Comparative analysis of regulatory elements in different germin-like protein gene promoters

Mahmood, Tariq; Nazar, Nazia; Yasmin, Tayyaba; Abbasi, Bilal Haider; Ahmad, Mushtaq; Naqvi, Syed Muhammad Saqlan

doi:10.5897/ajb09.1803

Cited by 12 publications

(4 citation statements)

References 35 publications

(31 reference statements)

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“…and Alternaria solani Sorauer] stresses (Ilyas et al, 2019;Munir et al, 2016). However, it is contradictory to the study of Mahmood et al, (2010) where ARA, W-box, GT-element and ACGT Sequence were common to 10 GLPs promoters of 5 plant species. CAAT box is part of the core promoter element with a consensus sequence of GGCCAATCT located upstream to the start codon of most eukaryotic genes and enhancer region playing important role in transcription (Etminan et al, 2018).…”

Section: Common Cis-regulatory Elementsmentioning

confidence: 97%

“…The highest number of elements were found in VvGLP6 (68 elements), lowest in VvGLP1 (44 elements), while VvGLP2, -3, -4, -5, and -7 contained 55, 64, 57, 53, and 52 TFBSs respectively. Previously, similar in silico approaches were adopted for the promoter study of 05 different plant species (Mahmood et al, 2010), EgGLP (Sassaki et al, 2015), and OsGLPs (Das et al, 2019;Ilyas et al, 2016a), etc. to get insight into their function and regulatory mechanism.…”

Section: Promoter Analysismentioning

confidence: 99%

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Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Ilyas

Rahman²,

Khan³

et al. 2024

Braz. J. Biol.

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Germin-like proteins (GLPs) play an important role against various stresses. Vitis vinifera L. genome contains 7 GLPs; many of them are functionally unexplored. However, the computational analysis may provide important new insight into their function. Currently, physicochemical properties, subcellular localization, domain architectures, 3D structures, N-glycosylation & phosphorylation sites, and phylogeney of the VvGLPs were investigated using the latest computational tools. Their functions were predicted using the Search tool for the retrieval of interacting genes/proteins (STRING) and Blast2Go servers. Most of the VvGLPs were extracellular (43%) in nature but also showed periplasmic (29%), plasma membrane (14%), and mitochondrial- or chloroplast-specific (14%) expression. The functional analysis predicted unique enzymatic activities for these proteins including terpene synthase, isoprenoid synthase, lipoxygenase, phosphate permease, receptor kinase, and hydrolases generally mediated by Mn+ cation. VvGLPs showed similarity in the overall structure, shape, and position of the cupin domain. Functionally, VvGLPs control and regulate the production of secondary metabolites to cope with various stresses. Phylogenetically VvGLP1, -3, -4, -5, and VvGLP7 showed greater similarity due to duplication while VvGLP2 and VvGLP6 revealed a distant relationship. Promoter analysis revealed the presence of diverse cis-regulatory elements among which CAAT box, MYB, MYC, unnamed-4 were common to all of them. The analysis will help to utilize VvGLPs and their promoters in future food programs by developing resistant cultivars against various biotic (Erysiphe necator and in Powdery Mildew etc.) and abiotic (Salt, drought, heat, dehydration, etc.) stresses.

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Section: Common Cis-regulatory Elementsmentioning

confidence: 97%

Section: Promoter Analysismentioning

confidence: 99%

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Ilyas

Rahman²,

Khan³

et al. 2024

Braz. J. Biol.

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“…Different stress resistance rice cultivars have been reported over the years (Lenka et al, 2011). Previously, 30 GLP genes in roots from japonica rice cultivar Nipponbare has been sequenced and studied (Mahmood et al, 2010). Notably, the japonica group cultivar Nipponbare genome has been completely sequenced and its sequence is available on public database.…”

Section: Analysis Of Protein -Dna Docking Findingmentioning

confidence: 99%

Isolation and In Silico Analysis of OsGLP12-3 Gene’s Promoter from Rice Cultivar Dilrosh-97

Durrani,

Asim,

Sohail

2023

SJA

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Germins and Germin-like proteins (GLPs) are the ubiquitous family of plant proteins that belong to the cupin superfamily and have been reported to play a major role in plant defense against pathogens attacks and different abiotic stresses. Current research deals with the study of cis-regulatory elements located in the promoter region of OsGLP12-3 gene of Nipponbare and newly sequenced Oryza sativa L. cultivar Dilrosh-97 using bioinformatics approach. The possible cis-acting regulatory elements were analyzed using PlantCARE and PlantPAN3.0. Phylogenetic tree was constructed using MEGA7 and docking of regulatory elements with the corresponding Transcription factors was performed using pyDockDNA. The OsGLP12-3 promoter region (1863bp) was PCR amplified using genomic DNA from Indica rice cultivar Dilrosh-97 and subsequently purified and sequenced. Sequence analysis using Plant Care online database revealed 32 different regulatory elements in Nipponbare while 31 different regulatory elements were found in Dilrosh-97. The cis-acting elements were found to be involved in plant hormonal inductions, developments and biotic and abiotic stress response. Notably, the OsGLP12-3 gene promoter from Dilrosh-97 was found to contain higher number of TATA-box and CAAT-box as compared to Nipponbare, reflecting it to be efficient in transcription initiation. Pairwise alignment using NCBI Nucleotide Blast tool showed 99% similarity between subject sequence (Nipponbare) and query sequence (Dilrosh-97). Localization of Transcription factors motif sequences indicate that the motifs including Homeodomain; TALE, NF-YB and GGAAAt in Nipponbare promoter and Alpha-amylase and B3 in Dilrosh-97 promoter were observed abundantly close to the transcriptional initiation site. Expression analysis using TENOR identified that OsGLP12-3 gene show high to minimal level of expression in response to different stress stimuli. Phylogenetic analysis of the Dilrosh-97 promoter sequence showed close relationship of this promoter with the Japonica rice cultivar Nipponbare. Three transcription factors including B3, GT-1 and NF-YB were subjected to docking with their corresponding cis-acting elements regulatory elements using pyDockDNA to evaluate the nature of interaction between the proteins and DNA sequences. The docking analysis revealed the hydrogen bonding interaction between cis-acting elements and their corresponding Transcription factors.

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“…For instance, OsGLP8-10 showed down-regulation in roots of both tolerant KS282 and sensitive Super Basmati rice variety only under drought stress whereas OsGLP8-12 was observed with upregulation under both drought and salt stress only in roots of Super Basmati (Anum et al 2022). Despite of the high sequence similarity in the gene regions of OsGLP genes, differential expression of OsGLP genes from same chromosome indicates the possible role of variation in promoter region (Mahmood et al 2010) and epigenetic effect such as DNA methylation in regulation of their expression. However, currently no report is available regarding the DNA methylation analysis in promoter region of OsGLP genes in contrasting rice cultivars under drought and salt stress.…”

Section: Introductionmentioning

confidence: 99%

The promoters of OsGLP genes exhibited differentially methylated sites under drought and salt stress in rice cultivars

et al. 2023

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DNA methylation at cytosine residues governs the regulation of stress responsive genes in plants to generate response against various environmental abiotic stress conditions. Here, we analyzed the epigenetic consequences of drought and salinity on cytosine methylation dynamics of promoter regions of stress responsive Germin-like protein (GLP) genes in rice (Oryza sativa). The bisul te sequencing technique was employed to identify differential methylation status at cytosine residues in selected promoter region of three OsGLP genes (OsGLP4-1, OsGLP8-10 and OsGLP8-12) in leaves and roots of two elite Indica rice cultivars (tolerant KS282 and sensitive Super Basmati) under drought and salt stress. Our results identi ed cultivar, tissue and stress-dependent differentially methylated cytosine residues, however, the extent of methylation was found to be different depending upon CGN, CHG and CHH sequence contexts. Among all three OsGLP genes, promoter region of OsGLP8-12 was observed with most methylated and differentially methylated sites depending upon a particular variety, tissue or stress condition whereas no methylated sites were observed in promoter region of OsGLP4-1 in all samples. Moreover, in promoter regions of OsGLP8-10 and OsGLP8-12, several differentially methylated sites in response to stress treatments were identi ed either near or within cis-regulatory elements (CREs) involved in gene regulation or abiotic stress response indicating the association between promoter methylation and regulation of OsGLP genes under drought and salinity. This study provides insights to argue that altered methylation status of speci c cytosine residues in the promoter regions of OsGLP genes can be a key regulatory mechanism associated with their regulation under abiotic stresses in contrasting rice cultivars.

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Comparative analysis of regulatory elements in different germin-like protein gene promoters

Cited by 12 publications

References 35 publications

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Analysis of Germin-like protein genes family in Vitis vinifera (VvGLPs) using various in silico approaches

Isolation and In Silico Analysis of OsGLP12-3 Gene’s Promoter from Rice Cultivar Dilrosh-97

The promoters of OsGLP genes exhibited differentially methylated sites under drought and salt stress in rice cultivars

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