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Differential sensitivity of Arabidopsis siRNA biogenesis mutants to genotoxic stress

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Abstract

Plant response to stress has been linked to different RNA-silencing processes and epigenetic mechanisms. Our recent results showed that Arabidopsis thaliana Dicer-like (DCL) mutants were impaired in transgenerational changes, recombination frequency and stress tolerance. We also found that transgenerational changes were dependent on changes in DNA methylation. Here, we hypothesized that plants deficient in the production of small RNAs would show an impaired abiotic stress response. To test this, we exposed A. thaliana dcl2, dcl3, dcl4, dcl2 dcl3 (d2d3), dcl2 dcl4 (d2d4), dcl2 dcl3 dcl4 (d2d3d4), nrpd1a, rdr2 and rdr6 mutants to methyl methane sulfonate (MMS). We found dcl4 and rdr6 to be more sensitive and dcl2, dcl3, d2d3 and rdr2 plants more resistant to MMS, as shown by fresh weight, root length and survival rate. The in vitro repair assay showed the lower ability of dcl2 and dcl3 to repair UV-damaged DNA. To summarize, we found that whereas mutants impaired in transactivating siRNA biogenesis were more sensitive to MMS, mutants impaired in natural antisense siRNA and heterochromatic siRNA biogeneses were more tolerant. Our data suggest that plant response to MMS is in part regulated through biogenesis of various siRNAs.

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Abbreviations

N7-MeG:

7-Methylguanine

ABA:

Abscisic acid

BER:

Base excision repair

DCL:

Dicer-like

DSBs:

Double-strand DNA breaks

HR:

Homologous recombination

MMS:

Methyl methane sulfonate

miRNA:

MicroRNA

MMR:

Mismatch repair

nat-siRNAs:

Natural antisense siRNAs

NHEJ:

Non-homologous end-joining

siRNAs:

Small interfering RNAs

ta-siRNAs:

Transactivating siRNAs

References

  • Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, Zhang P, Gruissem W, Meins F Jr, Hohn T, Pooggin MM (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34:462–471

    Article  CAS  PubMed  Google Scholar 

  • Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221

    Article  CAS  PubMed  Google Scholar 

  • Arnholdt-Schmitt B (2004) Stress-induced cell reprogramming. A role for global genome regulation? Plant Physiol 136:2579–2586

    Article  CAS  PubMed  Google Scholar 

  • Axtell MJ, Bowman JL (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci 13:343–349

    Article  CAS  PubMed  Google Scholar 

  • Bagherieh-Najjar MB, de Vries OM, Hille J, Dijkwel PP (2005) Arabidopsis RecQI4A suppresses homologous recombination and modulates DNA damage responses. Plant J 43:789–798

    Article  CAS  PubMed  Google Scholar 

  • Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366

    Article  CAS  PubMed  Google Scholar 

  • Blevins T, Rajeswaran R, Shivaprasad PV, Beknazariants D, Si-Ammour A, Park HS, Vazquez F, Robertson D, Meins F Jr, Hohn T, Pooggin MM (2006) Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res 34:6233–6246

    Article  CAS  PubMed  Google Scholar 

  • Blevins T, Pontes O, Pikaard CS, Meins F Jr (2009) Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS One 4:e5932

    Article  PubMed  Google Scholar 

  • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291

    Article  CAS  PubMed  Google Scholar 

  • Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollander J, Meins F Jr, Kovalchuk I (2010a) Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS One 5:e9514

  • Boyko A, Kovalchuk I (2010b) Transgenerational response to stress in Arabidopsis thaliana. Plant Signal Behav 5(8) [Epub ahead of print]

  • Chuck G, Candela H, Hake S (2009) Big impacts by small RNAs in plant development. Curr Opin Plant Biol 12:81–86

    Article  CAS  PubMed  Google Scholar 

  • Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, Matzke M (2009) A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J 28:48–57

    Article  CAS  PubMed  Google Scholar 

  • Dunoyer P, Himber C, Voinnet O (2005) DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet 37:1356–1360

    Article  CAS  PubMed  Google Scholar 

  • Gasciolli V, Mallory AC, Bartel DP, Vaucheret H (2005) Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15:1494–1500

    Article  CAS  PubMed  Google Scholar 

  • Grandbastien MA, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa AP, Le QH, Melayah D, Petit M, Poncet C, Tam SM, Van Sluys MA, Mhiri C (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 110:229–241

    Article  CAS  PubMed  Google Scholar 

  • Hanin M, Mengiste T, Bogucki A, Paszkowski J (2000) Elevated levels of intrachromosomal homologous recombination in Arabidopsis overexpressing the MIM gene. Plant J 24:183–189

    Article  CAS  PubMed  Google Scholar 

  • Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308:118–120

    Article  CAS  PubMed  Google Scholar 

  • Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19:926–942

    Article  CAS  PubMed  Google Scholar 

  • Johnson C, Sundaresan V (2007) Regulatory small RNAs in plants. EXS 97:99–113

    CAS  PubMed  Google Scholar 

  • Kaina B (2004) Mechanisms and consequences of methylating agent-induced SCEs and chromosomal aberrations: a long road traveled and still a far way to go. Cytogenet Genome Res 104:77–86

    Article  CAS  PubMed  Google Scholar 

  • Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet 40:670–675

    Article  CAS  PubMed  Google Scholar 

  • Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, Zhu JK, Staskawicz BJ, Jin H (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci USA 103:18002–18007

    Article  CAS  PubMed  Google Scholar 

  • Kovalchuk O, Burke P, Arkhipov A, Kuchma N, James SJ, Kovalchuk I, Pogribny I (2003) Genome hypermethylation in Pinus silvestris of Chernobyl—a mechanism for radiation adaptation? Mutat Res 529:13–20

    CAS  PubMed  Google Scholar 

  • Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 101:12753–12758

    Article  CAS  PubMed  Google Scholar 

  • Li A, Schuermann D, Gallego F, Kovalchuk I, Tinland B (2002) Repair of damaged DNA by Arabidopsis cell extract. Plant Cell 14:263–273

    Article  CAS  PubMed  Google Scholar 

  • Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC (2006) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res 16:1276–1288

    Article  CAS  PubMed  Google Scholar 

  • Mallory AC, Bouche N (2008) MicroRNA-directed regulation: to cleave or not to cleave. Trends Plant Sci 13:359–367

    Article  CAS  PubMed  Google Scholar 

  • Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10:512–519

    Article  CAS  PubMed  Google Scholar 

  • Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21:367–376

    Article  CAS  PubMed  Google Scholar 

  • Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 61(1):165–177

    Google Scholar 

  • Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613–622

    Article  CAS  PubMed  Google Scholar 

  • Pikaard C, Pontes O (2007) Heterochromatin: condense or excise. Nat Cell Biol 9:19–20

    Article  CAS  PubMed  Google Scholar 

  • Pontes O, Pikaard CS (2008) siRNA and miRNA processing: new functions for Cajal bodies. Curr Opin Genet Dev 18:197–203

    Article  CAS  PubMed  Google Scholar 

  • Pontes O, Costa-Nunes P, Vithayathil P, Pikaard CS (2009) RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Mol Plant 2:700–710

    Article  CAS  PubMed  Google Scholar 

  • Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 19(17):2030–2040

    Google Scholar 

  • Puchta H, Swoboda P, Gal S, Blot M, Hohn B (1995) Somatic intrachromosomal homologous recombination events in populations of plant siblings. Plant Mol Biol 28:281–292

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran V, Chen X (2008) Small RNA metabolism in Arabidopsis. Trends Plant Sci 13:368–374

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  PubMed  Google Scholar 

  • Shaked H, Avivi-Ragolsky N, Levy AA (2006) Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics 173:985–994

    Article  CAS  PubMed  Google Scholar 

  • Spoel SH, Dong X (2008) Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe 3:348–351

    Article  CAS  PubMed  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  CAS  PubMed  Google Scholar 

  • Takeda S, Tadele Z, Hofmann I, Probst AV, Angelis KJ, Kaya H, Araki T, Mengiste T, Mittelsten Scheid O, Shibahara K, Scheel D, Paszkowski J (2004) BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes Dev 18:782–793

    Article  CAS  PubMed  Google Scholar 

  • Taylor NL, Tan YF, Jacoby RP, Millar AH (2009) Abiotic environmental stress induced changes in the Arabidopsis thaliana chloroplast, mitochondria and peroxisome proteomes. J Proteomics 72:367–378

    Article  CAS  PubMed  Google Scholar 

  • Vaucheret H (2008) Plant ARGONAUTES. Trends Plant Sci 13:350–358

    Article  CAS  PubMed  Google Scholar 

  • Vazquez F (2006) Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci 11:460–468

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    Article  CAS  PubMed  Google Scholar 

  • Wiermer M, Feys BJ, Parker JE (2005) Plant immunity: the EDS1 regulatory node. Curr Opin Plant Biol 8:383–389

    Article  CAS  PubMed  Google Scholar 

  • Wyatt MD, Pittman DL (2006) Methylating agents and DNA repair responses: methylated bases and sources of strand breaks. Chem Res Toxicol 19:1580–1594

    Article  CAS  PubMed  Google Scholar 

  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104

    Article  PubMed  Google Scholar 

  • Xie Z, Allen E, Wilken A, Carrington JC (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA 102:12984–12989

    Article  CAS  PubMed  Google Scholar 

  • Yang JH, Seo HH, Han SJ, Yoon EK, Yang MS, Lee WS (2008) Phytohormone abscisic acid control RNA-dependent RNA polymerase 6 gene expression and post-transcriptional gene silencing in rice cells. Nucleic Acids Res 36:1220–1226

    Article  CAS  PubMed  Google Scholar 

  • Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19:2164–2175

    Article  CAS  PubMed  Google Scholar 

  • Zhang JF, Yuan LJ, Shao Y, Du W, Yan DW, Lu YT (2008) The disturbance of small RNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis. Plant Cell Environ 31:562–574

    Article  CAS  PubMed  Google Scholar 

  • Zheng B, Wang Z, Li S, Yu B, Liu JY, Chen X (2009) Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev 23:2850–2860

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We would like to thank Valentina Titova and Zoe Migicovsky for proofreading the manuscript. The authors acknowledge NSERC Discovery and HFSP grant to IK.

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Author notes

  1. Todd Blevins

    Present address: Department of Biology, Indiana University, Bloomington, IN, USA

Authors and Affiliations

  1. Department of Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, AB, T1K 3M4, Canada

    Youli Yao, Andriy Bilichak, Andrey Golubov & Igor Kovalchuk

  2. Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland

    Todd Blevins

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  1. Youli Yao
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  2. Andriy Bilichak
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Corresponding author

Correspondence to Igor Kovalchuk.

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Communicated by E. Guiderdoni.

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Yao, Y., Bilichak, A., Golubov, A. et al. Differential sensitivity of Arabidopsis siRNA biogenesis mutants to genotoxic stress. Plant Cell Rep 29, 1401–1410 (2010). https://doi.org/10.1007/s00299-010-0930-9

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  • DOI: https://doi.org/10.1007/s00299-010-0930-9

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