Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

Journal of Experimental Botany

Volumn 62, Issue 10, 2011, Pages 3563-3573

  Ding, Yanfei ^a,b   Chen, Zhen ^a   Zhu, Cheng ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b CHINA JILIANG UNIVERSITY   (China)

Author keywords

Cadmium; gene regulation; heavy metal tolerance; microarray; microRNA; rice; stress response

Indexed keywords

CADMIUM; MICRORNA;

ARTICLE; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE;

CADMIUM; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ORYZA SATIVA;

EID: 79960260124     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/err046     Document Type: Article

References (64)

1. Agalou A, Purwantomo S, Overnäs E, et al. 2008. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Molecular Biology 66, 87-103. (Pubitemid 50002672)
2. Apel K, Hirt H. 2004. Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annual Review of Plant Biology 55, 373-399. (Pubitemid 38940937)
3. Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell 15, 2730-2741. (Pubitemid 37470672)
4. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
5. Carrington JC, Ambros V. 2003. Role of microRNAs in plant and animal development. Science 301, 336-338. (Pubitemid 36877060)
6. Chen C, Ridzon DA, Broomer AJ, et al. 2005. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33, e179.
7. Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su Cl. 2006. Regulation of phosphate homeostasis by microRNA in Arabidopsis. The Plant Cell 18, 412-421. (Pubitemid 43951302)
8. Clemens S. 2001. Molecular mechanisms of plant metal tolerance and homeostasis. Planta 212, 475-486. (Pubitemid 32235425)
9. Cobbett C, Goldsbrough P. 2002. Phytochelatins and metallothioneins: roles in heavy metal detoxification and homeostasis. Annual Review of Plant Biology 53, 159-182. (Pubitemid 36257491)
10. Dai M, Hu Y, Ma Q, Zhao Y, Zhou DX. 2008. Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellins responses. Plant Molecular Biology 66, 289-301.
11. Dietz KJ, Baier M, Kramer U. 1999. Free radicals and reactive oxygen species as mediators of heavy metal toxicity in plants. In: Prasad MNV, Hagemeyer J, eds. Heavy metal stress in plants: from molecules to ecosystems. Berlin: Springer-Verlag, 73-97.
12. Ding YF, Zhu C. 2009. The role of microRNAs in copper and cadmium homeostasis. Biochemical and Biophysical Research Communications 386, 6-10.
13. Dolferus R, Jacobs M, Peacock WJ, Dennis ES. 1994. Differential interactions of promoter elements in stress responses of the Arabidopsis Adh gene. Plant Physiology 105, 1075-1087.
14. Friedrichsen DM, Joazeiro CA, Li J, Hunter T, Chory J. 2000. Brassinosteroid-insensitive-1 is a ubiquitously expressed leucine-rich repeat receptor serine/threonine kinase. Plant Physiology 123, 1247-1256.
15. Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. 2005. A miRNA involved in phosphate-starvation response in Arabidopsis. Current Biology 15, 2038-2043. (Pubitemid 41654628)
16. 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. The Plant Cell 17, 1376-1386. (Pubitemid 43138191)
17. Hall JL. 2002. Cellular mechanisms for heavy metal detoxification and tolerance. Journal of Experimental Botany 53, 1-11. (Pubitemid 34043136)
18. Hawker NP, Bowman JL. 2004. Roles for class III HD-Zip and KANADI genes in Arabidopsis root development. Plant Physiology 135, 2261-2270. (Pubitemid 39182803)
19. Henriksson E, Olsson ASB, Johannesson H, Johansson H, Hanson J, Engström P, Söderman E. 2005. Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiology 139, 509-518. (Pubitemid 43951633)
20. Huang SQ, Peng J, Qiu CX, Yang ZM. 2009. Heavy metal-regulated new microRNAs from rice. Journal of Inorganic Biochemistry 103, 282-287.
21. Huang SQ, Xiang AL, Che LL, Chen S, Li H, Song JB, Yang ZM. 2010. A set of miRNAs from Brassica napus in response to sulphate-deficiency and cadmium stress. Plant Biotechnology Journal 8, 887-899.
22. Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell 14, 787-799. (Pubitemid 38780852)
23. Jones-Rhoades MW, Bartel DP, Bartel B. 2006. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 57, 19-53. (Pubitemid 44061017)
24. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K. 1999. Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nature Biotechnology 17, 287-291. (Pubitemid 29122637)
25. Kuo MH, Nadeau ET, Grayhack EJ. 1997. Multiple phosphorylated forms of the Saccharomyces cerevisiae Mcm1 protein include an isoform induced in response to high salt concentrations. Molecular and Cellular Biology 17, 819-832. (Pubitemid 27044381)
26. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts P. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research 30, 325-327. (Pubitemid 34685468)
27. Liu H, Tian X, Li Y, Wu CA, Zheng C. 2008. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14, 836-843. (Pubitemid 351574905)
28. Liu Q, Zhang YC, Wang CY, Luo YC, Huang QJ, Chen SY, Zhou H, Qu LH, Chen YQ. 2009. Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Letters 583, 723-728.
29. Lozano R, Angosto T, Gómez P, Payán C, Capel J, Huijser P, Salinas J, Mart́nez-Zapater LM. 1998. Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-box genes. Plant Physiology 117, 91-100. (Pubitemid 128652782)
30. Lu C, Jeong DH, Kulkarni K, et al. 2008. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proceedings of the National Academy of Sciences USA 105, 4951-4956. (Pubitemid 351753852)
31. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL. 2005. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. The Plant Cell 17, 2186-2203. (Pubitemid 41672940)
32. 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, 883-898.
33. Osakabe Y, Maruyama K, Seki M, Satou M, Shinozaki K, Yamaguchi-Shinozaki K. 2005. Leucine-rich repeat receptor-like kinase1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis. The Plant Cell 17, 1105-1119. (Pubitemid 43142129)
34. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. 2003. Control of leaf morphogenesis by microRNAs. Nature 425, 257-263. (Pubitemid 37158395)
35. Pinto AP, Mota AM, De Varennes A, Pinto FC. 2004. Influence of organic matter on the uptake of cadmium, zinc, copper and iron by sorghum plants. Science of the Total Environment 326, 239-274.
36. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. 2005. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. The Plant Cell 17, 61-76. (Pubitemid 41672988)
37. Qi X, Zhang Y, Chai T. 2007. Characterization of a novel plant promoter specifically induced by heavy metal and identification of the promoter regions conferring heavy metal responsiveness. Plant Physiology 143, 50-59. (Pubitemid 46133616)
38. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. 2002. MicroRNAs in plants. Genes and Development 16, 1616-1626. (Pubitemid 34743323)
39. Rhoades M, Reinhart B, Lim L, Burge C, Bartel B, Bartel D. 2002. Prediction of plant microRNA targets. Cell 110, 513-520. (Pubitemid 35232294)
40. Rodriguez-Serrano M, Romero-Puertas MC, Pazmino DM, Testillano PS, Risueno MC, del Rio LA, Sandalio LM. 2009. Cellular response of pea plants to cadmium toxicity: cross talk between reactive oxygen species, nitric oxide, and calcium. Plant Physiology 150, 229-243.
41. Sandalio LM, Dalurzo HC, Gomez M, Romero-Puertas MC, del Rio LA. 2001. Cadmium-induced changes in the growth and oxidative metabolism of pea plants. Journal of Experimental Botany 52, 2115-2126. (Pubitemid 33044991)
42. Sanitàdi Toppiand L, Gabbrielli R. 1999. Response to cadmium in higher plants. Environmental and Experimental Botany 41, 105-130. (Pubitemid 29194798)
43. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. 2005. Specific effects of microRNAs on the plant transcriptome. Developmental Cell 8, 517-527. (Pubitemid 40450741)
44. Schützendübel A, Polle A. 2002. Plant responses to abiotic stress: heavy metal induced oxidative stress and protection by mycorrhization. Journal of Experimental Botany 53, 1351-1365. (Pubitemid 34544055)
45. Schützendübel A, Schwanz P, Teichmann T, Gross K, Langenfeld-Heyser R, Godbold DL, Polle L. 2001. Cadmium-induced changes in antioxidative systems, hydrogen peroxide content, and differentiation in Scots pine roots. Plant Physiology 127, 887-898. (Pubitemid 33112150)
46. Searle PF, Stuart GW, Palmiter RD. 1987. Metal regulatory elements of the mouse metallothionein-I gene. Experientia Supplementum 52, 407-414.
47. Sire C, Moreno AB, Garcia-Chapa M, Lopez-Moya JJ, San Segundo B. 2009. Diurnal oscillation in the accumulation of Arabidopsis microRNAs, miR167, miR168, miR171 and miR398. FEBS Letters 583, 1039-1044.
48. Siripornadulsil S, Train S, Verma DPS, Sayre RT. 2002. Molecular mechanisms of proline-mediated tolerance to toxic heavy metals in transgenic microalgae. The Plant Cell 14, 2837-2847. (Pubitemid 35326308)
49. Stuart GW, Searle PF, Palmiter RD. 1985. Identification of multiple metal regulatory elements in mouse metallothionein-I promoter by assaying synthetic sequences. Nature 317, 828-831. (Pubitemid 16195414)
50. Sunkar R, Girke T, Jain PK, Zhu JK. 2005. Cloning and characterization of microRNAs from rice. The Plant Cell 17, 1397-1411. (Pubitemid 43138193)
51. 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. The Plant Cell 18, 2051-2065. (Pubitemid 44260196)
52. Sunkar R, Zhou XF, Zheng Y, Zhang WX, Zhu JK. 2008. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology 8, 25.
53. Sunkar R, Zhu JK. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell 16, 2001-2019. (Pubitemid 39059724)
54. Thomine S, Wang R, Ward JM, Crawford NM, Schroeder JI. 2000. Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proceedings of the National Academy of Sciences USA 97, 4991-4996. (Pubitemid 30238670)
55. Tichtinsky G, Vanoosthuyse V, Cock JM, Gaude T. 2003. Making inroads into plant receptor kinase signalling pathways. Trends in Plant Science 8, 231-237. (Pubitemid 36726450)
56. Vaucheret H, Mallory AC, Bartel DP. 2006. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Molecular Cell 22, 129-136.
57. Vazquez F, Gasciolli V, Crete P, Vaucheret H. 2004. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Current Biology 14, 346-351. (Pubitemid 38300215)
58. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM. 2007. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Letters 581, 1464-1474. (Pubitemid 46452623)
59. Zhang W, Ruan J, Ho T, You Y, Yu T, Quatrano RS. 2005. Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid-and abiotic stress responsive genes in Arabidopsis thaliana. Bioinformatics 21, 3074-3081. (Pubitemid 41418459)
60. Zhang Y. 2005. miRU: an automated plant miRNA target prediction server. Nucleic Acids Research 33, w701-w704. (Pubitemid 44530014)
61. Zhang ZX, Wei LY, Zou XL, Tao YS, Liu ZJ, Zheng YL. 2008. Submergence-responsive microRNAs are potentially involved in the regulation of morphological and metabolic adaptations in maize root cells. Annals of Botany 102, 509-519.
62. Zhao BT, Liang RQ, Ge LF, Li W, Xiao HS, Lin H, Ruan K, Jin YX. 2007. Identification of drought-induced microRNAs in rice. Biochemical and Biophysical Research Communications 354, 585-590. (Pubitemid 46161364)
63. Zhou X, Ruan J, Wang G, Zhang W. 2007. Characterization and identification of microRNA core promoters in four model species. PLoS Computational Biology 3, e37.
64. Zhou ZS, Huang SQ, Yang ZM. 2008. Bioinformatic identification and expression analysis of new microRNAs from. Medicago truncatula. Biochemical and Biophysical Research Communications 374, 538-542.