Bioinformatic analysis of physicochemical properties, post-translational ‎modifications and domains of proteins involved in wheat salt tolerance

Asl Alizade, Arezoo; Toorchi, Mahmoud; Bandehhagh, Ali

doi:10.30473/cb.2024.70089.1942

Bioinformatic analysis of physicochemical properties, post-translational ‎modifications and domains of proteins involved in wheat salt tolerance

Document Type : Research Paper

Authors

Department of Plant Breeding and Biotechnology, Faculty of Agriculture, ‎University of Tabriz, Tabriz, Iran.

10.30473/cb.2024.70089.1942

Abstract

Salinity is one of the most important environmental stresses that disrupt the natural growth of plants. Plant use different mechanisms to cope with stress conditions, such as salinity, in which changes in protein expression is the most important one at molecular level. Changes in protein expression depends on their physicochemical changes such as half- life, stability index, iso-electric point, molecular weight, extinction coefficient etc. Furtermore, identification of motifs, patterns and protein domains make it possible to predict changes in the conformation, structure and proteins functions. In this research was selected a number of changed protein in expression under salinity stress in wheat based on the previous proteomic studies for further was selected bioinformatic analysis. Study Physicochemical properties of proteins by ProtParam software, identification of domains by InterProScan and CDD, identification patters for prediction of post translational modification by ScanProsite, similarity by Blast, alignment of similar proteins for identification of conserved block was performed by T-Coffee. Out of the 25 proteins associated with salinity stress, 20 proteins have a half-life more than 20 hours. The molecular weight of these proteins was varied between 13 to 117 kDa and 15 protein showed instability index of less than 40 and therefore classified as stable proteins. Investigation of proteins using TMHMM and Protscale softwares, it was found that Aquaporins, Plasma membrane intrinsic proteins, Plasma membrane ATPase and Rust resistance kinase Lr10 are highly hydrophobic proteins, whose major structure located inside the membranes. Out of 25 proteins, 8 proteins were selected and analyzed for identification of patterns, domains, structure and function. α-tubulin as a monomer participates with -tubulin to make α-tubulin dimer. Tubulin create a major part of microtubules that are essential for cell growth and division. This protein consisted of one pattern, Tubulin subunits alpha, beta and gamma signature domain namly PLN00221. For the Triosphosphate isomerase protein, a domain called TIM, which is involved in the catalytic mechanism and for the Calmodulin protein a domain called PTZ00184 was identified which is a calcium binding domain. For the Putative glycine decarbixylase subunit a domain called PRK01202 has been identified that has carboxylase activity. For Cu/Zn superoxide dismutase protein the domain called as SOD is involved in the absorption of superoxide. For Fructose-bisphosphate aldolase protein, the catalytic converter domain was identified as PLV02455 and for Hsp 70- Hsp 90 organizing protein, STI1 domain was identified with ATPase property. For the 2- Cys peroxiredoxin BAS 1 protein, for the PRX-Typ 2 cys domain that plays an important role in regulating oxidation- cell reduction.

Keywords

Main Subjects

Biotic and Abiotic stress

References

Abdullinasab, M., & Mortezavi, M. (2021). Bioinformatics study of LEA proteins involved in tolerance to drought stress in barley (Hordium vulgare L.) and rice (Oryza sativa L.). Agricultural Biotechnology Journal, 13(1), 159-182. doi: 10.22103/jab.2021.15483.1208 Arnold, K., Bordoli, L., Kopp, J., Schwede, T. (2006). The SWISS-MODEL workplace: A web-based enviroment for protein structure homology modeling. Bioinformatics, 22(2), 195-201. Banci, L., Bertini, I., Cramaro, F., Del Conte, R., & Silvia Viezzoli, M. (2002). The solution structure of reduced dimeric copper zinc superoxide dismutase. European Journal Biochemistry, 269: 1905-1915. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., & Sonnhammer, E. L. (2004). The Pfam protein families databse. Nucleic Acids Research, 32: 138-141. Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., Bansal, P., Bridge, A.J., Poux, S., Bougueleret, L., & Xenarios, I. (2016). UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Plant bioinformatics: methods and protocols, pp.23-54. Cantelli, G., Cochrane, G., & Brooksbank, C. (2021). The universal protein knowledgebase in 2021. Nucleic Acids Research, httpds://doi.org/10.1093/nar/gkaa1100. Caruso, G., Cavaliere, C., Guarino, C., Gubbiotti, R., Foglia, P., & Lagana, A. (2008). Identification of changes in Triticum durum L. leaf proteome in response to salt stress by two-dimensional electrophoresis and MALDI-TOF mass spectrometry, Analytical and Bioanalytical Chemistry, 391: 381-390. Chang, J., & Baldi, P. (2006). A machine learning information retrieval approach fold recognition. Bioinformatics, 22(12), 1456-1463. Claverie, J.M., & Notredame, C. (2011). Bioinformatics for Dummies, 2nd Edition 18. Wiley Pub. Dietz, K.J. (2008). Redox signal integration: from stimulus to networks and genes. Plant Physiology, 133: 459-468. Dorothea, B., & Ramanjulu, S. (2005). Drought and salt tolerance in plants. Critical Reviews in Plant Sciences, 24(1): 23-58. Fellerer, C., Schongruber, K., Soll, J., & Schwenkert, S. (2011). Cytosolic HSP90 cochaperones HOP and FKBP interact with freshly synthesized chloroplast preproteins of Arabidopsis. Molecular Plant. doi: 10.1093/mp/ssr037.Epud 2011 May 18. Findeisen, P., Muhlhausen, S., Dempewolf, S., Hertzog, J., Zietlow, A., Carlomango, T., & Kollmar, M. (2014). six subgroupsand extensive recent duplications charscterize the evolution of the eukaryotic tubulin protein family. Genome Biology, 6(9): 2274-2288. Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., & Eddy, S.R. (2014). Pfam: the protin families database. Nucleic Acids Research, 42, 222-30. Fleissner, R., Metzler, D., & Van Haeseler, A. (2005). Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology, 54(4), 548-561. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., & Ben-Tal, N. (2003). ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics Application Note, 19(1), 163-164. Hajduch, M., Rakwal, R., Agrawal, G.k., Yonekura, M., & Pretova, A. (2001). High-resolution two-dimensional electrophoresis separation of proteins from metal-stressed rice (Oryza sativa L.) leaves: Drastic reductions/fragmentation of ribulose-1, 5-bisphosphate carboxylase/ oxygenase and induction of stress-related proteins. Electrophoresis, 22, 2824-2831. Hashimoto, M., Toorchi, M., Matsushita, K., Iwasaki, Y., & Komatsu, S. (2009). Proteome analysis of rice root plasma membrane and detection of cold stress responsive proteins. Protein and Peptide Letters, 16, 685-697. Hesse, J., Thierauf, M., & Ponstingle, H. (1987). Tubulin sequence region beta 155-174 is involved in binding exchangeable guanosine triphosphate. Journal of Biology Chemistry, 262, 15472-15475. Hoffer, I. (2011). How mmuch protein do parenteral amino acid mixtures provide? The American Journal of Clinical Nutrition, 94, 1396-1398. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B., De Castro, E., Lachaize, C., Langendijk-Genevaux, P.S., & Sigrist, ©.J.A. 2007. The 20 years of PROSITE. Nucleic Acids Res. 36 (Database issue): D245–9. doi:10.1093/nar/gkm977 Jitrapakdee, S., & Wallace, J.C. (2003). The biotin enzyme family: conserved structural motifs and domain rearrangements. Current Protein and Peptide Science, 4(3), 217-229. Jonak, C., Okresz, L., Bogre, L., & Hirt, H. (2002). Complexity, cross talk and integration of plant MAP kinase signaling. Current Opinion in Plant Biology, 5, 415-424. Letunic, I., Copley, R.R., Plis, B., Pinkert, S., Schultz, J., & Boork, P. (2006). SMART 5: Domains in the context of genomes and networks. Nucleic Acids Research, 34(1), 257-260. Li, Y.C., Ren, J.P., Cho, M.J, Zhou, S.M., Kim, Y.B., & Buchanan, B.B. (2009). The level of expression of thioredoxin is linked to fundamental properties and applications of wheat seeds. Molecular Plant, 3: 430-441. Liu, J., & Zhu, J.-K. (1998). A calcium sensor homolog required for plant salt tolerance. Science, 280(5371), 1943-1945. Marchler-Bauer, A., Anderson, J.B., Chitsaz, F., Derbyshire, M.K., DeWeese-Scott, C., Fong, J.H., Geer, L.Y., Geer, R.C., Gonzales, N. R., & Gwadz, M. (2009). CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Research, 37, 205-210. Morgan, B.A., & Veal, E.A. (2007). Functions of typical 2-Cys peroxiredoxins in yeast. Subcell Biochemistry, 44, 253-256. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courceelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J.A., Silventoinen, V., Studholme, D.J., Vaughan, R., & Wu, C.H. (2005). Inter Pro, progress and status in 2005. Nucleic Acids Research, 33(1), 201-205. Nagarajan, D., Nanajkar, N. 2020. Encyclopedic Review Article. Wiki Journal of Science. doi: 10. 15347/wjs/2020.004. Noble, J., & Bailey, M. (2009). Quantitation of protein. Methods in Enzymology, 463, 73-95. Quevillon, E., Silventionen, V., Pillai, S., Harte, N., Mudler, N., Apweiler, R., & Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic Acids Research, 33, 116-120. Rakhit, R., & Chakrabartty, A. (2006). Structure, folding, and misfolding of Cu-Zn superoxide dismutase in amyotrophic lateral sclerosis. Biochimica et Biophysica Acta (BBA)- Molecular Basis of Disease, 1762 (11- 12), 1025-1037. Roslan, H.A., Hossain, M.D., & Gerunsin, J. (2017). Molecular and 3D- Structural Characterization of Fructose-1, 6-Bisphosphate Aldolase Derived From Metroxylon Sagu. Brazilian archives of Biology and Technology. Skopp, A., Stefanie, D., boyd, M., Liu. L., Duane, D., & Winkler, D. (2019). Copper-zinc superoxide dismutase (Sod 1) activation terminates interaction between its copper chaperone (Ccs) and the cytosolic metal-binding domain of the copper importer Ctr1. BioMetals. doi.org/10.1007/s 10534-0914-00206-3. Shigeoka, S., Ishikawa, T., Tamoi, M., Miyagawa, Y., Tekeda, T., Yabuta, T., Yabuta, Y., & Yoshimura, K. (2002). Regulation and functon of ascorbate peroxidase isoenzymes. Journal Experimental Botany, 53(372), 1305-1319. Sato, K., Sato, M., & Nakano, A. (2003). Rer1p, a retrieval receptor for ER membrane proteins, recognizes transmembrane domains in multiple modes. Molecular Biology of the Cell, 14(9), 3605-16. DOI: 10.1091/mbc.e02-12-0777. Stone, S. (2019). Role of the ubiquitin proteasome system in plant response to obiotic stress. International Review of Cell and Molecular Biology, 343, 65-110. Tammam, A.M.F., & Hemeda, M. (2008). Study of salt tolerance in wheat (Triticum aestivum L.) cultivar banysaifl. Australian Journal of Crop Sciense, 1(3), 115-125. Tamoi, M., Nagaoka, M., Yabuta, Y., & Koizumi, N. (2003). Osmotic stress tolerance of transgenic tobacco expressing a gene encoding a membrane-located receptor-like protein from tobacco plants. Plant Physiology, 131, 454-462. Turhan, H., & Baser, I. (2004). In vitro and vivo water stress in sunflower, Helianthus annuus L. Helia, 27, 227-236. Tuteja, N., & Sopory, S.K. (2008). Chemical signaling under abiotic stress enviroment in plants. Plant Signaling & Behavior, 3(8),525-536. Tyerman, S. D., Niemiets, C. M., & Bramley, H. (2002). Plant aquaporins: Multifunctional water and solute channels with expanding roles. Plant, Cell and Enviroment, 21, 173-194. Wang, W., Vinocur, B., Soseyov, O., & Altman, A. (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in Plant Science, 9, 244-252. Yildiz, M. (2007). Two-dimensional electrophretic analysis of Soluble leaf proteins of a salt sensitive (Triticum aestivum) and a salt tolerant (Triticum aestivum) cultivar in response to NaCl stress. Journal of Intergrative Plant Biology, 49(7), 975-981. Zdobnov, E.M., & Apweiler, R. (2001). InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17(9), 847-848.