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

Arpita Das,Rishu Sharma,Joydeep Banerjee,Krishnendu Pramanik,Saikat Gantait,Anil Kumar Singh

doi:10.1371/journal.pone.0211887

Arpita Das, Rishu Sharma + Show 4 more

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https://doi.org/10.1371/journal.pone.0211887

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Abstract

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.

Highlights

Germin-like proteins (GLP) belonging to cupin superfamily are evolutionary conserved plant glycoproteins [1]
RNAi-mediated gene silencing of rice germin-like protein1 (OsGLP1) depicted susceptibility of OsGLP1-down regulated plants to sheath blight and blast diseases of rice compared to untransformed control plants [7]
Characteristics of 40 OsGLP gene promoters of O. sativa retrieved from NCBI database have been depicted in Table 1 and their location on each chromosomes have been presented (Fig 1)

Summary

Introduction

Germin-like proteins (GLP) belonging to cupin superfamily are evolutionary conserved plant glycoproteins [1]. Majority of the GLP family members have been involved in biotic as well as abiotic stress responses [1, 3,4,5] in diverse plant. An interesting study on rice reported 12 OsGLP gene families as quantitative traits loci (QTL) associated with blast disease and all of those genes were present on chromosome number 8 [6]. RNAi-mediated gene silencing of rice germin-like protein (OsGLP1) depicted susceptibility of OsGLP1-down regulated plants to sheath blight and blast diseases of rice compared to untransformed control plants [7]. RNAi-mediated down-regulation of OsGLP1 has documented improved salt tolerance of transgenic lines during seed germination and early seedling growth compared to untransformed plant [3]. Another study has identified the expressional changes of 31 different OsGLP genes upon exposure to drought, salt, cold and heavy metal stresses [9]

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