scholarly journals Powerful Induction of Divergent tgs1-Rv3131 Genes in Mycobacterium tuberculosis Is Mediated by DevR Interaction with a High-Affinity Site and an Adjacent Cryptic Low-Affinity Site

2009 ◽  
Vol 191 (19) ◽  
pp. 6075-6081 ◽  
Author(s):  
Santosh Chauhan ◽  
Jaya Sivaswami Tyagi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Binding Site ◽  
Binding Sites ◽  
Target Genes ◽  
Promoter Activation ◽  
Transcription Start ◽  
High Affinity ◽  
Synergistic Activation ◽  
Dnase I Footprinting ◽  
High Affinity Site

ABSTRACT DevR activates the transcription of ∼48 genes in response to hypoxia and other stresses and triggers metabolic downshift and dormancy development in Mycobacterium tuberculosis. tgs1 and Rv3131 encode triacylglycerol synthase and a putative nitroreductase, respectively, and both are members of the DevR regulon. This study aimed to understand how a single putative DevR binding site identified previously could sustain powerful induction of divergent tgs1-Rv3131 genes. DNase I footprinting revealed that phosphorylated DevR in fact binds to two sites symmetrically located at −42.5 and −63.5 bp from transcription start points of both genes. DevR first bound to the high-affinity site, P, and cooperatively recruited another DevR molecule to the secondary low-affinity site, S, to activate tgs1-Rv3131 transcription by ∼210- and ∼110-fold, respectively. The presence of a single P site significantly reduced activation of tgs1 expression and abolished Rv3131 activity, reinforcing the requirement of two binding sites for robust expression in both directions. P site inversion abolished tgs1 but not Rv3131 transcription despite DevR occupancy at both sites. The lack of tgs1 expression is most likely due to disruption of its −35 promoter element rather than inversion of the binding site per se. We conclude that (i) an overlap of a DevR binding site and −35 sequence is indispensable for promoter activation, (ii) DevR interaction with two binding sites is obligatory for synergistic activation of tgs1-Rv3131 promoters, and (iii) DevR interaction with binding sites of different affinities offers scope for temporal and differential expression of target genes.

scholarly journals Ion–Ion Interactions at the Selectivity Filter

2000 ◽  
Vol 115 (4) ◽  
pp. 509-518 ◽  
Author(s):  
David Immke ◽  
Stephen J. Korn
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Selectivity Filter ◽  
Na Current ◽  
High Affinity ◽  
Ion Interactions ◽  
High Affinity Site ◽  
Maximal Block ◽  
Different Levels ◽  
External K

In the Kv2.1 potassium channel, binding of K+ to a high-affinity site associated with the selectivity filter modulates channel sensitivity to external TEA. In channels carrying Na+ current, K+ interacts with the TEA modulation site at concentrations ≤30 μM. In this paper, we further characterized the TEA modulation site and examined how varying K+ occupancy of the pore influenced the interaction of K+ with this site. In the presence of high internal and external [K+], TEA blocked 100% of current with an IC50 of 1.9 ± 0.2 mM. In the absence of a substitute permeating ion, such as Na+, reducing access of K+ to the pore resulted in a reduction of TEA efficacy, but produced little or no change in TEA potency (under conditions in which maximal block by TEA was just 32%, the IC50 for block was 2.0 ± 0.6 mM). The all-or-none nature of TEA block (channels were either completely sensitive or completely insensitive), indicated that one selectivity filter binding site must be occupied for TEA sensitivity, and that one selectivity filter binding site is not involved in modulating TEA sensitivity. At three different levels of K+ occupancy, achieved by manipulating access of internal K+ to the pore, elevation of external [K+] shifted channels from a TEA-insensitive to -sensitive state with an EC50 of ∼10 mM. Combined with previous results, these data demonstrate that the TEA modulation site has a high affinity for K+ when only one K+ is in the pore and a low affinity for K+ when the pore is already occupied by K+. These results indicate that ion–ion interactions occur at the selectivity filter. These results also suggest that the selectivity filter is the site of at least one low affinity modulatory effect of external K+, and that the selectivity filter K+ binding sites are not functionally interchangeable.

scholarly journals Characterization of Staphylococcus aureus SarA Binding Sites

2003 ◽  
Vol 185 (15) ◽  
pp. 4410-4417 ◽  
Author(s):  
Kristen M. Sterba ◽  
Samuel G. Mackintosh ◽  
Jon S. Blevins ◽  
Barry K. Hurlburt ◽  
Mark S. Smeltzer
Keyword(s):  
Staphylococcus Aureus ◽  
Binding Site ◽  
Binding Sites ◽  
Target Genes ◽  
Direct Interaction ◽  
Nucleotide Composition ◽  
Dna Fragments ◽  
Mobility Shift ◽  
High Affinity ◽  
Electrophoretic Mobility Shift Assays

ABSTRACT The staphylococcal accessory regulator locus (sarA) encodes a DNA-binding protein (SarA) that modulates expression of over 100 genes. Whether this occurs via a direct interaction between SarA and cis elements associated with its target genes is unclear, partly because the definitive characteristics of a SarA binding site have not been identified. In this work, electrophoretic mobility shift assays (EMSAs) were used to identify a SarA binding site(s) upstream of the SarA-regulated gene cna. The results suggest the existence of multiple high-affinity binding sites within the cna promoter region. Using a SELEX (systematic evolution of ligands by exponential enrichment) procedure and purified, recombinant SarA, we also selected DNA targets that contain a high-affinity SarA binding site from a random pool of DNA fragments. These fragments were subsequently cloned and sequenced. Randomly chosen clones were also examined by EMSA. These DNA fragments bound SarA with affinities comparable to those of recognized SarA-regulated genes, including cna, fnbA, and sspA. The composition of SarA-selected DNAs was AT rich, which is consistent with the nucleotide composition of the Staphylococcus aureus genome. Alignment of selected DNAs revealed a 7-bp consensus (ATTTTAT) that was present with no more than one mismatch in 46 of 56 sequenced clones. By using the same criteria, consensus binding sites were also identified upstream of the S. aureus genes spa, fnbA, sspA, agr, hla, and cna. With the exception of cna, which has not been previously examined, this 7-bp motif was within the putative SarA binding site previously associated with each gene.

The somatotrophic axis in young steers: influence of nutritional status and oestradiol-17β on hepatic high-and low-affinity somatotrophic binding sites

1988 ◽  
Vol 116 (2) ◽  
pp. 169-177 ◽  
Author(s):  
B. H. Breier ◽  
P. D. Gluckman ◽  
J. J. Bass
Keyword(s):  
Body Weight ◽  
Nutritional Status ◽  
Binding Site ◽  
Binding Sites ◽  
Dry Matter ◽  
Specific Binding ◽  
Scatchard Analysis ◽  
Binding Studies ◽  
High Affinity ◽  
High Affinity Site

ABSTRACT The binding of bovine GH (bGH) to hepatic membranes obtained from steers on either high (3% dry matter of body weight per day) or low (1% dry matter of body weight per day) planes of nutrition with or without an oestradiol-17β implant was studied (n = 5 per group). Binding studies were performed on both crude membrane homogenates and on 100 000 g microsomal membrane fractions; identical results were obtained using both preparations. In all four groups of animals, linear Scatchard plots were obtained, but following pretreatment of the membranes with MgCl2 to remove endogenously bound hormone, curvilinear plots were obtained in the groups on the high plane of nutrition. Analysis of these curves suggested the presence of a high- and low-affinity binding site, the high-affinity site being fully occupied in the absence of MgCl2 pretreatment. The specific binding of bGH in MgCl2-pretreated crude membranes was greater (P < 0·01) in well-fed steers (14·8 ± 1·6%) than in poorly fed steers (9·8 ± 0·9%). Scatchard analysis showed this to be due to the presence of a high-affinity site (dissociation constant (Kd) = 11·6 ± 3·3 pmol/l) in the well-fed animals only. In addition, there was an increase (P < 0·01) in the affinity, but not in the capacity, of the low-affinity site (Kd = 106·4 ± 22·8 pmol/l in well-fed steers and 197·0 ± 23·8 pmol/l in poorly fed steers). Oestradiol treatment was associated with an increase (P < 0·01) in specific binding at both planes of nutrition, but binding was higher (P < 0·01) in well-fed (24·8 ± 2·9%) than in poorly fed (15·6 ± 3·7%) steers. Scatchard analysis after MgCl2 pretreatment again showed a curvilinear plot at the high and a linear plot at the low nutritional plane. The effect of oestradiol was to increase (P < 0·001) the capacity of the high-affinity site from 1·87 ± 0·61 pmol/100 mg in the control well-fed group to 6·56 ± 1 ·2 pmol/100 mg. The capacity of the low-affinity site was increased (P < 0·01) from 20·1 ± 2·6 to 30·1 ± 3·2 pmol/100 mg in the well-fed group, with a similar change in the poorly fed group. Oestradiol had no effect on the apparent affinity of either binding site. These studies demonstrate a heterogeneity of somatotrophic binding sites of hepatic membranes in steers. The presence of a high-affinity site is determined by nutritional status, whereas oestradiol primarily affects receptor capacity. Thus nutrition and oestradiol have independent and qualitatively different effects on somatotrophic binding. As the rate of weight gain correlated (P < 0·01) with the capacity of the high-affinity site, it is suggested that somatotrophic receptor modulation is a primary factor in the regulation of somatic growth in the ruminant. J. Endocr. (1988) 116, 169–177

Generation of an agonistic binding site for blockers of the M3 muscarinic acetylcholine receptor

2008 ◽  
Vol 412 (1) ◽  
pp. 103-112 ◽  
Author(s):  
Doreen Thor ◽  
Angela Schulz ◽  
Thomas Hermsdorf ◽  
Torsten Schöneberg
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
G Protein ◽  
Binding Sites ◽  
Expression System ◽  
Muscarinic Acetylcholine Receptor ◽  
Intracellular Loop ◽  
Inverse Agonists ◽  
Yeast Expression System ◽  
High Affinity

GPCRs (G-protein-coupled receptors) exist in a spontaneous equilibrium between active and inactive conformations that are stabilized by agonists and inverse agonists respectively. Because ligand binding of agonists and inverse agonists often occurs in a competitive manner, one can assume an overlap between both binding sites. Only a few studies report mutations in GPCRs that convert receptor blockers into agonists by unknown mechanisms. Taking advantage of a genetically modified yeast strain, we screened libraries of mutant M3Rs {M3 mAChRs [muscarinic ACh (acetylcholine) receptors)]} and identified 13 mutants which could be activated by atropine (EC50 0.3–10 μM), an inverse agonist on wild-type M3R. Many of the mutations sensitizing M3R to atropine activation were located at the junction of intracellular loop 3 and helix 6, a region known to be involved in G-protein coupling. In addition to atropine, the pharmacological switch was found for other M3R blockers such as scopolamine, pirenzepine and oxybutynine. However, atropine functions as an agonist on the mutant M3R only when expressed in yeast, but not in mammalian COS-7 cells, although high-affinity ligand binding was comparable in both expression systems. Interestingly, we found that atropine still blocks carbachol-induced activation of the M3R mutants in the yeast expression system by binding at the high-affinity-binding site (Ki ∼10 nM). Our results indicate that blocker-to-agonist converting mutations enable atropine to function as both agonist and antagonist by interaction with two functionally distinct binding sites.

RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene

1991 ◽  
Vol 11 (7) ◽  
pp. 3642-3651 ◽  
Author(s):  
C Devlin ◽  
K Tice-Baldwin ◽  
D Shore ◽  
K T Arndt
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Binding Sites ◽  
Binding Activity ◽  
Micrococcal Nuclease ◽  
Mrna Levels ◽  
High Affinity ◽  
Steady State Levels

The major in vitro binding activity to the Saccharomyces cerevisiae HIS4 promoter is due to the RAP1 protein. In the absence of GCN4, BAS1, and BAS2, the RAP1 protein binds to the HIS4 promoter in vivo but cannot efficiently stimulate HIS4 transcription. RAP1, which binds adjacently to BAS2 on the HIS4 promoter, is required for BAS1/BAS2-dependent activation of HIS4 basal-level transcription. In addition, the RAP1-binding site overlaps with the single high-affinity HIS4 GCN4-binding site. Even though RAP1 and GCN4 bind competitively in vitro, RAP1 is required in vivo for (i) the normal steady-state levels of GCN4-dependent HIS4 transcription under nonstarvation conditions and (ii) the rapid increase in GCN4-dependent steady-state HIS4 mRNA levels following amino acid starvation. The presence of the RAP1-binding site in the HIS4 promoter causes a dramatic increase in the micrococcal nuclease sensitivity of two adjacent regions within HIS4 chromatin: one region contains the high-affinity GCN4-binding site, and the other region contains the BAS1- and BAS2-binding sites. These results suggest that RAP1 functions at HIS4 by increasing the accessibility of GCN4, BAS1, and BAS2 to their respective binding sites when these sites are present within chromatin.

A gonadotropin-releasing hormone type neuropeptide with a high affinity binding site for copper(ii) and nickel(ii)

Metallomics ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 404-414 ◽  
Author(s):  
Kevin K. Tran ◽  
Bhawantha M. Jayawardena ◽  
Maurice R. Elphick ◽  
Christopher E. Jones
Keyword(s):  
Binding Site ◽  
Gonadotropin Releasing Hormone ◽  
Affinity Binding ◽  
Asterias Rubens ◽  
High Affinity Binding ◽  
Releasing Hormone ◽  
High Affinity ◽  
Evolutionarily Conserved ◽  
High Affinity Site ◽  
High Affinity Binding Site

Gonadotropin releasing hormone from Asterias rubens binds Cu(ii) in a nitrogen-rich, high-affinity site. Cu(ii)-binding is an evolutionarily conserved feature of GnRH-type neuropeptides.

scholarly journals The binding of [3H]adenosine to synaptosomal and other preparations from the mammalian brain

1981 ◽  
Vol 194 (2) ◽  
pp. 611-620 ◽  
Author(s):  
M E Newman ◽  
J Patel ◽  
H McIlwain
Keyword(s):  
Binding Site ◽  
Adenosine Deaminase ◽  
Binding Capacity ◽  
Receptor Site ◽  
Mammalian Brain ◽  
Affinity Binding ◽  
Temperature Dependent ◽  
High Affinity ◽  
High Affinity Site ◽  
Uptake Process

1. A high-affinity adenosine-binding site with Kd(adenosine) 0.5-1.3 microM was demonstrated in particulate and synaptosomal fractions isolated from the cerebral cortex of guinea pig, rat and ox. 2. Binding of [3H]adenosine to this site was inhibited by theophylline and by 2-chloroadenosine, but not by four other adenosine analogues. 3. Endogenous adenosine, found to be present in some preparations at approx. 1 pmol/mg of protein, diminished the binding capacity of the preparations for [3H]adenosine. 4. Addition of the adenosine deaminase inhibitor erythro-9-[1-(1-hydroxyethyl)heptyl]-adenine revealed the presence of a second lower affinity binding site with Kd (adenosine) 5-9 microM and a higher maximal adenosine-binding capacity. The inhibitor partially blocked binding to the high-affinity site in preparations from which adenosine deaminase had been removed by washing. 5. To preparations of particulate fractions maintained under iso-osmotic conditions, adenosine attachment was non-saturable and temperature-dependent, indicating the existence of an active uptake process. 6. The location and binding constant of the high-affinity adenosine-binding site suggest that it corresponds to the receptor site for adenosine-activated adenylate cyclase.

Functional Differences in GATA-1 Affinity for Double Versus Single GATA-1 Binding Sites Dictate Synergistic Versus Antagonistic Interactions of PU.1 and GATA-1 in Myeloid Gene Transcription.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1608-1608
Author(s):  
Jian Du ◽  
Dharmesh Vyas ◽  
Qing Xi ◽  
Steven J. Ackerman
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Gene Transcription ◽  
Binding Sites ◽  
Zinc Fingers ◽  
Specific Expression ◽  
High Affinity ◽  
Dual Versus ◽  
P2 Promoter ◽  
Dual Site

Abstract Instructive roles for both GATA-1 and PU.1 have been demonstrated in hematopoiesis, and recent studies have identified both antagonistic and synergistic interactions between them in myeloid gene transcription and lineage development. In prior studies, we reported that PU.1 synergizes with rather than antagonizes GATA-1 for transactivation of a hallmark eosinophil gene, the major basic protein P2 promoter (MBP-P2), which possesses a novel dual (double) GATA-binding site, similar to the palindromic double site in the murine GATA-1 control locus that may specify eosinophil lineage-specific expression of GATA-1 and eosinophil development. To address the transcriptional mechanism for PU.1-GATA-1 synergy through the MBP-P2 dual GATA site, we investigated GATA-1 and PU.1 physical and functonal interactions via their binding sites in the MBP-P2 promoter. DNA binding affinities of GATA-1 and its C- versus N-terminal zinc fingers were assessed for single versus double GATA sites in the presence or absence of PU.1. Our results show that the dual GATA site strongly binds full length GATA-1 with higher affinity than either of the single sites, using both zinc fingers, but that mutant GATA-1 proteins with C-finger or N-finger deletions retain their ability to bind, albeit at lower affinity, to the dual site. DNA binding activities of the two zinc fingers with the dual GATA site were confirmed using peptides containing only the C-finger or N-finger region. Of note, formation of GATA-1 complexes with the dual GATA site was not inhibited by the addition of PU.1, whereas formation of binding complexes for mutants of GATA-1 containing only the C- or N-finger region could be completely inhibited in a dose-response fashion by PU.1. These unique features of PU.1/GATA-1 interactions on a dual versus single GATA-1 site were confirmed using peptides containing only the C- or N-finger regions of GATA-1. Our findings indicate that both zinc fingers of GATA-1 are involved in formation of the high-affinity GATA-1 complex with the dual site. Importantly, we show that the higher affinity dual GATA-1 site complex is not affected by the addition of PU.1, whereas formation of the binding complex with a single GATA-1 site is eliminated by PU.1, emphasizing the different mechanisms of GATA-1/PU.1 interactions on dual versus single GATA binding sites. Functional analyses by transactivation confirmed that synergistic activation of the MBP-P2 promoter by GATA-1 and PU.1 is mediated by their protein-protein interactions through this unique high affinity dual GATA-1 binding site. We suggest two possible mechanisms for PU.1/GATA-1 synergy on dual GATA sites: (1) PU.1 may change GATA-1 conformation and its high affinity for the dual site, enhancing its availability for interaction with the basal transcriptional machinery. Alternatively, (2) PU.1 could impede interactions of GATA-1 with a co-repressor, e.g. FOG-1, which we and others have shown represses GATA-1 function in the eosinophil lineage.

scholarly journals Electron microscopy of cervical-mucus glycoproteins and fragments therefrom. The use of colloidal gold to make visible ‘naked’ protein regions

1990 ◽  
Vol 265 (1) ◽  
pp. 169-177 ◽  
Author(s):  
J K Sheehan ◽  
I Carlstedt
Keyword(s):  
Electron Microscopy ◽  
Binding Site ◽  
Binding Sites ◽  
Colloidal Gold ◽  
Length Distribution ◽  
Cervical Mucus ◽  
High Affinity ◽  
Protein Rich ◽  
Peptide Region ◽  
Mucus Glycoproteins

Subunits of human cervical-mucus glycoproteins obtained by reductive cleavage of whole mucins and high-Mr glycopeptides (T-domains) obtained after their trypsin digestion were studied with electron microscopy after spreading the macromolecules in a monolayer of benzyldimethylalkylammonium chloride. Subunits were observed as linear and apparently flexible particles, with number- and weight-average lengths of 390 nm and 460 nm respectively. T-domains randomly distributed on the grid have number- and weight-average lengths of 90 nm and 103 nm respectively, whereas when aligned (possibly stretched by flow) they were longer, with number-average and weight-average lengths of 150 nm and 170 nm respectively. Subunits complexed with gold appeared as segmented structures, with a distribution of inter-gold distances similar to the length distribution for the relaxed T-domains. The whole mucins had few binding sites for gold, suggesting that reduction exposes hydrophobic protein-rich regions with high affinity for gold. Most T-domains had a binding site at one end, indicating the presence of a residual protruding naked peptide region. We conclude that mucins are assembled from subunits joined end-to-end, and that each subunit consists of alternating oligosaccharide ‘clusters’ (approx. 100 nm) and naked peptide regions which have (after reduction) a high affinity for colloidal gold.

Uptake of 3,5,3′-l-tri-iodothyronine in human erythrocytes

1989 ◽  
Vol 121 (3) ◽  
pp. 585-591 ◽  
Author(s):  
K. Yamauchi ◽  
R. Horiuchi ◽  
H. Takikawa
Keyword(s):  
Binding Sites ◽  
Binding Capacity ◽  
Human Erythrocytes ◽  
The Other ◽  
Transport Pathway ◽  
High Affinity ◽  
High Affinity Site ◽  
Maximum Binding Capacity ◽  
Energy Dependent ◽  
Dependent Pathway

ABSTRACT The mechanisms of 3,5,3′-l-tri-iodothyronine (T3) uptake into human erythrocytes were examined. Purified membranes of human erythrocytes were shown to have two classes of T3-binding sites with one being a high-affinity site (dissociation constant, 59·2±17·8 nmol/l; maximum binding capacity, 344·3 ± 95·5 fmol/μg protein). Furthermore, it was shown that there were two pathways for T3 uptake in human erythrocytes; one was saturable, stereospecific (T3»thyroxine > 3,5,3′-d-tri-iodothyronine), energydependent and dominant at 15 °C; the other was not displaced by unlabelled T3 and was energyindependent but did not occur by passive diffusion. The former pathway which, it is suggested, is a receptor-mediated transport pathway, was inhibited by monodansylcadaverine, phloretin or oligomycin at 15 or 37 °C, but the latter pathway was not inhibited by these inhibitors. Our results strongly suggest that uptake of T3 by the energy-independent pathway became predominant over the energy-dependent pathway at 37 °C and accounted for 83% of total T3 uptake of human erythrocytes. Journal of Endocrinology (1989) 121, 585–591

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