing protein, GPKOW; a nuclear RNA-binding protein regulated by protein kinase A. J Mol Signal 2011; 6: 10.
Piano F, Schetter AJ, Morton DG, et al. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol 2002; 12:1959–1964.
Clough SJ, Bent AF . Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 1998; 16:735–743.
Trapnell C, Pachter L, Salzberg SL . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105–1111.
Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511–515.
Yoo SD, Cho YH, Sheen J . Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2007; 2:1565–1572.
Wierzbicki AT, Haag JR, Pikaard CS . Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008; 135:635–648.
Acknowledgements
We thank Dr Anthony Millar (The Australian National University, Australian) for pMIR159b::GUS, Dr Bonnie Bartel (Rice University, USA) for pMIR398c::GUS and Dr H Vaucheret (Institut National de la Recherche Agronomique, France) for the hyl1-2 and ago1-25 mutants. This work was supported in part by China National Funds for Distinguished Young Scientists (31225015) and National Basic Research Program of China (2012CB910900) to Y Q.
Author information
Authors and Affiliations
Corresponding author
Additional information
( Supplementary information is linked to the online version of the paper on the Cell Research website.)
Supplementary information
Supplementary information, Table S1
Genes that are downregulated in the mos2-2 mutant (XLS 110 kb)
Supplementary information, Table S2
Genes that are upregulated in the mos2-2 mutant (XLS 42 kb)
Supplementary information, Table S3
Primers and probes (XLS 40 kb)
Supplementary information, Figure S1
Complementation of mos2-2 with p35S::FLAG-MOS2 transgene. (PDF 219 kb)
Supplementary information, Figure S2
Localization of MOS-YFP and HYL1-YFP in the root cells of transgenic plants expressing the YFP fusion proteins under the control of their native promoters. (PDF 273 kb)
Supplementary information, Figure S3
Detection of interactions between DCL1, HYL1, and SE in the Col-0 and mos2-2 cells. (PDF 467 kb)
Supplementary information, Figure S4
Diagrams that show the positions of primers in the pri-miRNA sequences. (PDF 231 kb)
Rights and permissions
About this article
Cite this article
Wu, X., Shi, Y., Li, J. et al. A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis. Cell Res 23, 645–657 (2013). https://doi.org/10.1038/cr.2013.23
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/cr.2013.23
Keywords
This article is cited by
-
MicroRNAs modulating nutrient homeostasis: a sustainable approach for developing biofortified crops
Protoplasma (2023)
-
Understanding the evolution of miRNA biogenesis machinery in plants with special focus on rice
Functional & Integrative Genomics (2023)
-
Accumulation of DNA damage alters microRNA gene transcription in Arabidopsis thaliana
BMC Plant Biology (2022)
-
MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal
BMC Plant Biology (2022)
-
Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
Nature Communications (2022)