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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

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.
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pone.0132618.g008: 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.

Mentions: The second group (FadR, n = 71; HutC, n = 28) consists of divergons where the distance between the sites in a pair linearly increases with the size of the intergenic region (Fig 6B). Thus, these sites are presumably independent, and each of them controls its own operon. There is also a trend towards increasing of the distance to the proximal site for both structural operons and operons with a TF gene, as the intergenic region grows, but this trend is not as prominent as in case of divergons with relatively constant inter-site distance (the first group) (Table 6, Fig 8A and 8B). The same tendencies were also observed in the control group in both FadR (n = 46) and HutC (n = 19) subfamilies (Table 6, Figs 5B and 8C). Thus, in the control group there is only one type of divergons, where the sites do not act co-operatively, and each likely regulates the adjacent operon.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132618.g008: 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.
Mentions: The second group (FadR, n = 71; HutC, n = 28) consists of divergons where the distance between the sites in a pair linearly increases with the size of the intergenic region (Fig 6B). Thus, these sites are presumably independent, and each of them controls its own operon. There is also a trend towards increasing of the distance to the proximal site for both structural operons and operons with a TF gene, as the intergenic region grows, but this trend is not as prominent as in case of divergons with relatively constant inter-site distance (the first group) (Table 6, Fig 8A and 8B). The same tendencies were also observed in the control group in both FadR (n = 46) and HutC (n = 19) subfamilies (Table 6, Figs 5B and 8C). Thus, in the control group there is only one type of divergons, where the sites do not act co-operatively, and each likely regulates the adjacent operon.

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