The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

<div> <div> <p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p> </div> </div>

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The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

10.26434/chemrxiv.12195372.v3 ◽

2021 ◽

Author(s):

Marina Corbella ◽

Qinghua Liao ◽

Catia Moreira ◽

Peter M. Kasson ◽

Shina Caroline Lynn Kamerlin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequences ◽

Dynamical Behavior ◽

Dna Recognition ◽

Tight Binding ◽

Binding Mode ◽

Binding Modes ◽

Efficient Design ◽

Terminal Loop

<div> <div> <p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p> </div> </div>

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The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

10.26434/chemrxiv.12195372.v2 ◽

2020 ◽

Author(s):

Marina Corbella ◽

Qinghua Liao ◽

Catia Moreira ◽

Peter M. Kasson ◽

Shina Caroline Lynn Kamerlin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequences ◽

Dynamical Behavior ◽

Dna Recognition ◽

Tight Binding ◽

Binding Mode ◽

Binding Modes ◽

Efficient Design ◽

Terminal Loop

<div> <div> <p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p> </div> </div>

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DNA recognition by nuclear receptors

Essays in Biochemistry ◽

10.1042/bse0400059 ◽

2004 ◽

Vol 40 ◽

pp. 59-72 ◽

Cited By ~ 51

Author(s):

Frank Claessens ◽

Daniel T Gewirth

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Nuclear Receptors ◽

Dna Sequences ◽

Dna Recognition ◽

Binding Domain ◽

Dna Binding Domain ◽

Core Motif ◽

Response Elements ◽

Sequence Recognition

The nuclear receptors constitute a large family of ligand-inducible transcription factors. The control of many genetic pathways requires the assembly of these nuclear receptors in defined transcription-activating complexes within control regions of ligand-responsive genes. An essential step is the interaction of the receptors with specific DNA sequences, called hormone-response elements (HREs). These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. HREs are bipartite elements that are composed of two hexameric core half-site motifs. The identity of the response elements resides in three features: the nucleotide sequence of the two core motif half-sites, the number of base pairs separating them and the relative orientation of the motifs. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension. Residues in the first module determine the specificity of the DNA recognition, while residues in the second module are involved in dimerization. Indeed, nuclear receptors bind to their HREs as either homodimers or heterodimers. Depending on the type of receptor, the C-terminal extension plays a role in sequence recognition, dimerization, or both. The DNA-binding domain is furthermore involved in several other functions including nuclear localization, and interaction with transcription factors and co-activators. It is also the target of post-translational modifications. The DNA-binding domain therefore plays a central role, not only in the correct binding of the receptors to the target genes, but also in the control of other steps of the action mechanism of nuclear receptors.

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Faculty Opinions recommendation of Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725289371.793525937 ◽

2016 ◽

Author(s):

Nicolas Buchler

Keyword(s):

Dna Binding ◽

Dna Recognition ◽

Binding Mode ◽

Structural Basis ◽

Winged Helix

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Role of nuclear receptors and hepatocyte-enriched transcription factors for Ntcp repression in biliary obstruction in mouse liver

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00319.2004 ◽

2005 ◽

Vol 289 (5) ◽

pp. G798-G805 ◽

Cited By ~ 46

Author(s):

Gernot Zollner ◽

Martin Wagner ◽

Peter Fickert ◽

Andreas Geier ◽

Andrea Fuchsbichler ◽

...

Keyword(s):

Transcription Factors ◽

Bile Acid ◽

Dna Binding ◽

Nuclear Receptors ◽

Farnesoid X Receptor ◽

Acid Uptake ◽

Mrna Levels ◽

Uptake System ◽

Duct Ligation

Expression of the main hepatic bile acid uptake system, the Na+-taurocholate cotransporter (Ntcp), is downregulated during cholestasis. Bile acid-induced, farnesoid X receptor (FXR)-mediated induction of the nuclear repressor short heterodimer partner (SHP) has been proposed as a key mechanism reducing Ntcp expression. However, the role of FXR and SHP or other nuclear receptors and hepatocyte-enriched transcription factors in mediating Ntcp repression in obstructive cholestasis is unclear. FXR knockout (FXR−/−) and wild-type (FXR+/+) mice were subjected to common bile duct ligation (CBDL). Cholic acid (CA)-fed and LPS-treated FXR−/− and FXR+/+ mice were studied for comparison. mRNA levels of Ntcp and SHP and nuclear protein levels of hepatocyte nuclear factor (HNF)-1α, HNF-3β, HNF-4α, retinoid X receptor (RXR)-α, and retinoic acid receptor (RAR)-α and their DNA binding were assessed. Hepatic cytokine mRNA levels were also measured. CBDL and CA led to Ntcp repression in FXR+/+, but not FXR−/−, mice, whereas LPS reduced Ntcp expression in both genotypes. CBDL and LPS but not CA induced cytokine expression and reduced levels of HNF-1α, HNF-3β, HNF-4α, RXRα, and RARα to similar extents in FXR+/+ and FXR−/−. DNA binding of these transactivators was unaffected by CA in FXR+/+ mice but was markedly reduced in FXR−/− mice. In conclusion, Ntcp repression by CBDL and CA is mediated by accumulating bile acids via FXR and does not depend on cytokines, whereas Ntcp repression by LPS is independent of FXR. Reduced levels of HNF-1α, RXRα, and RARα in CBDL FXR−/− mice and reduced DNA binding in CA-fed FXR−/− mice, despite unchanged Ntcp levels, indicate that these factors may have a minor role in regulation of mouse Ntcp during cholestasis.

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Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x1801110x ◽

2018 ◽

Vol 74 (10) ◽

pp. 656-663 ◽

Cited By ~ 2

Author(s):

Ruby Sharma ◽

Shanti P. Gangwar ◽

Ajay K. Saxena

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequence ◽

Structure Analysis ◽

Dna Sequences ◽

Space Group ◽

Class 1 ◽

Comparative Structure ◽

Ets Domain ◽

Promoter Dna

ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P41212 and of its complex with the E74 DNA sequence (DNA9) in space group C2221 were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA9 with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P65212 and of the ERGi–DNA12 complex in space group P41212 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi–DNA9 complex in space group C2221 forms a structure that is quite similar to that of the ERG–DNA12 complex in space group P41212. Upon superposition of the complexes, major conformational changes are observed at the 5′ and 3′ ends of DNA9, while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi–DNA9 structure with known structures of ETS class 1 protein–DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.

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Reprogrammable Recognition Codes in Bicoid Homeodomain-DNA Interaction

Molecular and Cellular Biology ◽

10.1128/mcb.20.20.7673-7684.2000 ◽

2000 ◽

Vol 20 (20) ◽

pp. 7673-7684 ◽

Cited By ~ 32

Author(s):

Vrushank Dave ◽

Chen Zhao ◽

Fan Yang ◽

Chang-Shung Tung ◽

Jun Ma

Keyword(s):

Dna Sequences ◽

Human Disease ◽

Dna Recognition ◽

Dna Interaction ◽

Morphogenetic Protein ◽

Different Types ◽

Disease Protein

ABSTRACT We describe experiments to determine how the homeodomain of the Drosophila morphogenetic protein Bicoid recognizes different types of DNA sequences found in natural enhancers. Our chemical footprint analyses reveal that the Bicoid homeodomain makes both shared and distinct contacts with a consensus site A1 (TAATCC) and a nonconsensus site X1 (TAAGCT). In particular, the guanine of X1 at position 4 (TAAGCT) is protected by Bicoid homeodomain. We provide further evidence suggesting that the unique arginine at position 54 (Arg 54) of the Bicoid homeodomain enables the protein to recognize X1 by specifically interacting with this position 4 guanine. We also describe experiments to analyze the contribution of artificially introduced Arg 54 to DNA recognition by other Bicoid-related homeodomains, including that from the human disease protein Pitx2. Our experiments demonstrate that the role of Arg 54 varies depending on the exact homeodomain framework and DNA sequences. Together, our results suggest that Bicoid and its related homeodomains utilize distinct recognition codes to interact with different DNA sequences, underscoring the need to study DNA recognition by Bicoid-class homeodomains in an individualized manner.

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Minireview: Nuclear Receptor-Controlled Steroid Hormone Synthesis and Metabolism

Molecular Endocrinology ◽

10.1210/me.2009-0212 ◽

2010 ◽

Vol 24 (1) ◽

pp. 11-21 ◽

Cited By ~ 16

Author(s):

Jinhan He ◽

Qiuqiong Cheng ◽

Wen Xie

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Steroid Hormones ◽

Nuclear Receptor ◽

Recent Progress ◽

Hormone Receptors ◽

Steroid Hormone ◽

Etiological Factor ◽

Hormone Synthesis

Abstract Steroid hormones are essential in normal physiology whereas disruptions in hormonal homeostasis represent an important etiological factor for many human diseases. Steroid hormones exert most of their functions through the binding and activation of nuclear hormone receptors (NRs or NHRs), a superfamily of DNA-binding and often ligand-dependent transcription factors. In recent years, accumulating evidence has suggested that NRs can also regulate the biosynthesis and metabolism of steroid hormones. This review will focus on the recent progress in our understanding of the regulatory role of NRs in hormonal homeostasis and the implications of this regulation in physiology and diseases.

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