In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice

Abstract

Germins (GERs) and germin-like proteins (GLPs) play important roles in responses to various stresses; however, their function is still not fully understood. Significant insight into their function can be obtained by analyzing their promoters. In the present study, the 5' upstream promoters (1000 bp) of 43 Asian rice (Oryza sativa var. Japonica) GLP genes were retrieved from the Plant Ensemble, based on the Rice Annotation Project database (RAP-DB). Phylogenetic analysis via MEGA6 showed a narrow genetic background (0.2%) with a Tajima neutrality value (π) of 0.69. Overall, 4234 transcription factor (TF) binding sites (TFBSs) were found on chromosomes 1, 2, 3, 4, 5, 8, 9, 11 and 12 via "MatInspector" from 90 different TF families using a total of 444. Common TFs and DiAlign analyses showed that Arabidopsis homeobox protein (AHBP), MYB-like proteins (MYBL) and vertebrate TATA-box-binding protein (VTBP) were the most abundant, common and evolutionarily conserved elements in the upstream region from 0 to -800. Finding their mutual interaction via Farmworker analysis uncovered three new cis-regulatory modules (VTBP_VTBP, MYBS_MYBS, and AHBP_VTBP), which appear to be decisive for OsGLPs regulation. In silico functional analysis via ModelInspector revealed 77 cis-regulatory modules, each comprised of two elements, among which DOFF_OPAQ_03 and GTBX_MYCL_01 were the most frequent and mostly found on chromosome 8 and 12, indicating that the combinatorial interaction of these elements has a fundamental role in various biological processes. The study revealed the importance of these elements in regulating the expression of OsGLPs that will help in predicting the role of these genes in various stresses and can have application in biotechnology.

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

“…In accordance with the previous report [70], in the present study also OsGLP promoters under chromosome 1, 3 and 9 exhibited maximum diversification. Interestingly, OsGLP1-1 and OsGLP1-2 were found to be located at different arms on chromosome 1, and this positional difference might be causing diversity between them.…”

“…Most of the OsGLP promoters on chromosomes 8 and 12 shared the highest sequence similarity and this might be due to the duplication of the genomic region including the presence of TFbs. In corroboration to our findings, OsGLP promoters analyzed using 1.0 kb promoter region also depicted the relatedness of the promoters on chromosomes 8 and 12 [70]. Although, according to our study certain promoters on chromosome 8 viz .…”

“…Although, according to our study certain promoters on chromosome 8 viz . OsGLP8-11 , -13 and -14 were distantly related, earlier study [70] depicted that OsGLP8-11 , -12 and -13 promoters were phylogenetically distinct from the rest of the OsGLP promoters on chromosome 8. This difference with earlier study might be due to the consideration of 1.5 kb promoter region in our study.…”

“…In a similar manner OsGLP3-7 and -8 promoters on chromosome 3 were phylogenetically closer probably due to their origin through tandem duplication in chromosome 3 while OsGLP3-4 , -5 and -6 were highly phylogenetically related due to their derivation through inverse tandem duplication (Figs 1 and 6). The phylogenetic differences among the rest of the OsGLP promoters under chromosome 3 and 9 might be due to the diversification in their TFbs as mentioned by earlier researchers also [70]. Another study on barley germin-like GER4 gene cluster revealed that barley genome contains tandemly duplicated genes ( GER4a-h ) and different GER4 promoters exhibited differential expression in response to biotic stress due to the available changes in their cis -regulatory region [14].…”

In silico comparative analysis of promoters derived from plant pararetroviruses

“…O$VTBP, TATA Binding Protein Factor (TBPF) is the second most abundant matrix family found in or promoter analysis. TBPF is a general transcription factor that binds to the TATA box of a gene's promoter [28] and is crucial for promoter activity equally in plants, animals and viruses in gene-specific expression [13,29]. These observations suggested the evolutionary importance of these motifs in which they are conserved by nature and presence in accordance with their demanding function.…”