Title

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

Authors

 Shipra Srivastava¹, Vijai Singh¹, Vipin Kumar¹, Praveen Chandra Verma^{2, 3}, Rajeev Srivastava¹, Vaishali Basu³, Vijayta Gupta³ and Anil Kumar Rawat^1, *

Affiliation

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

 akrbz@rediffmail.com; * Corresponding author

Article Type

Hypothesis

Date

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

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.

Keywords

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

Citation

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

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.