Merve KELEŞ, Tevfik Hasan CAN, Mehmet Cengiz BALOĞLU, Yasemin ÇELİK ALTUNOĞLU

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformaticsanalysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed.In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to theHsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. Whenthe estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominantin almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the ClaHsp genefamilies. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative Hspgene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about therelationships between Hsp genes and combined stresses.

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Al-Whaibi MH (2011). Plant heat-shock proteins: A mini review. Journel of King Saud University-Science 23: 139-150.
Bailey TL, Johnson J, Grant CE, Noble WS (2015). The MEME Suite. Nucleic Acids Research 43: W39-49.
Baloğlu MC, Eldem V, Hajyzadeh M, Unver T (2014a). Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS ONE 9 (4): e96014.
Baloğlu MC (2014b). Genome-wide in silico identification and comparison of Growth Regulating Factor (GRF) genes in the Cucurbitaceae family. Plant Omics Journal 7 (4): 260-270.
Baloğlu MC, Patir MG (2014c). Molecular characterization, 3D model analysis, and expression pattern of the CmUBC gene encoding the melon ubiquitin-conjugating enzyme under drought and salt stress conditions. Biochemical Genetics 52: 90-105.
Baloğlu MC, Inal B, Kavas M, Unver T (2014d). Diverse expression pattern of wheat transcription factors against abiotic stresses in wheat species. Gene 550 (1): 117-122.
Baloğlu MC, Ulu F, Altunoğlu YC, Pekol S, Alagoz G et al. (2015). Identification, molecular characterization and expression analysis of RPL24 genes in three Cucurbitaceae family members: cucumber, melon and watermelon. Biotechnology & Biotechnological Equipment 29: 1024-1034.
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN et al. (2000). The Protein Data Bank. Nucleic Acids Research 28 (1): 235-242.
Budak H Akpinar AB (2015). Plant miRNAs: biogenesis, organization and origins. Functional and Integrative Genomics 15 (5): 523- 531.
Büyük I, Fazlioğlu A, Aras S (2012). Relation between different concentrations of Cd+2 treatment and mRNA levels of 17.7 kDa heat-shock protein gene in Helianthus annuus plants. Journal of Biotechnology 161: 45.
Büyük İ, Soydam-Aydın S, Aras S (2012). Bitkilerin stres koşullarına verdiği moleküler cevaplar. Türk Hijyen ve Deneysel Biyoloji 69 (2): 97-110.
Cao F, Cheng H, Cheng S, Li L, Xu F et al. (2012). Expression of selected ginkgo biloba heat shock protein genes after cold treatment could be induced by other abiotic stress. International Journal of Molecular Sciences 13 (5): 5768-5788.
Collins JK, Wu G, Perkins-Veazie P, Spears K, Claypool PL et al. (2007). Watermelon consumption increases plasma arginine concentrations in adults. Nutrition 23 (3): 261-266.
Conesa A, Götz S (2008). Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 2008: 12.
Çelik Altunoğlu Y (2016a). Isı Şoku Protein Ailesinden Hsp70 Genlerinin Okaliptüs Genomunda Saptanması ve Karakterizasyonu. Kastamonu University, Journal of Forest Faculty 16( 2): 497-509.
Çelik Altunoğlu Y, Baloğlu P, Yer EN, Pekol S, Baloğlu MC (2016b). Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regulation 80 (2): 225-241. doi: 10.1007/s10725-016-0160-4
Çelik Altunoğlu Y, Baloğlu MC, Baloğlu 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 (1): 5-21. doi: 10.1007/s12298-016- 0405-8
Çelik Altunoğlu Y, Ünel NM, Baloğlu MC, Ulu F, Can TH et al. (2018). Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: perspective from a sunflower model for evaluation of gene expression pattern under drought stress. Biotechnology & Biotechnological Equipment 32 (4): 846-857. https://doi.org /10.1080/13102818.2018.1480421
Dai X, Zhao PX (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39: W155-159.
Ghatak A, Chaturvedi P, Nagler M, Roustan V, Lyon D et al. (2016). Comprehensive tissue-specific proteome analysis of drought stress responses in Pennisetum glaucum (L.) R. Br. (Pearl millet). Journal of Proteomics 143: 122-135.
Guan JC, Jinn TL, Yeh CH, Feng SP, Chen YM et al. (2004). Characterization of the genomic structures and selective expression profiles of nine class I small heat shock protein genes clustered on two chromosomes in rice (Oryza sativa L.). Plant Molecular Biology 56: 795-809.
Guleria P, Kumar Yadav S (2011). Identification of miR414 and Expression Analysis of Conserved miRNAs from Stevia rebaudiana. Genomics Proteomics Bioinformatics 9 (6): 211- 217.
Guo S, Zhang J, Sun H, Salse J, Lucas WJ et al. (2013). The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 45 (1): 51-58.
Hayashi T, Juliet PA, Matsui-Hirai H, Miyazaki A, Fukatsu A et al. (2005). L-citrulline and L-arginine supplementation retards the progression of high-cholesterol-diet–induced atherosclerosis in rabbits. Proceedings of the National Academy of Sciences USA 102 (38): 13681-13686.
Henle KJ, Jethmalani SM, Nagle W (1998). Stress proteins and glycoproteins (Review). International Journal of Molecular Medicine 1: 25-57.
Hill JE, Hemmingsen SM (2001). Arabidopsis thaliana type I and II chaperonins. Cell Stress Chaperones 6 (3): 190-200.
Hoagland DR, Arnon DI (1950). The Water-Culture Method for Growing Plants Without Soil. Berkeley, CA, USA: College of Agriculture, University of California. Hong SW, Vierling E (2001). Hsp101 is necessary for heat tolerance but dispensable for development and germination in the absence of stress. The Plant Journal 27 (1): 25-35.
Hu B, Jin J, Gua AY, Zhang H, Luo J et al. (2015). GSDS 2.0: an upgraded gene feature visualization server. Oxford JournalBioinformatics 31 (8): 1296-1297.
Hu W, Hu G, Han B (2009). Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Science 176 (4): 583-590.
Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J et al. (2002) bZIP transcription factors in Arabidopsis. Trends Plant Science 7 (3): 106-111.
Jiang SS, Lu YW, Li KF, Lin L, Zheng HY et al. (2014). Heat shock protein 70 is necessary for Rice stripe virus infection in plants. Molecular Plant Pathology 15: 907-917.
Jin Z, Xu W, Liu A (2014) Genomic surveys and expression analysis of bZIP gene family in castor bean (Ricinus communis L.). Planta 239: 299-312.
Kavas M, Kizildogan A, Gokdemir G, Baloğlu MC (2015). Genomewide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean Experimental and Clinical Sciences 14: 1187-1206. doi:10.17179/excli2015-600
Kavas M, Baloğlu MC, Atabay ES, Ziplar UT, Dasgan HY et al. (2016). Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration Molecular Genetics and Genomics 291: 129-143. doi:10.1007/s00438-015-1095-6
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015). The Phyre2 web portal for protein modelling, prediction and analysis. Nature Protocols 10 (6): 845-858.
Kong Q, Yuan J, Gao L, Zhao S, Jiang W et al. (2014). Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon. PloS One 9(2): e90612.
Kosova K, Vitamvas P, Urban MO, Prasil IT, Renaut J (2018). Plant abiotic stress proteomics: the major factors determining alterations in cellular proteome. Frontiers Plant Science 9: 122.
Krishna P, Gloor G (2001) The Hsp90 family of proteins in Arabidopsis thaliana. Cell Stress Chaperones 6 (3): 238-246.
Kumar RR, Nagarajan NS, Arunraj SP, Devanjan S, Rajun V et al. (2012). HSPIR: a manually annotated heat shock protein information resource. Bioinformatics 28 (21): 2853-2855.
Li X, Cao J (2015). Late embryogenesis abundant (LEA) gene family in maize: ıdentification, evolution, and expression profiles. Plant Molecular Biology Reporter 34 (1): 15-28. doi:10.1007/ s11105-015-0901-y
Lin BL, Wang JS, Liu HC, Chen RW, Meyer Y et al. (2001). Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress & Chaperones 6 (3): 201.
Livak K, Schmittgen T (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25 (4): 402-408.
Lund PA (2001). Molecular Chaperones in the Cell. Oxford, UK: Oxford University Press.
Lynch M, Conery JS (2000). The evolutionary fate and consequences of duplicate genes. Science 290 (5494): 1151-1155.
Martin J, Horwich AL, Harti UF (1992). Prevention of protein denaturation under heat stress by the chaperonin Hsp60. Science 258 (5084): 995-998.
Mayer M, Brehmer P, Gassler DCS, Bukau B (2001). Hsp70 chaperone machines. Advances in Protein Chemistry 59: 1-44. Milligan BG (2003). Maximum-likelihood estimation of relatedness. Genetics 163 (3): 1153-1167.
Mittler R (2006). Abiotic stress, the field environment and stress combination. Trends in Plant Science 11 (1): 15-19.
Muthusamy SK, Dalal M, Chinnusamy V, Bansal KC (2017). Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat. Journal of Plant Physiology 211: 100-113.
Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008). Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiology 146: 333- 350.
Perkins-Veazie P, Collins JK, Davis AR, Roberts W (2006). Carotenoid content of 50 watermelon cultivars. Journal of Agricultural and Food Chemistry 54: 2593-2597.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N (2005). InterProScan: protein domains identifier. Nucleic Acids Research 33: W116-W120.
Rajan VBV, D’Silva P (2009). Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors. Functional Integrative Genomics 9: 433-446.
Sarkar NK, Kim YK, Grover A (2009). Rice sHsp genes: genomic organization and expression profiling under stress and development. BMC Genomics 10 (1): 393.
Sarkar NK, Kundnani P, Grover A (2013). Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa). Cell Stress and Chaperones 18 (4): 427-437.
Scharf KD, Siddique M, Vierling E (2001). The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing α-crystallin domains (Acd proteins). Cell Stress & Chaperones 6 (3): 225-237.
Singh A, Singh U, Mittal D, Grover A (2010). Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes. BMC Genomics 11. doi:10.1186/1471-2164-11-95
Su P, Li H (2008). Arabidopsis stromal 70-kD heat shock proteins are essential for plant development and important for thermotolerance of germinating seeds 1[C][W][OA]. Plant Physiology 146 (3): 1231-1241.
Sun W, Montagu MV, Verbruggen N (2002). Small heat shock proteins and stress tolerance in plants. Biochim Biophys Acta 1577 (1): 1-9.
Sung DY, Vierling E, Guy CL (2001). Comprehensive expression profile analysis of the Arabidopsis Hsp70 gene family. Plant Physiology 126 (2): 789-800.
Suyama M, Torrents D, Bork P (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research 34: W609-W612.
Swindell WR, Huebner M, Weber AP, (2007). Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics 8: 125.
Tang S, Dong Y, Liang D, Zhang Z, Ye CY et al. (2015). Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing. Plant Molecular Biology Reporter 33 (3): 424-438.
Wang J, Zhou J, Zhang B, Vanitha J, Ramachandran S et al. (2011). Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum. Journal of Integrative Plant Biology 53 (3): 212-231.
Wang Y, Lin S, Song Q, Li K, Tao H et al. (2014). Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. BMC Genomics 15 (1): 344.
Wang W, Vinocur B, Shoseyov O, Altman A (2004). Role of plant heatshock proteins and molecular chaperones in the abiotic stress response. Trends in Plant Science 9 (5): 244-252.
Whitley D, Goldberg SP, Jordan WD (1999). Heat shock proteins: A review of the molecular chaperones. Journal of Vascular Surgery 29 (4): 748-751.
Yang Z, Gu S, Wang X, Li W, Tang Z et al. (2008). Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. Journal of Molecular Evolution 67 (3): 266-277.
Yang J, Zhang N, Ma C, Qu Y, Si H et al. (2013). Prediction and verification of microRNAs related to proline accumulation under drought stress in potato. Elsevier 46: 48-54.
Yer EN (2016). Drought-responsive Hsp70 gene analysis in populus at genome-wide level. Plant Molecular Biology Reporter 34 (2): 483-500.
Yer EN (2017). Isı şoku Protein Genlerinin (HSP) Bazı Populus Taksonlarında Fonksiyonel Genom Analizi ve Abiyotik Stres Koşullarında HSP Genlerinin İfade Seviyelerinin Belirlenmesi. Phd, T.C. Kastamonu University Institute of Science, Kastamonu, Turkey.
Yer EN, Baloğlu MC, Ayan S (2018). Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones. Gene 678: 324-336.
Young JC, Moarefi I, Hartl U (2001). Hsp90: a specialized but essential protein-folding tool. The Journal of Cell Biolog 154 (2): 267-273.
Zai WS, Miao LX, Xiong ZL, Zhang HL, Ma YR et al. (2017). Comprehensive identification and expression analysis of Hsp90s gene family in Solanum lycopersicum. Genetics and Molecular Research 14 (3): 7811-7820.
Zhang J, Liu B, Li J, Zhang L, Wang Y et al. (2015). Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses. BMC Genomics 16 (1): 181.