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In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes

Germin-like proteins (GLPs) are involved in biotic and abiotic stress tolerance in different plant species. Rice (Oryza sativa L.) genome contains about 40 GLP family member proteins in nine chromosomes. Although some of the rice GLP (OsGLP) promoters have been studied through in silico analysis as...

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Autores principales: Das, Arpita, Pramanik, Krishnendu, Sharma, Rishu, Gantait, Saikat, Banerjee, Joydeep
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375593/
https://www.ncbi.nlm.nih.gov/pubmed/30763346
http://dx.doi.org/10.1371/journal.pone.0211887
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author Das, Arpita
Pramanik, Krishnendu
Sharma, Rishu
Gantait, Saikat
Banerjee, Joydeep
author_facet Das, Arpita
Pramanik, Krishnendu
Sharma, Rishu
Gantait, Saikat
Banerjee, Joydeep
author_sort Das, Arpita
collection PubMed
description Germin-like proteins (GLPs) are involved in biotic and abiotic stress tolerance in different plant species. Rice (Oryza sativa L.) genome contains about 40 GLP family member proteins in nine chromosomes. Although some of the rice GLP (OsGLP) promoters have been studied through in silico analysis as well as experimentally, studies regarding the distribution pattern of the biotic and abiotic stress associated transcription factor binding sites (TFbs) in the promoter regions of OsGLP genes have not been attempted thoroughly. Several transcription factors (TFs) namely NAC, WRKY, bHLH, bZIP, MYB and AP2/ERF act as major TFs concerned with biotic as well as abiotic stress responses across various plant species. In the present study the in silico analysis was carried out using the 1.5 kilobases (kb) promoter regions from 40 different OsGLP genes for the presence of NAC, WRKY, bHLH, bZIP, MYB and AP2/ERF TFbs in it. Among various OsGLP gene promoters, OsGLP8-11 was found to contain highest number of tested TFbs in the promoter region whereas the promoter region of OsGLP5-1 depicted least amount of TFbs. Phylogenetic study of promoter regions of different OsGLP genes revealed four different clades. Our analyses could reveal the evolutionary significance of different OsGLP gene promoters. It can be presumed from the present findings as well as previous reports that OsGLP gene duplications and subsequent variations in the TFbs in OsGLP gene promoter regions might be the consequences of neofunctionalization of OsGLP genes and their promoters for biotic and abiotic stress tolerance in rice.
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spelling pubmed-63755932019-03-01 In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes Das, Arpita Pramanik, Krishnendu Sharma, Rishu Gantait, Saikat Banerjee, Joydeep PLoS One Research Article Germin-like proteins (GLPs) are involved in biotic and abiotic stress tolerance in different plant species. Rice (Oryza sativa L.) genome contains about 40 GLP family member proteins in nine chromosomes. Although some of the rice GLP (OsGLP) promoters have been studied through in silico analysis as well as experimentally, studies regarding the distribution pattern of the biotic and abiotic stress associated transcription factor binding sites (TFbs) in the promoter regions of OsGLP genes have not been attempted thoroughly. Several transcription factors (TFs) namely NAC, WRKY, bHLH, bZIP, MYB and AP2/ERF act as major TFs concerned with biotic as well as abiotic stress responses across various plant species. In the present study the in silico analysis was carried out using the 1.5 kilobases (kb) promoter regions from 40 different OsGLP genes for the presence of NAC, WRKY, bHLH, bZIP, MYB and AP2/ERF TFbs in it. Among various OsGLP gene promoters, OsGLP8-11 was found to contain highest number of tested TFbs in the promoter region whereas the promoter region of OsGLP5-1 depicted least amount of TFbs. Phylogenetic study of promoter regions of different OsGLP genes revealed four different clades. Our analyses could reveal the evolutionary significance of different OsGLP gene promoters. It can be presumed from the present findings as well as previous reports that OsGLP gene duplications and subsequent variations in the TFbs in OsGLP gene promoter regions might be the consequences of neofunctionalization of OsGLP genes and their promoters for biotic and abiotic stress tolerance in rice. Public Library of Science 2019-02-14 /pmc/articles/PMC6375593/ /pubmed/30763346 http://dx.doi.org/10.1371/journal.pone.0211887 Text en © 2019 Das et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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
Das, Arpita
Pramanik, Krishnendu
Sharma, Rishu
Gantait, Saikat
Banerjee, Joydeep
In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title_full In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title_fullStr In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title_full_unstemmed In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title_short In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
title_sort in-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375593/
https://www.ncbi.nlm.nih.gov/pubmed/30763346
http://dx.doi.org/10.1371/journal.pone.0211887
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