Isolation, Characterization and Expression Analysis of Hordeumvulgare 22 (HVA 22) Gene from Drought Tolerant Sugarcane Variety
![](/public/icon/gor.png)
![](/public/icon/pdf.png)
Abstract
Sugarcane is an important commercial crop in India. Water deficit stress is the major limitation for sustainable sugarcane production across the country. Owing to its socio-economic importance, predicted climate changes and increase in the possibility of water shortage, a drought responsive geneHordeumvulgare 22 (HVA 22) was cloned and characterized from drought tolerant sugarcane variety Co 740. The open reading frame of this gene is 945 bp that encodes for a single polypeptide of 314 amino acids. In silico analysis of HVA 22 using bioinformatics tools revealed the ~ 35.56 kDA size protein with theoretical pI 9.17, instability index 38.70, aliphatic index 66.53 and GRAVY of -0.742. Subcellular localization by WOLFPSORT server suggested that HVA 22 expression is localized in the nucleus, mitochondria and chloroplast. TMHMM analysis suggests that HVA 22 protein contains three transmembrane domains. SignalP showed no signal peptide and the phosphorylation sites viz. 30 serine, 8 threonine and 3 tyrosine residues were identified using Netphos server. The phylogenetic tree exhibited that HVA 22 from sugarcane variety Co 740 is closely associated with that of HVA 22 of Zea mays and Oryza sativa. qRT-PCR gene expression analysis showed that HVA 22 was differentially upregulated in drought tolerant and susceptible genotypes under water deficit stress conditions.
References
Amara I (2012) Abiotic stress in plants: Late Embryogenesis Abundant proteins. Barcelona. Spain
Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics, 18(2): 298-305
Buxbaum E (2007) Fundamentals of Protein Structure and Function. Springer Science and Business Media, LLC, New York.
Cao Y, Xiang X, Geng M, You Q, Huang X (2017) Effect of HbDHN1 and HbDHN2 genes on abiotic stress responses in Arabidopsis. Frontiers in Plant Science, 8: 470
Chandra S, Dutta AK, Chandrashekara KN, Acharya K (2017) In silico characterization, homology modeling of Camellia sinensischitinase and its evolutionary analyses with other plant chitinases. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 87(3): 685-695
Chen CN, Chu CC, Zentella R, Pan SM, Ho TH (2002) AtHVA 22 gene family in Arabidopsis: phylogenetic relationship, ABA and stress regulation, and tissue-specific expression. Plant Molecular Biology, 49(6): 631-642
Dharshini S, Chakravarthi M, Manoj VM, Naveenarani M, Kumar R, Meena M, Ram B, Appunu C (2016) De novo sequencing and transcriptome analysis of a low temperature tolerant Saccharum spontaneum clone IND 00-1037. Journal of Biotechnology, 231:280-294
Doerks T, Copley RR, Schultz J, Ponting CP, Bork P (2002) Systematic identification of novel protein domain families associated with nuclear functions. Genome Research, 12(1): 47-56
Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4): 783-791
Filiz E, Ozyigit II, Tombuloglu H, Koc I (2013) In silico comparative analysis of LEA (Late Embryogenesis Abundant) proteins in Brachypodiumdistachyon L. Plant Omics, 6(6): 433
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook. Humana press, 571-607
Goyal M, Chauhan S, Kumar P (2017) Insilico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris. Agricultural Science Digest, 37(3): 185-190
Grelet J, Benamar A, Teyssier E, Avelange-Macherel MH, Grunwald D, Macherel D (2005). Identification in pea seed mitochondria of a late-embryogenesis abundant protein able to protect enzymes from drying. Plant Physiology, 137(1): 157-167.
Guo WJ, Ho TH (2008). An abscisic acid-induced protein, HVA 22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. Plant Physiology, 147(4): 1710-1722
Guruprasad K, Reddy BB, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection, 4(2):155-161.
Han, Y, Zheng QS, Wei YP, Chen J, Liu R, Wan HJ (2015) In silico identification and analysis of phytoene synthase genes in plants. Genetics and Molecular Research, 14(3): 9412-9422.
Horton P, Keun-Joon P, Takeshi O, Naoya F, Hajime Harada CJ, Adams C, Kenta N (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Research, 35: W585–W587 Web Server issue.
Ikai A (1980) Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 8(6): 1895-1898
Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1. Journal of Molecular Biology, 305(3): 567-580
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7): 1870-1874
Kyte J, Doolittle RF (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1): 105-132.
Lakshmanan P, Robinson N (2014). Stress physiology: Abiotic stresses. Sugarcane: Physiology, Biochemistry and Functional Biology, 411-434.
Leprince O, Buitink J (2010) Desiccation tolerance: from genomics to the field. Plant Science, 179(6): 554-564
Letunic I, Doerks T, Bork P (2014) SMART: recent updates, new developments and status in 2015. Nucleic Acids Research, 43(1): 257-260
Livak KJ, Schmittgen TD (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods, 25(4): 402-408.
Lobell DB, Schlenker W, Costa-Roberts J (2011) Climate trends and global crop production since 1980. Science, 333(6042): 616-620
Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Archives of Biochemistry and Biophysics, 444(2): 139-158
McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16(4): 404-405
Nagaraju M, Reddy PS, Kumar SA, Kumar A, Suravajhala P, Ali A, Srivastava RK, Kishor PK, Rao DM (2018) Genome-wide in silico analysis of dehydrinsin Sorghum bicolor, Setariaitalica and Zea mays and quantitative analysis of dehydrin gene expressions under abiotic stresses in Sorghum bicolor. Plant Gene, 13: 64-75
Nakai K, Kanehisa M (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics, 14(4): 897-911.
N’Dong C, Danyluk J, Wilson KE, Pocock T, Huner NP, Sarhan F (2002) Cold-regulated cereal chloroplast late embryogenesis abundant-like proteins. Molecular characterization and functional analyses. Plant Physiology, 129(3): 1368-1381.
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford university press.
Nielsen H, Krogh A (1998) Prediction of signal peptides and signal anchors by a hidden Markov model (1998) Proceedings of International Conference Intelligent Systems for Molecular Biology, 6: 122-130
Rampino P, Pataleo S, Gerardi C, Mita G, Perrotta C (2006) Drought stress response in wheat: physiological and molecular analysis of resistant and sensitive genotypes. Plant Cell and Environment, 29(12): 2143-2152
Rumpi G, Upadhyay AD, Roy AK, Samik A (2017) Structural analysis of cytochrome C Genes of Major Carp and utility of Forensic Investigation. Journal of Forensic and Crime Investigation, 1(1): 1-8
Saha D, Rana RS, Arya L, Mondal TK (2017) Genomic organization and structural diversity of germin-like protein coding genes in foxtail millet (Setariaitalica L.). Agri Gene, 3:87-98
Sahay A, Shakya M (2010) Insilico Analysis and Homology Modelling of Antioxidant Proteins of Spinach. Journal of Proteomics and Bioinformatics, 3: 148-154
Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proceedings of the National Academy of Sciences, 95(11): 5857-5864
Sharon K, Suvarna S (2017) Cloning of HVA 22 Homolog from Aloe vera and preliminary study of transgenic plant development. International Journal of Pure and Applied Biosciences, 5(6): 1113-1121
Shen Q, Chen CN, Brands A, Pan SM, Tuan-Hua DH (2001) The stress-and abscisic acid-induced barley gene HVA 22: developmental regulation and homologues in diverse organisms. Plant Molecular Biology, 45(3): 327-340
Shen Q, Uknes SJ, Ho TH (1993) Hormone response complex in a novel abscisic acid and cycloheximide-inducible barley gene. Journal of Biological Chemistry, 268(31): 23652-60.
Sivamani E, Bahieldin A, Wraith JM, Al-Niemi T, Dyer WE, Ho TH, Qu R (2000) Improved biomass productivity and water use efficiency under water deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene. Plant Science, 155(1): 1-9
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25(24): 4876-4882
Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta, 218(1): 1-4
Xu D, Duan X, Wang B, Hong B, Ho TH, Wu R (1996) Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiology, 110(1): 249-257
Yadav DK, Shukla D, Tuteja N (2014) Isolation, in silico characterization, localization and expression analysis of abiotic stress-responsive rice G-protein β subunit (RGB1). Plant Signaling &BeHVAior, 9(5): e28890
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 Biology, 12(1): 140.
Yaqoob U, Kaul T, Nawchoo IA (2016) In-silico analysis, structural modelling and phylogenetic analysis of Acetohydroxy acid synthase gene of Oryza sativa. Medicinal and Aromatic Plants (Los Angel), 5(272): 2167-0412
Downloads
Submitted
Published
Issue
Section
License
It is mandatory on the part of the corresponding author to furnish the article declaration form at the time of submission of the manuscript or after acceptance.
Authors who publish with JSR agree to the following terms:
- Authors retain copyright and grant JSR right of first publication with the work simultaneously licensed under Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
Society for Sugarcane Research and Development