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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 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.
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pone.0132618.g004: 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.

Mentions: For both FadR- (n = 96) and HutC-subfamily (n = 94) divergons comprising a TF gene in one of the operons we observed an approximately linear increase of the distance between the site and the start of each gene in the divergon, as the intergenic distance increased (Fig 4A and 4B). The same tendency was also observed for the control divergons (FadR, n = 33; HutC, n = 23) (Fig 4C; due to the complete match only one regression line is visible). Thus, single sites usually tend to be localized approximately in the middle of the intergenic spacer, although in the divergons with TF genes they usually are slightly closer to the structural operon (Table 3, Fig 4).


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 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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132618.g004: 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.
Mentions: For both FadR- (n = 96) and HutC-subfamily (n = 94) divergons comprising a TF gene in one of the operons we observed an approximately linear increase of the distance between the site and the start of each gene in the divergon, as the intergenic distance increased (Fig 4A and 4B). The same tendency was also observed for the control divergons (FadR, n = 33; HutC, n = 23) (Fig 4C; due to the complete match only one regression line is visible). Thus, single sites usually tend to be localized approximately in the middle of the intergenic spacer, although in the divergons with TF genes they usually are slightly closer to the structural operon (Table 3, Fig 4).

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