Redefining fundamental concepts of transcription initiation in bacteria

• Published in: Nature reviews. Genetics Vol. 21; no. 11; pp. 699 - 714
• Main Authors: Mejía-Almonte, Citlalli, Busby, Stephen J. W., Wade, Joseph T., van Helden, Jacques, Arkin, Adam P., Stormo, Gary D., Eilbeck, Karen, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.11.2020; Nature Publishing Group; Springer Nature
• Subjects: 631/114/2184; 631/208/200; 631/326/41/2530; 631/337/572/2102; Agriculture; Animal Genetics and Genomics; Bacteria; Bacteria - genetics; Bacterial genetics; BASIC BIOLOGICAL SCIENCES; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Cancer Research; Computer applications; Escherichia coli; Expert Recommendation; Gene expression; Gene Expression Regulation, Bacterial; Gene Function; Gene regulation; Genetic aspects; Genetic research; Genetic transcription; Genetics; Genomes; Human Genetics; Life Sciences; Operon; Prediction models; Promoter Regions, Genetic; Regulon; Transcription Factors - physiology; Transcription initiation; Transcription Initiation, Genetic; United States; Sequence annotation; Transcriptional regulatory elements; Bacterial genomics; Gene regulation
• ISSN: 1471-0056; 1471-0064; 1471-0064
• DOI: 10.1038/s41576-020-0254-8

Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics. In this Expert Recommendation, the authors review the definitions of classic concepts relating to bacterial gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on bacterial gene regulation.