Abstract
Key message
The binding site for miR398 in an isoform of Cu/Zn superoxide dismutase (CSD1) is eliminated by alternative splicing to bypass miR398-mediated gene down-regulation under drought stress.
Abstract
MicroRNA (miRNA) binding sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generate functional MBSs in target transcripts. MBSs can also be excluded during splicing of pre-messenger RNA, leading to different regulation among isoforms. Previous studies have shown that levels of Cu/Zn superoxide dismutase (CSD) are down-regulated by miR398. In this study, sequences and transcript levels of peanut CSD1 isoforms (AhCSD1-1, AhCSD1-2.1, and AhCSD1-2.2) were analyzed under the drought stress. Results demonstrated that a miR398 binding site is eliminated in AhCSD1-2.2 as a consequence of alternative splicing, which bypasses miRNA-mediated down-regulation under drought stress. This alternative isoform was not only identified in peanut but also in soybean and Arabidopsis. In addition, transgenic Arabidopsis plants expressing AhCSD1 were more tolerant to osmotic stress. We hypothesize that the level of AhCSD1 is increased to allow diverse plant responses to overcome environmental challenges even in the presence of increased miR398 levels. These findings suggest that studies on the role of alternatively spliced MBSs affecting transcript levels are important for understanding plant stress responses.
Similar content being viewed by others
References
Afonso-Grunz F, Müller S (2015) Principles of miRNA–mRNA interactions: beyond sequence complementarity. Cell Mol Life Sci 72:3127–3141. doi:10.1007/s00018-015-1922-2
Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159. doi:10.1146/annurev-arplant-050312-120043
Azevedo Neto AD, Nogueira RJMC, Melo Filho PA, Santos RC (2009) Physiological and biochemical responses of peanut genotypes to water deficit. J Plant Interact 5:1–10 doi:10.1080/17429140902999243
Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743
Dang P, Chen C (2013) Modified method for combined DNA and RNA isolation from peanut and other oil seeds. Mol Biol Rep 40:1563–1568. doi:10.1007/s11033-012-2204-9
Ding Y, Tao Y, Zhu C (2013) Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot 64(11):3077–3086. doi:10.1093/jxb/ert164
Fang Y, Xie K, Xiong L (2014) Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J Exp Bot 65:2119–2135
Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930. doi:10.1016/j.plaphy.2010.08.016
Guan Q, Lu X, Zeng H, Zhang Y, Zhu J (2013) Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis. Plant J 74:840–851. doi:10.1111/tpj.12169
Jing X et al (2015) Overexpression of copper/zinc superoxide dismutase from mangrove Kandelia candel in tobacco enhances salinity tolerance by the reduction of reactive oxygen species in chloroplast. Front Plant Sci. doi:10.3389/fpls.2015.00023
Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799. doi:10.1016/j.molcel.2004.05.027
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53. doi:10.1146/annurev.arplant.57.032905.105218
Kitagawa N et al (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21:1758–1763. doi:10.1093/bioinformatics/bti253
Krapovickas A, Walton CG, Williams DE, Simpson CE (2007) Taxonomy of the genus Arachis (Leguminosae). Bonplandia 16:7–205. doi:10.2307/41941433
Kulcheski FR, Marcelino-Guimaraes FC, Nepomuceno AL, Abdelnoor RV, Margis R (2010) The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Anal Biochem 406:185–192. doi:10.1016/j.ab.2010.07.020
Leal-Bertioli SCM et al (2012) The effect of tetraploidization of wild Arachis on leaf morphology and other drought-related traits. Environ Exp Bot 84:17–24. doi:10.1016/j.envexpbot.2012.04.005
Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605–1619
Marquez Y, Brown JWS, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22:1184–1195. doi:10.1101/gr.134106.111
Mazzucotelli E, Mastrangelo AM, Crosatti C, Guerra D, Stanca AM, Cattivelli L (2008) Abiotic stress response in plants: when post-transcriptional and post-translational regulations control transcription. Plant Sci 174:420–431. doi:10.1016/j.plantsci.2008.02.005
Mehta R et al (2013) Coat protein-mediated transgenic resistance of peanut (Arachis hypogaea L.) to peanut stem necrosis disease through Agrobacterium-mediated genetic transformation Indian. J Virol 24:205–213. doi:10.1007/s13337-013-0157-9
Ni Z, Hu Z, Jiang Q, Zhang H (2012) Overexpression of gma-MIR394a confers tolerance to drought in transgenic Arabidopsis thaliana. Biochem Biophys Res Commun 427:330–335
Ni Z, Hu Z, Jiang Q, Zhang H (2013) GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant Mol Biol 82:113–129. doi:10.1007/s11103-013-0040-5
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 12:1484–1495
Park SY et al (2007) The senescence-induced staygreen protein regulates chlorophyll degradation. Plant Cell 19:1649–1664. doi:10.1105/tpc.106.044891
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626. doi:10.1101/gad.1004402
Remans T, Opdenakker K, Guisez Y, Carleer R, Schat H, Vangronsveld J, Cuypers A (2012) Exposure of Arabidopsis thaliana to excess Zn reveals a Zn-specific oxidative stress signature. Environ Exp Bot 84:61–71. doi:10.1016/j.envexpbot.2012.05.005
Ryan BM, Robles AI, Harris CC (2010) Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 10:389–402. doi:10.1038/nrc2867
Song JB, Gao S, Sun D, Li H, Shu XX, Yang ZM (2013) miR394 and LCR are involved in Arabidopsis salt and drought stress responses in an abscisic acid-dependent manner. BMC Plant Biol 13:210. doi:10.1186/1471-2229-13-210
Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21:805–811. doi:10.1016/j.semcdb.2010.04.001
Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019. doi:10.1105/tpc.104.022830
Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18:2051–2065. doi:10.1105/tpc.106.041673
Sunkar R, Li Y-F, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203. doi:10.1016/j.tplants.2012.01.010
Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231:705–716. doi:10.1007/s00425-009-1078-0
Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs plant. Methods 3:12. doi:10.1186/1746-4811-3-12
Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genom 12:367. doi:10.1186/1471-2164-12-367
Wu C-T, Chiou C-Y, Chiu H-C, Yang U-C (2013) Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element. BMC Genom 14:1–12. doi:10.1186/1471-2164-14-438
Wu J, Zhang J, Li X, Xu J, Wang L (2016) Identification and characterization of a PutCu/Zn-SOD gene from Puccinellia tenuiflora (Turcz.) Scribn. et Merr. Plant Growth Regul 79:55–64. doi:10.1007/s10725-015-0110-6
Xia K et al (2012) OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS ONE 7:e30039
Yamasaki H, Abdel-Ghany SE, Cohu CM, Kobayashi Y, Shikanai T, Pilon M (2007) Regulation of copper homeostasis by micro-RNA in Arabidopsis. J Biol Chem 282:16369–16378. doi:10.1074/jbc.M700138200
Yang X, Zhang H, Li L (2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J 70:421–431. doi:10.1111/j.1365-313X.2011.04882.x
Yi F, Xie S, Liu Y, Qi X, Yu J (2013) Genome-wide characterization of microRNA in foxtail millet (Setaria italica). BMC Plant Biol 13:212
Zhang X et al (2015) Molecular analysis of the chloroplast Cu/Zn-SOD gene (AhCSD2) in peanut. Crop J 3:246–257. doi:10.1016/j.cj.2015.03.006
Zhao CZ et al (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10:3. doi:10.1186/1471-2229-10-3
Zhou M, Luo H (2014) Role of microRNA319 in creeping bentgrass salinity and drought stress response. Plant Signal Behav 9(4):e28700. doi:10.4161/psb.28700
Zhou M, Li D, Li Z, Hu Q, Yang C, Zhu L, Luo H (2013) Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol 161:1375–1391. doi:10.1104/pp.112.208702
Acknowledgements
This work was supported in part by the USDA National Institute of Food and Agriculture, Hatch Project 221820. We thank Drs. Maria Balota, Ruth Grene, Xiaofeng Wang, Eva Collakova and Qian Zhang for valuable suggestions.
Author information
Authors and Affiliations
Contributions
SP and EG designed of the work, SP performed research, SP analyzed data, SP and EG wrote the paper.
Corresponding author
Ethics declarations
Conflict of interest
All authors declare that they have no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Park, SY., Grabau, E. Bypassing miRNA-mediated gene regulation under drought stress: alternative splicing affects CSD1 gene expression. Plant Mol Biol 95, 243–252 (2017). https://doi.org/10.1007/s11103-017-0642-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-017-0642-4