| Structural highlights
Function
[RDR2_ARATH] RNA-dependent direct polymerase involved in the production of small interfering RNAs (siRNAs). Required for the biogenesis of endogenous siRNAs of 24 nucleotide which derive from heterochromatin and DNA repeats such as transposons or endogenous gene tandem repeats, such as repeats present in FWA gene. Involved in transcriptional gene silencing (TGS). Component of the RNA-directed DNA methylation (RdDM) silencing pathway that utilizes siRNAs to guide DNA methyltransferases to asymmetric cytosines. Involved in control of flowering time through RdDM of FWA locus. Required for reception of long-distance mRNA silencing in the shoot. Required for the formation of telomeric siRNAs and the RNA-dependent DNA methylation of asymmetric cytosines in telomeric (5'-CCCTAAA-3') repeats.[1] [2] [3] [4] [5] [6] [7] [8] [9]
Publication Abstract from PubMed
RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In Arabidopsis, RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 A, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.
Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2.,Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JC, Takagi Y, Pikaard CS Proc Natl Acad Sci U S A. 2021 Dec 21;118(51). pii: 2115899118. doi:, 10.1073/pnas.2115899118. PMID:34903670[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004 May;2(5):E104. doi: 10.1371/journal.pbio.0020104. Epub 2004 Feb, 24. PMID:15024409 doi:http://dx.doi.org/10.1371/journal.pbio.0020104
- ↑ Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science. 2005 Apr 1;308(5718):118-20. doi: 10.1126/science.1106910. Epub 2005 Feb, 3. PMID:15692015 doi:http://dx.doi.org/10.1126/science.1106910
- ↑ Ronemus M, Vaughn MW, Martienssen RA. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell. 2006 Jul;18(7):1559-74. doi: 10.1105/tpc.106.042127. Epub 2006 Jun, 23. PMID:16798886 doi:http://dx.doi.org/10.1105/tpc.106.042127
- ↑ Chan SW, Zhang X, Bernatavichute YV, Jacobsen SE. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 2006 Nov;4(11):e363. doi: 10.1371/journal.pbio.0040363. PMID:17105345 doi:http://dx.doi.org/10.1371/journal.pbio.0040363
- ↑ Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell. 2007 May;19(5):1507-21. doi: 10.1105/tpc.107.051540. Epub 2007 May, 25. PMID:17526749 doi:http://dx.doi.org/10.1105/tpc.107.051540
- ↑ Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carroll BJ. Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14741-6. doi:, 10.1073/pnas.0706701104. Epub 2007 Sep 4. PMID:17785412 doi:http://dx.doi.org/10.1073/pnas.0706701104
- ↑ Vrbsky J, Akimcheva S, Watson JM, Turner TL, Daxinger L, Vyskot B, Aufsatz W, Riha K. siRNA-mediated methylation of Arabidopsis telomeres. PLoS Genet. 2010 Jun 10;6(6):e1000986. doi: 10.1371/journal.pgen.1000986. PMID:20548962 doi:http://dx.doi.org/10.1371/journal.pgen.1000986
- ↑ Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar;6(3):344-54. doi: 10.4161/epi.6.3.14242. Epub 2011 Mar 1. PMID:21150311 doi:http://dx.doi.org/10.4161/epi.6.3.14242
- ↑ Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell. 2012 Dec 14;48(5):811-8. doi: 10.1016/j.molcel.2012.09.027. Epub 2012, Nov 8. PMID:23142082 doi:http://dx.doi.org/10.1016/j.molcel.2012.09.027
- ↑ Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JC, Takagi Y, Pikaard CS. Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2. Proc Natl Acad Sci U S A. 2021 Dec 21;118(51). pii: 2115899118. doi:, 10.1073/pnas.2115899118. PMID:34903670 doi:http://dx.doi.org/10.1073/pnas.2115899118
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