Identification of the DEAD-box RNA helicase family members in grapevine reveals that VviDEADRH25a confers tolerance to drought stress

doi:10.1016/S2095-3119(21)63870-4

摘要/Abstract

摘要：

DEAD-box是RNA解旋酶家族中最大的亚家族之一，在植物的生长发育及其逆境胁迫中发挥着关键作用。此前有研究表明了DEAD-box基因在拟南芥和番茄、水稻等作物物种干旱胁迫响应中的潜力，但有关葡萄DEAD-box基因的功能尚不清楚。本研究在葡萄中共鉴定出40个DEAD-box基因，并对其蛋白序列特征、基因结构、染色体位置、顺式作用元件进行了分析，并比较了VviDEADRHs在干旱胁迫下的表达模式，筛选出9个可能在葡萄干旱胁迫过程中发挥关键作用VviDEADRHs (VviDEADRH10c，-13，-22，-25a，-25b，-33，-34，-36，-39)。结合qRT-PCR结果，选择VviDEADRH25a进行功能验证。在拟南芥中过表达VviDEADRH25a促使植株对干旱胁迫更加敏感，电解质渗透率和丙二醛含量均显著增加，叶绿素含量、超氧化物歧化酶 (SOD)、过氧化物酶 (POD)、过氧化氢酶 (CAT)和抗坏血酸过氧化物酶 (APX)酶活性显著降低。此外，VviDEADRH25a过表达植株中与干旱胁迫相关的几个标记基因 (AtCOR15a、AtRD29a、AtERD15、AtP5CS1) 的表达水平下调。综上所述，本研究为葡萄DEAD-box RNA解旋酶基因的结构、进化提供了理论基础，为提高葡萄干旱耐受性研究提供了新的见解。

Abstract: Grapevine growing areas are increasingly affected by drought, which has greatly limited global wine production and quality. DEAD-box is one of the largest subfamilies of the RNA helicase family, and its members play key roles in the growth and development of plants and their stress responses. Previous studies have shown the potential of DEAD-box genes in the drought stress responses of Arabidopsis and tomato, rice, and other crop species. However, information about DEAD-box genes in grapevine remains limited. In this report, a total of 40 DEAD-box genes were identified in grapevine and their protein sequence characteristics and gene structures were analyzed. By comparing the expression profiles of VviDEADRHs in response to drought stress in different grapevine varieties, nine candidate genes (VviDEADRH10c, -13, -22, -25a, -25b, -33, -34, -36, and -39) were screened based on expression profiling data. Combined with qRT-PCR results, VviDEADRH25a was selected for functional verification. Heterologous overexpression of VviDEADRH25a in Arabidopsis showed the transgenic plants were more sensitive to drought stress than the control. Both electrolyte permeability and malondialdehyde content were significantly increased in transgenic plants, whereas the chlorophyll content and superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) enzyme activities were significantly decreased. Furthermore, VviDEADRH25a-overexpressing plants showed down-regulated expression levels of several drought stress-related marker genes, namely AtCOR15a, AtRD29A, AtERD15, and AtP5CS1, which indicated that they participated in the drought stress response. In summary, this study provides new insights into the structure, evolution, and participation of DEAD-box RNA helicase genes in the response to drought stress in grapevines.

Key words: grapevine , gene family identification , drought stress , DEAD-box RNA helicase , overexpression

. [J]. Journal of Integrative Agriculture, 2022, 21(5): 1357-1374.

YANG Sheng-di, GUO Da-long, PEI Mao-song, WEI Tong-lu, LIU Hai-nan, BIAN Lu, YU Ke-ke, ZHANG Guo-hai, YU Yi-he. Identification of the DEAD-box RNA helicase family members in grapevine reveals that VviDEADRH25a confers tolerance to drought stress[J]. Journal of Integrative Agriculture, 2022, 21(5): 1357-1374.

参考文献

Apel K, Hirt H. 2004. Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annual Review of Plant Biology, 55, 373–399.
Baek W, Lim C W, Lee S C. 2018. A DEAD-box RNA helicase, RH8, is critical for regulation of ABA signalling and the drought stress response via inhibition of PP2CA activity. Plant, Cell & Environment, 41, 1593–1604.
Banavath J N, Chakradhar T, Pandit V, Konduru S, Guduru K K, Akila C S, Podha S, Puli C O R. 2018. Stress inducible overexpression of AtHDG11 leads to improved drought and salt stress tolerance in peanut (Arachis hypogaea L.). Frontiers in Chemistry, 6, 34.
Banu S A, Huda K M K, Tuteja N. 2014. Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrobacterium-mediated transient assay. Plant Signaling & Behavior, 9, e28992.
Cai J, Meng X Q, Li G, Dong T T, Sun J, Xu T, Li Z Y, Han Y H, Zhu M K. 2018. Identification, expression analysis, and function evaluation of 42 tomato DEAD-box RNA helicase genes in growth development and stress response. Acta Physiologiae Plantarum, 40, 1–11.
Causton H C, Ren B, Koh S S, Harbison C T, Kanin E I, Jennings E G, Lee T I, True H L, Lander E S, Young R A. 2001. Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of the Cell, 12, 323–337.
Chen C J, Chen H, Zhang Y, Thomas H, Frank M, He Y H, Xia R. 2020. TBtools - An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13, 1194–1202.
Chen J, Zhang Y J, Liu J B, Xia M X, Wang W, Shen F F. 2014. Genome-wide analysis of the RNA helicase gene family in Gossypium raimondii. International Journal of Molecular Sciences, 15, 4635–4656.
Chen R C, Wu P W, Cao D Y, Tian H Q, Chen C K, Zhu B Z. 2019. Edible coatings inhibit the postharvest berry abscission of table grapes caused by sulfur dioxide during storage. Postharvest Biology and Technology, 152, 1–8.
Consortium T G. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635.
Craig E A, Gross C A. 1991. Is hsp70 the cellular thermometer? Trends in Biochemical Sciences, 16, 135–140.
Du Y T, Zhao M J, Wang C T, Gao Y, Wang Y X, Liu Y W, Chen M, Chen J, Zhou Y B, Xu Z S, Ma Y Z. 2018. Identification and characterization of GmMYB118 responses to drought and salt stress. BMC Plant Biology, 18, 1–18.
Fanizza G, Ricciardi L. 2015. Influence of drought stress on shoot, leaf growth, leaf water potential, stomatal resistance in wine grape genotypes (Vitis vinifera L.). Vitis, 29, 371.
Gasch A P, Spellman P T, Kao C M, Carmelharel O, Eisen M B, Storz G, Botstein D, Brown P O. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell, 11, 4241–4257.
Gaut B S, Morton B R, McCaig B C, Clegg M T. 1996. Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proceedings of the National Academy of Sciences of the United States of America, 93, 10274–10279.
Grimplet J, Adam-Blondon A F, Bert P F, Bitz O, Cantu D, Davies C, Delrot S, Pezzotti M, Rombauts S, Cramer G R. 2014. The grapevine gene nomenclature system. BMC Genomics, 15, 1–14.
Guan Q M, Wu J M, Zhang Y Y, Jiang C H, Liu R Y, Chai C L, Zhu J H. 2013. A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell, 25, 342–356.
Guo R R, Qiao H B, Zhao J, Wang X H, Tu M X, Guo C L, Wan R, Li Z, Wang X P. 2018. The grape VlWRKY3 gene promotes abiotic and biotic stress tolerance in transgenic Arabidopsis thaliana. Frontiers in Plant Science, 9, 545.
Harindra-Champa W A, Gill M I S, Mahajan B V C, Bedi S. 2015. Exogenous treatment of spermine to maintain quality and extend postharvest life of table grapes (Vitis vinifera L.) cv. Flame Seedless under low temperature storage. LWT-Food Science and Technology, 60, 412–419.
Hilliker A K, Gao Z, Jankowsky E, Parker R. 2011. The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Molecular Cell, 43, 962–972.
Le Hir R, Castelain M, Chakraborti D, Moritz T, Dinant S, Bellini C. 2017. AtbHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana. Physiologia Plantarum, 160, 312–327.
Hondele M, Sachdev R, Heinrich S, Wang J, Vallotton P, Fontoura B M A, Weis K. 2019. DEAD-box ATPases are global regulators of phase-separated organelles. Nature, 573, 144–148.
Hopper D W, Ghan R, Schlauch K, Cramer G R. 2016. Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance. BMC Plant Biology, 16, 118–118.
Hou H M, Jia H, Yan Q, Wang X P. 2018. Overexpression of a SBP-Box gene (VpSBP16) from Chinese wild Vitis species in Arabidopsis improves salinity and drought stress tolerance. International Journal of Molecular Sciences, 19, 940.
Hsu Y F, Chen Y C, Hsiao Y C, Wang B J. Lin S Y, Cheng W H, Jauh G Y, Harada J J, Wang C S. 2014. AtRH57, a DEAD-box RNA helicase, is involved in feedback inhibition of glucose-mediated abscisic acid accumulation during seedling development and additively affects pre-ribosomal RNA processing with high glucose. The Plant Journal, 77, 119–135.
Huang C K, Huang L F, Huang J J, Wu S J, Ye C H, Lu C A. 2010. A DEAD-box protein, AtRH36, is essential for female gametophyte development and is involved in rRNA biogenesis in Arabidopsis. Plant and Cell Physiology, 51, 694–706.
Iserman C, Altamirano C D, Jegers C, Friedrich U, Zarin T, Fritsch A W, Mittasch M, Domingues A, Hersemann L, Jahnel M. 2020. Condensation of Ded1p promotes a translational switch from housekeeping to stress protein production. Cell, 181, 487–497.
Jackson D I, Lombard P B. 1993. Environmental and management practices affecting grape composition and wine quality - A review. American Journal of Enology and Viticulture, 44, 409–430.
Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463–467.
Ji X R, Yu Y H, Ni P Y, Zhang G H, Guo D L. 2019. Genome-wide identification of small heat-shock protein (HSP20) gene family in grape and expression profile during berry development. BMC Plant Biology, 19, 1–15.
Kant P, Kant S, Gordon M, Shaked R, Barak S. 2007. STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, two DEAD-box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses. Plant Physiology, 145, 814–830.
Kim J S, Kim K A, Oh T R, Park C M, Kang H. 2008. Functional characterization of DEAD-box RNA helicases in Arabidopsis thaliana under abiotic stress conditions. Plant and Cell Physiology, 49, 1563–1571.
Kruger C, Benecke B. 1981. In vitro translation of Drosophila heat-shock and non-heat-shock mRNAs in heterologous and homologous cell-free systems. Cell, 23, 595–603.
Van Leeuwen C, Tregoat O, Chone X, Bois B, Pernet D, Gaudillere J. 2009. Vine water status is a key factor in grape ripening and vintage quality for red Bordeaux wine. How can it be assessed for vineyard management purposes. OENO One, 43, 121–134.
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30, 325–327.
Li D Y, Liu H Z, Zhang H J, Wang X, Song F M. 2008. OsBIRH1, a DEAD-box RNA helicase with functions in modulating defence responses against pathogen infection and oxidative stress. Journal of Experimental Botany, 59, 2133–2146.
Linder P. 2006. Dead-box proteins: A family affair - Active and passive players in RNP-remodeling. Nucleic Acids Research, 34, 4168–4180.
Linder P, Owttrim G W. 2009. Plant RNA helicases: linking aberrant and silencing RNA. Trends in Plant Science, 14, 344–352.
Lindquist S. 1986. The heat-shock response. Annual Review of Biochemistry, 55, 1151–1191.
Livak K J, Schmittgen T. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆CT method. Methods, 25, 402–408.
Montpetit B, Thomsen N D, Helmke K J, Seeliger M A, Berger J M, Weis K. 2011. A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature, 472, 238–242.
Nawaz G, Kang H. 2019. Rice OsRH58, a chloroplast DEAD-box RNA helicase, improves salt or drought stress tolerance in Arabidopsis by affecting chloroplast translation. BMC Plant Biology, 19, 1–11.
Owttrim G W. 2006. RNA helicases and abiotic stress. Nucleic Acids Research, 34, 3220–3230.
Pandey S, Muthamilarasan M, Sharma N, Chaudhry V, Dulani P, Shweta S, Jha S, Mathur S, Prasad M. 2019. Characterization of DEAD-box family of RNA helicases in tomato provides insights into their roles in biotic and abiotic stresses. Environmental and Experimental Botany, 158, 107–116.
Park J, Nguyen K T, Park E, Jeon J S, Choi G. 2013. DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis. Plant Cell, 25, 927–943.
Park J J, Yi J, Yoon J, Cho L H, Ping J, Jeong H J, Cho S K , Kim W T, An G. 2011. OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment. The Plant Journal, 65, 194–205.
Rocak S, Linder P. 2004. DEAD-box proteins: the driving forces behind RNA metabolism. Nature Reviews Molecular Cell Biology, 5, 232–241.
Romero P, Fernandezfernandez J I, Martinezcutillas A. 2010. Physiological thresholds for efficient regulated deficit-irrigation management in winegrapes grown under semiarid conditions. American Journal of Enology and Viticulture, 61, 300–312.
Stonebloom S, Burch-Smith T, Kim I, Meinke D, Mindrinos M, Zambryski P. 2009. Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata. Proceedings of the National Academy of Sciences of the United States of America, 106, 17229–17234.
Storti R V, Scott M P, Rich A, Pardue M L. 1980. Translational control of protein synthesis in response to heat shock in D. melanogaster cells. Cell, 22, 825–834.
Tanner N K, Linder P. 2001. DExD/H box RNA helicases: From generic motors to specific dissociation functions. Molecular Cell, 8, 251–262.
Teng K Q, Li J Z, Liu L, Han Y C, Du Y X, Zhang J, Sun H Z, Zhao Q Z. 2014. Exogenous ABA induces drought tolerance in upland rice: The role of chloroplast and ABA biosynthesis-related gene expression on photosystem II during PEG stress. Acta Physiologiae Plantarum, 36, 2219–2227.
Tuteja N. 2003. Plant DNA helicases: The long unwinding road. Journal of Experimental Botany, 54, 2201–2214.
Umate P, Tuteja R, Tuteja N. 2010. Genome-wide analysis of helicase gene family from rice and Arabidopsis: A comparison with yeast and human. Plant Molecular Biology, 73, 449–465.
Vashisht A A, Tuteja N. 2006. Stress responsive DEAD-box helicases: A new pathway to engineer plant stress tolerance. Journal of Photochemistry and Photobiology (B: Biology), 84, 150–160.
Wan R, Liu J R, Yang Z M, Zhu P P, Cao Q H, Xu T. 2020. Genome-wide identification, characterisation and expression profile analysis of DEAD-box family genes in sweet potato wild ancestor Ipomoea trifida under abiotic stresses. Genes Genomics, 42, 325–335.
Wang Q, Liu J, Wang Y, Zhao Y, Jiang H, Cheng B. 2015. Systematic analysis of the maize PHD-finger gene family reveals a subfamily involved in abiotic stress response. International Journal of Molecular Sciences, 16, 23517–23544.
Xu R R, Zhang S Z, Huang J G, Zheng C C. 2013. Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: A comparison with Arabidopsis and Oryza sativa. PLoS ONE, 8, e78982.
Yu Y, Xu W R, Wang, J, Wang L, Yao W K, Yang Y Z, Xu Y, Ma F L, Du Y J, Wang Y J. 2013. The Chinese wild grapevine (Vitis pseudoreticulata) E3 ubiquitin ligase Erysiphe necator-induced RING finger protein 1 (EIRP1) activates plant defense responses by inducing proteolysis of the VpWRKY11 transcription factor. New Phytologist, 200, 834–846.
Yu Y H, Bian L, Jiao Z L, Yu K K, Wan Y T, Zhang G H, Guo D L. 2019a. Molecular cloning and characterization of a grapevine (Vitis vinifera L.) serotonin N-acetyltransferase (VvSNAT2) gene involved in plant defense. BMC Genomics, 20, 1–13.
Yu Y H, Ni Z Y, Wang Y, Wan H N, Hu Z, Jiang Q Y, Sun X J, Zhang H. 2019b. Overexpression of soybean miR169c confers increased drought stress sensitivity in transgenic Arabidopsis thaliana. Plant Science, 285, 68–78.
Zhang L C, Zhao G Y, Xia C, Jia J Z, Liu X, Kong X Y. 2012. A wheat R2R3-MYB gene, TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. Journal of Experimental Botany, 63, 5873–5885.
Zhu M K, Chen G P, Dong T T, Wang L L, Zhang J L, Zhao Z P, Hu Z L. 2015. SlDEAD31, a putative DEAD-box RNA helicase gene, regulates salt and drought tolerance and stress-related genes in tomato. PLoS ONE, 10, e0133849