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

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Author(s): Shipra Srivastava | Vijai Singh | Vipin Kumar | Praveen Chandra Verma | Rajeev Srivastava | Vaishali Basu | Vijayta Gupta | Anil Kumar Rawat

Journal: Bioinformation
ISSN 0973-2063

Volume: 3;
Issue: 4;
Start page: 174;
Date: 2008;
Original page

Keywords: RNA polymerase binding site | 16S ribosomal RNA gene | transcription factor | promoter region | Acinetobacter | PCR

ABSTRACT
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.
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