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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.

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.

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References
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Crop Biotechnology
Volume 13, Issue 45 - Serial Number 45
March 2024
Pages 63-75
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