ArticleBMC bioinformatics2008
Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 24 citations in OpenAlex.
- Cell-Free Protein Synthesis by Diversifying Bacterial Transcription Machinery.Biotech (Basel (Switzerland)) · 2021Article
- Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning.Journal of molecular biology · 2021Article
- PromoterPredict: sequence-based modelling ofPeerJ · 2018Article
- Unveiling Mycoplasma hyopneumoniae promoters: sequence definition and genomic distribution.DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
- PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.BMC research notes · 2011Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- Gains and unexpected lessons from genome-scale promoter mapping.Nucleic acids research · 2009Article
- Regulation by transcription factors in bacteria: beyond description.FEMS microbiology reviews · 2009Review
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Authors and funding
3 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundBacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes.
resultsWe describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I sigma70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the alpha subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the sigma70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions.
conclusionThe triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance.
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