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Plant Biology

Alternative splicing regulates autophagy in response to environmental stresses in cucumber (Cucumis sativus)

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Article: 2195987 | Received 01 Dec 2022, Accepted 08 Feb 2023, Published online: 04 Apr 2023

References

  • Calixto CP, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JW. 2018. Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell. 30(7):1424–1444.
  • Capovilla G, Delhomme N, Collani S, Shutava I, Bezrukov I, Symeonidi E, de Francisco Amorim M, Laubinger S, Schmid M. 2018. PORCUPINE regulates development in response to temperature through alternative splicing. Nat Plants. 4(8):534–539.
  • Chaudhary S, Kalkal M. 2021. Rice transcriptome analysis reveals nitrogen starvation modulates differential alternative splicing and transcript usage in various metabolism-related genes. Life. 11(4):285.
  • Chung T, Suttangkakul A, Vierstra RD. 2009. The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol. 149(1):220–234.
  • Dai Z, Dong S, Miao H, Liu X, Han J, Li C, Gu X, Zhang S. 2022. Genome-wide identification of TIFY genes and their response to various pathogen infections in cucumber (Cucumis sativus L.). Sci Hortic. 295:110814.
  • Filichkin SA, Mockler TC. 2012. Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes. Biol Direct. 7(1):1–15.
  • Ganie SA, Reddy AS. 2021. Stress-induced changes in alternative splicing landscape in rice: functional significance of splice isoforms in stress tolerance. Biology. 10(4):309.
  • Gao R, Luo Y, Yun F, Wu X, Wang P, Liao W. 2021. Genome-wide identification, expression profile, and alternative splicing analysis of CAMTA family genes in cucumber (Cucumis sativus L.). Agronomy. 11(9):1827.
  • Han Y, Yang Y, Wang Y, Elsheery NI, Ding G. 2021. Genome-wide identification and expression analysis of autophagy genes in cucumber. Res Sq. doi:10.21203/rs.3.rs-359244/v1.
  • Huang S, Li R, Zhang Z, Li LI, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, et al. 2009. The genome of the cucumber, Cucumis sativus L. Nat Genet. 41(12):1275–1281.
  • Huo L, Guo Z, Jia X, Sun X, Wang P, Gong X, Ma F. 2020. Increased autophagic activity in roots caused by overexpression of the autophagy-related gene MdATG10 in apple enhances salt tolerance. Plant Sci. 294:110444.
  • John S, Olas JJ, Mueller-Roeber B. 2021. Regulation of alternative splicing in response to temperature variation in plants. J Exp Bot. 72(18):6150–6163.
  • Kazan K. 2003. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends Plant Sci. 8(10):468–471.
  • Kim DJ. 2004. A study of cotyledon senescence in cucumber (Cucumis sativus L.) based on expressed sequence tags and gene expression. J Plant Biol. 47(3):244–253.
  • Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, Baba M, Baehrecke EH, Bahr BA, Ballabio A, et al. 2008. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy. 4(2):151–175.
  • Laloum T, Martín G, Duque P. 2018. Alternative splicing control of abiotic stress responses. Trends Plant Sci. 23(2):140–150.
  • Lam PY, Wang L, Lo C, Zhu FY. 2022. Alternative splicing and its roles in plant metabolism. Int J Mol Sci. 23(13):7355.
  • Liu C, Ma H, Wu J, Huang Q, Liu JO, Yu L. 2013. Arginine68 is an essential residue for the C-terminal cleavage of human Atg8 family proteins. BMC Cell Biol. 14(1):1–12.
  • Liu Y, Bassham DC. 2012. Autophagy: pathways for self-eating in plant cells. Annu Rev Plant Biol. 63:215–237.
  • Liu Y, Xiong Y, Bassham DC. 2009. Autophagy is required for tolerance of drought and salt stress in plants. Autophagy. 5(7):954–963.
  • Ma SH, He GQ, Navarro-Payá D, Santiago A, Cheng YZ, Jiao JB, Li H-J, Zuo D-D, Sun H-T, Pei M-S, et al. 2023. Global analysis of alternative splicing events based on long-and short-read RNA sequencing during grape berry development. Gene. 852:147056.
  • Matsukura S, Mizoi J, Yoshida T, Todaka D, Ito Y, Maruyama K, … Yamaguchi-Shinozaki K. 2010. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Mol Genet Genomics. 283(2):185–196.
  • Mizushima N. 2007. Autophagy: process and function. Genes Dev. 21(22):2861–2873.
  • Oka M, Shimoda Y, Sato N, Inoue J, Yamazaki T, Shimomura N, Fujiyama H. 2012. Abscisic acid substantially inhibits senescence of cucumber plants (Cucumis sativus) grown under low nitrogen conditions. J Plant Physiol. 169(8):789–796.
  • Ouyang DY, Xu LH, He XH, Zhang YT, Zeng LH, Cai JY, Ren S. 2013. Autophagy is differentially induced in prostate cancer LNCaP, DU145 and PC-3 cells via distinct splicing profiles of ATG5. Autophagy. 9(1):20–32.
  • Palusa SG, Ali GS, Reddy AS. 2007. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J. 49(6):1091–1107.
  • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 40(12):1413–1415.
  • Park SM, Ou J, Chamberlain L, Simone TM, Yang H, Virbasius CM, Ali A, Zhu L, Mukherjee S, Raza A, Green MR. 2016. U2AF35 (S34F) promotes transformation by directing aberrant ATG7 pre-mRNA 3′ end formation. Mol Cell. 62(4):479–490.
  • Pei D, Zhang W, Sun H, Wei X, Yue J, Wang H. 2014. Identification of autophagy-related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses. Plant Cell Rep. 33(10):1697–1710.
  • Pérez-Martín M, Pérez-Pérez ME, Lemaire SD, Crespo JL. 2014. Oxidative stress contributes to autophagy induction in response to endoplasmic reticulum stress in Chlamydomonas reinhardtii. Plant Physiol. 166(2):997–1008.
  • Pérez-Pérez ME, Florencio FJ, Crespo JL. 2010. Inhibition of target of rapamycin signaling and stress activate autophagy in Chlamydomonas reinhardtii. Plant Physiol. 152(4):1874–1888.
  • Punzo P, Grillo S, Batelli G. 2020. Alternative splicing in plant abiotic stress responses. Biochem Soc Trans. 48(5):2117–2126.
  • Rigo R, Bazin J, Crespi M, Charon C. 2019. Alternative splicing in the regulation of plant–microbe interactions. Plant Cell Physiol. 60(9):1906–1916.
  • Rose TL, Bonneau L, Der C, Marty-Mazars D, Marty F. 2006. Starvation-induced expression of autophagy-related genes in Arabidopsis. Biol Cell. 98(1):53–67.
  • Signorelli S, Tarkowski ŁP, Van den Ende W, Bassham DC. 2019. Linking autophagy to abiotic and biotic stress responses. Trends Plant Sci. 24(5):413–430.
  • Song XS, Hu WH, Mao WH, Ogweno JO, Zhou YH, Yu JQ. 2005. Response of ascorbate peroxidase isoenzymes and ascorbate regeneration system to abiotic stresses in Cucumis sativus L. Plant Physiol Biochem. 43(12):1082–1088.
  • Sreeratree J, Butsayawarapat P, Chaisan T, Somta P, Juntawong P. 2022. RNA-Seq reveals waterlogging-triggered root plasticity in mungbean associated with ethylene and jasmonic acid signal integrators for root regeneration. Plants. 11(7):930.
  • Su W, Bao Y, Yu X, Xia X, Liu C, Yin W. 2020. Autophagy and its regulators in response to stress in plants. Int J Mol Sci. 21(23):8889.
  • Sun X, Wang P, Jia X, Huo L, Che R, Ma F. 2018a. Improvement of drought tolerance by overexpressing MdATG18a is mediated by modified antioxidant system and activated autophagy in transgenic apple. Plant Biotechnol J. 16(2):545–557.
  • Sun Y, Hou H, Song H, Lin K, Zhang Z, Hu J, Pang E. 2018b. The comparison of alternative splicing among the multiple tissues in cucumber. BMC Plant Biol. 18(1):1–12.
  • Suttangkakul A, Li F, Chung T, Vierstra RD. 2011. The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. Plant Cell. 23(10):3761–3779.
  • Wang P, Nolan TM, Yin Y, Bassham DC. 2020a. Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis. Autophagy. 16(1):123–139.
  • Wang Y, Xu J, Ge M, Ning L, Hu M, Zhao H. 2020b. High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize. BMC Genomics. 21(1):1–19.
  • Wei L, Deng XG, Zhu T, Zheng T, Li PX, Wu JQ, Zhang DW, Lin HH. 2015. Ethylene is involved in brassinosteroids induced alternative respiratory pathway in cucumber (Cucumis sativus L.) seedlings response to abiotic stress. Front Plant Sci. 6:982.
  • Xia K, Liu TAO, Ouyang J, Wang R, Fan T, Zhang M. 2011. Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.). DNA Res. 18(5):363–377.
  • Xin M, Wang L, Liu Y, Feng Z, Zhou X, Qin Z. 2017. Transcriptome profiling of cucumber genome expression in response to long-term low nitrogen stress. Acta Physiol Plant. 39(6):1–11.
  • Yan X, Bai D, Song H, Lin K, Pang E. 2021. Alternative splicing during fruit development among fleshy fruits. BMC Genomics. 22(1):1–14.
  • Yang Z, Klionsky DJ. 2009. An overview of the molecular mechanism of autophagy. Autophagy Infect Immunity. 1–32.
  • Yoshimoto K, Hanaoka H, Sato S, Kato T, Tabata S, Noda T, Ohsumi Y. 2004. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. Plant Cell. 16(11):2967–2983.
  • Zhang J, Yang W, Yue J, Liu Y, Pei D, Wang H. 2020. The responses of wheat autophagy and ATG8 family genes to biotic and abiotic stresses. J Plant Growth Regul. 39(2):867–876.
  • Zheng J, Liu F, Zhu C, Li X, Dai X, Yang B, Zou X, Ma Y. 2019. Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses. PLoS One. 14(7):e0219775.
  • Zhou J, Wang J, Cheng Y, Chi YJ, Fan B, Yu JQ, Chen Z. 2013. NBR1-mediated selective autophagy targets insoluble ubiquitinated protein aggregates in plant stress responses. PLoS Genet. 9(1):e1003196.