Contribution of bacterial promoter elements to transcription start site detection accuracy

Abstract

© 2017 World Scientific Publishing Europe Ltd. Accurately detecting transcription start sites (TSS) is a starting point for understanding gene transcription, and an important ingredient in a number of applications necessary for functional gene annotation, such as gene and operon predictions. Available methods for TSS detection in bacteria use very different description of the bacterial promoter structure and all of them show low accuracy. It is therefore unclear which promoter features should be included in TSS recognition, and how their accuracy impacts the search detection. We here address this question for σ70 and σE (an alternative σ factor) promoters in E. coli. We find that -35 element, which is considered exchangeable, and is often not included in TSS search, contributes to the search accuracy equally (for σ70), or more (for σE) than the ubiquitous -10 element. Surprisingly, the sequence of the spacer between -35 and -10 promoter elements, which is commonly included in TSS detection, significantly decreases the search accuracy for σ70 promoters. However, the spacer sequence improves the search accuracy for σE promoters, which we attribute to a presence of sequence conservation. Overall, there is as much as 50% false positive reduction for optimally implemented promoter features in σ70, underlying necessity for accurate promoter element alignments.