PJB-2023-184
ISOLATION AND IN SILICO ANALYSIS OF OsGLP12-3 GENE’S PROMOTER FROM RICE CULTIVAR DILLROSH-97
Irfan Safdar Durrani
Abstract
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 TFs 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 PlantCARE online database revealed 32 different regulatory elements in Nipponbare while 31 different regulatory elements were found in Dilrosh-97. The cis-acting elements were fund 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 TFs motif sequences indicate that the motifs including Homeodomain; TALE, NF-YB and GGAAAt in Nippponbare 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 TFs.
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