Distinct substrate specificities of Arabidopsis DCL3 and DCL4

Nucleic Acids Research

Volumn 42, Issue 3, 2014, Pages 1845-1856

  Nagano, Hideaki ^a   Fukudome, Akihito ^a   Hiraguri, Akihiro ^a   Moriyama, Hiromitsu ^a   Fukuhara, Toshiyuki ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; ARABIDOPSIS PROTEIN; DICER; DICER LIKE 3 PROTEIN; DICER LIKE 4 PROTEIN; DOUBLE STRANDED RNA; PHOSPHATE; POTASSIUM CHLORIDE; SMALL INTERFERING RNA; SODIUM CHLORIDE; UNCLASSIFIED DRUG; URIDINE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME PHOSPHORYLATION; ENZYME SPECIFICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN RNA BINDING; RNA CLEAVAGE;

ADENOSINE; ARABIDOPSIS PROTEINS; PHOSPHORYLATION; RIBONUCLEASE III; RNA CLEAVAGE; RNA, DOUBLE-STRANDED; SUBSTRATE SPECIFICITY; URIDINE;

EID: 84896727803     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1077     Document Type: Article

References (40)

1. Hamilton, A.J. and Baulcombe, D.C. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950-952.
2. Zamore, P.D., Tuschl, T., Sharp, P.A. and Bartel, D.P. (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25-33.
3. Bernstein, E., Caudy, A.A., Hammond, S.M. and Hannon, G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363-366.
4. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
5. Ketting, R.F., Fischer, S.E., Bernstein, E., Sijen, T., Hannon, G.J. and Plasterk, R.H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev., 15, 2654-2659.
6. 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.
7. Liu, Q., Rand, T.A., Kalidas, S., Du, F., Kim, H.E., Smith, D.P. and Wang, X. (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921-1925.
8. Colmenares, S.U., Buker, S.M., Buhler, M., Dlakic, M. and Moazed, D. (2007) Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol. Cell, 27, 449-461.
9. MacRae, I.J., Zhou, K. and Doudna, J.A. (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat. Struct. Mol. Biol., 14, 934-940.
10. Elbashir, S.M., Lendeckel, W. and Tuschl, T. (2001) RNA interference is mediated by 21-And 22-nucleotide RNAs. Genes Dev., 15, 188-200.
11. Zhang, H., Kolb, F.A., Jaskiewicz, L., Westhof, E. and Filipowicz, W. (2004) Single processing center models for human Dicer and bacterial RNase III. Cell, 118, 57-68.
12. Macrae, I.J., Zhou, K., Li, F., Repic, A., Brooks, A.N., Cande, W.Z., Adams, P.D. and Doudna, J.A. (2006) Structural basis for doublestranded RNA processing by Dicer. Science, 311, 195-198.
13. Ye, X., Paroo, Z. and Liu, Q. (2007) Functional anatomy of the Drosophila microRNA-generating enzyme. J. Biol. Chem., 282, 28373-28378.
14. Lee, Y.S., Nakahara, K., Pham, J.W., Kim, K., He, Z., Sontheimer, E.J. and Carthew, R.W. (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell, 117, 69-81.
15. 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.
16. Park, J.E., Heo, I., Tian, Y., Simanshu, D.K., Chang, H., Jee, D., Patel, D.J. and Kim, V.N. (2011) Dicer recognizes the 5 end of RNA for efficient and accurate processing. Nature, 475, 201-205.
17. 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.
18. Mukherjee, K., Campos, H. and Kolaczkowski, B. (2013) Evolution of animal and plant Dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. Mol. Biol. Evol., 30, 627-641.
19. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
20. Xie, Z., Johansen, L.K., Gustafson, A.M., Kasschau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E. and Carrington, J.C. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol., 2, e104.
21. Vaucheret, H. (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev., 20, 759-771.
22. Blevins, T., Rajeswaran, R., Shivaprasad, P.V., Beknazariants, D., Si-Ammour, A., Park, H.S., Vazquez, F., Robertson, D., Meins, F. Jr, Hohn, T. et al. (2006) Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res., 34, 6233-6246.
23. Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K.D., Carrington, J.C. and Voinnet, O. (2006) Hierarchical action and inhibition of plant DICER-LIKE proteins in antiviral defense. Science, 313, 68-71.
24. Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J. and Jacobsen, S.E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet., 38, 721-725.
25. Qu, F., Ye, X. and Morris, T.J. (2008) Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc. Natl Acad. Sci. USA, 105, 14732-14737.
26. Hamilton, A., Voinnet, O., Chappell, L. and Baulcombe, D. (2002) Two classes of short interfering RNA in RNA silencing. EMBO J., 21, 4671-4679.
27. Siomi, H. and Siomi, M.C. (2009) On the road to reading the RNA-interference code. Nature, 457, 396-404.
28. Tang, G., Reinhart, B.J., Bartel, D.P. and Zamore, P.D. (2003) A biochemical framework for RNA silencing in plants. Genes Dev., 17, 49-63.
29. Qi, Y., Denli, A.M. and Hannon, G.J. (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell, 19, 421-428.
30. 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.
31. Fukudome, A., Kanaya, A., Egami, M., Nakazawa, Y., Hiraguri, A., Moriyama, H. and Fukuhara, T. (2011) Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNAcleaving activity of Arabidopsis Dicer-like 4. RNA, 17, 750-760.
32. Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A. and Carrington, J.C. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol., 5, e57.
33. Mimura, T., Dietz, K.J., Kaiser, W., Schramm, M.J., Kaiser, G. and Heber, U. (1990) Phosphate transport across biomembranes and cytosolic phosphate homeostasis in barley leaves. Planta, 180, 139-146.
34. Szittya, G., Silhavy, D., Molnár, A., Havelda, Z., Lovas, A., Lakatos, L., Bánfalvi, Z. and Burgyán, J. (2003) Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation. EMBO J., 22, 633-640.
35. Haag, J.R., Ream, T.S., Marasco, M., Nicora, C.D., Norbeck, A.D., Pasa-Tolic, L. and Pikaard, C.S. (2012) 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, 48, 811-818.
36. Lister, R., OMalley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. and Ecker, J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
37. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C. et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 50 terminal nucleotide. Cell, 133, 116-127.
38. Takeda, A., Iwasaki, S., Watanabe, T., Utsumi, M. and Watanabe, Y. (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol., 49, 493-500.
39. Havecker, E.R., Wallbridge, L.M., Hardcastle, T.J., Bush, M.S., Kelly, K.A., Dunn, R.M., Schwach, F., Doonan, J.H. and Baulcombe, D.C. (2010) The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell, 22, 321-334.
40. Hiraguri, A., Itoh, R., Kondo, N., Nomura, Y., Aizawa, D., Murai, Y., Koiwa, H., Seki, M., Shinozaki, K. and Fukuhara, T. (2005) Specific interactions between Dicer-like proteins and HYL1/DRB family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol. Biol., 57, 173-188.