Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties

Abstract

Understanding the attributes that confer promoter activity is essential for gene regulation, gene prediction and sequence annotation. It is a challenging problem to detect promoter regions, either in silico or by experiments. In this report, we show that the stress induced DNA duplex destabilization sites (SIDD) in prokaryotic genomes under negative superhelical stresses, as occurs in vivo, are closely associated with specific promoter regions. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is the most informative DNA property of promoter regions in the E. coli K12 genome. Our method using SIDD as a sole predictor performs better than other promoter prediction programs in detecting promoter sequences in E. coli or Bacillus subtilis. We show that, by combining SIDD properties with -10 motif scores in a linear discrimination function, one can achieve better than 80% accuracy in predicting promoter sequences.