scholarly journals Mobilization of Chimeric oriT Plasmids by F and R100-1: Role of Relaxosome Formation in Defining Plasmid Specificity

2000 ◽  
Vol 182 (14) ◽  
pp. 4022-4027 ◽  
Author(s):  
Richard A. Fekete ◽  
Laura S. Frost
Keyword(s):  
Binding Sites ◽  
Integration Host Factor ◽  
Affinity Binding ◽  
High Affinity Binding ◽  
High Affinity ◽  
Negative Dominance ◽  
Transfer Apparatus

ABSTRACT Cleavage at the F plasmid nic site within the origin of transfer (oriT) requires the F-encoded proteins TraY and TraI and the host-encoded protein integration host factor in vitro. We confirm that F TraY, but not F TraM, is required for cleavage atnic in vivo. Chimeric plasmids were constructed which contained either the entire F or R100-1 oriT regions or various combinations of nic, TraY, and TraM binding sites, in addition to the traM gene. The efficiency of cleavage atnic and the frequency of mobilization were assayed in the presence of F or R100-1 plasmids. The ability of these chimeric plasmids to complement an F traM mutant or affect F transfer via negative dominance was also measured using transfer efficiency assays. In cases where cleavage at nic was detected, R100-1 TraI was not sensitive to the two-base difference in sequence immediately downstream of nic, while F TraI was specific for the F sequence. Plasmid transfer was detected only when TraM was able to bind to its cognate sites within oriT. High-affinity binding of TraY in cis to oriTallowed detection of cleavage at nic but was not required for efficient mobilization. Taken together, our results suggest that stable relaxosomes, consisting of TraI, -M, and -Y bound to oriT are preferentially targeted to the transfer apparatus (transferosome).

Temperature-dependence of the DnaA–DNA interaction and its effect on the autoregulation of dnaA expression

2012 ◽  
Vol 449 (2) ◽  
pp. 333-341 ◽  
Author(s):  
Chiara Saggioro ◽  
Anne Olliver ◽  
Bianca Sclavi
Keyword(s):  
Temperature Dependence ◽  
Binding Sites ◽  
Dna Interaction ◽  
Bacterial Dna ◽  
Dnaa Protein ◽  
High Affinity ◽  
Key Factor

The DnaA protein is a key factor for the regulation of the timing and synchrony of initiation of bacterial DNA replication. The transcription of the dnaA gene in Escherichia coli is regulated by two promoters, dnaAP1 and dnaAP2. The region between these two promoters contains several DnaA-binding sites that have been shown to play an important role in the negative auto-regulation of dnaA expression. The results obtained in the present study using an in vitro and in vivo quantitative analysis of the effect of mutations to the high-affinity DnaA sites reveal an additional effect of positive autoregulation. We investigated the role of transcription autoregulation in the change of dnaA expression as a function of temperature. While negative auto-regulation is lost at dnaAP1, the effects of both positive and negative autoregulation are maintained at the dnaAP2 promoter upon lowering the growth temperature. These observations can be explained by the results obtained in vitro showing a difference in the temperature-dependence of DnaA–ATP binding to its high- and low-affinity sites, resulting in a decrease in DnaA–ATP oligomerization at lower temperatures. The results of the present study underline the importance of the role for autoregulation of gene expression in the cellular adaptation to different growth temperatures.

Zinc Trafficking 1. Probing the Roles of Proteome, Metallothionein, and Glutathione

Metallomics ◽  
2021 ◽  
Author(s):  
Afsana Mahim ◽  
Mohammad Mahim ◽  
David H Petering
Keyword(s):  
Carbonic Anhydrase ◽  
Binding Sites ◽  
Affinity Binding ◽  
Conditional Stability ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Conditional Stability Constant ◽  
High Affinity Binding ◽  
High Affinity

Abstract The cellular trafficking pathways that conduct zinc to its sites of binding in functional proteins remain largely unspecified. In this study, the hypothesis was investigated that non-specific proteomic binding sites serve as intermediates in zinc trafficking. Proteome from pig kidney LLC-PK1 cells contains a large concentration of such sites, displaying an average conditional stability constant of 1010-11, that are dependent on sulfhydryl ligands to achieve high affinity binding of zinc. As a result, the proteome competes effectively with induced metallothionein for Zn2+ upon exposure of cells to extracellular Zn2+ or during in vitro direct competition. The reaction of added Zn2+ bound to proteome with apo-carbonic anhydrase was examined as a potential model for intracellular zinc trafficking. The extent of this reaction was inversely dependent upon proteome concentration and under cellular conditions thought to be negligible. The rate of reaction was strictly first order in both Zn2+ and apo-carbonic anhydrase and also considered to be insignificant in cells. Adding the low molecular weight fraction of cell supernatant to the proteome markedly enhanced the speed of this reaction, a phenomenon dependent on the presence of glutathione. In agreement, inclusion of glutathione accelerated the reaction in a concentration-dependent manner. The implications of abundant high affinity binding sites for Zn2+ within the proteome are considered in relation to their interaction with glutathione in the efficient delivery of Zn2+ to functional binding sites and in the operation of fluorescent zinc sensors as a tool to observe zinc trafficking.

scholarly journals The TorR High-Affinity Binding Site Plays a Key Role in Both torR Autoregulation and torCADOperon Expression in Escherichia coli

2000 ◽  
Vol 182 (4) ◽  
pp. 961-966 ◽  
Author(s):  
Mireille Ansaldi ◽  
Gwénola Simon ◽  
Michèle Lepelletier ◽  
Vincent Méjean
Keyword(s):  
Escherichia Coli ◽  
Binding Site ◽  
Binding Sites ◽  
Response Regulator ◽  
Regulatory System ◽  
Affinity Binding ◽  
High Affinity Binding ◽  
High Affinity ◽  
High Affinity Binding Site

ABSTRACT In the presence of trimethylamine N-oxide (TMAO), the TorS-TorR two-component regulatory system induces thetorCAD operon, which encodes the TMAO respiratory system ofEscherichia coli. The sensor protein TorS detects TMAO and transphosphorylates the response regulator TorR which, in turn, activates transcription of torCAD. The torRgene and the torCAD operon are divergently transcribed, and the short torR-torC intergenic region contains four direct repeats (the tor boxes) which proved to be TorR binding sites. The tor box 1-box 2 region covers thetorR transcription start site and constitutes a TorR high-affinity binding site, whereas box 3 and box 4 correspond to low-affinity binding sites. By using torR-lacZ operon fusions in different genetic backgrounds, we showed that thetorR gene is negatively autoregulated. Surprisingly, TorR autoregulation is TMAO independent and still occurs in atorS mutant. In addition, this negative regulation involves only the TorR high-affinity binding site. Together, these data suggest that phosphorylated as well as unphosphorylated TorR binds the box 1-box 2 region in vivo, thus preventing RNA polymerase from binding to the torR promoter whatever the growth conditions. By changing the spacing between box 2 and box 3, we demonstrated that the DNA motifs of the high- and low-affinity binding sites must be close to each other and located on the same side of the DNA helix to allow induction of the torCAD operon. Thus, prior TorR binding to the box 1-box 2 region seems to allow cooperative binding of phosphorylated TorR to box 3 and box 4.

scholarly journals Common and Variable Contributions of Fis Residues to High-Affinity Binding at Different DNA Sequences

2006 ◽  
Vol 188 (6) ◽  
pp. 2081-2095 ◽  
Author(s):  
Leah S. Feldman-Cohen ◽  
Yongping Shao ◽  
Derrick Meinhold ◽  
Charmi Miller ◽  
Wilfredo Colón ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Binding Motif ◽  
Affinity Binding ◽  
Flanking Sequence ◽  
Binding Assays ◽  
High Affinity Binding ◽  
High Affinity

ABSTRACT Fis is a nucleoid-associated protein that interacts with poorly related DNA sequences with a high degree of specificity. A difference of more than 3 orders of magnitude in apparent Kd values was observed between specific (Kd , ∼1 to 4 nM) and nonspecific (Kd , ∼4 μM) DNA binding. To examine the contributions of Fis residues to the high-affinity binding at different DNA sequences, 13 alanine substitutions were generated in or near the Fis helix-turn-helix DNA binding motif, and the resulting proteins were purified. In vitro binding assays at three different Fis sites (fis P II, hin distal, and λ attR) revealed that R85, T87, R89, K90, and K91 played major roles in high-affinity DNA binding and that R85, T87, and K90 were consistently vital for binding to all three sites. Other residues made variable contributions to binding, depending on the binding site. N84 was required only for binding to the λ attR Fis site, and the role of R89 was dramatically altered by the λ attR DNA flanking sequence. The effects of Fis mutations on fis P II or hin distal site binding in vitro generally correlated with their abilities to mediate fis P repression or DNA inversion in vivo, demonstrating that the in vitro DNA-binding effects are relevant in vivo. The results suggest that while Fis is able to recognize a minimal common set of DNA sequence determinants at different binding sites, it is also equipped with a number of residues that contribute to the binding strength, some of which play variable roles.

scholarly journals Role of Mg2+ in the structure and activity of maize (Zea mays L.) isocitrate lyase: indications for hysteretic behaviour

1997 ◽  
Vol 327 (1) ◽  
pp. 171-176 ◽  
Author(s):  
Sonia BEECKMANS ◽  
A. Salam KHAN ◽  
Edilbert VAN DRIESSCHE
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Isocitrate Lyase ◽  
Affinity Binding ◽  
High Affinity Binding ◽  
High Affinity ◽  
Activity Measurements ◽  
Enzyme Molecules ◽  
Structure And Activity

The role of Mg2+ in the structure and activity of maize isocitrate lyase has been studied by CD, limited proteolysis, protection by ligands against inactivation, and activity measurements at various metal concentrations. From CD and trypsinolysis experiments, the existence of high-affinity binding sites for Mg2+ was demonstrated, and a KdME of 200 μM was determined. Both free enzyme (E) and enzyme molecules with high-affinity sites occupied (ME) are catalytically competent, the former showing 40% of the activity of the latter. Mg2+ thus acts as a non-essential activator. A second Mg2+-binding site with a KdMEM of 6 mM was revealed from protection experiments by increasing Mg2+ concentrations against inactivation. From activity measurements at different Mg2+ concentrations, the affinity of the enzyme for the Mg2+–isocitrate complex (MI) was determined to be KdE(MI) = 9 μM. Maize isocitrate lyase was shown to display hysteretic behaviour. Filling the low-affinity binding sites with Mg2+ induces a conformational change in the high-affinity binding sites resulting in an even higher affinity for Mg2+ (KdME* = 40 μM). On lowering the Mg2+ concentration again, the enzyme only responds slowly: the time needed for all enzyme molecules to return to the conformation at which KdME is 200 μM was found to be 60 min. Finally it was shown that the high-affinity binding site for Mg2+ is not formed at low (4 °C) temperature.

EFFECT OF FUROSEMIDE ON PLATELET AGGREGATION AND ON ALPHA-ADRENOCEPTOR-DENSITY IN MAN.

1987 ◽  
Author(s):  
A Kribben ◽  
E Fritschka ◽  
M Sibold ◽  
M Fassbender ◽  
A Distler ◽  
...  
Keyword(s):  
Platelet Aggregation ◽  
Binding Sites ◽  
Ex Vivo ◽  
Platelet Rich Plasma ◽  
Affinity Binding ◽  
Pressor Effect ◽  
High Affinity Binding ◽  
Alpha Adrenoceptor ◽  
High Affinity

Furosemide (FUR) reduces the ∝2-adrenoceptor- (∝2-R) mediated pressor effect of norepinephrine. Since it has been shown that FUR reduces platelet aggregation ( AGG) we studied the effect of FUR on α2-R as well as that on the ∝2-R-medi ated epinephrine ( EPI)-induced AGG a) ex vivo and b) in vitro. For comparison the effect of FUR on ADP-induced AGG was also studied. Methods: a) 8 normotensive men received FUR (30 mg b. i.d. ) for 3 weeks. EPI- (1 μmol/1) and ADP- (1 μmol/1) induced platelet AGG were measured before as well as after 3 weeks of FUR application with a semiautomatic device ( APACT) . Platelet ∝2-R-density was measured by 3H-yohimbine-binding and the fraction of high-affinity binding-sites was measured by competi tion of 3H-yohimbine with EPI. b) Platelet-rich plasma was incubated with FUR (1 mmol/1) for 10 min at 37 °C and AGG was measured (n=7) as described. Results: a) FUR decreased ∝2-R-densi ty from 293± 28 to 251±; 21 fmol/mg protein (p< 0.01) and high affinity binding sites from 64± 3 to 55± 5 % (p< 0.01). FUR inhibited ADP-induced AGG ex vivo while EPI-induced AGG did not change (table). b) In vitro FUR inhibited total ADP-induced AGG from 7 4 ± 4 to 45± 8 % (p< 0. 01) while again EPI-induced AGG did not change.Conclusions: The results suggest separate effects of FUR on α2 R-density and on platelet AGG. Although FUR decreased < r2-R, EPI-induced platelet AGG remained unchanged. Since FUR inhibited ADP-induced AGG ex vivo as well as in vitro FUR may interfere directly with the mechanism of ADP-induced platelet AGG.

scholarly journals High-affinity binding sites for VIP in renal cortical membranes: Possible role of VIP in renal transport

1991 ◽  
Vol 39 (2) ◽  
pp. 266-272 ◽  
Author(s):  
Daniel Kniaz ◽  
◽  
Peyman Pahlavan ◽  
Daiva Valaitis ◽  
Jose A.L. Arruda
Keyword(s):  
Binding Sites ◽  
Affinity Binding ◽  
Renal Transport ◽  
High Affinity Binding ◽  
High Affinity ◽  
Cortical Membranes
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