Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing

Nucleic Acids Research

Volumn 41, Issue 19, 2013, Pages 9129-9140

  Iwata, Yuji ^a,b   Takahashi, Masateru ^a   Fedoroff, Nina V ^a   Hamdan, Samir M ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b Osaka Prefecture University   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; DICER LIKE 1 PROTEIN; JAGGED1; MICRORNA; RECOMBINANT PROTEIN; RNA; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

AMINO TERMINAL SEQUENCE; ARABIDOPSIS; ARTICLE; BACULOVIRUS EXPRESSION SYSTEM; IN VITRO STUDY; INSECT CELL; IONIC STRENGTH; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; RNA BINDING; RNA CLEAVAGE; RNA PROCESSING; RNA SPLICING;

ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CALCIUM-BINDING PROTEINS; CELL CYCLE PROTEINS; GENE EXPRESSION REGULATION, PLANT; INTERCELLULAR SIGNALING PEPTIDES AND PROTEINS; MEMBRANE PROTEINS; MICRORNAS; OSMOLAR CONCENTRATION; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE III; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; SEQUENCE DELETION; SF9 CELLS; SPODOPTERA;

EID: 84886083746     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt667     Document Type: Article

References (43)

1. Voinnet, O. (2009) Origin, biogenesis, and activity of plant microRNAs. Cell, 136, 669-687.
2. Kim, V.N., Han, J. and Siomi, M.C. (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol, 10, 126-139.
3. Han, M.H., Goud, S., Song, L. and Fedoroff, N. (2004) The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl Acad. Sci. USA, 101, 1093-1098.
4. Lobbes, D., Rallapalli, G., Schmidt, D.D., Martin, C. and Clarke, J. (2006) SERRATE: a new player on the plant microRNA scene. EMBO Rep., 7, 1052-1058.
5. Yang, L., Liu, Z., Lu, F., Dong, A. and Huang, H. (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J., 47, 841-850.
6. Vazquez, F., Gasciolli, V., Crete, P. and Vaucheret, H. (2004) The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol., 14, 346-351.
7. Fang, Y. and Spector, D.L. (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr. Biol., 17, 818-823.
8. Fujioka, Y., Utsumi, M., Ohba, Y. and Watanabe, Y. (2007) Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol., 48, 1243-1253.
9. Kurihara, Y., Takashi, Y. and Watanabe, Y. (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA, 12, 206-212.
10. Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J.U., Ratsch, G. and Weigel, D. (2008) Dual roles of the nuclear capbinding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 105, 8795-8800.
11. Yu, B., Bi, L., Zheng, B., Ji, L., Chevalier, D., Agarwal, M., Ramachandran, V., Li, W., Lagrange, T., Walker, J.C. et al. (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl Acad. Sci. USA, 105, 10073-10078.
12. Kim, S., Yang, J.Y., Xu, J., Jang, I.C., Prigge, M.J. and Chua, N.H. (2008) Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol., 49, 1634-1644.
13. Li, J., Yang, Z., Yu, B., Liu, J. and Chen, X. (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol., 15, 1501-1507.
14. Park, M.Y., Wu, G., Gonzalez-Sulser, A., Vaucheret, H. and Poethig, R.S. (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl Acad. Sci. USA, 102, 3691-3696.
15. Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R. and Chen, X. (2005) Methylation as a crucial step in plant microRNA biogenesis. Science, 307, 932-935.
16. Chaabane, S.B., Liu, R., Chinnusamy, V., Kwon, Y., Park, J.H., Kim, S.Y., Zhu, J.K., Yang, S.W. and Lee, B.H. (2012) STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res., 41, 1984-1997.
17. Ren, G., Xie, M., Dou, Y., Zhang, S., Zhang, C. and Yu, B. (2012) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc. Natl Acad. Sci. USA, 109, 12817-12821.
18. Han, J., Lee, Y., Yeom, K.H., Nam, J.W., Heo, I., Rhee, J.K., Sohn, S.Y., Cho, Y., Zhang, B.T. and Kim, V.N. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell, 125, 887-901.
19. Song, L., Axtell, M.J. and Fedoroff, N.V. (2010) RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr. Biol., 20, 37-41.
20. Werner, S., Wollmann, H., Schneeberger, K. and Weigel, D. (2010) Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr. Biol., 20, 42-48.
21. Mateos, J.L., Bologna, N.G., Chorostecki, U. and Palatnik, J.F. (2010) Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Curr. Biol., 20, 49-54.
22. Addo-Quaye, C., Snyder, J.A., Park, Y.B., Li, Y.F., Sunkar, R. and Axtell, M.J. (2009) Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA, 15, 2112-2121.
23. Bologna, N.G., Mateos, J.L., Bresso, E.G. and Palatnik, J.F. (2009) A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J, 28, 3646-3656.
24. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev, 16, 1616-1626.
25. Kurihara, Y. and Watanabe, Y. (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. USA, 101, 12753-12758.
26. Yang, S.W., Chen, H.Y., Yang, J., Machida, S., Chua, N.H. and Yuan, Y.A. (2010) Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure, 18, 594-605.
27. Wu, F., Yu, L., Cao, W., Mao, Y., Liu, Z. and He, Y. (2007) The N-terminal double-stranded RNA binding domains of Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing. Plant Cell, 19, 914-925.
28. Machida, S., Chen, H.Y. and Adam Yuan, Y. (2011) Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE. Nucleic Acids Res., 39, 7828-7836.
29. Dong, Z., Han, M.H. and Fedoroff, N. (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc. Natl Acad. Sci. USA, 105, 9970-9975.
30. Schneider, C.A., Rasband, W.S. and Eliceiri, K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat. Methods, 9, 671-675.
31. Prigge, M.J. and Wagner, D.R. (2001) The arabidopsis serrate gene encodes a zinc-finger protein required for normal shoot development. Plant Cell, 13, 1263-1279.
32. Myong, S., Cui, S., Cornish, P.V., Kirchhofer, A., Gack, M.U., Jung, J.U., Hopfner, K.P. and Ha, T. (2009) Cytosolic viral sensor RIG-I is a 5′-triphosphate-dependent translocase on double-stranded RNA. Science, 323, 1070-1074.
33. Cenik, E.S., Fukunaga, R., Lu, G., Dutcher, R., Wang, Y., Tanaka Hall, T.M. and Zamore, P.D. (2011) Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol. Cell, 42, 172-184.
34. Welker, N.C., Maity, T.S., Ye, X., Aruscavage, P.J., Krauchuk, A.A., Liu, Q. and Bass, B.L. (2011) Dicer's helicase domain discriminates dsRNA termini to promote an altered reaction mode. Mol. Cell, 41, 589-599.
35. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B. and Radmark, O. (2002) Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864-5874.
36. Zhang, H., Kolb, F.A., Brondani, V., Billy, E. and Filipowicz, W. (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875-5885.
37. Gregory, R.I., Chendrimada, T.P., Cooch, N. and Shiekhattar, R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123, 631-640.
38. Jinek, M. and Doudna, J.A. (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature, 457, 405-412.
39. Tsutsumi, A., Kawamata, T., Izumi, N., Seitz, H. and Tomari, Y. (2011) Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat. Struct. Mol. Biol., 18, 1153-1158.
40. Liu, C., Axtell, M.J. and Fedoroff, N.V. (2012) The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis. Plant Physiol., 159, 748-758.
41. Wang, L., Song, X., Gu, L., Li, X., Cao, S., Chu, C., Cui, X., Chen, X. and Cao, X. (2013) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis. Plant Cell, 25, 715-727.
42. Gruber, J.J., Zatechka, D.S., Sabin, L.R., Yong, J., Lum, J.J., Kong, M., Zong, W.X., Zhang, Z., Lau, C.K., Rawlings, J. et al. (2009) Ars2 links the nuclear cap-binding complex to RNA interference and cell proliferation. Cell, 138, 328-339.
43. Sabin, L.R., Zhou, R., Gruber, J.J., Lukinova, N., Bambina, S., Berman, A., Lau, C.K., Thompson, C.B. and Cherry, S. (2009) Ars2 regulates both miRNA- and siRNA-dependent silencing and suppresses RNA virus infection in Drosophila. Cell, 138, 340-351.