Analysis of nucleotide binding to Dictyostelium myosin II motor domains containing a single tryptophan near the active site

Dictyostelium myosin II motor domain constructs containing a single tryptophan residue near the active sites were prepared in order to characterize the process of nucleotide binding. Tryptophan was introduced at positions 113 and 131, which correspond to those naturally present in vertebrate skeletal muscle myosin, as well as position 129 that is also close to the adenine binding site. Nucleotide (ATP and ADP) binding was accompanied by a large quench in protein fluorescence in the case of the tryptophans at 129 and 131 but a small enhancement for that at 113. None of these residues was sensitive to the subsequent open-closed transition that is coupled to hydrolysis (i.e. ADP and ATP induced similar fluorescence changes). The kinetics of the fluorescence change with the F129W mutant revealed at least a three-step nucleotide binding mechanism, together with formation of a weakly competitive off-line intermediate that may represent a nonproductive mode of nucleotide binding. Overall, we conclude that the local and global conformational changes in myosin IIs induced by nucleotide binding are similar in myosins from different species, but the sign and magnitude of the tryptophan fluorescence changes reflect nonconserved residues in the immediate vicinity of each tryptophan. The nucleotide binding process is at least three-step, involving conformational changes that are quite distinct from the open-closed transition sensed by the tryptophan Trp(501) in the relay loop.     

Nonimmune binding of Ig to Clostridium perfringens. Preferential binding of IgM and aggregated IgG

In an attempt to find a bacterial IgM receptor, a large number of bacterial strains of different species were screened for the ability to bind human IgM. Certain strains of the anaerobic bacterium Clostridium perfringens were found to bind a major fraction of polyclonal IgM. One bacterial strain showed a particularly high binding capacity and was studied in more detail. This strain is also able to bind a minor fraction of polyclonal IgA and IgG. Inhibition experiments indicate that the different Ig classes bind to one and the same R structure. The ability of the strain to bind polyclonal Ig is correlated to the number of subunits in the Ig. This correlation can most simply be explained by increasing avidity with increasing number of subunits. In agreement with this hypotheses, experiments with aggregated IgG show that binding ability increases with aggregate size. Experiments with Ig fragments indicate that the binding structure in Ig is located in the F(ab')2 region. The ability of this bacterial strain to bind a majority of IgM molecules as well as aggregated IgG is potentially useful in immunologic work and represents a new type of Ig binding to bacteria.     

Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human proteins

Our recent studies have been aimed at understanding the mechanisms regulating apical protein sorting in polarized epithelial cells. In particular, we have been investigating how lipid rafts serve to sort apical proteins in the biosynthetic pathway. The recent findings that lipid domains are too small or transient to host apically destined cargo have led to newer versions of the hypothesis that invoke proteins required for lipid domain coalescence and stabilization. MAL (myelin and lymphocyte protein) and its highly conserved family member, MAL2, have emerged as possible regulators of this process in the direct and indirect apical trafficking pathways respectively. To test this possibility, we took a biochemical approach. We determined that MAL, but not MAL2, self-associates, forms higher-order cholesterol-dependent complexes with apical proteins and promotes the formation of detergent-resistant membranes that recruit apical proteins. Such biochemical properties are consistent with a role for MAL in raft coalescence and stabilization. These findings also support a model whereby hydrophobic mismatch between the long membrane-spanning helices of MAL and the short-acyl-chain phospholipids in the Golgi drive formation of lipid domains rich in raft components that are characterized by a thicker hydrophobic core to alleviate mismatch.     

The relationship between cytotoxic effect and binding to mammalian cultured cells of Clostridium perfringens enterotoxin

Abstract The relationship between the cytotoxic effect and binding to different cell lines of Clostridium perfringens enterotoxin was investigated. The enterotoxin released ⁵¹Cr from Vero and MDCK cells labeled with Na₂-⁵¹CrO₄. The effect varied depending upon the dose of enterotoxin and the duration and temperature of the interaction. The enterotoxin gave no effect on FL, KB, or L-929 cells. [¹²⁵I]Enterotoxin bound specifically to Vero and MDCK cells via a binding site of distinct nature, but not to FL, KB, or L-929 cells. The number of the binding sites located on one MDCK cell (1.98 × 10⁶ sites/cell) was three times that on one Vero cell (5.64 × 10⁵ sites/cell), although the binding affinity of MDCK cell ( K _a/ 3.76 × 10⁷ M⁻¹) was 0.1 that of Vero cells ( K _a/ 3.23 × 10⁸ M⁻¹). Binding of the enterotoxin to susceptible cells was temperature-independent.     

Response of Clostridium perfringens and its L form to bacteriocins of C. perfringens

Clostridium perfringens strain No. 28 and its penicillin-induced stable L form were treated with 10 different bacteriocins of C. perfringens. Viable count and labelled amino acid incorporation experiments revealed that the L form was sensitive to two and possibly three bacteriocins to which the bacillus was not, while both forms were commonly sensitive to two other bacteriocins and resistant to five others. Adsorption of bacteriocin, immunity factors, or perhaps uptake of bacteriocin might be proposed to explain the responses of these organisms to bacteriocins.     

Biochemical and molecular characterization of a novel choline-specific glycerophosphodiester phosphodiesterase belonging to the nucleotide pyrophosphatase/phosphodiesterase family

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) are ubiquitous membrane-associated or secreted ectoenzymes that release nucleoside 5'-monophosphate from a variety of nucleotides and nucleotide derivatives. The mammalian NPP family comprises seven members, but only three of these (NPP1-3) have been studied in some detail. Previously we showed that lysophospholipase D, which hydrolyzes lysophosphatidylcholine (LPC) to produce lysophosphatidic acid, is identical to NPP2. More recently an uncharacterized novel NPP member (NPP7) was shown to have alkaline sphingomyelinase activity. These findings raised the possibility that other members of the NPP family act on phospholipids. Here we show that the sixth member of the NPP family, NPP6, is a choline-specific glycerophosphodiester phosphodiesterase. The sequence of NPP6 encodes a transmembrane protein containing an NPP domain with significant homology to NPP4, NPP5, and NPP7/alkaline sphingomyelinase. When expressed in HeLa cells, NPP6 was detected in both the cells and the cell culture medium as judged by Western blotting and by enzymatic activity. Recombinant NPP6 efficiently hydrolyzed the classical substrate for phospholipase C, p-nitrophenyl phosphorylcholine, but not the classical nucleotide phosphodiesterase substrate, p-nitrophenyl thymidine 5'-monophosphate. In addition, NPP6 hydrolyzed LPC to form monoacylglycerol and phosphorylcholine but not lysophosphatidic acid, showing it has a lysophospholipase C activity. NPP6 showed a preference for LPC with short (12:0 and 14:0) or polyunsaturated (18:2 and 20:4) fatty acids. It also hydrolyzed glycerophosphorylcholine and sphingosylphosphorylcholine efficiently. In mice, NPP6 mRNA was predominantly detected in kidney with a lesser expression in brain and heart, and in human it was detected in kidney and brain. The present results suggest that NPP6 has a specific role through the hydrolysis of polyunsaturated LPC, glycerophosphorylcholine, or sphingosylphosphorylcholine in these organs.     

Susceptibility of Clostridium perfringens to C-C fatty acids

AIMS: To determine susceptibility of Clostridium perfringens strains CCM 4435(T) and CNCTC 5459 to C(2)-C(18) fatty acids, and evaluate influence of pH in cultures grown on glucose. Straw particles were added to cultures to simulate the presence of solid phase of the digestive tract milieu. METHODS AND RESULTS: Antimicrobial activity of fatty acids was expressed as a concentration at which only 50% of the initial glucose was utilized. Lauric acid showed the highest antimicrobial activity, followed by myristic, capric, oleic and caprylic acid. Only strain CNCTC 5459 was susceptible to linoleic acid. Neither caproic acid and acids with a shorter carbon chain nor palmitic and stearic acid influenced substrate utilization. The antimicrobial activity of myristic, oleic and linoleic acid decreased when clostridia were grown in the presence of straw particles. In cultures of both strains treated with capric and lauric acid at pH 5.0-5.3, the number of viable cells was <10(2) ml(-1). Only lauric acid reduced number of viable cells of both strains below 10(2) ml(-1) at pH > 6. Transmission electron microscopy revealed separation of inner and outer membranes and cytoplasma disorganization in cells treated with lauric acid. CONCLUSIONS: Lauric acid had the highest activity towards C. perfringens among fatty acid tested. Its activity was not influenced by the presence of solid particles and did not cease at pH > 6. SIGNIFICANCE AND IMPACT OF THE STUDY: Lauric acid might be a means for control of clostridial infections in farm animals.     

Growth Response of Clostridium perfringens to Oxidative Stress

The sensitivity of Clostridium perfringens strain 13 to oxygen and its toxic derivatives was investigated in a new, defined medium (MMP). Exponentially growing cells in MMP medium were very sensitive to exposure to air by vigorous shaking. When exposed to air, the cells survived only 1hour and then rapidly died. Addition of cysteine, ascorbic acid, or yeast extract to the medium significantly increased vegetative cell survival without inducing sporulation. The level of toxicity of peroxyl and hydroperoxyl radicals, generated by H₂O₂, t-butyl hydroperoxide or ethanol, was very similar with and without air exposure. By contrast, plumbagin or menadione, which generate superoxide radicals in the presence of oxygen, caused high levels of cell death only in aerobiosic culture. Growth-arrested cells were more resistant to H₂O₂and to redox-cycling agents than were exponentially growing cells, but the resistance required de novo synthesis of proteins. An adaptive response to oxidative stress was also suggested by the higher level of cell resistance to H₂O₂and to ethanol when cells were pretreated with sublethal doses of these oxidants.     

Identification of the structural and functional domains of the large serine recombinase TnpX from Clostridium perfringens

Members of the large serine resolvase family of site-specific recombinases are responsible for the movement of several mobile genetic elements; however, little is known regarding the structure or function of these proteins. TnpX is a serine recombinase that is responsible for the movement of the chloramphenicol resistance elements of the Tn4451/3 family. We have shown that TnpX binds differentially to its transposon and target sites, suggesting that resolvase-like excision and insertion were two distinct processes. To analyze the structural and functional domains of TnpX and, more specifically, to define the domains involved in protein-DNA and protein-protein interactions, we conducted limited proteolysis studies on the wild-type dimeric TnpX(1-707) protein and its functional truncation mutant, TnpX(1-597). The results showed that TnpX was organized into three major domains: domain I (amino acids (aa) 1-170), which included the resolvase catalytic domain; domain II (aa 170-266); and domain III (aa 267-707), which contained the dimerization region and two separate regions involved in binding to the DNA target. A small polypeptide (aa 533-587) was shown to bind specifically to the TnpX binding sites providing further evidence that it was the primary DNA binding region. In addition, a previously unidentified DNA binding site was shown to be located between residues 583 and 707. Finally, the DNA binding and multerimization but not the catalytic functions of TnpX could be reconstituted by recombining separate polypeptides that contain the N- and C-terminal regions of the protein. These data provide evidence that TnpX has separate catalytic, DNA binding, and multimerization domains.     

Site-specific effects of zinc on the activity of family II pyrophosphatase

Family II pyrophosphatases (PPases), recently found in bacteria and archaebacteria, are Mn(2+)-containing metalloenzymes with two metal-binding subsites (M1 and M2) in the active site. These PPases can use a number of other divalent metal ions as the cofactor but are inactive with Zn(2+), which is known to be a good cofactor for family I PPases. We report here that the Mg(2+)-bound form of the family II PPase from Streptococcus gordonii is nearly instantly activated by incubation with equimolar Zn(2+), but the activity thereafter decays on a time scale of minutes. The activation of the Mn(2+)-form by Zn(2+) was slower but persisted for hours, whereas activation was not observed with the Ca(2+)- and apo-forms. The bound Zn(2+) could be removed from PPase by prolonged EDTA treatment, with a complete recovery of activity. On the basis of the effect of Zn(2+) on PPase dimerization, the Zn(2+) binding constant appeared to be as low as 10(-12) M for S. gordonii PPase. Similar effects of Zn(2+) and EDTA were observed with the Mg(2+)- and apo-forms of Streptococcus mutans and Bacillus subtilis PPases. The effects of Zn(2+) on the apo- and Mg(2+)-forms of HQ97 and DE15 B. subtilis PPase variants (modified M2 subsite) but not of HQ9 variant (modified M1 subsite) were similar to that for the Mn(2+)-form of wild-type PPase. These findings can be explained by assuming that (a) the PPase tightly binds Mg(2+) and Mn(2+) at the M2 subsite; (b) the activation of the corresponding holoenzymes by Zn(2+) results from its binding to the M1 subsite; and (c) the subsequent inactivation of Mg(2+)-PPase results from Zn(2+) migration to the M2 subsite. The inability of Zn(2+) to activate apo-PPase suggests that Zn(2+) binds more tightly to M2 than to M1, allowing direct binding to M2. Zn(2+) is thus an efficient cofactor at subsite M1 but not at subsite M2.     

Identification and isolation of the binding substance for Clostridium perfringens enterotoxin on Vero cells

Abstract To identify the binding substance for Clostridium perfringens enterotoxin (CPE), the CPE-binding substances metabolically labelled with [³H]leucine on CPE-susceptible (Vero) and resistant (L-929) cells were analyzed by solubilization, immunoprecipitation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and fluorography. The CPE-binding substance was found on Vero cells, but not on L-929 cells. The molecular weight of the CPE-binding substance was found to be 60 000 on SDS-PAGE. The CPE-binding substances were isolated from Vero cells and Balb/c mouse intestinal brush border membranes by affinity chromatography on CPE-coupled Sepharose 4B. They were homogeneous substances with molecular weights of 60 000 on SDS-PAGE and inhibited to the same extent the binding reaction of ¹²⁵I-labeled CPE with Vero cells. These results suggests that the CPE-binding substances are the receptors of CPE on these cells.     

Effects of gyrase mutation on the growth kinetics of ciprofloxacin-resistant strains of Clostridium perfringens

To investigate the effect of gyrA mutation on resistance of Clostridium perfringens to fluoroquinolones, a ciprofloxacin-resistant mutant was developed. The mutant had a single substitution in gyrA at position 87 (Asp to Tyr) and no additional mutations in gyrB, parC or parE. The MIC values of gatifloxacin and ciprofloxacin for this strain were 16 and 32-fold higher than those for the wild type, which were 0.125 and 0.250 microg/mL, respectively. The resistant mutant grew equally well in the presence or absence of 5 microg/mL of ciprofloxacin or 1 microg/mL of gatifloxacin and grew to lower cell densities with up to 30 microg/mL of ciprofloxacin or 5 microg/mL of gatifloxacin. Higher concentrations of fluoroquinolones resulted in increases in the time required to reach the end of the exponential phase and in lower cell densities at the end. The efflux pump inhibitor reserpine did not affect susceptibility to fluoroquinolones. The substitution of Asp 87 to Tyr in gyrA may have protected C. perfringens from low concentrations of ciprofloxacin and gatifloxacin and enabled survival and growth at higher concentrations.     

Nonequivalence of the nucleotide binding domains of the ArsA ATPase

The arsRDABC operon of Escherichia coli plasmid R773 encodes the ArsAB pump that catalyzes extrusion of the metalloids As(III) and Sb(III), conferring metalloid resistance. The catalytic subunit, ArsA, is an ATPase with two homologous halves, A1 and A2, connected by a short linker. Each half contains a nucleotide binding domain. The overall rate of ATP hydrolysis is slow in the absence of metalloid and is accelerated by metalloid binding. The results of photolabeling of ArsA with the ATP analogue 8-azidoadenosine 5'-[alpha-(32)P]-triphosphate at 4 degrees C indicate that metalloid stimulation correlates with a >10-fold increase in affinity for nucleotide. To investigate the relative contributions of the two nucleotide binding domains to catalysis, a thrombin site was introduced in the linker. This allowed discrimination between incorporation of labeled nucleotides into the two halves of ArsA. The results indicate that both the A1 and A2 nucleotide binding domains bind and hydrolyze trinucleotide, even in the absence of metalloid. Sb(III) increases the affinity of the A1 nucleotide binding domain to a greater extent than the A2 nucleotide binding domain. The ATP analogue labeled with (32)P at the gamma position was used to measure hydrolysis of trinucleotide at 37 degrees C. Under these catalytic conditions, both nucleotide binding domains hydrolyze ATP, but hydrolysis in A1 is stimulated to a greater degree by Sb(III) than A2. These results suggest that the two homologous halves of the ArsA may be functionally nonequivalent.     

Purification and characterization of Clostridium perfringens 120-kilodalton collagenase and nucleotide sequence of the corresponding gene.

Clostridium perfringens type C NCIB 10662 produced various gelatinolytic enzymes with molecular masses ranging from approximately 120 to approximately 80 kDa. A 120-kDa gelatinolytic enzyme was present in the largest quantity in the culture supernatant, and this enzyme was purified to homogeneity on the basis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified enzyme was identified as the major collagenase of the organism, and it cleaved typical collagenase substrates such as azocoll, a synthetic substrate (4-phenylazobenzyloxy-carbonyl-Pro-Leu-Gly-Pro-D-Arg [Pz peptide]), and a type I collagen fibril. In addition, a gene (colA) encoding a 120-kDa collagenase was cloned in Escherichia coli. Nested deletions were used to define the coding region of colA, and this region was sequenced; from the nucleotide sequence, this gene encodes a protein of 1,104 amino acids (M(r), 125,966). Furthermore, from the N-terminal amino acid sequence of the purified enzyme which was found in this reading frame, the molecular mass of the mature enzyme was calculated to be 116,339 Da. Analysis of the primary structure of the gene product showed that the enzyme was produced with a stretch of 86 amino acids containing a putative signal sequence. Within this stretch was found PLGP, the amino acid sequence constituting the Pz peptide. This sequence may be implicated in self-processing of the collagenase. A consensus zinc-binding sequence (HEXXH) suggested for vertebrate Zn collagenases is present in this bacterial collagenase. Vibrio alginolyticus collagenase and Achromobacter lyticus protease I showed significant homology with the 120-kDa collagenase of C. perfringens, suggesting that these three enzymes are evolutionarily related.     

Expression and delivery of an endolysin to combat Clostridium perfringens

Clostridium perfringens is a cause for increasing concern due to its responsibility for severe infections both in humans and animals, especially poultry. To find new control strategies to treat C. perfringens infection, we investigated the activity and delivery of a bacteriophage endolysin. We identified a new endolysin, designated CP25L, which shows similarity to an N-acetylmuramoyl-l-alanine amidase domain and is distinct from other C. perfringens endolysins whose activity has been demonstrated in vitro. The cp25l gene was cloned and expressed in Escherichia coli, and the gene product demonstrated lytic activity against all 25 C. perfringens strains tested. The probiotic strain Lactobacillus johnsonii FI9785 was engineered to deliver the endolysin to the gastrointestinal tract. The integration of the nisRK two-component regulatory system from the Lactococcus lactis nisin A biosynthesis operon into the chromosome of L. johnsonii allowed constitutive expression of the endolysin under the control of the nisA promoter (P _nisA ), while the use of a signal peptide (SLPmod) led to successful secretion of the active endolysin to the surrounding media. The high specificity and activity of the endolysin suggest that it may be developed as an effective tool to enhance the control of C. perfringens by L. johnsonii in the gastrointestinal tract.     

A trimetal site and substrate distortion in a family II inorganic pyrophosphatase

We report the first crystal structures of a family II pyrophosphatase complexed with a substrate analogue, imidodiphosphate (PNP). These provide new insights into the catalytic reaction mechanism of this enzyme family. We were able to capture the substrate complex both by fluoride inhibition and by site-directed mutagenesis providing complementary snapshots of the Michaelis complex. Structures of both the fluoride-inhibited wild type and the H98Q variant of the PNP-Bacillus subtilis pyrophosphatase complex show a unique trinuclear metal center. Each metal ion coordinates a terminal oxygen on the electrophilic phosphate and a lone pair on the putative nucleophile, thus placing it in line with the scissile bond without any coordination by protein. The nucleophile moves further away from the electrophilic phosphorus site, to the opposite side of the trimetal plane, upon binding of substrate. In comparison with earlier product complexes, the side chain of Lys296 has swung in and so three positively charged side chains, His98, Lys205 and Lys296, now surround the bridging nitrogen in PNP. Finally, one of the active sites in the wild-type structure appears to show evidence of substrate distortion. Binding to the enzyme may thus strain the substrate and thus enhance the catalytic rate.