Abstract
The Late Embryogenesis Abundant (LEA) protein gene family is associated with salt and drought stress tolerance in many plant species. However, the number of LEA-encoding genes in the grape (Vitis vinifera) genome has not been previously determined. Here, we conducted a phylogenetic analysis to identify individual members of the LEA gene family in V. vinifera. This analysis identified 60 members of this gene family classified into nine subfamilies (DHN, LEA1, LEA2, LEA3, LEA4, LEA5, LEA6, WHY and SMP) in the grape genome. With 35 members, the LEA2 subfamily constituted the largest subgroup. LEA-encoding genes are non-randomly distributed across most grape chromosomes, suggesting that, similarly to other species, a significant portion of VvLEAs was originated by segmental or tandem duplications. Bioinformatic analyses suggested that the majority of the grape LEA2 proteins is associated with plasma membrane whilst many members of other families are likely to be found in different subcellular locations such as cytoplasm, nucleus and mitochondria. The promoters of these genes contain cis-acting sequence elements associated with stress responses. Expression profiles of a subset of LEA-encoding genes from publically available Affymetrix Vitis vinifera (grape) Genome Array expression data showed that these genes are responsive to salt and dehydration. We also experimentally studied stress-responsive expression patterns of VvDHN1 encoding a dehydrin (DHN) and VvLEA D29L (VvLEA D29Like) encoding a LEA4 protein in the grape cultivar V. vinifera L. cvs. Cabernet Sauvignon (CS) and the rootstock Solonis X riparia 1616 C (1616 C) under salt- and PEG-induced drought stress by qRT-PCR. Both VvDHN1 and VvLEA D29L responded very strongly to these stresses in 1616 C whilst VvLEA D29L was induced only in CS. In response to PEG, VvLEA D29L was induced in both genotypes whilst VvDHN1 showed induction only in CS. Overall, our results suggest the LEA gene family is associated with stress tolerance and manipulation of these genes might provide increased stress tolerance in grapes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Artur MAS, Zhao T, Ligterink W, Schranz ME, Hilhorst HW (2018) Dissecting the genomic diversification of LATE EMBRYOGENESIS ABUNDANT (LEA) protein gene families in plants. Genome Biol Evol 11(2):459–471. https://doi.org/10.1093/gbe/evy248
Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58. https://doi.org/10.1080/07352680590910410
Battaglia M, Covarrubias AA (2013) Late embryogenesis abundant (LEA) proteins in legumes. Front Plant Sci 4:190. https://doi.org/10.3389/fpls.2013.00190
Bies-Ethève N, Gaubier-Comella P, Debures A, Lasserre E, Jobet E, Raynal M, Cooke R, Delseny M (2008) Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana. Plant Mol Biol 67:107–124. https://doi.org/10.1007/s11103-008-9304-x
Cao J, Li X (2015) Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum). Planta 241:757–772. https://doi.org/10.1007/s00425-014-2215-y
Cao Y, Xiang X, Geng M, You Q, Huang X (2017) Effect of HbDHN1 and HbDHN2 genes on abiotic stress responses in Arabidopsis. Front Plant Sci 8:470. https://doi.org/10.3389/fpls.2017.00470
Celik Altunoglu Y, Baloglu MC, Baloglu P, Yer EN, Kara S (2017) Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. Physiol Mol Biol Plants 23:5–21. https://doi.org/10.1007/s12298-016-0405-8
Charfeddine S, Saïdi MN, Charfeddine M, Gargouri-Bouzid R (2015) Genome-wide identification and expression profiling of the late embryogenesis abundant genes in potato with emphasis on dehydrins. Mol Biol Rep 42:1163–1174. https://doi.org/10.1007/s11033-015-3853-2
Close TJ (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol Plant 97:795–803. https://doi.org/10.1111/j.1399-3054.1996.tb00546.x
Cramer GR, Ergül A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC (2007) Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7:111–134. https://doi.org/10.1007/s10142-006-0039-y
Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res 46(W1):W49–W54. https://doi.org/10.1093/nar/gky316
Daldoul S, Guillaumie S, Reustle GM, Krczal G, Ghorbel A, Delrot S, Mliki A, Höfer MU (2010) Isolation and expression analysis of salt induced genes from contrasting grapevine (Vitis vinifera L.) cultivars. Plant Sci 179:489–498. https://doi.org/10.1016/j.plantsci.2010.07.017
Du D, Zhang Q, Cheng T, Pan H, Yang W, Sun L (2013) Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 40:1937–1946. https://doi.org/10.1007/s11033-012-2250-3
Gambino G, Perrone I, Gribaudo I (2008) A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal 19:520–525. https://doi.org/10.1002/pca.1078
Gao J, Lan T (2016) Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli. Sci Rep 6:19467. https://doi.org/10.1038/srep19467
Gao C, Liu Y, Wang C, Zhang K, Wang Y (2014) Expression profiles of 12 late embryogenesis abundant protein genes from Tamarix hispida in response to abiotic stress. Sci World J 2014:1–9. https://doi.org/10.1155/2014/868391
Godoy JA, Lunar R, Torres-Schumann S, Moreno J, Rodrigo RM, Pintor-Toro JA (1994) Expression, tissue distribution and subcellular localization of dehydrin TAS14 in salt-stressed tomato plants. Plant Mol Biol 26:1921–1934
Hanana M, Deluc L, Fouquet R, Daldoul S, Léon C, Barrieu F, Ghorbel A, Mliki A, Hamdi S (2008) Identification et caractérisation d’un gène de réponseà la déshydratation rd22 chez la vigne (Vitis vinifera L.). C R Biologies 331:569–578. https://doi.org/10.1016/j.crvi.2008.05.002
Hand SC, Menze MA, Toner M, Boswell L, Moore D (2011) LEA proteins during water stress: not just for plants anymore. Annu Rev Physiol 73:115–134. https://doi.org/10.1146/annurev-physiol-012110-142203
Hanin M, Brini F, Ebel C, Toda Y, Takeda S, Masmoudi K (2011) Plant dehydrins and stress tolerance: versatile proteins for complex mechanisms. Plant Signal Behav 6:1503–1509. https://doi.org/10.4161/psb.6.10.17088
Hopper DW, Ghan R, Cramer GR (2014) A rapid dehydration leaf assay reveals stomatal response differences in grapevine genotypes. Hortic Res 1:2. https://doi.org/10.1038/hortres.2014.2
Howell GS (1987) Vitis rootstocks. In: Rom RC, Carlson RF (Eds.), Rootstocks for fruit crops. A Wiley Pinter Science Publication, John Wiley and Sons, NewYork, Inc p. 451–72.
Huang Z, Zhong XJ, He J, Jin SH, Guo HD, Yu XF, Zhou Y-J, Li X, Ma MD, Chen QB, Long H (2016) Genome-wide identification, characterization, and stress-responsive expression profiling of genes encoding LEA (Late Embryogenesis Abundant) proteins in Moso bamboo (Phyllostachys edulis). PLoS One 11:e0165953. https://doi.org/10.1371/journal.pone.0165953
Hundertmark M, Hincha DK (2008) LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 9:118. https://doi.org/10.1186/1471-2164-9-118
Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Biol 47:377–403. https://doi.org/10.1146/annurev.arplant.47.1.377
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Lan T, Gao J, Zeng QY (2013) Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa. Tree Genet Genomes 9:253–264. https://doi.org/10.1007/s11295-012-0551-2
Li X, Cao J (2016) Late Embryogenesis Abundant (LEA) gene family in maize: identification, evolution, and expression profiles. Plant Mol Biol Report 34:15–28. https://doi.org/10.1007/s11105-015-0901-y
Liang Y, Xiong Z, Zheng J, Xu D, Zhu Z, Xiang J, Gan J, Raboanatahiry N, Yin Y, Li M (2016) Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus. Sci Rep 6:24265. https://doi.org/10.1038/srep24265
Ling H, Zeng X, Guo S (2016) Functional insights into the late embryogenesis abundant (LEA) protein family from Dendrobium officinale (Orchidaceae) using an Escherichia coli system. Sci Rep 6:39693. https://doi.org/10.1038/srep39693
Liu Y, Wang L, Xing X, Sun L, Pan J, Kong X, Zhang M, Li D (2013) ZmLEA3, a multifunctional group 3 LEA protein from maize (Zea mays L.), is involved in biotic and abiotic stresses. Plant Cell Physiol 54:944–959. https://doi.org/10.1093/pcp/pct047
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Luo D, Hou X, Zhang Y, Meng Y, Zhang H, Liu S, Wang X, Chen R (2019) CaDHN5, a dehydrin gene from pepper, plays an important role in salt and osmotic stress responses. Int J Mol Sci 20:E1989. https://doi.org/10.3390/ijms20081989
Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, Zhou Z, Zhang Z, Salih H, Wang K, Liu F (2018a) Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 19:6. https://doi.org/10.1186/s12863-017-0596-1
Magwanga RO, Lu P, Kirungu JN, Dong Q, Hu Y, Zhou Z, Cai X, Wang X, Hou Y, Wang K, Liu F (2018b) Cotton Late Embryogenesis Abundant (LEA2) genes promote root growth and confer drought stress tolerance in transgenic Arabidopsis thaliana. G3 (Bethesda) 8:2781–2803. https://doi.org/10.1534/g3.118.200423
Mirás-Avalos JM, Intrigliolo DS (2017) Grape composition under abiotic constrains: water stress and salinity. Front Plant Sci 8:851. https://doi.org/10.3389/fpls.2017.00851
Mota APZ, Oliveira TN, Vinson CC, Williams TCR, Costa MMC, Araujo ACG, Danchin EGJ, Grossi-de-Sá MF, Guimaraes PM, Brasileiro ACM (2019) Contrasting effects of wild Arachis dehydrin under abiotic and biotic stresses. Front Plant Sci 10:497. https://doi.org/10.3389/fpls.2019.004
Mullins MG, Bouquet A, Williams LE (1992) Biology of the grapevine. Cambridge University Press. p. 239
Muvunyi B, Yan Q, Wu F, Min X, Yan Z, Kanzana G, Wang Y, Zhang J (2018) Mining Late Embryogenesis Abundant (LEA) family genes in Cleistogenes songorica, a xerophyte perennial desert plant. Int J Mol Sci 19:3430. https://doi.org/10.3390/ijms19113430
Nagaraju M, Kumar SA, Reddy PS, Kumar A, Rao DM, Kavi Kishor PB (2019) Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PLoS One 14:e0209980. https://doi.org/10.1371/journal.pone.0209980
Padgett-Johnson M, Williams LE, Walker MA (2003) Vine water relations, gas exchange, and vegetative growth of seventeen Vitis species grown under irrigated and nonirrigated conditions in California. J Amer Soc Hort Sci 128(2):269–276. https://doi.org/10.21273/JASHS.128.2.0269
Pagliarani C, Vitali M, Ferrero M, Vitulo N, Incarbone M, Lovisolo C, Valle G, Schubert A (2017) The accumulation of miRNAs differentially modulated by drought stress is affected by grafting in grapevine. Plant Physiol 173:2180–2195. https://doi.org/10.1104/pp.16.01119
Pantaleo V, Vitali M, Boccacci P, Miozzi L, Cuozzo D, Chitarra W, Mannini F, Lovisolo C, Gambino G (2016) Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress. Sci Rep 6:20167. https://doi.org/10.1038/srep20167
Parra CS, Aguirreolea J, Sánchez-Díaz M, Irigoyen JJ, Morales F (2010) Effects of climate change scenarios on Tempranillo grapevine (Vitis vinifera L.) ripening: response to a combination of elevated CO2 and temperature, and moderate drought. Plant Soil 337:179–191. https://doi.org/10.1007/s11104-010-0514-z
Paul A, Kumar S (2013) Dehydrin2 is a stress-inducible, whereas Dehydrin1 is constitutively expressed but up-regulated gene under varied cues in tea [Camellia sinensis (L.) O. Kuntze]. Mol Biol Rep 40:3859–3863. https://doi.org/10.1007/s11033-012-2466-2
Pedrosa AM, Martins CDPS, Gonçalves LP, Costa MGC (2015) Late Embryogenesis Abundant (LEA) constitutes a large and diverse family of proteins involved in development and abiotic stress responses in sweet orange (Citrus sinensis L. Osb.). PLoS One 10:e0145785. https://doi.org/10.1371/journal.pone.0145785
Pelah D, Wang W, Altman A, Shoseyov O, Bartels D (1997) Differential accumulation of water stress-related proteins, sucrose synthase and soluble sugars in Populus species that differ in their water stress response. Physiol Plant 99:153–159. https://doi.org/10.1111/j.1399-3054.1997.tb03443.x
Prior LD, Grieve AM, Slavich PG, Cullis BR (1992) Sodium chloride and soil texture interactions in irrigated field grown Sultana grapevines. III. Soil and root system effects. Aust J Agric Res 43:1085–1100. https://doi.org/10.1071/AR9921085
Roubelakis-Angelakis KA, Zivanovitc SB (1991) A new culture medium for in vitro rhizogenesis of grapevine (Vitis spp.) genotypes. HortSci 26:1551–1553
Serra I, Strever A, Myburgh PA, Deloire A (2014) The interaction between rootstocks and cultivars (Vitis vinifera L.) to enhance drought tolerance in grapevine. Aust J Grape Wine Res 20:1–14. https://doi.org/10.1111/ajgw.12054
Sharma A, Kumar D, Kumar S, Rampuria S, Reddy AR, Kirti PB (2016) Ectopic expression of an atypical hydrophobic group 5 LEA protein from wild peanut, Arachis diogoi confers abiotic stress tolerance in tobacco. PLoS One 11:e0150609. https://doi.org/10.1371/journal.pone.0150609
Suprunova T, Krugman T, Fahima T, Chen G, Shams I, Korol A, Nevo E (2004) Differential expression of dehydrin genes in wild barley, Hordeum spontaneum, associated with resistance to water deficit. Plant Cell Environ 27:1297–1308. https://doi.org/10.1111/j.1365-3040.2004.01237.x
Tattersall EA, Grimplet J, DeLuc L, Wheatley MD, Vincent D, Osborne C, Ergül A, Lomen E, Blank RR, Schlauch KA, Cushman JC, Cramer GR (2007) Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress. Funct Integr Genomics 7:317–333
Vincent D, Ergül A, Bohlman MC, Tattersall EA, Tillett RL, Wheatley MD, Woolsey R, Quilici DR, Joets J, Schlauch K, Schooley DA, Cushman JC, Cramer GR (2007) Proteomic analysis reveals differences between Vitis vinifera L. cv. Chardonnay and cv. Cabernet Sauvignon and their responses to water deficit and salinity. J Exp Bot 58:1873–1892. https://doi.org/10.1093/jxb/erm012
Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218:1–14. https://doi.org/10.1007/s00425-003-1105-5
Wang XS, Zhu HB, Jin GL, Liu HL, Wu WR, Zhu J (2007) Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.). Plant Sci 172:414–420. https://doi.org/10.1016/j.plantsci.2006.10.004
Wong DCJ, Lopez Gutierrez R, Gambetta GA, Castellarin SD (2017) Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine. DNA Res 24:311–326
Wu C, Hu W, Yan Y, Tie W, Ding Z, Guo J, He G (2018) The Late Embryogenesis Abundant protein family in cassava (Manihot esculenta Crantz): genome-wide characterization and expression during abiotic stress. Molecules 23:1196. https://doi.org/10.3390/molecules23051196
Xiao H, Nassuth A (2006) Stress-and development-induced expression of spliced and unspliced transcripts from two highly similar dehydrin 1 genes in V. riparia and V. vinifera. Plant Cell Rep 25:968–977. https://doi.org/10.1007/s00299-006-0151-4
Yang Y, He M, Zhu Z, Li S, Xu Y, Zhang C, Singer SD, Wang Y (2012) Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. BMC Plant Biol 12:140. https://doi.org/10.1186/1471-2229-12-140
Yang J, Zhao S, Zhao B, Li C (2018) Overexpression of TaLEA3 induces rapid stomatal closure under drought stress in Phellodendron amurense Rupr. Plant Sci 277:100–109. https://doi.org/10.1007/s00299-006-0151-4
Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins: structure, Funct Bioinformatics 64:643–651
Zhu JK, Hasegawa PM, Bressan RA, Bohnert HJ (1997) Molecular aspects of osmotic stress in plants. Crit Rev Plant Sci 16:253–277. https://doi.org/10.1080/07352689709701950
Acknowledgements
This study is dedicated in memory of Ibrahime Mohammed, who died in 2015.
Funding
IM was supported by a scholarship from the Turks Abroad and Related Communities (YTB) program.
Data archiving statementThe NCBI accession numbers of the Vitis vinifera protein sequences used in phylogenetic analysis are given in the text and also in Supplementary Table 1.
Author information
Authors and Affiliations
Contributions
AE designed and outlined the research. Mİ, FM, CYÖ and SDA conducted the experiments. UK analysed the data. KK, FM and CYÖ drafted manuscript. AE, KK and BÇA edited the manuscript. All authors read and approved the manuscript.
Corresponding author
Additional information
Communicated by M. Troggio
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Supplementary Table 1
The number of LEA protein family genes identified in the grape genome and their chromosomal locations. (DOCX 18 kb)
Supplementary Table 2
Published examples of LEA gene families in different plant species. (DOCX 17 kb)
Supplementary Table 3
The distribution of various cis-acting promoter elements in the promoters of LEA encoding genes in grapes (Vitis vinifera). (DOCX 18 kb)
Supplementary Table 4
psRNATarget analysis of V. vinifera miRNA targeted LEA encoding genes. (DOCX 22 kb)
Rights and permissions
About this article
Cite this article
İbrahime, M., Kibar, U., Kazan, K. et al. Genome-wide identification of the LEA protein gene family in grapevine (Vitis vinifera L.). Tree Genetics & Genomes 15, 55 (2019). https://doi.org/10.1007/s11295-019-1364-3
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11295-019-1364-3