Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
By Carl Kingsford, Kunmi Ayanbule, Steven L. Salzberg. Genome Biology, 2007
518 citations recorded by the source corpus.
BackgroundIn 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.ResultsWe 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.ConclusionOur 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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6c861e0d58dd04107f235d413b5a3958cb99a3aa
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In Genetics
In Molecular Biology
- Oscar P. Kuipers
- Robert E. W. Hancock
- Raymond Lo
- Anne de Jong
- Jan Kok
- Fiona S. L. Brinkman
- Geoffrey L. Winsor
Citations in the corpus
- ARNold: A web tool for the prediction of Rho-independent transcription terminators (2011, methodology): “4,5,7 Another class uses generic motif detection algorithms, such as Erpin, 8 that takes as input a sequence alignment, or RNAmotif, 3 that uses an expert-made descriptor to represent sequence, structure and thermodynamic constraints.”
- BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins (2018, methodology): “TranTermHP terminator prediction (18) was additionally implemented in the BAGEL4 pipeline.”
- Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes (2010, methodology): “We also incorporated updated Rho-independent transcription terminator predictions using TransTermHP (33) and computationally-identified inverted repeats (palindromes) using EMBOSS’s Palindrome software (34).”
- Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, methodology): “As a complement to manually curated transcriptional units, we provide computationally predicted rho-independent transcription terminators based on TransTermHP (27).”