Limits...
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

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.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4494728&req=5

pone.0132618.g006: 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.

Mentions: In both FadR (n = 100) and HutC (n = 60) subfamilies, we observe two fractions of divergons with a TF gene (Table 4, Fig 5A). The first group includes divergons (FadR, n = 29; HutC, n = 32) where the distance between double sites is relatively constant (Fig 6A). In this group, the distance to the proximal binding site tends to be higher for longer intergenic regions in both structural operons and operons with a TF gene (Table 5, Fig 7A and 7B). Thus, double sites in this group of divergons usually tend to be localized near the center of the intergenic area, and we may conclude that they form a pair involved in the co-operative control of both operons.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132618.g006: 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.
Mentions: In both FadR (n = 100) and HutC (n = 60) subfamilies, we observe two fractions of divergons with a TF gene (Table 4, Fig 5A). The first group includes divergons (FadR, n = 29; HutC, n = 32) where the distance between double sites is relatively constant (Fig 6A). In this group, the distance to the proximal binding site tends to be higher for longer intergenic regions in both structural operons and operons with a TF gene (Table 5, Fig 7A and 7B). Thus, double sites in this group of divergons usually tend to be localized near the center of the intergenic area, and we may conclude that they form a pair involved in the co-operative control of both operons.

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