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

Suvorova IA, Korostelev YD, Gelfand MS - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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pone.0132618.g001: 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.

Mentions: The common consensus of all analyzed binding sites of FadR-subfamily TFs is an A/T-rich palindromic sequence with conserved TKGT/ACMA boxes (Fig 1), likely the most important for the DNA-protein interaction. As was mentioned earlier, the typical distance between GT and AC in most FadR-subfamily TF-binding sites is 3 nt (DgoR, ExuR, FadR, GlcC, LldR, PdhR etc), although in several orthologous groups it is 2 nt (e.g., GntR, HpxS, HypR, MdcY, PrpR, UxuR). The latter sites were included into the dataset (Spreadsheet FadR in S1 File) for further analysis after insertion of a single-nucleotide gap into the center of the motif.


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

Suvorova IA, Korostelev YD, Gelfand MS - PLoS ONE (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494728&req=5

pone.0132618.g001: 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.
Mentions: The common consensus of all analyzed binding sites of FadR-subfamily TFs is an A/T-rich palindromic sequence with conserved TKGT/ACMA boxes (Fig 1), likely the most important for the DNA-protein interaction. As was mentioned earlier, the typical distance between GT and AC in most FadR-subfamily TF-binding sites is 3 nt (DgoR, ExuR, FadR, GlcC, LldR, PdhR etc), although in several orthologous groups it is 2 nt (e.g., GntR, HpxS, HypR, MdcY, PrpR, UxuR). The latter sites were included into the dataset (Spreadsheet FadR in S1 File) for further analysis after insertion of a single-nucleotide gap into the center of the motif.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.

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.

No MeSH data available.


Related in: MedlinePlus