Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.

Autor: Suvorova IA; Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia., Gelfand MS; Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia.; Skolkovo Institute of Science and Technology, Moscow, Russia.
Jazyk: angličtina
Zdroj: Frontiers in microbiology [Front Microbiol] 2021 Jun 10; Vol. 12, pp. 675815. Date of Electronic Publication: 2021 Jun 10 (Print Publication: 2021).
DOI: 10.3389/fmicb.2021.675815
Abstrakt: The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW 3-4 RYGRAMC and TGRAACAN 1-2 TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18-22 nucleotides between their centers. We predict protein-DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein-DNA interaction trends.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2021 Suvorova and Gelfand.)
Databáze: MEDLINE
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