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Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat

Wheat is a major staple food and has been extensively grown around the globe. Sessile nature of plants has exposed them to a lot of biotic and abiotic stresses including fungal pathogen attack. Puccinia graminis f.sp. tritici causes stem rust in the wheat crop and leads to 70% decrease in its produc...

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Autores principales: Numan, Muhammad, Bukhari, Shazia Anwer, Rehman, Mahmood-ur-, Mustafa, Ghulam, Sadia, Bushra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8432781/
https://www.ncbi.nlm.nih.gov/pubmed/34506613
http://dx.doi.org/10.1371/journal.pone.0257392
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author Numan, Muhammad
Bukhari, Shazia Anwer
Rehman, Mahmood-ur-
Mustafa, Ghulam
Sadia, Bushra
author_facet Numan, Muhammad
Bukhari, Shazia Anwer
Rehman, Mahmood-ur-
Mustafa, Ghulam
Sadia, Bushra
author_sort Numan, Muhammad
collection PubMed
description Wheat is a major staple food and has been extensively grown around the globe. Sessile nature of plants has exposed them to a lot of biotic and abiotic stresses including fungal pathogen attack. Puccinia graminis f.sp. tritici causes stem rust in the wheat crop and leads to 70% decrease in its production. Pathogenesis-related (PR) proteins provide plants with defense against different fungal pathogens as these proteins have antifungal activities. This study was designed to screen Pakistani wheat varieties for PR2 and PR3 proteins and their in silico characterization. PR2 and PR3 genes were screened and isolated by PCR amplification from wheat variety Chenab-70 and Frontana, respectively. The nucleotide sequences of PR2 and PR3 genes were deposited in GenBank with accession numbers MT303867 and MZ766118, respectively. Physicochemical properties, secondary and tertiary structure predictions, and molecular docking of protein sequences of PR2 and PR3 were performed using different bioinformatics tools and software. PR2 and PR3 genes were identified to encode β–1,3–glucanase and chitinase proteins, respectively. Molecular docking of both PR2 and PR3 proteins with beta-glucan and chitin (i.e. their respective ligands) showed crucial amino acid residues involved in molecular interactions. Conclusively, molecular docking analysis of β–1,3–glucanase and chitinase proteins revealed crucial amino acid residues which are involved in ligand binding and important interactions which might have important role in plant defense against fungal pathogens. Moreover, the active residues in the active sties of these proteins can be identified through mutational studies and resulting information might help understanding how these proteins are involved in plant defense mechanisms.
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spelling pubmed-84327812021-09-11 Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat Numan, Muhammad Bukhari, Shazia Anwer Rehman, Mahmood-ur- Mustafa, Ghulam Sadia, Bushra PLoS One Research Article Wheat is a major staple food and has been extensively grown around the globe. Sessile nature of plants has exposed them to a lot of biotic and abiotic stresses including fungal pathogen attack. Puccinia graminis f.sp. tritici causes stem rust in the wheat crop and leads to 70% decrease in its production. Pathogenesis-related (PR) proteins provide plants with defense against different fungal pathogens as these proteins have antifungal activities. This study was designed to screen Pakistani wheat varieties for PR2 and PR3 proteins and their in silico characterization. PR2 and PR3 genes were screened and isolated by PCR amplification from wheat variety Chenab-70 and Frontana, respectively. The nucleotide sequences of PR2 and PR3 genes were deposited in GenBank with accession numbers MT303867 and MZ766118, respectively. Physicochemical properties, secondary and tertiary structure predictions, and molecular docking of protein sequences of PR2 and PR3 were performed using different bioinformatics tools and software. PR2 and PR3 genes were identified to encode β–1,3–glucanase and chitinase proteins, respectively. Molecular docking of both PR2 and PR3 proteins with beta-glucan and chitin (i.e. their respective ligands) showed crucial amino acid residues involved in molecular interactions. Conclusively, molecular docking analysis of β–1,3–glucanase and chitinase proteins revealed crucial amino acid residues which are involved in ligand binding and important interactions which might have important role in plant defense against fungal pathogens. Moreover, the active residues in the active sties of these proteins can be identified through mutational studies and resulting information might help understanding how these proteins are involved in plant defense mechanisms. Public Library of Science 2021-09-10 /pmc/articles/PMC8432781/ /pubmed/34506613 http://dx.doi.org/10.1371/journal.pone.0257392 Text en © 2021 Numan et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Numan, Muhammad
Bukhari, Shazia Anwer
Rehman, Mahmood-ur-
Mustafa, Ghulam
Sadia, Bushra
Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title_full Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title_fullStr Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title_full_unstemmed Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title_short Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat
title_sort phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (pr2 and pr3) genes from bread wheat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8432781/
https://www.ncbi.nlm.nih.gov/pubmed/34506613
http://dx.doi.org/10.1371/journal.pone.0257392
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