Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum)

BMC Plant Biology

Volumn 12, Issue , 2012, Pages

  Tang, She ^a   Wang, Yu ^a   Li, Zefeng ^a   Gui, Yijie ^a   Xiao, Bingguang ^b   Xie, Jiahua ^c   Zhu, Qian Hao ^d   Fan, Longjiang ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b Yunnan Academy of Tobacco Agricultural Sci and China Tobacco Breeding Research Center at Yunnan   (China)

^c NORTH CAROLINA CENTRAL UNIVERSITY   (United States)

^d CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; NICOTIANA OBTUSIFOLIA; NICOTIANA TABACUM;

MICRORNA; PLANT RNA; SMALL INTERFERING RNA;

ARTICLE; GENETICS; PLANT LEAF; PLANT ROOT; TOBACCO;

MICRORNAS; PLANT LEAVES; PLANT ROOTS; RNA, PLANT; RNA, SMALL INTERFERING; TOBACCO;

EID: 84862809328     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-12-28     Document Type: Article

References (62)

1. Zamore PD, Haley B. Ribo-gnome: the big world of small RNAs. Science 2005, 309(5740):1519-1524. 10.1126/science.1111444, 16141061.
2. Vazquez F. Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci 2006, 11(9):460-468. 10.1016/j.tplants.2006.07.006, 16893673.
3. Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev 2007, 21(23):3123-3134. 10.1101/gad.1595107, 2081978, 18003861.
4. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
5. Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet 2006, 38(Suppl):S31-S36.
6. Willmann MR, Poethig RS. Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 2007, 10(5):503-511. 10.1016/j.pbi.2007.07.004, 2080797, 17709279.
7. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23(20):4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
8. Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O. In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev 2004, 18(18):2237-2242. 10.1101/gad.307804, 517516, 15371337.
9. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002, 16(13):1616-1626. 10.1101/gad.1004402, 186362, 12101121.
10. Kurihara Y, Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 2004, 101(34):12753-12758. 10.1073/pnas.0403115101, 515125, 15314213.
11. Zhang X, Zhao H, Gao S, Wang WC, Katiyar-Agarwal S, Huang HD, Raikhel N, Jin H. Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(*)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. Mol Cell 2011, 42(3):356-366. 10.1016/j.molcel.2011.04.010, 21549312.
12. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 2006, 57:19-53. 10.1146/annurev.arplant.57.032905.105218, 16669754.
13. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JD. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312(5772):436-439. 10.1126/science.1126088, 16627744.
14. Chen X. Small RNAs - secrets and surprises of the genome. Plant J 2010, 61(6):941-958. 10.1111/j.1365-313X.2009.04089.x, 3062250, 20409269.
15. Khraiwesh B, Zhu JK, Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 2011,
16. Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2003, 15(11):2730-2741. 10.1105/tpc.016238, 280575, 14555699.
17. Chen XM. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303(5666):2022-2025. 10.1126/science.1088060, 12893888.
18. Zhu QH, Helliwell CA. Regulation of flowering time and floral patterning by miR172. J Exp Bot 2011, 62(2):487-495. 10.1093/jxb/erq295, 20952628.
19. Achard P, Herr A, Baulcombe DC, Harberd NP. Modulation of floral development by a gibberellin-regulated microRNA. Development 2004, 131(14):3357-3365. 10.1242/dev.01206, 15226253.
20. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121(2):207-221. 10.1016/j.cell.2005.04.004, 15851028.
21. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 2004, 18(19):2368-2379. 10.1101/gad.1231804, 522987, 15466488.
22. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 2004, 16(1):69-79. 10.1016/j.molcel.2004.09.028, 15469823.
23. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 2008, 18(9):1456-1465. 10.1101/gr.075572.107, 2527712, 18687877.
24. Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V, Sundaresan V, Vance V, Bowman LH. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 2009, 19(8):1429-1440. 10.1101/gr.089854.108, 2720183, 19584097.
25. Benowitz NL. Pharmacology of nicotine: addiction, smoking-induced disease, and therapeutics. Annu Rev Pharmacol Toxicol 2009, 49:57-71. 10.1146/annurev.pharmtox.48.113006.094742, 2946180, 18834313.
26. Fagerstrom K. The epidemiology of smoking: health consequences and benefits of cessation. Drugs 2002, 62(Suppl 2):1-9.
27. Steppuhn A, Gase K, Krock B, Halitschke R, Baldwin IT. Nicotine's defensive function in nature. PLoS Biol 2004, 2(8):E217. 10.1371/journal.pbio.0020217, 509292, 15314646.
28. Chintapakorn Y, Hamill JD. Antisense-mediated down-regulation of putrescine N-methyltransferase activity in transgenic Nicotiana tabacum L. can lead to elevated levels of anatabine at the expense of nicotine. Plant Mol Biol 2003, 53(1-2):87-105.
29. Saitoh F, Mona M, Kawashima N. The alkaloid contents of sixty Nicotiana species. Phytochemistry 1985, 24(3):477-480.
30. Baldwin IT, Karb MJ, Ohnmeiss TE. Allocation of 15 N from nitrate to nicotine: production and turnover of a damage-induced mobile defense. Ecology 1994, 75(6):1703-1713.
31. Kutchan T. Alkaloid biosynthesis-the basis for metabolic engineering of medicinal plants. Plant Cell 1995, 7(7):1059-1070. 160910, 12242397.
32. Baldwin IT. An ecologically motivated analysis of plant-herbivore interactions in native tobacco. Plant Physiol 2001, 127(4):1449-1458. 10.1104/pp.010762, 1540177, 11743088.
33. Hibi N, Higashiguchi S, Hashimoto T, Yamada Y. Gene expression in tobacco low-nicotine mutants. Plant Cell 1994, 6(5):723-735. 160471, 8038607.
34. Hibi N, Fujita T, Hatano M, Hashimoto T, Yamada Y. Putrescine N-methyltransferase in cultured roots of hyoscyamus albus: n-butylamine as a potent inhibitor of the transferase both in Vitro and in Vivo. Plant Physiol 1992, 100(2):826-835. 10.1104/pp.100.2.826, 1075632, 16653064.
35. Katoh A, Shoji T, Hashimoto T. Molecular cloning of N-methylputrescine oxidase from tobacco. Plant Cell Physiol 2007, 48(3):550-554. 10.1093/pcp/pcm018, 17283012.
36. Sinclair SJ, Johnson R, Hamill JD. Analysis of wound-induced gene expression in Nicotiana species with contrasting alkaloid profiles. Funct Plant Biol 2004, 31:721-729.
37. Sinclair SJ, Murphy KJ, Birch CD, Hamill JD. Molecular characterization of quinolinate phosphoribosyltransferase (QPRtase) in Nicotiana. Plant Mol Biol 2000, 44(5):603-617. 10.1023/A:1026590521318, 11198422.
38. Deboer KD, Lye JC, Aitken CD, Su AK, Hamill JD. The A622 gene in Nicotiana glauca (tree tobacco): evidence for a functional role in pyridine alkaloid synthesis. Plant Mol Biol 2009, 69(3):299-312. 10.1007/s11103-008-9425-2, 19011764.
39. Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 2010, 232(6):1289-1308. 10.1007/s00425-010-1255-1, 20803216.
40. Kim HJ, Baek KH, Lee BW, Choi D, Hur CG. In silico identification and characterization of microRNAs and their putative target genes in Solanaceae plants. Genome 2011, 54(2):91-98. 10.1139/G10-104, 21326365.
41. Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, Wu SH. 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci USA 2010, 107(34):15269-15274. 10.1073/pnas.1001738107, 2930544, 20643946.
42. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 2007, 19(3):926-942. 10.1105/tpc.107.050062, 1867363, 17400893.
43. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18(10):758-762. 10.1016/j.cub.2008.04.042, 2583427, 18472421.
44. Zhou M, Gu L, Li P, Song X, Wei L, Chen Z, Cao X. Degradome sequencing reveals endogenous small RNA targets in rice (<i>Oryza sativa</i> L. <i>ssp. indica</i>). Frontiers Biol 2010, 5(1):67-90.
45. Addo-Quaye C, Miller W, Axtell MJ. CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 2009, 25(1):130-131. 10.1093/bioinformatics/btn604, 3202307, 19017659.
46. Itaya A, Bundschuh R, Archual AJ, Joung JG, Fei Z, Dai X, Zhao PX, Tang Y, Nelson RS, Ding B. Small RNAs in tomato fruit and leaf development. Biochim Biophys Acta 2008, 1779(2):99-107.
47. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 2002, 110(4):513-520. 10.1016/S0092-8674(02)00863-2, 12202040.
48. Zhang S, Liu Y. Activation of salicylic acid-induced protein kinase, a mitogen-activated protein kinase, induces multiple defense responses in tobacco. Plant Cell 2001, 13(8):1877-1889. 139126, 11487699.
49. Romeis T, Piedras P, Zhang S, Klessig DF, Hirt H, Jones JD. Rapid Avr9- and Cf-9 -dependent activation of MAP kinases in tobacco cell cultures and leaves: convergence of resistance gene, elicitor, wound, and salicylate responses. Plant Cell 1999, 11(2):273-287. 144176, 9927644.
50. Lagudah ES, Moullet O, Appels R. Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat. Genome 1997, 40(5):659-665. 10.1139/g97-087, 9352645.
51. Richter TE, Ronald PC. The evolution of disease resistance genes. Plant Mol Biol 2000, 42(1):195-204. 10.1023/A:1006388223475, 10688137.
52. Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouche N, Gasciolli V, Vaucheret H. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol 2006, 16(9):927-932. 10.1016/j.cub.2006.03.035, 16682354.
53. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A. miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 2010, 22(4):1104-1117. 10.1105/tpc.109.072553, 2879756, 20363771.
54. Mallory AC, Dugas DV, Bartel DP, Bartel B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 2004, 14(12):1035-1046. 10.1016/j.cub.2004.06.022, 15202996.
55. Guo HS, Xie Q, Fei JF, Chua NH. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 2005, 17(5):1376-1386. 10.1105/tpc.105.030841, 1091761, 15829603.
56. Pandey SP, Baldwin IT. RNA-directed RNA polymerase 1 (RdR1) mediates the resistance of Nicotiana attenuata to herbivore attack in nature. Plant J 2007, 50(1):40-53. 10.1111/j.1365-313X.2007.03030.x, 17346266.
57. Pandey SP, Shahi P, Gase K, Baldwin IT. Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata. Proc Natl Acad Sci USA 2008, 105(12):4559-4564. 10.1073/pnas.0711363105, 2290812, 18339806.
58. Lu C, Meyers BC, Green PJ. Construction of small RNA cDNA libraries for deep sequencing. Methods 2007, 43(2):110-117. 10.1016/j.ymeth.2007.05.002, 17889797.
59. Zhang JY, Xu YY, Huan Q, Chong K. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 2009, 10:449. 10.1186/1471-2164-10-449, 2759970, 19772667.
60. German MA, Luo S, Schroth G, Meyers BC, Green PJ. Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 2009, 4(3):356-362. 10.1038/nprot.2009.8, 19247285.
61. Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP. TOBFAC: the database of tobacco transcription factors. BMC Bioinforma 2008, 9:53.
62. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh Chem 1994, 125:167-188.