Genome-wide Prediction and Annotation of Burkholderia Pseudomallei AraC/XylS Family Transcription Regulator

Article type: Research Article

Authors: Lim, Boon-San | Chong, Chan-Eng | Zamrod, Zulkeflie | Nathan, Sheila^; | Mohamed, Rahmah^;

Affiliations: School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia | Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, 43600 Bangi, Selangor, Malaysia

Note: [] Corresponding author. E-mail: sheila@pkrisc.cc.ukm.my

Abstract: Many members of the AraC/XylS family transcription regulator have been proven to play a critical role in regulating bacterial virulence factors in response to environmental stress. By using the Hidden Markov Model (HMM) profile built from the alignment of a 99 amino acid conserved domain sequence of 273 AraC/XylS family transcription regulators, we detected a total of 45 AraC/XylS family transcription regulators in the genome of the Gram-negative pathogen, Burkholderia pseudomallei. Further in silico analysis of each detected AraC/XylS family transcription regulatory protein and its neighboring genes allowed us to make a first-order guess on the role of some of these transcription regulators in regulating important virulence factors such as those involved in three type III secretion systems and biosynthesis of pyochelin, exopolysaccharide (EPS) and phospholipase C. This paper has demonstrated an efficient and systematic genome-wide scale prediction of the AraC/XylS family that can be applied to other protein families.

Keywords: AraC/XylS, α-helix-turn-α-helix, hidden Markov model, Burkholderia pseudomallei

Journal: In Silico Biology, vol. 7, no. 4-5, pp. 389-397, 2007