Prediction of Transcription Terminators in Prokaryotes

Carl Kingsford

Center for Bioinformatics & Computational Biology, University of Maryland, College Park

In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes, helping to delimit operons, and thus improve genome annotation. I will describe TransTermHP, a new computational method to rapidly and accurately find Rho-independent transcription terminators. We have used TransTermHP to predict the locations of terminators in 343 prokaryotic genomes, which represents the largest collection of such predictions available. Using our predictions, we explore the relationship between these terminators and another type of genomic motif: exogenous DNA uptake signal sequences. In Neisseria and Pasteurellaceae, for example, terminators are often formed by closely spaced, complementary instances of these uptake signals. We provide the first discussion of potential uptake signals in Haemophilus ducreyi and Mannheimia succiniciproducens, and we explore the preference for a particular configuration of uptake signal sequences within terminators.

Joint work with Kunmi Ayanbule and Steven Salzberg.