Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing
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- 作者：Lei Chen (1) (2)
Tianzuo Wang (1) (2)
Mingui Zhao (1)
Qiuying Tian (1)
Wen-Hao Zhang (1) - 关键词：Aluminum toxicity ; High ; throughput sequencing ; Medicago ; MicroRNA
- 刊名：Planta
- 出版年：2012
- 出版时间：February 2012
- 年：2012
- 卷：235
- 期：2
- 页码：375-386
- 全文大小：488KB
- 参考文献：1. Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357-365 CrossRef
2. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207-21 CrossRef
3. Alonso-Peral MM, Li JY, Li YJ, Allen RS, Schnippenkoetter W, Ohms S, White RG, Millar AA (2010) The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in / Arabidopsis. Plant Physiol 154:757-71 CrossRef
4. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277-79 CrossRef
5. Bari R, Pant BD, Stitt M, Scheible WR (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141:988-99 CrossRef
6. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-97 CrossRef
7. Chen X (2004) A microRNA as a translational repressor of / APETALA2 in / Arabidopsis flower development. Science 303:2022-025 CrossRef
8. Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in / Lotus japonicus. Plant J 39:487-12 CrossRef
9. Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 103:29-8 CrossRef
10. Doncheva S, Amenos M, Poschenrieder C, Barcelo J (2005) Root cell patterning: a primary target for aluminum toxicity in maize. J Exp Bot 56:1213-220 CrossRef
11. Fang Y, Spector DL (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living / Arabidopsis plants. Curr Biol 17:818-23 CrossRef
12. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158 CrossRef
13. Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor / NAC1 to downregulate auxin signals for / Arabidopsis lateral root development. Plant Cell 17:1376-386 CrossRef
14. Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in / Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 21:3119-132 CrossRef
15. Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T (2008) Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44:3-2 CrossRef
16. Hammond-Kosack KE, Parker JE (2003) Deciphering plant-pathogen communication: fresh perspectives for molecular resistance breeding. Curr Opin Biotech 14:177-93 CrossRef
17. Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang WX, Sunkar R (2009) Cloning and characterization of small RNAs from / Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 184:85-8 CrossRef
18. Jian X, Zhang L, Li G, Wang X, Cao X, Fang X, Chen F (2010) Identification of novel stress-regulated microRNAs from / Oryza sativa L. Genomics 95:47-5 CrossRef
19. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787-99 CrossRef
20. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19-3 CrossRef
21. Kochian LV, Pineros MA, Hoekenga OA (2005) The physiology, genetics and molecular biology of plant aluminum resistance and toxicity. Plant Soil 274:175-95 CrossRef
22. Kollmeier M, Felle HH, Horst WJ (2000) Genotypical differences in aluminum resistance of maize are expressed in the distal part of the transition zone. Is reduced basipetal auxin flow involved in inhibition of root elongation by aluminum? Plant Physiol 122:945-56 CrossRef
23. Kurihara Y, Watanabe Y (2004) / Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 101:12753-2758 CrossRef
24. Lee RC, Ambros V (2001) An extensive class of small RNAs in / Caenorhabditis elegans. Science 294:862-64 CrossRef
25. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38:803-14 CrossRef
26. Lelandais-Briere C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M (2009) Genome-wide / Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 21:2780-796 CrossRef
27. Li WX, Oono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Jin H, Zhu JK (2008a) The / Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20:2238-251 CrossRef
28. Li R, Li Y, Kristiansen K, Wang J (2008b) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-14 CrossRef
29. Liang G, Yang FX, Yu DQ (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in / Arabidopsis thaliana. Plant J 62:1046-057
30. Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC (2007) Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J 52:133-46
31. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in / Arabidopsis thaliana. RNA 14:836-43 CrossRef
32. Liu DM, Song Y, Chen ZX, Yu DQ (2009) Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol Plant 136:223-36
33. Liu XD, Huang J, Wang Y, Khanna K, Xie ZX, Owen HA, Zhao DZ (2010) The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in microRNA160a, in organogenesis and the mechanism regulating its expression. Plant J 62:416-28
34. Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605-619 CrossRef
35. Lobbes D, Rallapalli G, Schmidt DD, Martin C, Clarke J (2006) SERRATE: a new player on the plant microRNA scene. EMBO Report 7:1052-058 CrossRef
36. Lu C, Fedoroff N (2000) A mutation in the Arabidopsis / HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12:2351-366 CrossRef
37. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A (2010) miR390, / Arabidopsis TAS3 tasiRNAs, and their / AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 22:1104-117 CrossRef
38. Meng Y, Huang F, Shi Q, Cao J, Chen D, Zhang J, Ni J, Wu P, Chen M (2009) Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant. Planta 230:883-98 CrossRef
39. Mestre P, Baulcombe DC (2006) Elicitor-mediated oligomerization of the tobacco N disease resistance protein. Plant Cell 18:491-01 CrossRef
40. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK (2008) Criteria for annotation of plant microRNAs. Plant Cell 20:3186-190 CrossRef
41. Noutoshi Y, Ito T, Seki M, Nakashita H, Yoshida S, Marco Y, Shirasu K, Shinozaki K (2005) A single amino acid insertion in the WRKY domain of the Arabidopsis TIR-NBS-LRR-WRKY-type disease resistance protein SLH1 (sensitive to low humidity 1) causes activation of defense responses and hypersensitive cell death. Plant J 43:873-88 CrossRef
42. Pant BD, Buhtz A, Kehr J, Scheible WR (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J 53:731-38 CrossRef
43. Park W, Li J, Song R, Messing J, Chen X (2002) CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in / Arabidopsis thaliana. Curr Biol 12:1484-495 CrossRef
44. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in / Arabidopsis thaliana. Genes Dev 20:3407-425 CrossRef
45. Rengel Z, Zhang WH (2003) Role of dynamics of intracellular calcium in aluminum-toxicity syndrome. New Phytol 159:295-14 CrossRef
46. Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during / Arabidopsis seed germination. Plant J 49:592-06 CrossRef
47. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110:513-20 CrossRef
48. Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF (2010) Control of cell proliferation in / Arabidopsis thaliana by microRNA miR396. Development 137:103-12 CrossRef
49. Ryan PR, Ditomaso JM, Kochian LV (1993) Aluminum toxicity in roots—an investigation of spatial sensitivity and the role of the root cap. J Exp Bot 44:437-46 CrossRef
50. Ryan PR, Tyerman SD, Sasaki T, Furuichi T, Yamamoto Y, Zhang WH, Delhaize E (2011) The identification of aluminum-resistance genes provides opportunities for enhancing crop production on acid soils. J Exp Bot 62:9-0 CrossRef
51. Schommer C, Palatnik JF, Aggarwal P, Chetelat A, Cubas P, Farmer EE, Nath U, Weigel D (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. Plos Biol 6:1991-001 CrossRef
52. Sivaguru M, Horst WJ (1998) The distal part of the transition zone is the most aluminum-sensitive apical root zone of maize. Plant Physiol 116:155-63 CrossRef
53. Sun P, Tian QY, Zhao MG, Dai XY, Huang JH, Li LH, Zhang WH (2007) Aluminum-induced ethylene production is associated with inhibition of root elongation in / Lotus japonicus L. Plant Cell Physiol 48:1229-235 CrossRef
54. Sun P, Tian QY, Chen J, Zhang WH (2010) Aluminum-induced inhibition of root elongation in / Arabidopsis is mediated by ethylene and auxin. J Exp Bot 61:347-56 CrossRef
55. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001-019 CrossRef
56. Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in / Arabidopsis is mediated by down-regulation of miR398 and important for oxidative stress tolerance. Plant Cell 18:2051-065 CrossRef
57. Sunkar R, Chinnusamy V, Zhu J, Zhu JK (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12:301-09 CrossRef
58. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MPS, Moulton V, Dalmay T (2008) High-throughput sequencing of / Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9:593 CrossRef
59. Taylor GJ, Blamey FPC, Edwards DG (1998) Antagonistic and synergistic interactions between aluminum and manganese on growth of / Vigna unguiculata at low ionic strength. Physiol Plant 104:183-94 CrossRef
60. Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM (2009) miR398 and miR408 are up-regulated in response to water deficit in / Medicago truncatula. Planta 231:705-16 CrossRef
61. Trinh TH, Ratet P, Kondorosi E, Durand P, Kamate K, Bauer P, Kondorosi A (1998) Rapid and efficient transformation of diploid / Medicago truncatula and / Medicago sativa ssp. / falcata lines improved in somatic embryogenesis. Plant Cell Rep 17:345-55 CrossRef
62. Valdes-Lopez O, Yang SS, Aparicio-Fabre R, Graham PH, Reyes JL, Vance CP, Hernandez G (2010) MicroRNA expression profile in common bean ( / Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity. New Phytol 187:805-18 CrossRef
63. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204-216
64. Wang TZ, Chen L, Zhao MG, Tian QY, Zhang WH (2011) Identification of drought-responsive microRNAs and their targets in / Medicago truncatula by genome-wide high-throughput sequencing and degradome analysis. BMC Genomics 12:367
65. Wu F, Yu L, Cao W, Mao Y, Liu Z, He Y (2007) The N-terminal double-stranded RNA binding domains of / Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing. Plant Cell 19:914-25 CrossRef
66. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465-75 CrossRef
67. Yang S, Gao M, Xu C, Gao J, Deshpande S, Lin S, Roe BA, Zhu H (2008) Alfalfa benefits from / Medicago truncatula: the RCT1 gene from / M. truncatula confers broad-spectrum resistance to anthracnose in alfalfa. Proc Natl Acad Sci USA 105:12164-2169 CrossRef
68. Yang ZB, You JF, Xu MY, Yang ZM (2009) Interaction between aluminum toxicity and manganese toxicity in soybean ( / Glycine max). Plant Soil 319:277-89 CrossRef
69. Yao YY, Guo GG, Ni ZF, Sunkar R, Du JK, Zhu JK, Sun QX (2007) Cloning and characterization of microRNAs from wheat ( / Triticum aestivum L.). Genome Biol 8:120 CrossRef
70. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS (2010) Auxin regulation of the / microRNA390-dependent transacting small interfering RNA pathway in / Arabidopsis lateral root development. Nucleic Acids Res 38:1382-391 CrossRef
71. Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC, Chen X (2008) The FHA domain proteins DAWDLE in / Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA 105:10073-0078 CrossRef
72. Zhang J, Xu Y, Huan Q, Chong K (2009) Deep sequencing of / Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10:449 CrossRef
73. Zhou ZS, Huang SQ, Yang ZM (2008) Bioinformatic identification and expression analysis of new microRNAs from / Medicago truncatula. Biochem Biophys Res Comm 374:538-42 CrossRef
74. Zhou LG, Liu YH, Liu ZC, Kong DY, Duan M, Luo LJ (2010) Genome-wide identification and analysis of drought-responsive microRNAs in / Oryza sativa. J Exp Bot 61:4157-168 CrossRef
75. Zuker M (2003) M-fold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-415 CrossRef - 作者单位：Lei Chen (1) (2)
Tianzuo Wang (1) (2)
Mingui Zhao (1)
Qiuying Tian (1)
Wen-Hao Zhang (1)
1. State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, People’s Republic of China
2. Graduate University of the Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
文摘
MicroRNAs (miRNAs) play important roles in response of plants to biotic and abiotic stresses. Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. However, there has been limited report on the involvement of miRNAs in response of plants to toxic Al3+. To identify Al3+-responsive miRNAs at whole-genome level, high-throughput sequencing technology was used to sequence libraries constructed from root apices of the model legume plant Medicago truncatula treated with and without Al3+. High-throughput sequencing of the control and two Al3+-treated libraries led to generation of 17.1, 14.1 and 17.4?M primary reads, respectively. We identified 326 known miRNAs and 21 new miRNAs. Among the miRNAs, expression of 23 miRNAs was responsive to Al3+, and the majority of Al3+-responsive mRNAs was down-regulated. We further classified the Al3+-responsive miRNAs into three groups based on their expression patterns: rapid-responsive, late-responsive and sustained-responsive miRNAs. The majority of Al3+-responsive miRNAs belonged to the ‘rapid-responsive-category, i.e. they were responsive to short-term, but not long-term Al3+ treatment. The Al3+-responsive miRNAs were also verified by quantitative real-time PCR. The potential targets of the 21 new miRNAs were predicted to be involved in diverse cellular processes in plants, and their potential roles in Al3+-induced inhibition of root growth were discussed. These findings provide valuable information for functional characterization of miRNAs in Al3+ toxicity and tolerance.