Abstract
The MocR-subfamily transcription factors (MocR-TFs) characterized by the GntR-family DNA-binding domain and aminotransferase-like sensory domain are broadly distributed among certain lineages of Bacteria. Characterized MocR-TFs bind pyridoxal 5′-phosphate (PLP) and control transcription of genes involved in PLP, gamma aminobutyric acid (GABA) and taurine metabolism via binding specific DNA operator sites. To identify putative target genes and DNA binding motifs of MocR-TFs, we performed comparative genomics analysis of over 250 bacterial genomes. The reconstructed regulons for 825 MocR-TFs comprise structural genes from over 200 protein families involved in diverse biological processes. Using the genome context and metabolic subsystem analysis we tentatively assigned functional roles for 38 out of 86 orthologous groups of studied regulators. Most of these MocR-TF regulons are involved in PLP metabolism, as well as utilization of GABA, taurine and ectoine. The remaining studied MocR-TF regulators presumably control genes encoding enzymes involved in reduction/oxidation processes, various transporters and PLP-dependent enzymes, for example aminotransferases. Predicted DNA binding motifs of MocR-TFs are generally similar in each orthologous group and are characterized by two to four repeated sequences. Identified motifs were classified according to their structures. Motifs with direct and/or inverted repeat symmetry constitute the majority of inferred DNA motifs, suggesting preferable TF dimerization in head-to-tail or head-to-head configuration. The obtained genomic collection of in silico reconstructed MocR-TF motifs and regulons in Bacteria provides a basis for future experimental characterization of molecular mechanisms for various regulators in this family.
Highlights
Transcription factors (TFs) are proteins that recognize specific cis-regulatory DNA sequences to either stimulate or repress transcription of genes
For the comparative analysis of MocR-TF regulons, we selected a set of 390 representative genomes from 43 diverse taxonomic groups of Bacteria that excludes closely related strains and species and which is most suitable for the comparative genomics-based regulon reconstruction (Table S1a, available in the online Supplementary Material)
The entire set of 974 identified MocR-TFs was broken into taxonomic collection-specific groups that were further analysed using the comparative genomics approach
Summary
Transcription factors (TFs) are proteins that recognize specific cis-regulatory DNA sequences (transcription factor binding sites, TFBSs) to either stimulate or repress transcription of genes. The GntR family is a large and widespread group of bacterial TFs that regulate various biological processes including utilization of sugars and other carbon sources, and amino acid and fatty acid metabolism (Haydon & Guest, 1991; Rigali et al, 2002). TFs from the GntR family (GntR-TFs) contain a conserved N-terminal DNA-binding domain with the helix–turn–helix (HTH) motif, but differ in their C-terminal effector-binding. Depending on the structure of a C-terminal domain, GntR-TFs are classified into six subfamilies (Rigali et al, 2002, 2004)
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