Redefining fundamental concepts of transcription initiation in bacteria

Citlalli Mejía-Almonte, Stephen J.W. Busby, Joseph T. Wade, Jacques van Helden, Adam P. Arkin, Gary D. Stormo, Karen Eilbeck, Bernhard O. Palsson, James E. Galagan, Julio Collado-Vides*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)699-714
Number of pages16
JournalNature Reviews Genetics
Volume21
Issue number11
DOIs
Publication statusPublished - 1 Nov 2020

Bibliographical note

Funding Information:
C.M.-A. is a doctoral student from the Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), and has received CONACyT fellowship 576333. J.C.-V. acknowledges funding by Universidad Nacional Autónoma de México (UNAM) and the National Institutes of Health (5R01GM110597-04, 1RO1GM131643-01A1 and R01GM077678). J.C.-V. acknowledges being on sabbatical leave at the Center for Genomic Regulation, Barcelona, Spain. B.O.P. acknowledges the support of the Galletti Endowment at UC San Diego. The authors acknowledge J. Soffer, S. Gama-Castro and H. Salgado for useful discussions, and D. W. Sant for updating the definitions in Sequence Ontology. The authors also acknowledge the highly valuable suggestions from the referees.

Publisher Copyright:
© 2020, Springer Nature Limited.

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