Characterization of regulatory elements in OsRGLP2 gene promoter from different rice accessions through sequencing and in silico evaluation

Mahmood, Tariq; Tahir, T; Munir, Faiza

doi:10.1016/j.compbiolchem.2018.02.015

Cited by 6 publications

(17 citation statements)

References 38 publications

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“…Similarly, the GUS gene controlled by the OsRGLP1 promoter showed strong activity in the root when tested against drought, ABA, wounding, and salinity . A similar result was also noted for the OsRGLP2 promoter. , In the same way, the JA-mediated role of OsGER4 in crown root development was also confirmed in rice . Likewise, a moderate response was noted in seedlings, anthers, seminal roots, etc., which is similar to the expression of germin-like oxalate oxidase in seedlings of Hordeum vulgare and Beta vulgaris L .…”

Section: Resultssupporting

confidence: 61%

“… 94 A similar result was also noted for the OsRGLP2 promoter. 95 , 96 In the same way, the JA-mediated role of OsGER4 in crown root development was also confirmed in rice. 33 Likewise, a moderate response was noted in seedlings, anthers, seminal roots, etc., which is similar to the expression of germin-like oxalate oxidase in seedlings of Hordeum vulgare ( 93 ) and Beta vulgaris L. 97 However, foliar leaf, blade, shoot, etc.…”

Section: Resultsmentioning

confidence: 57%

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Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

Ilyas¹,

Ali

Binjawhar

et al. 2023

ACS Omega

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Germin (GER) and germin-like proteins (GLPs) play an important role in various plant processes. Zea mays contains 26 germin-like protein genes ( ZmGLPs ) located on chromosomes 2, 4, and 10; most of which are functionally unexplored. The present study aimed to characterize all ZmGLPs using the latest computational tools. All of them were studied at a physicochemical, subcellular, structural, and functional level, and their expression was predicted in plant development, against biotic and abiotic stresses using various in silico approaches. Overall, ZmGLPs showed greater similarity in their physicochemical properties, domain architecture, and structure, mostly localized in the cytoplasmic or extracellular regions. Phylogenetically, they have a narrow genetic background with a recent history of gene duplication events on chromosome 4. Functional analysis revealed novel enzymatic activities of phosphoglycolate phosphatase, adenosylhomocysteinase, phosphoglycolate phosphatase-like, osmotin/thaumatin-like, and acetohydroxy acid isomeroreductase largely mediated by disulfide bonding. Expression analysis revealed their crucial role in the root, root tips, crown root, elongation and maturation zones, radicle, and cortex with the highest expression being observed during germination and at the maturity levels. Further, ZmGLPs showed strong expression against biotic ( Aspergillus flavus , Colletotrichum graminicola , Cercospora zeina , Fusarium verticillioides , and Fusarium virguliforme ) while limited expression was noted against abiotic stresses. Concisely, our results provide a platform for additional functional exploration of the ZmGLP genes against various environmental stresses.

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Section: Resultssupporting

confidence: 61%

Section: Resultsmentioning

confidence: 57%

Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

Ilyas¹,

Ali

Binjawhar

et al. 2023

ACS Omega

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“…We used LncTar (Li et al, 2015) and found that lncRNA fantom3_9230106C11 had no effects on the mRNAs of these transcription factors. The Consite Predication Database (Mahmood et al, 2018) showed that transcription factors Gata1, Gklf, SOX17, S8, and Ahr-ARNT may be bound to the promoter of LncRNA fantom3_9230106C11. In addition to transcription factors, a wide range of miRNAs contribute to Th2 differentiation, i.e., miR-17∼92, miR-29, miR-126, miR-132-3p, miR-148a, mir-24, mir-27, mir-19, and mir-155 were confirmed to regulate Th2 differentiation (Istomine et al, 2016; Pua et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma

Wang

Chen

et al. 2019

Front. Genet.

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Background and Aims Although long non-coding RNAs (lncRNAs) have been linked to many diseases including asthma, little is known about lncRNA transcriptomes of CD4 + T cells in asthma. The present study aimed to explore the lncRNAs profile in the CD4 + T cells from the mouse model of acute asthma. Methods Next generation sequencing for lncRNAs and mRNAs was performed on CD4+ T cells from asthma and control mice. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed to predict the functions and signal pathways for the aberrant lncRNAs. The selected lncRNAs were further measured using quantitative real-time PCR (polymerase chain reaction) and observed in the fluorescence in situ hybridization (FISH). The lncRNA–mRNA co-expression network was constructed via Pearson’s correlation coefficient and Cytoscape 3.6. Results Next generation sequencing revealed 36 up-regulated lncRNAs and 98 down-regulated lncRNAs in acute asthma compared with controls. KEGG pathway analysis showed that cytokine-cytokine receptor interaction had the highest enrichment scores. A co-expression network was constructed in which 23 lncRNAs and 301 mRNAs altered formed a total of 12424 lncRNA and mRNA pairs. To validate the RNA sequencing results, we measured the 4 different lncRNAs using qPCR. The lncRNA fantom3_9230106C11 was significantly reduced in CD4+ T cells of asthma. Bioinformatics analysis showed that lncRNA fantom3_9230106C11 had the potential to interact with many miRNAs and transcription factors related to Th2 differentiation. Conclusion This study provided the first evidence for different expression of lncRNAs of CD4+T cells in asthma and may serve as a template for further, larger functional in-depth analyses regarding asthma molecular lncRNAs.

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“…The basic local alignment search tool (BLAST) was used to detect the similarity between sequences. Nucleotide Blast (BLASTn) was applied to find the sequence’s resemblance with previously submitted sequences in the sequence databases (). − The sequences which show a high level of similarity were selected for the phylogenetic analysis which includes the sequences from the Sorghum bicolor , Setaria italica , Zea mays , O. sativa Japonica group and Panicum hallii , Dichanthelium oligosanthes , Triticum uratru , Hordeum vulgare subspp. Vulgare, Aegilops tauschi subspp.…”

Section: Methodsmentioning

confidence: 99%

“…The HADDOCK web server, which is accessible online at , was used to perform protein–DNA docking. PyMol, the Molecular Graphic System, which is accessible online at (), was used to visualize the graphic analysis of every model . Additionally, the TENOR “The Encyclopedia of Rice” database, available online at (), was used to predict and understand gene’s regulatory characteristics, in terms of gene expression, which is governed by cis -acting elements that are the Transcription-factor binding sites located on the promoter.…”

Section: Methodsmentioning

confidence: 99%

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

Ahmad,

Ullah,

Ullah

et al. 2024

ACS Omega

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Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.

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Characterization of regulatory elements in OsRGLP2 gene promoter from different rice accessions through sequencing and in silico evaluation

Cited by 6 publications

References 38 publications

Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

Next Generation Sequencing for Long Non-coding RNAs Profile for CD4+ T Cells in the Mouse Model of Acute Asthma

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

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