9/17/2023 0 Comments Terminator sequence definitionIn some bacteria, such as Escherichia coli, a large fraction of termination is mediated by the Rho protein or its homologs (reviewed in ). The importance of Rho-independent termination varies across bacteria. These termination signals typically consist of a short, often GC-rich hairpin followed by a sequence enriched in thymine residues. Rho-independent (also known as intrinsic) terminators are sequence motifs found in many prokaryotes that cause the transcription of DNA to RNA to stop. Our software and predictions are freely available. Our new fast and accurate method for detecting transcription terminators has allowed us to identify and analyze terminators in many new genomes and to identify DNA uptake signal sequences in several species where they have not been previously reported. In the process, we provide the first discussion of potential uptake signals in Haemophilus ducreyi and Mannheimia succiniciproducens, and we discuss the preference for a particular configuration of uptake signal sequences within terminators. We quantify the propensity for terminators to include these sequences. In Neisseria and Pasteurellaceae, terminator hairpins are frequently formed by closely spaced, complementary instances of exogenous DNA uptake signal sequences. Outside the Firmicutes division, we find that Rho-independent termination plays a large role in the Neisseria and Vibrio genera, the Pasteurellaceae (including the Haemophilus genus) and several other species. In Bacillus subtilis, we can detect 93% of known terminators with a false positive rate of just 6%, comparable to the best-known methods. We predict the locations of terminators in 343 prokaryotic genomes, representing the largest collection of predictions available. We describe TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators. Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes and can improve genome annotation. In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop.
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