The applicability of the dimeric heterosynthon concept to molecules with equivalent binding sites. A DFT study of crystalline urea–H2O2

RSC Advances ◽  
2015 ◽  
Vol 5 (37) ◽  
pp. 29601-29608 ◽  
Author(s):  
A. G. Medvedev ◽  
A. V. Shishkina ◽  
P. V. Prikhodchenko ◽  
O. Lev ◽  
M. V. Vener
Keyword(s):  
Binding Sites ◽  
Dft Study ◽  
Two Component ◽  
Limited Applicability ◽  
Crystalline Urea

The limited applicability of the dimeric heterosynthon concept to a two-component urea–H2O2crystal is reported.

Biophysical and physiological characterization of ZraP from Escherichia coli, the periplasmic accessory protein of the atypical ZraSR two-component system

2015 ◽  
Vol 472 (2) ◽  
pp. 205-216 ◽  
Author(s):  
Isabelle Petit-Härtlein ◽  
Kevin Rome ◽  
Eve de Rosny ◽  
Florian Molton ◽  
Carole Duboc ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Zinc Binding ◽  
Accessory Protein ◽  
Two Component System ◽  
Physiological Characterization ◽  
Metal Binding Sites ◽  
Two Component ◽  
Zinc Resistance

ZraP is an octamer containing four interfacial metal-binding sites contributing to dimer stability. Zinc binding enhances its chaperone properties and zinc-bound ZraP represses the expression of the zraPSR operon. None of the Zra proteins are involved in zinc resistance.

scholarly journals FNR-Mediated Oxygen-Responsive Regulation of the nrdDG Operon of Escherichia coli

2003 ◽  
Vol 185 (17) ◽  
pp. 5310-5313 ◽  
Author(s):  
T. Boston ◽  
T. Atlung
Keyword(s):  
Binding Sites ◽  
Response Regulator ◽  
The Other ◽  
Class Iii ◽  
Wild Type ◽  
Anaerobic Conditions ◽  
Two Component ◽  
Oxygen Conditions ◽  
Responsive Regulation ◽  
Transcript Start Site

ABSTRACT Transcription of the nrdDG operon, which encodes the class III nucleotide reductase, which is only active under anaerobic conditions, was strongly induced after a shift to anaerobiosis. The induction was completely dependent on the transcriptional activator FNR and was independent of the ArcA-ArcB two-component response regulator system. The nrdD transcript start site was mapped to a position immediately downstream of two FNR binding sites. Transcription of the other two nucleotide reductase operons, nrdAB and nrdEF, did not respond to oxygen conditions in a wild-type background, but nrdAB expression was increased in the fnr mutant under anaerobic conditions.

scholarly journals Interplay of π-stacking and inter-stacking interactions in two-component crystals of neutral closed-shell aromatic compounds: periodic DFT study

RSC Advances ◽  
2020 ◽  
Vol 10 (47) ◽  
pp. 27899-27910 ◽  
Author(s):  
Sona M. Melikova ◽  
Alexander P. Voronin ◽  
Jaroslaw Panek ◽  
Nikita E. Frolov ◽  
Anastasia V. Shishkina ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Aromatic Compounds ◽  
Closed Shell ◽  
Dft Study ◽  
Organic Crystals ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Two Component ◽  
Periodic Dft

The interplay of π-stacking and inter-stacking interactions in two-component organic crystals without conventional hydrogen bonds.

scholarly journals Acid-Induced Activation of the Urease Promoters Is Mediated Directly by the ArsRS Two-Component System of Helicobacter pylori

2005 ◽  
Vol 73 (10) ◽  
pp. 6437-6445 ◽  
Author(s):  
Michael Pflock ◽  
Simone Kennard ◽  
Isabel Delany ◽  
Vincenzo Scarlato ◽  
Dagmar Beier
Keyword(s):  
Helicobacter Pylori ◽  
Binding Sites ◽  
Response Regulator ◽  
Two Component System ◽  
Component System ◽  
Nickel Ions ◽  
Colonization Factor ◽  
Two Component ◽  
Ph Conditions ◽  
Responsive Regulation

ABSTRACT The nickel-containing enzyme urease is an essential colonization factor of the human gastric pathogen Helicobacter pylori which enables the bacteria to survive the low-pH conditions of the stomach. Transcription of the urease genes is positively controlled in response to increasing concentrations of nickel ions and acidic pH. Here we demonstrate that acid-induced transcription of the urease genes is mediated directly by the ArsRS two-component system. Footprint analyses identify binding sites of the phosphorylated ArsR response regulator within the ureA and ureI promoters. Furthermore, deletion of a distal upstream ArsR binding site of the ureA promoter demonstrates its role in acid-dependent activation of the promoter. In addition, acid-induced transcription of the ureA gene is unaltered in a nikR mutant, providing evidence that pH-responsive regulation and nickel-responsive regulation of the ureA promoter are mediated by independent mechanisms involving the ArsR response regulator and the NikR protein.

scholarly journals DNA Interaction and Phosphotransfer of the C4-Dicarboxylate- Responsive DcuS-DcuR Two-Component Regulatory System from Escherichia coli

2004 ◽  
Vol 186 (6) ◽  
pp. 1879-1889 ◽  
Author(s):  
Aly E. Abo-Amer ◽  
Jonathan Munn ◽  
Kerry Jackson ◽  
Murat Aktas ◽  
Paul Golby ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Polyacrylamide Gel Electrophoresis ◽  
Regulatory System ◽  
Dna Interaction ◽  
Binding Motif ◽  
Pas Domain ◽  
Prosthetic Group ◽  
Two Component

ABSTRACT The DcuS-DcuR system of Escherichia coli is a two-component sensor-regulator that controls gene expression in response to external C4-dicarboxylates and citrate. The DcuS protein is particularly interesting since it contains two PAS domains, namely a periplasmic C4-dicarboxylate-sensing PAS domain (PASp) and a cytosolic PAS domain (PASc) of uncertain function. For a study of the role of the PASc domain, three different fragments of DcuS were overproduced and examined: they were PASc-kinase, PASc, and kinase. The two kinase-domain-containing fragments were autophosphorylated by [γ-32P]ATP. The rate was not affected by fumarate or succinate, supporting the role of the PASp domain in C4-dicarboxylate sensing. Both of the phosphorylated DcuS constructs were able to rapidly pass their phosphoryl groups to DcuR, and after phosphorylation, DcuR dephosphorylated rapidly. No prosthetic group or significant quantity of metal was found associated with either of the PASc-containing proteins. The DNA-binding specificity of DcuR was studied by use of the pure protein. It was found to be converted from a monomer to a dimer upon acetylphosphate treatment, and native polyacrylamide gel electrophoresis suggested that it can oligomerize. DcuR specifically bound to the promoters of the three known DcuSR-regulated genes (dctA, dcuB, and frdA), with apparent KD s of 6 to 32 μM for untreated DcuR and ≤1 to 2 μM for the acetylphosphate-treated form. The binding sites were located by DNase I footprinting, allowing a putative DcuR-binding motif [tandemly repeated (T/A)(A/T)(T/C)(A/T)AA sequences] to be identified. The DcuR-binding sites of the dcuB, dctA, and frdA genes were located 27, 94, and 86 bp, respectively, upstream of the corresponding +1 sites, and a new promoter was identified for dcuB that responds to DcuR.

scholarly journals Regulation of the α-Crystallin Gene acr2 by the MprAB Two-Component System of Mycobacterium tuberculosis

2007 ◽  
Vol 189 (17) ◽  
pp. 6213-6221 ◽  
Author(s):  
Xiuhua Pang ◽  
Susan T. Howard
Keyword(s):  
Protein Synthesis ◽  
Mycobacterium Tuberculosis ◽  
Molecular Chaperone ◽  
Binding Sites ◽  
Deletion Mutant ◽  
Housekeeping Genes ◽  
Mrna Levels ◽  
Two Component System ◽  
Component System ◽  
Two Component

ABSTRACT Coordinated regulation of molecular chaperones is an important feature of the bacterial stress response. The small molecular chaperone gene acr2 of Mycobacterium tuberculosis is activated by exposure to several stresses, including heat and the detergent sodium dodecyl sulfate (SDS). In this study, we show that acr2 is directly regulated by the MprAB two-component system, and that MprAB has both positive and negative effects on acr2 expression. mRNA analyses showed that acr2 expression levels were lower under SDS stress and control conditions but higher under heat shock in an mprAB deletion mutant than they were in the parental strain. Parental expression patterns were restored in an mprAB-complemented strain. Western blotting using an anti-Acr2 antibody showed that Acr2 protein synthesis correlated with mRNA levels. Primer extension identified one transcriptional start point (TSP) for acr2 in all three strains under control and stress conditions. Electrophoresis mobility shift assays revealed multiple MprA binding sites in the acr2 promoter, including one downstream and three upstream of the acr2 TSP, with one overlapping the binding sites predicted for SigE, SigH, and HspR. DNA footprinting confirmed that MprA protected large sections of the acr2 promoter region. Expression of several housekeeping genes under SDS stress also was evaluated, revealing the upregulation of large molecular chaperone genes and, unexpectedly, sigA, with slightly lower sigA mRNA levels detected in the mprAB deletion mutant than in the wild type. In contrast to Acr2, SigA protein synthesis did not correlate with mRNA expression. Overall, the data indicated that MprA has complex interactions with the acr2 promoter and indirect effects on major housekeeping genes.

scholarly journals Comparative analysis of Caulobacter chromosome replication origins

Microbiology ◽  
2009 ◽  
Vol 155 (4) ◽  
pp. 1215-1225 ◽  
Author(s):  
S. M. Shaheen ◽  
Marie-Claude Ouimet ◽  
Gregory T. Marczynski
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Caulobacter Crescentus ◽  
Chromosome Replication ◽  
Integration Host Factor ◽  
Site Directed Mutagenesis ◽  
Replication Origins ◽  
Two Component ◽  
Replication Control ◽  
Dnaa Box

Caulobacter crescentus (CB15) initiates chromosome replication only in stalked cells and not in swarmers. To better understand this dimorphic control of chromosome replication, we isolated replication origins (oris) from freshwater Caulobacter (FWC) and marine Caulobacter (MCS) species. Previous studies implicated integration host factor (IHF) and CcrM DNA methylation sites in replication control. However, ori IHF and CcrM sites identified in the model FWC CB15 were only conserved among closely related FWCs. DnaA boxes and CtrA binding sites are established CB15 ori components. CtrA is a two-component regulator that blocks chromosome replication selectively in CB15 swarmers. DnaA boxes and CtrA sites were found in five FWC and three MCS oris. Usually, a DnaA box and a CtrA site were paired, suggesting that CtrA binding regulates DnaA activity. We tested this hypothesis by site-directed mutagenesis of an MCS10 ori which contains only one CtrA binding site overlapping a critical DnaA box. This overlapping site is unique in the whole MCS10 genome. Selective DnaA box mutations decreased replication, while selective CtrA binding site mutations increased replication of MCS10 ori plasmids. Therefore, both FWC and MCS oris use CtrA to repress replication. Despite this similarity, phylogenetic analysis unexpectedly shows that CtrA usage evolved separately among these Caulobacter oris. We discuss consensus oris and convergent ori evolution in differentiating bacteria.

scholarly journals Regulatory Targets of the Response Regulator RR_1586 from Clostridioides difficile Identified Using a Bacterial One-Hybrid Screen

2018 ◽  
Vol 200 (23) ◽  
Author(s):  
Skyler D. Hebdon ◽  
Smita K. Menon ◽  
George B. Richter-Addo ◽  
Elizabeth A. Karr ◽  
Ann H. West
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Target Genes ◽  
Response Regulator ◽  
Self Regulation ◽  
Transport Systems ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Two Component

ABSTRACT The Clostridioides difficile R20291 genome encodes 57 response regulator proteins that, as part of two-component signaling pathways, regulate adaptation to environmental conditions. Genomic and transcriptomic studies in C. difficile have been limited, due to technical challenges, to the analysis of either high-throughput screens or high-priority targets, such as primary regulators of toxins or spore biology. We present the use of several technically accessible and generally applicable techniques to elucidate the putative regulatory targets of a response regulator, RR_1586, involved in sporulation of the hypervirulent C. difficile strain R20291. A DNA-binding specificity motif for RR_1586 was determined using a bacterial one-hybrid assay originally developed for Drosophila transcription factors. Comparative bioinformatics approaches identified and in vitro experiments confirmed RR_1586 binding sites upstream of putative target genes, including those that encode phosphate ion transporters, spermidine/putrescine biosynthesis and transport pathways, ABC type transport systems, known regulators of sporulation, and genes encoding spore structural proteins. Representative examples of these regulatory interactions have been tested and confirmed in Escherichia coli-based reporter assays. Finally, evidence of possible regulatory mechanisms is also presented. A working model includes self-regulation by RR_1586 and phosphorylation-dependent and -independent DNA binding at low- and high-fidelity binding sites, respectively. Broad application of this and similar approaches is anticipated to be an important catalyst for the study of gene regulation by two-component systems from pathogenic or technically challenging bacteria. IMPORTANCE Clostridioides difficile spores survive under harsh conditions and can germinate into actively dividing cells capable of causing disease. An understanding of the regulatory networks controlling sporulation and germination in C. difficile could be exploited for therapeutic advantage. However, such studies are hindered by the challenges of working with an anaerobic pathogen recalcitrant to genetic manipulation. Although two-component response regulators can be identified from genetic sequences, identification of their downstream regulatory networks requires further development. This work integrates experimental and bioinformatic approaches, which provide practical advantages over traditional transcriptomic analyses, to identify the putative regulon of the C. difficile response regulator RR_1586 by first screening for protein-DNA interactions in E. coli and then predicting regulatory outputs in C. difficile.

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