A single dicer gene is required for efficient gene silencing associated with two classes of small antisense RNAs in mucor circinelloides

Eukaryotic Cell

Volumn 8, Issue 10, 2009, Pages 1486-1497

  De Haro, Juan P ^a   Calo, Silvia ^a   Cervantes, María ^a   Nicolás, Francisco E ^a,b   Torres Martinez, Santiago ^a   Ruiz Vázquez, Rosa M ^a  

^a UNIVERSITY OF MURCIA   (Spain)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; FUNGAL PROTEIN; FUNGAL RNA; RIBONUCLEASE III; SMALL INTERFERING RNA;

ARTICLE; ENZYMOLOGY; GENETICS; METABOLISM; MUCOR; MUTATION; RNA INTERFERENCE;

FUNGAL PROTEINS; MUCOR; MUTATION; RIBONUCLEASE III; RNA INTERFERENCE; RNA, ANTISENSE; RNA, FUNGAL; RNA, SMALL INTERFERING;

FUNGI; MUCOR; MUCOR CIRCINELLOIDES;

EID: 70349696860     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.00191-09     Document Type: Article

References (39)

1. Alexander, W. G., N. B. Raju, H. Xiao, T. M. Hammond, T. D. Perdue, R. L. Metzenberg, P. J. Pukkila, and P. K. T. Shiu. 2008. DCL-I colocalizes with other components of the MSUD machinery and is required for silencing. Fungal Genet. Biol. 45:719-727.
2. Brodersen, P., and O. Voinnet. 2006. The diversity of RNA silencing pathways in plants. Trends Genet. 22:268-280.
3. Catalanotto, C., M. Pallota, P. ReFalo, M. S. Sach, L. Vaysie, G. Macino, and C. Cogoni. 2004. Redundancy of the two dicer genes in transgene induced posttranscriptional gene silencing in Neurospora crassa. Mol. Cell. Biol. 24:2536-2545. (Pubitemid 38326007)
4. Choudhary, S., H. C. Lee, M. Maiti, Q. He, P. Cheng, Q. Liu, and Y. Liu. 2007. A double-stranded-RNA response program important for RNA interference efficiency. Mol. Cell. Biol. 27:3995-4005.
5. Ghildiyal, M., and P. D. Zamore. 2009. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10:94-108.
6. Goldoni, M., G. Azzalin, G. Macino, and C. Cogoni. 2004. Efficient gene silencing by expression of double stranded RNA in Neurospora crassa. Fungal Genet. Biol. 41:1016-1024.
7. Gurr, S. J., S. E. Unkles, and J. R. Kinghorn. 1987. The structure and organization of nuclear genes of filamentous fungi, p. 93-139. In J. R. Kinghorn (ed.), Gene structure in eukaryotic microbes. IRL Press, Oxford, United Kingdom.
8. Henderson, I. R., X. Zhang, C. Lu, L. Johnson, B. C. Meyers, P. J. Green, and S. E. Jacobsen. 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 38:721-725.
9. Jaskiewicz, L., and W. Filipowicz. 2008. Role of Dicer in posttranscriptional RNA silencing. Curr. Top. Microbiol. Immunol. 320:77-97.
10. Kadotani, N., H. Nakayashiki, Y. Tosa, and S. Mayama. 2004. One of the two Dicer-like proteins in the filamentous fungi Magnaporthe oryzae genome is responsible for hairpin RNA-triggered RNA silencing and related small interfering RNA accumulation. J. Biol. Chem. 279:44467-44474.
11. Lee, H. C., S. S. Chang, S. Choudhary, A. P. Aalto, M. Maiti, D. H. Bamford, and Y. Liu. 2009. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459:274-278.
12. Lee, Y. S., K. Nakahara, J. W. Pham, K. Kim, Z. He, E. J. Ontheimer, and R. W. Carthew. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117:69-81.
13. MacRae, I. J., K. Zhou, F. Li, A. Repic, A. N. Brooks, W. Z. Cande, P. D. Adams, and J. A. Doudna. 2006. Structural basis for double-stranded RNA processing by Dicer. Science 311:195-198. (Pubitemid 43108178)
14. Maiti, M., H. C. Lee, and Y. Liu. 2007. QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev. 21:590-600.
15. Michielse, C. B., K. Salim, P. Ragas, A. F. Ram, B. Kudla, B. Jarry, P. J. Punt, and C. A. van den Hondel. 2004. Development of a system for integrative and stable transformation of the zygomycete Rhizopus oryzae by Agrobacterium-mediated DNA transfer. Mol. Genet. Genomics 271:499-510.
16. Nakayashiki, H., and Q. B. Nguyen. 2008. RNA interference: roles in fungal biology. Curr. Opin. Microbiol. 11:494-502.
17. Nakayashiki, H., N. Kadotani, and S. Mayama. 2006. Evolution and diversification of RNA silencing proteins in fungi. J. Mol. Evol. 63:127-135.
18. Nicolás, F. E., S. Torres-Martínez, and R. M. Ruiz-Vázquez. 2003. Two classes of small antisense RNAs in fungal RNA silencing triggered by nonintegrative transgenes. EMBO J. 22:3983-3991. (Pubitemid 36975724)
19. Nicolás, F. E., J. P. de Haro, S. Torres-Martínez, and R. M. Ruiz-Vázquez. 2007. Mutants defective in a Mucor circinelloides dicer-like gene are not compromised in siRNA silencing but display developmental defects. Fungal Genet. Biol. 44:504-516.
20. Nicolás, F. E., S. Calo, L. Murcia-Flores, V. Garre, R. M. Ruiz-Vázquez, and S. Torres Martínez. 2008. A RING-finger photocarotenogenic repressor involved in asexual sporulation in Mucor circinelloides. FEMS Microbiol. Lett. 280:81-88.
21. Nicolás, F. E., S. Torres-Martínez, and R. M. Ruiz-Vázquez. 2009. Transcriptional activation increases RNA silencing efficiency and stability in the fungus Mucor circinelloides. J. Biotechnol. 142:123-126.
22. Ocampo, J., L. Fernandez Nunez, F. Silva, E. Pereyra, S. Moreno, V. Garre, and S. Rossi. 1 May 2009. A subunit of protein kinase A regulates growth and differentiation in the fungus Mucor circinelloides. Eukaryot. Cell, doi: 10.1128/EC.00026-09.
23. Punt, P. J., M. A. Dingemanse, A. Kuyvenhoven, R. D. Soede, P. H. Pouwels, and C. A. van der Hondel. 1990. Functional elements in the promoter region of the Aspergillus nidulans gpdA gene encoding glyceraldehyde-3-phosphate dehydrogenase. Gene 93:101-109.
24. Qi, Y., and G. J. Hannon. 2005. Uncovering RNAi mechanisms in plants: biochemistry enters the foray. FEBS Lett. 579:5899-5903. (Pubitemid 41484135)
25. Quiles-Rosillo, M. D., S. Torres-Martinez, and V. Garre. 2003. cigA, a lightinducible gene involved in vegetative growth in Mucor circinelloides is regulated by the carotenogenic repressor crgA. Fungal Genet. Biol. 38:122-132.
26. Roncero, M. I. G. 1984. Enrichment method for the isolation of auxotrophic mutants of Mucor using the polyene antibiotic N-glycosyl-polyfungin. Carlsberg Res. Commun. 49:685-690.
27. Ruiz-Pérez, V. L., F. J. Murillo, and S. Torres-Martínez. 1995. PkpA, a novel Phycomyces blakesleeanus serine/threonine protein kinase. Curr. Genet. 28: 309-316.
28. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
29. Segers, G. C., X. Zhang, F. Deng, Q. Sun, and D. L. Nuss. 2007. Evidence that RNA silencing functions as an antiviral defense mechanism in fungi. Proc. Natl. Acad. Sci. USA 104:12902-12906.
30. Shiu, P. K. T., N. B. Raju, D. Zickler, and R. L. Metzenberg. 2001. Meiotic silencing by unpaired DNA. Cell 107:905-916.
31. Siomi, H., and M. C. Siomi. 2009. On the road to reading the RNA-interference code. Nature 457:396-404.
32. Skory, C. D. 2004. Repair of plasmid DNA used for transformation of Rhizopus oryzae by gene conversion. Curr. Genet. 45:302-310.
33. Skory, C. D., and A. S. Ibrahim. 2007. Native and modified lactate dehydrogenase expression in a fumaric acid producing isolate Rhizopus oryzae 99-880. Curr. Genet. 52:23-33.
34. Smith, N. A., S. P. Singh, M. B. Wang, P. A. Stoutjesdijk. A. G. Green, and P. M. Waterhouse. 2000. Total silencing by intron-spliced hairpin RNAs. Nature 407:319-320.
35. Tomari, Y., and P. D. Zamore. 2005. Perspective: machines for RNAi. Genes Dev. 19:517-529.
36. Velayos, A., J. L. Blasco, M. I. Alvarez, E. A. Iturriaga, and A. P. Eslava. 2000. Blue-light regulation of phytoene dehydrogenase (carB) gene expression in Mucor circinelloides. Planta 210:938-946.
37. Wolff, A. M., and J. Arnau. 2002. Cloning of glyceraldehyde-3-phosphate dehydrogenase-encoding genes in Mucor circinelloides (syn. racemosus) and use of the gpdl promoter for recombinant protein production. Fungal Genet. Biol. 35:21-29.
38. Xie, Z., L. K. Johansen, A. M. Gustafson, K. D. Kasschau, A. D. Lellis, D. Zilberman, S. E. Jacobsen, and J. C. Carrington. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2:E104. (Pubitemid 39234476)
39. Zhang, X., G. C. Segers, Q. Sun, F. Deng, and D. L. Nuss. 2008. Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependent pathway. Virology 82:2613-2619.