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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (04): 581-590.doi: 10.3724/SP.J.1006.2014.00581

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

A Comparison of Cadmium-Accumulation-Associated Genes Expression and Molecular Regulation Mechanism between Two Rice Cultivars (Oryza sativa L. subspecies japonica)

HUANG Zhi-Xiong1,2,WANG Fei-Juan2,JIANG Han2,LI Zhi-Lan3,DING Yan-Fei2,JIANG Qiong2,TAO Yue-Liang4,ZHU Cheng1,2,*   

  1. 1 State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; 2 Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China JiLiang University, Hangzhou 310018, China; 3 Nature Science Foundation Committee of Zhejiang Province, Hangzhou 310012, China; 4 College of Life and Environment Sciences, Wenzhou University, Wenzhou 325035, China
  • Received:2013-09-09 Revised:2014-01-12 Online:2014-04-12 Published:2014-02-17
  • Contact: 朱诚,E-mail: pzhch@cjlu.edu.cn; Tel: 0571-86914510 E-mail:21007016@zju.edu.cn

Abstract:

In plants, as in other eukaryotes, endogenous small interfering RNAs (siRNAs), a class of small non-coding RNAs, andDNA methylation regulate gene expression in developmental processes and adaptating to environmental stresses, including Cd stress. Cadmium (Cd) is a non-essential heavy metal and highly toxic to plants. To investigate the regulatory role of siRNAs and DNA methylation on genes involved in heavy metals transport, we compared these genes’ expression profiles between a high Cd-accumulating rice (Oryza sativa L. subspecies japonica) cultivar (Xiushui 11) and a low Cd-accumulating rice cultivar (Xiushui110). At five rice development stages investigated, the difference of these genes expression level between the two rice cultivars was not significant except OsPCR1, indicating OsPCR1 may be important in Cd transport in rice. Furthermore, quantitative real time PCR (qRT-PCR) was performed to examine the expression level of a siRNA matched OsPCR1 second exon. Results indicated that the expression level of the siRNA negatively correlated with OsPCR1 expression level at the five stages. In addition, McrBC-qRT-PCR technology was used to determine DNA methylation level, showing that OsPCR1 expression level also negatively correlated with OsPCR1 second exon methylation level. These results of regulatory roles of siRNA and DNA methylation on OsPCR1 expression will contribute to the studies on OsPCR1 function and rice breeding for low Cd accumulation.

Key words: siRNA, DNA methylationOsPCR1, Rice (Oryza sativa L.), Cadmium accumulation

[1]Uraguchi S, Kamiya T, Sakamoto T, Kssai K, Sato Y, Nagamura Y, Yoshida A, Kyozuka J, Ishikawa S, Fujiwara T. Low-affinity cation transporter (OsLCT1) regulates cadmium transport into rice grains. Proc Natl Acad Sci USA, 2011, 108: 20959–20964



[2]Ueno D, Koyama E, Yamaji N, Ma J F. Physiological, genetic, and molecular characterization of a high-Cd-accumulating rice cultivars, Jarjan. J Exp Bot, 2011, 62: 2262–2272



[3]Uraguchi S, Mori S, Kuramata M, Kawasaki A, Arao T, Ishikawa S. Root-to-shoot Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice. J Exp Bot, 2009, 60: 2677–2688



[4]Takahashi R, Ishimaru Y, Senoura T, Shimo H, Ishikawa S, Arao T, Nakanishi H, Nishizawa N K. The OsNRAMP1 iron transporter is involved in Cd accumulation in rice. J Exp Bot, 2011, 62: 4843–4850



[5]Kuramata M, Masuya S, Takahashi Y, Kitagawa E, Inoue C, Ishikawa S, Youssefian S, Kusano T. Novel cysteine-rich peptides from Digitaria ciliaris and Oryza sativa enhance tolerance to cadmium by limiting its cellular accumulation. Plant Cell Physiol, 2009, 50: 106–117



[6]Shen G M, Zhu C, Du Q Z. Genome-wide identification of PHYTOCHELATIN and PHYTOCH_SYNTH domain-containing phytochelatin family from rice. Electronic J Biol, 2010, 6:73–79



[7]Shimo H, Ishimaru Y, An G, Yamakawa T, Nakanishi H, Nishizawa N K. Low cadmium (LCD), a novel gene related to cadmium tolerance and accumulation in rice. J Exp Bot, 2011, 62: 5727–5734



[8]Song W Y, Choi K S, Alexis D A, Martinoia E, Lee Y. Brassica juncea plant cadmium resistance 1 protein (BjPCR1) facilitates the radial transport of calcium in the root. Proc Natl Acad Sci USA, 2010, 108: 1908–19813



[9]Song W Y, Choi K S, Kim D Y, Geisler M, Park J, Vincenzetti V, Schellenberg M, Kim S H, Lim Y P, Noh E W, Lee Y, Martinoia E. Arabidopsis PCR2 is a zinc exporter involved in both zinc extrusion and long-distance zinc transport. Plant Cell, 2010, 22: 2237–2252



[10]Cobbett C, Goldsbrough P. Phytochelatins and metallothioneins: roles in heavy metal detoxification and homeostasis. Annu Rev Plant Biol, 2002, 53: 159–182



[11]Song W Y, Hörtensteiner S, Tomioka R, Lee Y, Martinoia E. Common functions or only phylogenetically related? The large family of PLAC8 motif-containing/PCR genes. Mol Cells, 2011, 31: 1–7



[12]Song W Y, Martinoia E, Lee J, Kim D, Kim D Y, Vogt E, Shim D, Choi K S, Hwang I, Lee Y. A novel family of cys-rich membrane proteins mediates cadmium resistance in Arabidopsis. Plant Physiol, 2004, 135: 1027–1039



[13]Borsani O, Zhu J, Verslues P E, Sunkar R, Zhu J K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell, 2005, 123: 1279–1291



[14]Carthew R W, Sontheimer E J. Origins and mechanisms of miRNA and siRNAs. Cell, 2009, 136: 642–655



[15]Moldovan D, Spriggs A, Yang J, Pogson B J, Dennis E S, Wilson I W. Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot, 2010, 61: 165–177



[16]Yan Y, Zhang Y, Sun Z, Fu Y, Chen X, Fang R. Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice. Plant J, 2011, 65: 820–828



[17]Yao Y, Ni Z, Peng H, Sun F, Xin M, Sunkar R, Zhu J K, Sun Q. Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L. ). Funct Integr Genomic, 2010, 10: 187–190



[18]Kim V N, Han J, Siomi M C. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol, 2009, 10: 126–139



[19]Hannon G J. RNA interference. Nature, 2002, 418: 244–251



[20]Song J J, Smith S K, Hannon G J, Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 2004, 305: 1434–1437



[21]Law J A, Jacobsen S E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 2010, 11: 204–220



[22]Chan S W L, Henderson I R, Jacobsen S E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet, 2005, 6: 351–360



[23]Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollander J. Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of dicer-like proteins. PLoS One, 2010, 5: e9514



[24]Choi C S, Sano H. Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics, 2007, 277: 589–600



[25]Greco M, Chiappetta A, Bruno L, Bitonti M B. In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning. J Exp Bot, 2012, 63: 695–709



[26]Verhoeven K J F, Jansen J J, Dijk P J, Biere A. Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol, 2010, 185: 1108–1118



[27]Raj S, Brautigen K, Hamanishi E T, Wilkins O, Thomas B R, Schroeder W, Mansfield S D, Plant A L, Campbell M M. Clone history shapes populous drought response. Proc Natl Acad Sci USA, 2011, 108: 12521–12526



[28]Ball M P, Li J B, Gao Y, Lee J H, LeProust E M, Park I H, Xie B, Daley G Q, Church G M. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol, 2009, 27: 361–368



[29]Hellman A, Chess A. Gene Body-specific methylation on the active X chromosome. Science, 2007, 315: 1141–1143



[30]Lister R, Pelizzola M, Dowen R H, Hawkins R D, Hon G, Tonti-Filippini J, Nery J R, Lee L, Ye Z, Ngo Q M, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar A H, Thomson J A, Ren B, Ecker J R. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 2009, 462: 315–322



[31]Kawanabe T, Fujimoto R, Sasaki T, Taylor J M, Dennis E S. A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis. Gene, 2012, 506: 301–309



[32]Zilberman D, Gehring M, Tran R K, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet, 2007, 39: 61–69



[33]Suzuki M M, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet, 2008, 9: 465–476



[34]He J, Zhu C, Ren Y, Yan Y, Jiang D. Genotypic variation in grain cadmium concentration of lowland rice. J Plant Nutr Soil Sci, 2006, 169: 711–716



[35]何俊瑜,任艳芳,朱诚,蒋德安. 镉胁迫对不同水稻品种种子萌发、幼苗生长和淀粉酶活性的影响. 中国水稻科学, 2008, 22: 399–404



He J Y, Ren Y F, Zhu C, Jiang D A. Effects of cadmium stress on seed germination, seedling growth, and amylase activities in rice. Chin J Rice Sci, 2008, 22: 399–404 (in Chinese with English abstract)



[36]Ding Y, Chen Z, Zhu C. Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot, 2011, 62: 3563–3573



[37]Pfaffl M W. A new mathematical model for relative quantification in real-time RT-PCR. Nucl Acids Res, 2001, 29: e45



[38]Serra I A, Procaccini G, Intrieri M C, Migliaccio M, Mazzuca S, Innocenti A M. Comparison of ISSR and SSR markers for analysis of genetic diversity in the seagrass Posidonia oceanica. Marine Ecology Progress Series, 2007, 338: 71–79



[39]Teixeira F K, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga M F, Voinnet O, Wincker P, Esteller M, Colot V. A role for RNAi in the selective correction of DNA methylation defects. Science, 2009, 323: 1600–1604



[40]Johnson C, Bowman L, Adai A T, Vance V, Sundaresan V. CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic Acids Res, 2007, 35: D829–D833



[41]Brandeis M, Ariel M, Cedar H. Dynamics of DNA methylation during development. Bioessays, 1993, 15: 709–713



[42]赵嵘, 胡丽玲, 孔繁强, 左爱军. PXR基因外显子3甲基化与肠癌细胞对5氟尿嘧啶的耐药性相关. 中国生物化学与分子生物学报, 2013, 29: 63–69



Zhao R, Hu L L, Kong F Q, Zuo A J. Association between pregnane X receptor gene exon3 methylation with 5-fluorouracil resistance of the colon cancer cells. Chin J Biochem Mol Biol, 2013, 29: 63–69 (in Chinese with English abstract)



[43]Hohn T, Corsten S, Rieke S, Muller M, Rothnie H. Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci USA, 1996, 93: 8334–8339



[44]Rountree M R, Selker E U. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev, 1997, 11: 2383–2395



[45]Xiao Z, Wang C, Mo D, Li J, Chen Y, Zhang Z, Cong P. Promoter CpG methylation status in porcine Lyn is associated with its expression levels. Gene, 2012, 511: 73–78



[46]Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen S E, Robinson G E, Maleszka R. DNA methylation dynamics, metabolic fluxes, genesplicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci USA, 2012, 109: 4968–4973



[47]Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, 2011, 479: 74–79
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