Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum

Gene

Volumn 501, Issue 1, 2012, Pages 52-62

  Bai, Miao ^a   Yang, Guo Shun ^a   Chen, Wen Ting ^a   Mao, Zhen Chuan ^b,c   Kang, Hou Xiang ^b,c   Chen, Guo Hua ^b   Yang, Yu Hong ^b,c   Xie, Bing Yan ^b,c  

^a HUNAN AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

Author keywords

MicroRNA; Phylogenetic analysis; RNA silencing; Tomato yellow leaf curl virus

Indexed keywords

ARGONAUTE PROTEIN; DICER; MICRORNA; RNA DIRECTED RNA POLYMERASE;

ABIOTIC STRESS; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE EXPRESSION; GENE SILENCING; GENE STRUCTURE; GENOME; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT VIRUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TOMATO; TOMATO YELLOW LEAF CURL VIRUS; VIRUS INFECTION;

AMINO ACID SEQUENCE; ARGONAUTE PROTEINS; CHROMOSOME MAPPING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; RIBONUCLEASE III; RNA REPLICASE; SEQUENCE HOMOLOGY, AMINO ACID; SOLANUM; STRESS, PHYSIOLOGICAL;

DICOTYLEDONEAE; LYCOPERSICON ESCULENTUM; TOMATO YELLOW LEAF CURL VIRUS;

EID: 84860552254     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.02.009     Document Type: Article

References (52)

1. Akbergenov R., et al. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res. 2006, 2:462-471.
2. Antignus Y., Cohen S. Cloning of tomato yellow leaf curl virus (TYLCV) and the complete nucleotide sequence of a mild infectious clone. Phytopathology 1994, 707-712.
3. Aoki K., et al. Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics 2010, 210.
4. Baumberger N., Baulcombe D.C. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. PNAS 2005, 33:11928-11933.
5. Borges F., Pereira P.A., Slotkin R.K., Martienssen R.A., Becker J.D. MicroRNA activity in the Arabidopsis male germline. J. Exp. Bot. 2011, 5:1611.
6. Brodersen P., et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008, 5880:1185-1190.
7. Curaba J., Chen X. Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. J. Biol. Chem. 2008, 6:3059.
8. Czosnek H., Laterrot H. A worldwide survey of tomato yellow leaf curl viruses. Arch. Virol. 1997, 7:1391-1406.
9. Díaz-Pendón J.A., Ding S.-W. Direct and indirect roles of viral suppressors of RNA silencing in pathogenesis. Annu. Rev. Phytopathol. 2008, 1:303-326.
10. Deleris A., Gallego-Bartolome J., Bao J., Kasschau K.D., Carrington J.C., Voinnet O. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 2006, 5783:68-71.
11. Diaz-Pendon J.A., Li F., Li W.X., Ding S.W. Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 2007, 6:2053-2063.
12. Ding S.-W. RNA-based antiviral immunity. Nat. Rev. Immunol. 2010, 9:632-644.
13. Donaire L., Barajas D., Martinez-Garcia B., Martinez-Priego L., Pagan I., Llave C. Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs. J. Virol. 2008, 11:5167-5177.
14. Fagard M., Boutet S., Morel J.B., Bellini C., Vaucheret H. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl. Acad. Sci. India A 2000, 21:11650.
15. Finn R.D., et al. The Pfam protein families database. Nucleic Acids Res. 2011, 1-12.
16. Fukudome A., et al. Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4. RNA 2011, 4:750.
17. Fusaro A.F., et al. RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep. 2006, 11:1168-1175.
18. Gasciolli V., Mallory A.C., Bartel D.P., Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 2005, 16:1494-1500.
19. Gu Z., Cavalcanti A., Chen F.C., Bouman P., Li W.H. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 2002, 3:256-262.
20. Harvey J.J.W., et al. An antiviral defense role of AGO2 in plants. PLoS One 2011, 1:e14639.
21. Hutvagner G., Simard M.J. Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 2008, 1:22-32.
22. Kapoor M., et al. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 2008, 451.
23. Kasschau K.D., et al. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007, 3:e57.
24. Kimura S., Sinha N. Tomato (Solanum lycopersicum): A Model Fruit-Bearing Crop. Cold Spring Harb Protoc. 2008, 11:1-9.
25. Kurihara Y., Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. PNAS 2004, 34:12753-12758.
26. Llave C. Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci. 2010, 12:701-707.
27. Lu C., et al. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 2006, 10:1276-1288.
28. Lund E. Nuclear export of MicroRNA precursors. Science 2004, 5654:95-98.
29. MacRae I.J., Doudna J.A. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr. Opin. Struct. Biol. 2007, 1:138-145.
30. Mallory A., Vaucheret H. Form, function, and regulation of ARGONAUTE proteins. Plant Cell 2010, 12:3879-3889.
31. Manavella P.A., Weigel D., Wu L. Argonaute10 as a miRNA locker. Cell 2011, 2:173-174.
32. Margis R., et al. The evolution and diversification of Dicers in plants. FEBS Lett. 2006, 10:2442-2450.
33. Montgomery T.A., et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 2008, 1:128-141.
34. Mueller L.A., et al. The tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL). Comp. Funct. Genom. 2005, 3:153-158.
35. Mueller L.A.L., et al. A snapshot of the emerging tomato genome sequence. Plant Genome 2009, 1:78-92.
36. Qi X., Bao F.S., Xie Z. Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS One 2009, 3:356-363.
37. Qi Y., Denli A.M., Hannon G.J. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 2005, 3:421-428.
38. Qian Y., Cheng Y., Cheng X., Jiang H., Zhu S., Cheng B. Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize. Plant Cell Rep. 2011, 1-17.
39. Raja P., Sanville B.C., Buchmann R.C., Bisaro D.M. Viral genome methylation as an epigenetic defense against geminiviruses. J. Virol. 2008, 18:8997-9007.
40. Schiebel W., et al. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 1998, 12:2087-2101.
41. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 8:1596-1599.
42. Vaistij F.E., Jones L. Compromised virus-induced gene silencing in RDR6-deficient plants. Plant Physiol. 2009, 3:1399-1407.
43. Vaucheret H. Plant Argonautes. Trends Plant Sci. 2008, 7:350-358.
44. Vaucheret H., Vazquez F., Crete P., Bartel D.P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 2004, 10:1187-1197.
45. Wang X.B., et al. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. PNAS 2010, 1:484-489.
46. Xie Z., Allen E., Wilken A., Carrington J.C. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. PNAS 2005, 36:12984-12989.
47. Xie Z., Fan B., Chen C., Chen Z. An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense. PNAS 2001, 11:6516-6521.
48. Xie Z., et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004, 642-652.
49. Yoshikawa M., Peragine A., Park M.Y., Poethig R.S. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Gene Dev. 2005, 18:2164.
50. Yu D., Fan B., MacFarlane S.A., Chen Z. Analysis of the involvement of an inducible Arabidopsis RNA-dependent RNA polymerase in antiviral defense. Mol. Plant Microbe Interact. 2003, 3:206-216.
51. Zhang H., Gong H., Zhou X. Molecular characterization and pathogenicity of tomato yellow leaf curl virus in China. Virus Genes 2009, 2:249-255.
52. Zhu H., et al. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 2011, 2:242-256.