ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0

Abstract

DNA-binding transcription factors (TFs) have a central role in regulation of gene expression at the transcription initiation level. These proteins have been experimentally described in multiple bacterial and archaeal genomes. These descriptions have allowed their prediction in complete genomes. In this work, we collected 1784 experimentally validated TFs across 25 bacterial and seven archaeal phyla, including Gammaproteobacteria, Bacillota, and Actinomycetota in bacteria and Thermoproteota and Thermococci in archaea. The collection of regulatory proteins was organized into a relational database, named ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes or ENTRAF. The database shows the experimental evidence for all the TFs [protein structure information (X-ray or NMR structural data); binding of purified proteins; footprinting assays; site mutation; in vitro transcription assay; and PRiMer extension analysis, among others], their global regulatory roles (carbon source assimilation, virulence, antibiotic resistance, stress, and DNA damage), evolutionary families, and structural classifications. In addition, we achieved a global description of the collection in terms of their regulatory mechanisms (activation, repression, and dual activities), structural diversity, functional categories, and protein families. We consider that this collection of well-annotated TFs could be used as a benchmark, enhancing the predictions for this class of proteins in complete genomes. The complete collection of TFs is available at https://entraf.iimas.unam.mx and https://github.com/BioIIMAS/ENTRAF.