Open AccessRewiring the specificity of extracytoplasmic function sigma factors
Author(s) -
Horia Todor,
Hendrik Osadnik,
Elizabeth A. Campbell,
Kevin S. Myers,
Hao Li,
Timothy J. Donohue,
Carol A. Gross
Publication year - 2020
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2020204117
Subject(s) - gene , sigma factor , biology , computational biology , function (biology) , genome , genetics , bacterial genome size , regulator , regulation of gene expression , phenotype , gene expression , promoter
Significance Bacterial phenotypes require the concerted expression of multiple genes, usually coordinated by a transcriptional regulator. Although the functions of many genes in sequenced bacterial genomes can be inferred, the regulatory networks that coordinate their expression are only known in a few model systems. Using a bioinformatic and experimental approach, we solve the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major class of bacterial regulators. We develop and use a high-stringency pipeline to predict the genes regulated by 67% of ECF σs in >10,000 species, providing a comprehensive look at the role of a broadly distributed family of gene regulatory proteins. This conceptual and computational framework is potentially applicable to other bacterial regulators.