Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

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 and can improve genome annotation. Previous computational methods...

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Vydáno v:	Genome biology Ročník 8; číslo 2; s. R22 - 1504
Hlavní autoři:	Kingsford, Carleton L, Ayanbule, Kunmi, Salzberg, Steven L
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England BioMed Central 21.02.2007
Témata:	Algorithms Bacillus subtilis Bacteria - genetics Computational Biology - methods computer software DNA DNA - genetics genome Genomics - methods Haemophilus ducreyi Mannheimia Microsatellite Repeats - genetics Neisseria prediction prokaryotic cells Regulatory Sequences, Nucleic Acid - genetics RNA signal peptide Software transcription (genetics) Transcription, Genetic - genetics Vibrio
ISSN:	1474-760X, 1465-6906, 1474-760X, 1465-6914
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Shrnutí:	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 and can improve genome annotation. Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider. We describe TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators. We predict the locations of terminators in 343 prokaryotic genomes, representing the largest collection of predictions available. In Bacillus subtilis, we can detect 93% of known terminators with a false positive rate of just 6%, comparable to the best-known methods. 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 Neisseria and Pasteurellaceae, terminator hairpins are frequently formed by closely spaced, complementary instances of exogenous DNA uptake signal sequences. We quantify the propensity for terminators to include these sequences. 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. 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. Our software and predictions are freely available.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1474-760X 1465-6906 1474-760X 1465-6914
DOI:	10.1186/gb-2007-8-2-r22