Identification of regulatory elements in 16S rRNA gene of Acinetobacter species isolated from water sample




 Shipra Srivastava1, Vijai Singh1, Vipin Kumar1, Praveen Chandra Verma2, 3, Rajeev Srivastava1, Vaishali Basu3, Vijayta Gupta3 and Anil Kumar Rawat1, *





1Biotechnology and Bioinformatics Division, BIOBRAINZ, 566/29 J, Jai Prakash Nagar, Alambagh, Lucknow 226005, U.P., India; 2Department of Biotechnology, Madhav Institute of Technology and Science, Gwaliar; 3Present address: National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P. India


Email; * Corresponding author


Phone 91 0522 4042284


Article Type




received October 15, 2008; accepted November 10, 2008; published December 06, 2008


A bacterial strain, designated AcBz01, was isolated from a water sample collected from Gomti River, Lucknow, India, and identified using a molecular approach. On the basis of the bacterial 16S rRNA gene sequence phylogeny and comparison of this gene sequence with sequences in Ribosomal Database project II, evidence given in this study, it is proposed that isolate is closely related to members of the genus Acinetobacter. Identification and annotation of regulatory elements in the 16S rRNA gene and characterization of their interaction with the respective transcription factor can provide basis for better understanding of the mechanism of network of gene interaction of functionally related genes. The identification of such sites is relevant for locating promoter boundary of a gene and it also allows the prediction of specific gene expression pattern and response to disturbances in a known signaling pathway. Computational identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Acinetobacter sp. was performed using BPROM tool. We predicted the regulatory elements are TSS, -10 box, -35 box and three Transcription Factor (narP, ompR and fadR) with their binding sites in the upstream region of 16S rRNA gene of Acinetobacter sp. AcBz01. The GenBank accession number for 16S rRNA gene of Acinetobacter sp. AcBz01 is EU931637.



RNA polymerase binding site; 16S ribosomal RNA gene; transcription factor; promoter region; Acinetobacter; PCR




 Srivastava et al., Bioinformation 3(4): 173-176 (2008)

Edited by


P. Kangueane








Biomedical Informatics




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