Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/ XylS family transcription regulator

Boon San Lim, Chan Eng Chong, Zulkeflie Zamrod, Sheila Nathan, Rahmah Mohamed

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)389-397
Number of pages9
JournalIn Silico Biology
Volume7
Issue number4-5
Publication statusPublished - 2007

Fingerprint

Burkholderia pseudomallei
Virulence Factors
Transcription
Regulator
Annotation
Genome
Genes
Conserved Sequence
Prediction
Type C Phospholipases
Computer Simulation
Proteins
Amino Acids
Biosynthesis
Protein
Pathogens
Hidden Markov models
Secretion
Guess
Amino acids

Keywords

  • α-helix-turn-α-helix
  • AraC/XylS
  • Burkholderia pseudomallei
  • Hidden Markov Model

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/ XylS family transcription regulator. / Lim, Boon San; Chong, Chan Eng; Zamrod, Zulkeflie; Nathan, Sheila; Mohamed, Rahmah.

In: In Silico Biology, Vol. 7, No. 4-5, 2007, p. 389-397.

Research output: Contribution to journalArticle

Lim, Boon San ; Chong, Chan Eng ; Zamrod, Zulkeflie ; Nathan, Sheila ; Mohamed, Rahmah. / Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/ XylS family transcription regulator. In: In Silico Biology. 2007 ; Vol. 7, No. 4-5. pp. 389-397.
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