GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution

Abstract

The GNTR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GNTR family, FADR, HUTC, and YTRA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FADR, HUTC, and YTRA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FADR, HUTC, and YTRA subfamilies, which may play role in the binding of additional TF-subunits.

Fig 1. Heat map of correlations between amino acids and nucleotides for FadR-subfamily TFs and their binding sites.

Sequence logos of HTH DNA-binding domains and corresponding binding sites are shown on the top and to the left of the heat map, respectively. The total height of the symbols in each position equals the positional information content, whereas the height of individual symbols is proportional to the positional amino acid or nucleotide frequency. The correlation scores are color ramped from yellow to red for amino acid-nucleotide pairs with statistical significance greater than an automatically defined threshold (with red assigned for the most correlated pair). The violet-black palette is used for other pairs.

Fig 2. Heat map of correlations between amino acids and nucleotides for HutC-subfamily TFs and their binding sites.

Notation as in Fig 1.

Fig 3. Heat map of correlations between amino acids and nucleotides for YtrA-subfamily TFs and their binding sites.

Notation as in Fig 1.

Fig 4. Distances between regulated genes and TF-binding sites in divergons with single sites.

A—operons with a TF gene; B—operons with structural genes only; C—the control group (includes divergons without TF genes). The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Each dot corresponds to one site. The regression lines are shown. Blue color denotes the FadR subfamily; red color, the HutC subfamily.

Fig 5. Distances between double sites in divergons.

A—divergons with a TF gene; B—the control group. The vertical axis is the inter-site distance. The horizontal axis is the intergenic distance. Notation as in Fig 4.

Fig 6. Two groups of divergons with double sites.

A—the first group (constant inter-site distance); B—the second group (increasing inter-site distance). For details, see the text. The vertical axis is the inter-site distance. The horizontal axis is the intergenic distance. Notation as in Fig 4.

Fig 7. Distances between regulated genes and proximal TF-binding sites in divergons with common double sites.

A—operons with a TF gene; B—operons with structural genes only. The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Notation as in Fig 4.

Fig 8. Distances between regulated genes and proximal TF-binding sites in divergons with separate double sites.

A—operons with a TF gene; B—operons with structural genes only; C—the control group. The vertical axis is the distance between the site center and the start codon. The horizontal axis is the intergenic distance. Notation as in Fig 4.

Fig 9. Positioning of additional boxes and control pseudoboxes.

True binding half-sites are shown in blue; additional boxes, in violet; pseudoboxes, in red arrows. For details, see the text.

Fig 10. Distribution of S_near and S_random in the FadR, HutC and YtrA subfamilies.

The vertical axis—the number of S values falling in the given interval. The horizontal axis—intervals of S values. Blue color denotes S_near values; red color—S_random values. FadR subfamily data is shown in continuous lines; HutC subfamily, in dotted lines; YtrA subfamily, in dashed lines.