Journal of Applied Biological Chemistry

The Korean Society for Applied Biological Chemistry (한국응용생명화학회)
권호 표지
DOI QR코드

DOI QR Code

Non-coding RNAs Associated with Biotic and Abiotic Stresses in Plants

  • Kang, Han-Chul (Department of Functional Bio-material, National Academy of Agricultural Science, Rural Development Administration) ;
  • Yoon, Sang-Hong (Department of Functional Bio-material, National Academy of Agricultural Science, Rural Development Administration) ;
  • Lee, Chang-Muk (Department of Functional Bio-material, National Academy of Agricultural Science, Rural Development Administration) ;
  • Koo, Bon-Sung (Department of Functional Bio-material, National Academy of Agricultural Science, Rural Development Administration)
  • Received : 2012.03.29
  • Accepted : 2012.05.15
  • Published : 2012.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Many of biochemical or physiological processes can be regulated by non-coding RNAs as well as coding RNAs in plants, animals and microbes. Recently, many small RNAs including microRNAs (miRNAs) and endogenous small interference RNAs (siRNAs) and long non-coding RNAs have been discovered from ubiquitous organisms including plants. Biotic and abiotic stresses are main causal agents of crop losses all over the world. Much efforts have been performed for understanding the complex mechanism of stress responses. Up to date, many of these researches have been related with the identification and investigation of stress-related proteins, showing limitation to resolve the complex mechanism. Recently, non-coding RNAs as well as coding genes have been gradually interested because of its potential roles in plant stress responses as well as other biophysical aspects. In this review, various potential roles of non-coding RNAs, especially miRNAs and siRNAs, are reviewed in relation with plant biotic and abiotic stresses.

Keywords

References

  1. Achard P, Herr A, Baulcombe DC, and Harberd NP (2004) Modulation of floral development by a gibberellins-regulated microRNA. Development 13, 3357-65.
  2. Agorio A and Vera P (2007) Agronaute4 is required for resistance to Pseudomonas syringae in Arabidopsis. Plant Cell 19, 3778-90. https://doi.org/10.1105/tpc.107.054494
  3. Akbergenev R, Si-Ammour A, Bievins T, and Amin I (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34, 462-71. https://doi.org/10.1093/nar/gkj447
  4. Allen E, Xie Z, Gustafson AM, and Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207-21. https://doi.org/10.1016/j.cell.2005.04.004
  5. Bari R, Pant B, Stitt M, and Scheible WR (2006) microRNA399 and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141, 988- 99. https://doi.org/10.1104/pp.106.079707
  6. Bartel DP (2004) microRNAs; genomics, biogenesis, mechanism and function. Cell 116, 281-97. https://doi.org/10.1016/S0092-8674(04)00045-5
  7. Baulcombe D (2004) RNA silencing in plants. Nature 431, 356-63. https://doi.org/10.1038/nature02874
  8. Bazzini AA, Hopp HE, and Beachy RN (2007) Infection and coaccumulation of tobacco mosaic virus proteins alter microRNA levels, correlating with symptom and plant development. Proc Natl Acad Sci USA 104, 12157- 62. https://doi.org/10.1073/pnas.0705114104
  9. Ben AB, Wirth S, Merchan F, laporte P, Carafa Y, Hirsch J et al. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19, 57-69.
  10. Borsani O, Zhu J, Verslues PE, Sunkar R, and Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279-91. https://doi.org/10.1016/j.cell.2005.11.035
  11. Carr JP, Marsh LE, Lomonossoff GP, Sekiya ME, and Zaitlin (1992) Resistance to tobacco mosaic virus induced by the 54-kDa gene sequence requires expression of the 54-kDa protein. Mol Plant Microbe Interact 5, 397-404. https://doi.org/10.1094/MPMI-5-397
  12. Chendrimada TP, Finn KJ, Baillat D, Gregory RI, Liebharber S, Pasquinelli A et al. (2007) microRNA silencing through RISC recruitment of elF6. Nature 447, 823-8. https://doi.org/10.1038/nature05841
  13. Costa FF (2010) Non-coding RNAs: meet thy masters. Bioessays 32, 599- 608. https://doi.org/10.1002/bies.200900112
  14. Ding SW and Vionnet O (2007) Antiviral immunity directed by small RNAs. Cell 140, 413-26.
  15. Dunoyer P, Lecellier CH, Parizotto EA, and Himber C (2004) Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16, 1235-50. https://doi.org/10.1105/tpc.020719
  16. Dunoyer P and Vionnet O (2005) The complex interplay between plant viruses and host RNA silencing pathway. Curr Opin Plant Biol 8, 415- 23. https://doi.org/10.1016/j.pbi.2005.05.012
  17. Ellendorff U, Fradin EF, Jonge R, and Thomma BP (2009) RNA silencing is required for Arabidopsis defence against Verticillium wilt disease. J Exp Bot 60, 591-602. https://doi.org/10.1093/jxb/ern306
  18. Eulalio A, Huntzinger E, and Izaurralde E (2008) Getting to the root of miRNA-mediated gene silencing. Cell 132, 9-14. https://doi.org/10.1016/j.cell.2007.12.024
  19. Fahlgren, Howell MD, Kasschau K, and Chapman E (2007) High-throughput sequencing of Arabidopsis microRNAs. Plos One 2, 219-23. https://doi.org/10.1371/journal.pone.0000219
  20. Fuji H, Chiou TJ, Lin SI, Aung K, and Zhu JK (2005) A miRNA involved in phosphate starvation response in Arabidopsis. Curr Biol 15, 2038-43. https://doi.org/10.1016/j.cub.2005.10.016
  21. Gao P, Bai X, Yang L, Lv D, Pan X, LI Y et al. (2011) osaMIR393; a salinity and alkaline stress-related microRNA gene. Mol Biol Rep 38, 237-42. https://doi.org/10.1007/s11033-010-0100-8
  22. He H, Cai L, Skogerbo G, Deng W, and Liu T (2006) Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Res 34, 2976-83. https://doi.org/10.1093/nar/gkl371
  23. Heredia M and Jansen RP (2004) mRNA localization and the cytoskeleton. Curr Opin Cell Biol 16, 80-5. https://doi.org/10.1016/j.ceb.2003.11.002
  24. Isam F, Bjorn V, Ralf R, Wolfgang RH, and Wolfgang F (2007) Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. Plant Biol 7, 13-7.
  25. Jia X, Wang WX, REN L, Chen QJ, and Mendu V (2009) Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana. Plant Mol Biol 71, 51-9. https://doi.org/10.1007/s11103-009-9508-8
  26. Jones-Rhoades MW and Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14, 787-99. https://doi.org/10.1016/j.molcel.2004.05.027
  27. Jones-Rhoades MW, Bartel DP, and Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57, 19-53. https://doi.org/10.1146/annurev.arplant.57.032905.105218
  28. Kanno T and Habu Y (2011) siRNA-mediated chromatin maintenance and its function in Arabidopsis thaliana. Biochim Biophys Acta 1809, 444-51. https://doi.org/10.1016/j.bbagrm.2011.05.002
  29. Katiyar-Agawall S and Jin H (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 48, 225-46. https://doi.org/10.1146/annurev-phyto-073009-114457
  30. Katiyar-Agawall S, Gao S, Smith V, and Jin H (2007) A novel class of bacteria induces small RNAs in Arabidopsis. Genes Dev 21, 3123-34. https://doi.org/10.1101/gad.1595107
  31. Kawaji H and Hayashizaki Y (2008) Exploration of small RNAs. Plos One 4, 3334-6.
  32. Khraiwesh B, Zhu JK, and Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819, 137-48. https://doi.org/10.1016/j.bbagrm.2011.05.001
  33. Kim VN (2005) microRNA biogenesis: coordinate cropping and dicing. Nat Rev Mol Cell Biol 6, 376-85. https://doi.org/10.1038/nrm1644
  34. Lee RC, Feinbaum RL, and Ambros V (1993) The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-54. https://doi.org/10.1016/0092-8674(93)90529-Y
  35. Li H, Dong Y, Yin H, Wang N, Yang J, and Liu X (2011) Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol 11, 170-81. https://doi.org/10.1186/1471-2229-11-170
  36. Liu HH, Tian X, Li YU, Wu CA, and Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14, 836-43. https://doi.org/10.1261/rna.895308
  37. Llave C, Xie Z, Kasschau KD, and Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053-6. https://doi.org/10.1126/science.1076311
  38. Lu SF, Sun YH, Shi R, Clark C, Li L, and Chiang VL (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17, 2186-203. https://doi.org/10.1105/tpc.105.033456
  39. Mallory AC and Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38, 31-6. https://doi.org/10.1038/ng1791
  40. Meister G (2007) miRNAs: get an early star on translational silencing. Cell 131, 25-8. https://doi.org/10.1016/j.cell.2007.09.021
  41. Mishra AK, Agarwall S, Jain CK, and Rani V (2009) High GC content:critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana. Bioinformation 4, 151-4. https://doi.org/10.6026/97320630004151
  42. Morris KV (2005) Si-RNA-mediated transcriptional gene silencing: the potential mechanism and a possible role in the histone code. Cell Mol life Sci 62, 3057-66. https://doi.org/10.1007/s00018-005-5182-4
  43. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312, 436-9. https://doi.org/10.1126/science.1126088
  44. Navarro L, Jay F, Nomura K, He SY, and Voinnet O (2008) Suppression of the microRNA pathway by bacterial effector protein. Science 321, 964- 7. https://doi.org/10.1126/science.1159505
  45. Ponting CP, Oliver PL, and Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136, 629-41. https://doi.org/10.1016/j.cell.2009.02.006
  46. Prasanth KV and Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the genome complexity conundrum. Genes Dev 21, 11-42. https://doi.org/10.1101/gad.1484207
  47. Raja P, Sanville BC, Buchmann RC, and Bisaro DM (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J Viol 82, 8997-9007.
  48. Rother S and Meister G (2011) Small RNAs derived from non-coding RNAs. Biochimie 93, 1905-15. https://doi.org/10.1016/j.biochi.2011.07.032
  49. Ruiz-Ferrer V and Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60, 485-510. https://doi.org/10.1146/annurev.arplant.043008.092111
  50. Shami M, Pontier D, Lahmy S, Braun L, and Picart C (2007) Reiterated WG/ GW motifs form functionally and evolutionally conserved agronautebinding platforms in RNAi-related components. Genes Dev 21, 2539-44. https://doi.org/10.1101/gad.451207
  51. Simon-Mateo C and Garcia JA (2006) MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism. J Virol 80, 2429-36. https://doi.org/10.1128/JVI.80.5.2429-2436.2006
  52. Sunkar R and Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16, 2001-19. https://doi.org/10.1105/tpc.104.022830
  53. SunKar R and Zhu JK (2007) MicroRNAs and short-interfering RNAs in plants. J Intergrative Plant Biol 49, 817-26. https://doi.org/10.1111/j.1744-7909.2007.00499.x
  54. Swiezewski S, Liu F, Magusin A, and Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462, 799-802. https://doi.org/10.1038/nature08618
  55. Takeda A, Tsukuda M, Mizumoto H, and Okamato K (2005) Plant RNA virus suppresses RNA silencing through viral replication. EMBO J 24, 3147- 57. https://doi.org/10.1038/sj.emboj.7600776
  56. Trindade I, Capitao C, Dalmay T, Fevereiro MO, and Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231, 705-16. https://doi.org/10.1007/s00425-009-1078-0
  57. Tsuji H, Aya K, and Ueguchi-Tanaka M (2006) GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anothers. Plant J 47, 427-44. https://doi.org/10.1111/j.1365-313X.2006.02795.x
  58. Untiveros M, Fiuentes S, and Salazar L (2007) Synergistic interactions of sweet potato chlorotic stunt virus (Crinivirus) with Carla, Cucumo, Ipomo and potyviruses infecting sweet potato. Plant Disease 91, 669-76. https://doi.org/10.1094/PDIS-91-6-0669
  59. Xie X, Kasschau KD, and Carrington JC (2003) Negative feedback regulation of Dicer-like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 13, 784-9. https://doi.org/10.1016/S0960-9822(03)00281-1
  60. Vaucheret H, Vazquez F, Crete P, and Bartel DP (2004) The action of argonaute 1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18, 1187-97. https://doi.org/10.1101/gad.1201404
  61. Wang JF, Zhou H, Chen YQ, Luo QJ, and QU LH (2004) Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res 32, 1688-95. https://doi.org/10.1093/nar/gkh332
  62. Zhao B, Ge L, Liang R, Li W, and Ruan K (2009) Members of miR169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10, 29-34. https://doi.org/10.1186/1471-2199-10-29
  63. Zhou L, Liu Y, Liu Z, Kong D, Duan M, and Luo L (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61, 4157-68. https://doi.org/10.1093/jxb/erq237
  64. Zhou X, Wang G, Sutoh K, Zhu JK, and Zhang W (2008) Identification of cold-inducible miRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1031, 780-8.
  65. Zhou X, Wang G, and Zhang W (2007) UV-responsive microRNA genes in Arabidopsis thaliana. Mol Syst Biol 3, 103-9.