Characterization of surface binding sites in glycoside hydrolases: A computational study

Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty‐five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut‐off differences in each SBSs with different ligand size, molecular docking were performed. Molecular docking results were used to refine SBSs classification and binding sites cut‐off. Docking results predicted putative ligands positions and displayed dependence of the ligands binding mode to the structural type of SBSs. Physicochemical properties of SBSs were calculated for all docking results with YASARA Structure. The results showed that all SBSs are hydrophilic, while their charges could vary and depended to ligand size and defined cut‐off. Surface binding sites type B had highest average values of solvent accessible surface area. Analysis of interactions showed that hydrophobic interactions occur more than hydrogen bonds, which is related to the presence of aromatic residues and carbohydrates interactions.     

Ethylene binding sites in higher plants

A review of work carried out on ethylene binding in higher plants is presented. The use of radio-labelled displacement assays has identified specific ¹⁴C-ethylene binding in all tissues so far studied. virtually all higher plants studied contain at least two classes of ethylene binding site, one of which fully associates and dissociates in about 2 h and a class of sites that takes up to 20 h to become fully saturated. Although the types of site differ in their rate constants of association they have similar and high affinities for ethylene.A series of Arabidopsis thaliana mutants shown to vary in sensitivity to ethylene have been analysed for ¹⁴C-ethylene binding. One mutant, eti 5, which was shown to be unaffected by ethylene concentrations of up to 10,000 L L^–1 was also shown to exhibit reduced binding. In vivo and in vitro studies on pea have shown that ethylene binding can be detected in this tissue. In vitro studies have shown that both membrane and cytosolic fractions contain measurable amounts of ethylene binding. Interestingly, cytosolic ethylene binding consisted only of the fast associating/dissociating type.Developing cotyledons of Phaseolus vulgaris contain a higher concentration of ethylene binding sites that other tissues and only contain the slow dissociating component. These facets have allowed the purification of ethylene binding protein(s) (EBP) from this tissue. The proteins which bind ethylene can be resolved into two bands of 26 and 28 kDa on semi-denaturing PAGE and the proteins appear to be single entities on a 2-D gels.Data will be presented which indicate a possible role for heterotrimetric G-proteins in the early stages of the ethylene signal transduction pathway.     

Membrane-associated binding sites for indoleacetic acid in the rice coleoptile

As described previously, the sensitivity of rice (Oryza sativa L.) coleoptiles to auxin is modulated by oxygen. Under anoxia, coleoptile elongation is insensitive to exogenously applied indole-3-acetic acid (IAA), whereas its sensitivity increases in air in the presence of the exogenous stimulus. Here we report the presence of two independent classes of membrane-bound IAA-binding sites in air-grown coleoptiles. Their binding activity is strictly correlated with the system's sensitivity to IAA. We designate them as site A (high affinity) and site B (low affinity). Site A shows a relatively fast response to anoxia, and is highly specific for auxins. Regulation of site-A binding activity through ATP, whose availability decreases under anoxia, is postulated. A role as auxin carrier is suggested for site B.Abbreviations ABS(s) auxin-binding site(s) - IAA indole-3-acctic acid - NAA 2-naphthaleneacetic acid - ION3 valinomycin, nigericin, carbonylcyanide p-trifluoromethoxyphenyl hydrazone Dedicated to the memory of Professor G. Torti, who passed away on 2 May, 1988     

Temperature-sensitive,lipopolysaccharide-deficient mutants of Salmonella typhimurium

Two mutants of Salmonella typhimurium LT2, which were temperature-sensitive for lipopolysaccharide (LPS) synthesis, were isolated from a galE ^- strain based on their resistance to phage C21 and sensitivity to sodium deoxycholate at 42°C. They produced LPS of chemotype Rc at 30°C and deep-rough LPS at 42°C. P22-mediated transductional analysis showed that the mutations responsible for temperature sensitivity are located in the rfa cluster where several genes involved in the synthesis of the LPS core are mapped. A plasmid, carrying rfaC, D and F genes of Escherichia coli K-12, complemented these mutations. These genes are responsible for the synthesis of the inner-core region of the LPS molecule. This indicates that genetic defects in these temperature-sensitive mutants affect the inner-core region of LPS.     

Effects of water salinity on melatonin levels in plasma and peripheral tissues and on melatonin binding sites in European sea bass (Dicentrarchus labrax)

Sea bass is an euryhaline fish that lives in a wide range of salinities and migrates seasonally from lagoons to the open sea. However, to date, the influence of water salinity on sea bass melatonin levels has not been reported. Here, we evaluated the differences in plasma and tissue melatonin contents and melatonin binding sites in sea bass under four different salinity levels: seawater (36‰), isotonic water (15‰), brackish water (4‰) and freshwater (0‰). The melatonin content was evaluated in plasma, whole brain, gills, intestine and kidney, while melatonin binding sites were analyzed in different brain regions and in the neural retina. Plasma melatonin levels at mid-dark varied, the lowest value occurring in seawater (102 pg/mL), and the highest in freshwater (151 pg/mL). In gills and intestine, however, the highest melatonin values were found in the seawater group (209 and 627 pg/g tissue, respectively). Melatonin binding sites in the brain also varied with salinity, with the highest density observed at the lower salinities in the optic tectum, cerebellum and hypothalamus (30.3, 13.0, and 8.0 fmol/mg protein, respectively). Melatonin binding sites in the retina showed a similar pattern, with the highest values being observed in freshwater. Taken together, these results reveal that salinity influences melatonin production and modifies the density of binding sites, which suggests that this hormone could play a role in timing seasonal events in sea bass, including those linked to fish migration between waters of different salinities for reproduction and spawning.     

Comparative effect of methioninyl adenylate on the growth of Salmonella typhimurium and Pseudomonas aeruginosa

The bacteriostatic effect of methioninyl adenylate (MAMP)—a specific inhibitor of the enzyme methionyl-tRNA synthetase—was investigated on Salmonella typhimurium and Pseudomonas aeruginosa.0.1 mM of this molecule added to the culture, inhibits the growth of S. typhimurium. The inhibition is specifically reversible by 0.1 mM L-methionine. In the same conditions even 1–2 mM MAMP has a very slight effect on the growth rate of P. aeruginosa and only during the first two generations. The same observation was made with the two other members of the fluorescens group P. fluorescens and P. putida.The growth rate of P. testosteroni with 1 mM MAMP in the medium is similar to the growth rate of P. aeruginosa but the other member of the acidovorans group P. acidovorans is much more affected by the same concentration of the inhibitor. — P. multivorans is inhibited by MAMP like P. acidovorans but with a somewhat higher yield at the end of the culture.—MAMP has no effect on P. alcaligenes.The possible reasons for the weak bacteriostatic effect of MAMP on P. aeruginosa were investigated. It was established that the inhibitor enters the cells and is not used as a carbon and energy source. The intracellular methionine concentration in S. typhimurium and in P. aeruginosa is about the same and does not increase when bacteria are cultivated with MAMP. The MTS of the two microorganisms is inhibited by MAMP in vitro to about the same extent. Furthermore the tRNA^met from P. aeruginosa are fully acylated after 3 to 4 generations with this compound. Nevertheless MAMP elicits higher MTS activity in P. aeruginosa and in P. acidovorans after 1 h of incubation. The most striking difference between S. typhimurium and P. aeruginosa is that the intra and extracellular level of 5phosphodiesterase which degrades MAMP is 10–20 fold higher in the second than in the first species.Non Standard Abbreviations MAMP Methioninyl adenylate - MTS methionyl-tRNA synthetase (EC 6.1.1.10) - VTS valyl-tRNA synthetase (EC 6.1.1.0) - Tris trihydroxymethylaminomethane Dedicated to Prof. R. Y. Stanier on the occasion of his 60th birthday     

DNA binding site specificity of the Neurospora global nitrogen regulatory protein NIT2: Analysis with mutated binding sites

NIT2, a positive-acting regulatory protein in Neurospora crassa, activates the expression of a series of unlinked structural genes that encode nitrogen catabolic enzymes. NIT2 binding sites in the promoter regions of nit3, alc and lao have at least two GATA sequence elements. We have examined the binding affinity of the NIT2 protein for the yeast DAL5 wild-type upstream activation sequence UAS_NTR, which contains two GATA elements, and for a series of mutated binding sites, each differing from the wild-type site by a single base. Substitution for individual nucleotides within 5 or 3 sequences that flank the GATA elements had only modest effects upon NIT2 binding. In contrast, nearly all substitutions within the GATA elements almost completely eliminated NIT2 binding, demonstrating the importance of the GATA sequence for NIT2 binding. Four high-affinity binding sites for the NIT2 protein were found within a central region of the nit-2 gene itself.     

The isolation and mapping of EF-Tu mutations in Salmonella typhimurium

Summary The first isolation of EF-Tu mutations in Salmonella typhimurium is reported. The mutations were isolated by selecting for resistance to the antibiotic mocimycin (= kirromycin). The mocimycin resistant phenotype is the result of mutations in each of two genes, tufA and tufB. Strains mutant in only one of the two tuf genes are sensitive to mocimycin. The spontaneous mutation rate of each of the two tuf genes to a mocimycin resistant phenotype differs by an order of magnitude. tufA maps at minute 71–72, closely linked to rpsL. tufB maps at minute 88–89, closely linked to rpoB. These map positions correspond to the locations of tufA and tufB in E. coli.Abbreviations EF-Tu protein elongation factor Tu - MOC mocimycin     

Mutagenicity of structurally related phenylazo-3-pyridines inSalmonella typhimurium

Studies were conducted to explore structure-activity relationships for 4'-N,Ndimethylamino-1'-phenylazo-3-pyridine and nine structurally related compounds in Salmonella typhimuriunz tester strains TA1535, TA100, TA1537, TA1538, TA98. Each compound was tested for mutagenicity at five or more concentrations that varied from 10-5000 pglplate. We used the standard plate test and the investigations were carried out both in the absence and presence of Aroclor-1254induced rat-liver homogenate and the components of the NADPHgenerating system. Negative response was observed for 4'-N,N-dimethylamino-1'-phenylazo-3-pyridine and five of its analogues (4'-N,N-diethylamino-1'phenylazo-3-pyridine; 4'-N,N-di-(-hydroxyethylamino)-1'phenylazo-3-pyridine; 4'-N-methylamino sulfonic acid-1'-phenylazo-3-pyrldine; 4'-N,N-dimethylamino-. 6'-acetamido-1'phenylazo-3-pyridine, and 4'-N,N-di-(-hydroxyethylamino)-6'-methyl-1'phenylazo-3-pyridine). When S9 induced by Aroclor-1254 was present, the compound 4'-N,N-dimethylamino-6-methoxy-1'phenylazo-3-pyridine exhibited mulagenic activity in the two strains TA1538 and TA98. The compound 4' ,6'-diamino-3-methyl-1'-phenylazo-3-pyridine was also mutagenic, both in the presence and in the absence of S9 mix. The two compounds 4'-NjVdimethylamino-6-butoxy-1'-phenylazo-3-pyridine and 4'N,N-di-(-hydroxyethylamino)-1'-phenylazo-3-[6-N,N-di-(-hydroxyethylamino)]-pyridine were either weakly mutagenic or nonmutagenic. On the basis of these data, it is concluded that the mutagenicity of phenylazo-3-pyrzdines, like monocyclic aromatic amines and azo dyes, is influenced by the nature of the substifuent chemical groups and their positions in the molecular structure of the compounds.     

Mutations affecting a regulated, membrane-associated esterase in Salmonella typhimurium LT2

Mutations at the apeA locus in Salmonella typhimurium lead to loss of a soluble enzyme (protease I) that hydrolyzes the chromogenic endoprotease substrate N-acetyl phenylalanine -naphthyl ester. We have isolated pseudorevertants of S. typhimurium apeA mutations that have regained the ability to hydrolyze this compound. These pseudorevertants contain mutations (apeR) that lead to overproduction of a membrane-bound esterase different from protease I. The apeR locus is phage P1 cotransducible with ilvC (83 map units) and is unlinked to apeA. Mutations at still another locus, apeE, lead to loss of the membrane-associated esterase. The apeE locus is P1 cotransducible with purE (12 map units). In an apeE-lacZ operon fusion strain, an apeR mutation increases the level of -galactosidase approximately 60-fold. We propose that apeR encodes a repressor of apeE. The evidence available suggests that the ApeE protein is not a protease.     

OmpR and EnvZ are pleiotropic regulatory proteins: positive regulation of the tripeptide permease (tppB) of Salmonella typhimurium

Summary The tppB locus of Salmonella typhimurium encodes the anaerobically-induced tripeptide permease. We have demonstrated that expression of tppB requires the function of the ompR and envZ gene products, originally identified as positive regulatory proteins required for the osmotic regulation of porin expression. Significantly, tppB expression is not osmotically regulated. We have also identified three additional genes whose expression depends on OmpR. Thus OmpR and EnvZ serve a more general regulatory role than has previously been supposed. This study provides the first detailed genetic analysis of the ompB locus of S. typhimurium.     

Detection of small cryptic plasmids in Salmonella typhimurium strain LT2

Small cryptic plasmids of molecular weights ranging from 1 to 3 Mdal were detected by electron microscopy in Salmonella typhimurium strain LT2 (ColIb). They were divided into different size classes. Two of the cryptic plasmids were transferred simultaneously with ColIb to Escherichia coli.List of Abbreviations TES buffer 0.05 M tris-HCl pH 8.0, 0.05 M NaCl, 0.005 M Na₂ EDTA - TCG medium tris-casamino acid-glucose medium - cpm counts per min     

Energetics of glucose uptake in Salmonella typhimurium

We have studied the energetics of glucose uptake in Salmonella typhimurium. Strain PP418 transprots glucose via the phosphoenolpyruvate: glucose phosphotransferase system, while strain PP1705 lacks this system and can only use the galactose permease for glucose uptake. These two strains were cultured anaerobically in glucose-limited chemostats. Both strains produced ethanol and acetate in equimolar amounts but a significant difference was observed in the molar growth yield on glucose (Y _Glc). It is suggested that this difference is due to a difference in the energetics of the glucose uptake systems in the two strains.Assuming an equal Y _ATP for both strains, we could calculate that uptake of 1 mole of glucose via the galactose permease consumes the equivalent of 0.5 mole of ATP. With the additional assumption that one proton is transported in symport with one glucose molecule, these results imply a stoichiometry of two protons per ATP hydrolysed.Abbreviations PTS Phosphoenolpyruvate: carbohydrate phosphotransferase system - D dilution rate (h^-1 - DW dry weight - GalP galactose permease - EtOH ethanol - HAc acetate - Lact lactate - Suc succinate - HFo formate - Glc Glucose - Y _Glc, Y _ATP yield of cells per glucose or ATP - q specific production rate     

Allosterically linked noncompetitive antagonist binding sites in the resting nicotinic acetylcholine receptor ion channel

Previous studies have established the presence of overlapping binding sites for the noncompetitive antagonists (NCAs) amobarbital, tetracaine, and 3-trifluoromethyl-3-(m-[(125)I]iodophenyl) diazirine ([(125)I]TID) within the ion channel of the Torpedo nicotinic acetylcholine receptor (AChR) in the resting state. These well-characterized NCAs and competitive radioligand binding and photolabeling experiments were employed to better characterize the interaction of the dissociative anesthetics ketamine and thienylcycloexylpiperidine (TCP) with the resting AChR. Our experiments yielded what appear to be conflicting results: (i) both ketamine and TCP potentiated [(125)I]TID photoincorporation into AChR subunits; and (ii) ketamine and TCP had very little effect on [(14)C]amobarbital binding. Nevertheless, (iii) both ketamine and TCP completely displaced [(3)H]tetracaine binding (K(i)s approximately 20.9 and 2.0 microM, respectively) by a mutually exclusive mechanism. To reconcile these results we propose that, in the resting ion channel, TCP and ketamine bind to a site that is spatially distinct from the TID and barbiturate locus, while tetracaine bridges both binding sites.     

Adaptive response to cold temperatures and characterization of cspA in Salmonella typhimurium LT2

Salmonella typhimurium is a major foodborne microbial pathogen which primarily contaminates poultry products causing salmonellosis in humans. S. typhimurium LT2 cultures, when transferred from 37 °C to 5 °C or 10 °C, showed an initial lag period in growth with an approximate generation time of 10–25 h. Western blot assay using E. coli CS7.4 antibody and analysis of radiolabeled total cellular proteins from S. typhimurium cultures after exposure to 10 °C or 5 °C showed elevated expression of a major cold shock protein, CS7.4. Identification of a decreased level of CS7.4 at 37 °C suggests that the expression of this protein may require a large temperature downshift. Putative regulatory protein binding segment on the 5-untranslated region referred as Fragment 7 in S. typhimurium exhibited a 90.6% and a 56.25% nucleotide sequence identity when compared with the Fragment 7 of E. coli and S. enteritidis, respectively. The differences in the nucleotide sequence within the Fragment 7 between S. typhimurium and S. enteritidis may explain the differential expression of CspA at 37 °C. The nucleotide sequence of the open reading frame of S. typhimurium cspA gene showed a single base difference at 816 bp position from a G to a C which altered the amino acid residue from a glycine to an alanine. In addition to CspA, an elevated expression of a 105 kDa, and decreased expression of 6 proteins were evidenced when cultures of S. typhimurium were exposed to 10 °C or 5 °C. Differential expression of the CspA and other proteins in S. typhimurium following exposure to cold temperatures suggest that adaptation and continued growth and survival at cold temperatures in this pathogen may be aided by these cold-responsive proteins.     

Influence of short chain fatty acids and lysine on Salmonella typhimurium cadA expression

In Salmonella typhimurium, cadA has a role in virulence expression and is an inducible gene that responds to external lysine concentration. In this study, a strain of S. typhimurium carrying a cadA: lacZ fusion was used to determine if the induction of cadA occurred under different lysine concentrations and mildly acid conditions in the presence of short chain fatty acids. Aliquots of an 18-h culture of S. typhimurium were placed on fresh media containing different lysine concentrations at pH 5.8 adjusted by addition of HCl or by 1 M short chain fatty acids (SCFA, acetic, propionic and butyric acid) stock solution. After an induction period of 2 h, -galactosidase activities were assayed. Expression of cadA in rich medium was significantly higher than that of minimal medium at neutral pH and different lysine concentrations. In contrast, at pH 5.8, there was a significant increase in cadA expression, particularly when pH was adjusted using HCl at all lysine levels. Addition of a mixture of organic acids yielded an overall lower cadA expression at all lysine levels studied when compared to HCl. However, each SCFA challenge (individual or as a mixture) caused a high level of expression, both at neutral and acidic pH. Based on these results it is apparent that in the presence of external lysine, SCFA and nutrient availability can influence cadA expression in S. typhimurium.