Probing the relation between protein–protein interactions and DNA binding for a linker mutant of the bacterial nucleoid protein H-NS

2014 ◽  
Vol 1844 (2) ◽  
pp. 339-345 ◽  
Author(s):  
Mara Giangrossi ◽  
Kathelijne Wintraecken ◽  
Roberto Spurio ◽  
Renko de Vries
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Bacterial Nucleoid

scholarly journals Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher R. Horne ◽  
Hariprasad Venugopal ◽  
Santosh Panjikar ◽  
David M. Wood ◽  
Amy Henrickson ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Dna Binding ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nutrient Source ◽  
Cryo Electron Microscopy ◽  
Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

scholarly journals Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions

2003 ◽  
Vol 17 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Raj Kumar ◽  
E. Brad Thompson
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Hormone Receptors ◽  
Nuclear Hormone Receptor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Protein Protein Interactions ◽  
Carboxy Terminal ◽  
And Function ◽  
Terminal Domains

Abstract The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.

scholarly journals Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins.

1990 ◽  
Vol 10 (9) ◽  
pp. 4565-4573 ◽  
Author(s):  
L J Ransone ◽  
P Wamsley ◽  
K L Morley ◽  
I M Verma
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Chimeric Protein ◽  
Domain Swapping ◽  
Amino Terminus ◽  
Protein Protein Interactions ◽  
Amino Terminal ◽  
Nih 3T3 ◽  
Basic Region

The products of the Jun and Fos proto-oncogenes form a heterodimer that binds to and activates transcription from 12-O-tetradecanoylphorbol-13-acetate-responsive promoter elements (TGACTCA) and AP-1-binding sites (TGACATCA). These two proteins belong to a family of related transcription factors which contain similar domains required for protein dimerization and DNA binding but display different protein and DNA binding specificities. The basic region, required for DNA binding, is followed by a leucine zipper structure, a domain that mediates protein-protein interactions. To assess the role of these two domains in three related proteins, Fos, Jun, and CREB, we carried out extensive domain-swapping analysis. We found that (i) dimers formed by two Jun leucine zipper-containing proteins were unable to bind DNA as efficiently as a Fos-Jun combination, regardless of the source of the basic region; (ii) the Fos leucine zipper was unable to form either homo- or heterodimers with a chimeric protein containing a Fos leucine zipper; (iii) the Fos basic region was capable of binding to an AP-1 site; (iv) replacement of the Jun amino terminus with that of CREB had little effect on dimerization, whereas replacement with the amino terminus of Fos disrupted both protein-protein and protein-DNA interactions; (v) changes in relative affinities of the Fos and Jun basic regions for the AP-1 element were dependent on the secondary contributions of amino-terminal residues; and (vi) the Fos-Jun chimeric constructs cooperated in transcriptional transactivation of the Jun promoter in NIH 3T3 cells.

scholarly journals Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein–protein interactions

1998 ◽  
Vol 8 (8) ◽  
pp. 452-458 ◽  
Author(s):  
Sanjay Vashee ◽  
Karsten Melcher ◽  
W.Vivianne Ding ◽  
Stephen Albert Johnston ◽  
Thomas Kodadek
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Protein Protein Interactions

scholarly journals Anti-inflammatory functions of the glucocorticoid receptor require DNA binding

2020 ◽  
Vol 48 (15) ◽  
pp. 8393-8407
Author(s):  
Laura Escoter-Torres ◽  
Franziska Greulich ◽  
Fabiana Quagliarini ◽  
Michael Wierer ◽  
Nina Henriette Uhlenhaut
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Protein Interactions ◽  
Transcriptional Activation ◽  
Drug Target ◽  
Immunosuppressive Drug ◽  
Rna Seq ◽  
Protein Protein Interactions ◽  
Inflammatory Conditions ◽  
Anti Inflammatory

Abstract The glucocorticoid receptor is an important immunosuppressive drug target and metabolic regulator that acts as a ligand-gated transcription factor. Generally, GR’s anti-inflammatory effects are attributed to the silencing of inflammatory genes, while its adverse effects are ascribed to the upregulation of metabolic targets. GR binding directly to DNA is proposed to activate, whereas GR tethering to pro-inflammatory transcription factors is thought to repress transcription. Using mice with a point mutation in GR’s zinc finger, that still tether via protein–protein interactions while being unable to recognize DNA, we demonstrate that DNA binding is essential for both transcriptional activation and repression. Performing ChIP-Seq, RNA-Seq and proteomics under inflammatory conditions, we show that DNA recognition is required for the assembly of a functional co-regulator complex to mediate glucocorticoid responses. Our findings may contribute to the development of safer immunomodulators with fewer side effects.

Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins

1990 ◽  
Vol 10 (9) ◽  
pp. 4565-4573
Author(s):  
L J Ransone ◽  
P Wamsley ◽  
K L Morley ◽  
I M Verma
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Chimeric Protein ◽  
Domain Swapping ◽  
Amino Terminus ◽  
Protein Protein Interactions ◽  
Amino Terminal ◽  
Nih 3T3 ◽  
Basic Region

The products of the Jun and Fos proto-oncogenes form a heterodimer that binds to and activates transcription from 12-O-tetradecanoylphorbol-13-acetate-responsive promoter elements (TGACTCA) and AP-1-binding sites (TGACATCA). These two proteins belong to a family of related transcription factors which contain similar domains required for protein dimerization and DNA binding but display different protein and DNA binding specificities. The basic region, required for DNA binding, is followed by a leucine zipper structure, a domain that mediates protein-protein interactions. To assess the role of these two domains in three related proteins, Fos, Jun, and CREB, we carried out extensive domain-swapping analysis. We found that (i) dimers formed by two Jun leucine zipper-containing proteins were unable to bind DNA as efficiently as a Fos-Jun combination, regardless of the source of the basic region; (ii) the Fos leucine zipper was unable to form either homo- or heterodimers with a chimeric protein containing a Fos leucine zipper; (iii) the Fos basic region was capable of binding to an AP-1 site; (iv) replacement of the Jun amino terminus with that of CREB had little effect on dimerization, whereas replacement with the amino terminus of Fos disrupted both protein-protein and protein-DNA interactions; (v) changes in relative affinities of the Fos and Jun basic regions for the AP-1 element were dependent on the secondary contributions of amino-terminal residues; and (vi) the Fos-Jun chimeric constructs cooperated in transcriptional transactivation of the Jun promoter in NIH 3T3 cells.

Synergistic activation of transcription is mediated by the N-terminal domain of Drosophila fushi tarazu homeoprotein and can occur without DNA binding by the protein

1993 ◽  
Vol 13 (3) ◽  
pp. 1599-1609
Author(s):  
J Ananthan ◽  
R Baler ◽  
D Morrissey ◽  
J Zuo ◽  
Y Lan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Binding Activity ◽  
Protein Protein Interactions ◽  
Fushi Tarazu ◽  
Combinatorial Regulation ◽  
Dna Binding Activity ◽  
Culture Cells ◽  
Synergistic Activation ◽  
Activation Of Transcription

Synergistic activation of transcription by Drosophila segmentation genes in tissue culture cells provides a model with which to study combinatorial regulation. We examined the synergistic activation of an engrailed-derived promoter by the pair-rule proteins paired (PRD) and fushi tarazu (FTZ). Synergistic activation by PRD requires regions of the homeodomain or adjacent sequences, and that by FTZ requires the first 171 residues. Surprisingly, deletion of the FTZ homeodomain does not reduce the capacity of the protein for synergistic activation, although this mutation abolishes any detectable DNA-binding activity. This finding suggests that FTZ can function through protein-protein interactions with PRD or other components of the homeoprotein transcription complex, adding a new layer of mechanisms that could underlie the functional specificities and combinatorial regulation of homeoproteins.

scholarly journals Synergistic activation of transcription is mediated by the N-terminal domain of Drosophila fushi tarazu homeoprotein and can occur without DNA binding by the protein.

1993 ◽  
Vol 13 (3) ◽  
pp. 1599-1609 ◽  
Author(s):  
J Ananthan ◽  
R Baler ◽  
D Morrissey ◽  
J Zuo ◽  
Y Lan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Binding Activity ◽  
Protein Protein Interactions ◽  
Fushi Tarazu ◽  
Combinatorial Regulation ◽  
Dna Binding Activity ◽  
Culture Cells ◽  
Synergistic Activation ◽  
Activation Of Transcription

Synergistic activation of transcription by Drosophila segmentation genes in tissue culture cells provides a model with which to study combinatorial regulation. We examined the synergistic activation of an engrailed-derived promoter by the pair-rule proteins paired (PRD) and fushi tarazu (FTZ). Synergistic activation by PRD requires regions of the homeodomain or adjacent sequences, and that by FTZ requires the first 171 residues. Surprisingly, deletion of the FTZ homeodomain does not reduce the capacity of the protein for synergistic activation, although this mutation abolishes any detectable DNA-binding activity. This finding suggests that FTZ can function through protein-protein interactions with PRD or other components of the homeoprotein transcription complex, adding a new layer of mechanisms that could underlie the functional specificities and combinatorial regulation of homeoproteins.

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