Abstract
Identification of promoters and their regulatory elements are the most important phases in bioinformatics. To understand the regulation of gene expression, identification, and analysis of promoters region, motif and CpG islands are the most important steps. The accurate prediction of promoter’s is basic for proper interpretation of gene expression patterns, construction and understanding of genetic regulatory system. Therefore, the objective of this study was to analyze the promoter region, motif such as a transcription factor and CpG islands in AraC family transcriptional regulator ACP92 genes of Herbaspirillum seropedicae. The analysis was carried out by identifying transcription start sites in ACP92 genome sequences taken from the H. seropedicae assembly of NCBI genome browser, and 29 ACP92 genes sequences. Accordingly, transcription start sites (TSS) were identified, and the result indicated that 37.9% had more than one TSS whereas only 62.1% had one TSS. In the analysis, seven motifs were identified from the thought sequences and MV6 was revealed the common promoter motif for all (100%) in H. seropedicae ACP92 gene that serves as binding sites for transcription factors which shared a minimum of 48.27%. Based on a common motif MV6 to find out similar motifs using TOMTOM from the databases of prokaryotes DNA, most of them are transcription factors of fur family. The others are bacterial histone-like protein family, matp and sigma-54 factor family also transcription factor families that are binding candidate to MV6. H. seropedicae ACP92 genes are CpG Island which implies that the regulation of gene expression plays an important role.
Highlights
Seven motifs were identified from the thought sequences and MV6 was revealed the common promoter motif for all (100%) in H. seropedicae ACP92 gene that serves as binding sites for transcription factors which shared a minimum of 48.27%
Herbaspirillum seropedicae is a genus of bacteria that found in roots, stems, and leaves in association with economically important species of Poaceae family such as maize (Zea mays), rice (Oryza sativa), sorghum (Sorghum bicolor), sugar cane (Saccharum officinarum) [1]
The AraC family of transcriptional regulators, present in bacterial species is involved in a variety of cellular processes from carbon metabolism to stress responses and its regulation according to Munson and Scott [6]
Summary
Herbaspirillum seropedicae is a genus of bacteria that found in roots, stems, and leaves in association with economically important species of Poaceae family such as maize (Zea mays), rice (Oryza sativa), sorghum (Sorghum bicolor), sugar cane (Saccharum officinarum) [1]. It’s commonly found in forage grasses such as elephant grass and tropical fruits like pineapple and banana [2] It is a nitrogen-fixing Proteobacterium isolated from the rhizosphere and tissues of several economically important plants species [3]. H. seropedicae is well-characterized class of diazotrophic bacteria capable of establishing endophytic associations and promoting plant-growth of important cereals and forage grasses [4]. It was studied as a model of bacterial entry into host plants and plant growth promotion [5]. In AraC family transcriptional regulator ACP92 genes of H. seropedicae are a potential transcriptional regulator that involved in a variety of cellular processes, transcriptional control and expression of genes by binding to specific promoter regions both at transcriptional and post-translational levels
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