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At least 865 records · Page 48Linked to original sources
PubMed1975

Influence of molecular structure on the tolerogenicity of bacterial dextrans. II. The alpha1--3-linked epitope of dextran B1355.

Dextran B1355 is a branched glucose polymer containing 57 per cent alpha1--6, 35 per cent alpha1--3 and 8 per cent alpha1--2/1--4 linkages. Direct PFC responses to B1355 can be measured with sheep RBC sensitized with its O-stearoyl or palmitoyl derivative, and, as shown by inhibition analysis, are specific for an eptiope which is dependent on alpha1--3 linkages. B1355 is a potent immunogen in BALB/c mice producing peak PFC levels which approach 10(6) per spleen following an optimal dose of 1 mg. By contrast, the alpha-1--3-linked epitope of B1355 is feebly tolerogenic, for even 10 mg still induces a strong initial response. Mice given 1--10 mg sustain PFC levels 1--2 log10 above background for several months, but do not respond further to restimulation. Full recovery is attained by their spleen cells within 1 week of transfer into irradiated recipients. Deeper tolerance to this epitope was attained in vivo only when these larger doses of B1355 were injected during cyclophosphamide suppression. Two exceptions to this weak tolerogenicty were found. First, BALB/c spleen cells developed durable partial alpha1--3 tolerance following 2-hour incubation with B1355 in vitro. Second, CBA mice were fully tolerized by doses of 1 mg upwards. It is argued from these and other data in the accompanying papers that the relative resistance of BALB/c mice to induction of alpha1--3 tolerance is explicable neither as part of a more general phenomenon based on macrophage activity nor as due to an inadequate epitope density. A possible explanation based on features of the genetically determined high alpha1--3 responsiveness of BALB/c B cells is discussed.

Animals↗
PubMed1975

Influence of molecular structure of the tolerogenicity of bacterial dextrans. III. Dissociation between tolerance and immunity to the alpha1--6- and alpha1--3-linked epitopes of dextran B1355.

Dextran B1355 induces a direct PFC response detectable with dextran B512-sensitized red cells which is directed towards an alpha1--6-linked glucose epitope. This response is distinguishable from the alpha1--3-linked specificity assayed by homologous sensitization in that: (a) it is totally suppressed in donors previously rendered tolerant of B512; (b) the PFC are sensitive to inhibition by B512 and isomaltohexaose. The alpha1--6 epitope of B1355 is less immunogenic in BALB/c mice than that with alpha1--3 linkage, inducing a lower amplitude of response and requiring a 100-fold greater minimal dose, while conversely, it is the more effective tolerogen. No alpha1--6-specific response develops in 50 per cent of mice given 10 mg of B1355 and all become totally unresponsive within 14 days. This tolerant state remains stable when spleen cells are transferred to irradiated recipients. By comparison, parallel depression of the alpha1--3 response is not great and rapidly lost by similar transfer. No correlation was observed between the levels of alpha1--6 suppression and alpha1--3 response induced by 10 mg of B1355 in individual mice. The dissociative aspects of the responses to these two epitopes present on the same molecule are discussed in relation to some current theories of B-cell tolerance induction. It is argued that the present findings are contrary to those models which attribute a causal role to mitogenic overstimulation or failure to generate an extrinsic 'second signal'.

Animals↗
PubMed2000

The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target.

Type I signal peptidases are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidases are unique serine proteases that utilize a Ser/Lys catalytic dyad mechanism in place of the classical Ser/His/Asp catalytic triad mechanism. They represent a potential novel antibiotic target at the bacterial membrane surface. This review will discuss the bacterial signal peptidases that have been characterized to date, as well as putative signal peptidase sequences that have been recognized via bacterial genome sequencing. We review the investigations into the mechanism of Escherichia coli and Bacillus subtilis signal peptidase, and discuss the results in light of the recent crystal structure of the E. coli signal peptidase in complex with a beta-lactam-type inhibitor. The proposed conserved structural features of Type I signal peptidases give additional insight into the mechanism of this unique enzyme.

Amino Acid Sequence↗
PubMed2006

Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.

Amino Acid Sequence↗
PubMed1998

Structure and switching of bacterial flagellar filaments studied by X-ray fiber diffraction.

Bacterial motility involves switching between the left and right supercoiled states of the flagellar filament. The polymorphism of this assembly of identical flagellin molecules has presented a structural puzzle. Supercoiling has been attributed to coexistence of two conformational states of the 11 nearly axially aligned protofilament strands of subunits. The helical parameters of straight filaments in the left (L) and right (R) lattice states have now been accurately determined by X-ray fiber diffraction. The 9 A resolution electron density map of the R-type filament, refined from the X-ray data, reveals the interlocked alpha-helical segments of the core portion, which constitute the inner and outer tubes. While the inner-tube domain interactions remain invariant, the strand joints in the outer tube can switch between the L- and R-state by 2-3 A axial shifts, which change the strand periodicity of approximately 50 A by 0.8 A. This bi-stable quaternary switching results in supercoiling. Based on the measured helical parameters of the L and R lattices and the switching model, the twist and curvature calculated for the ten possible supercoils are in quantitative accord with observed supercoiled forms of flagellar filaments.

Crystallography, X-Ray↗
PubMed2001

Solution structure of HI0257, a bacterial ribosome binding protein.

A novel bacterial ribosome binding protein, protein Y (also known as YfiA), was recently shown to reside at the 30S/50S subunit interface and to stabilize the ribosomal 70S complex against dissociation at low magnesium ion concentrations. We report here the three-dimensional NMR structure in solution of a homologue from Haemophilus influenzae, HI0257, that has 64% sequence identity to protein Y. The 107 residue protein has a beta-alpha-beta-beta-beta-alpha folding topology with two parallel alpha-helices packed against the same side of a four-stranded beta-sheet. The closest structural relatives are proteins with the double-stranded RNA-binding domain (dsRBD) motif although there is little (<10%) sequence homology. The most immediate differences between the dsRBD and HI0257 structures are that (1) HI0257 has a larger beta-sheet motif with an extra beta-strand at the N-terminus, (2) the helices are parallel in HI0257 but at an angle of about 30 degrees to each other in the dsRBD, and (3) HI0257 lacks the extended loop commonly seen between the first and second beta-strands of the dsRBD. Further, an analysis of the surface electrostatic potential in HI0257 and the dsRBD family reveals significant differences in the location of contiguous positively (and negatively) charged regions. The structural data, in combination with sequence analysis of HI0257 and its homologues, suggest that the most likely mode of RNA recognition for HI0257 may be distinct from that of the dsRBD family of proteins.

Amino Acid Sequence↗
PubMed1987

[Antigenic bacterial polysaccharides. 24. The structure of the O-specific polysaccharide chain of Salmonella arizonae 063 (Arizona 08) lipopolysaccharide].

The O-specific polysaccharide chain of the Salmonella arizonae O63 lipopolysaccharide is composed of D-glucose, D-galactose, N-acetyl-D-galactosamine, and 3-acetamido-3,6-dideoxy-D-galactose (Fuc3NAc) residues in the ratio 1:1:2:1. On the basis of methylation analysis and calculations of 13C-NMR-spectra of the polysaccharide and of the product of its selective cleavage with anhydrous hydrogen fluoride, the linear polymer lacking 3-acetamido-3,6-dideoxygalactose, it was concluded that the polysaccharide has the following structure: (Formula: see text).

Antigens, Bacterial↗
PubMed1988

[Antigenic bacterial polysaccharides. 28. The structure of the O-specific lipopolysaccharide chain of Pseudomonas syringae pv. atrofaciens K-1025 and Pseudomonas holci 90a (serogroup II)].

Lipopolysaccharides of serologically related strains of Pseudomonas syringae pv. atrofaciens K-1025 and Pseudomonas holci 90a possess the identical O-specific polysaccharide chains, representing a homopolymer of D-rhamnose. On the basis of methylation, partial and complete Smith degradation, and analysis by 1H- and 13C-NMR-spectroscopy, it was concluded that the repeating unit of the polysaccharide is a branched pentasaccharide of the following structure: (formula; see text)

Antigens, Bacterial↗
PubMed2005

Involvement of the Escherichia coli O157:H7(pO157) ecf operon and lipid A myristoyl transferase activity in bacterial survival in the bovine gastrointestinal tract and bacterial persistence in farm water troughs.

Escherichia coli O157:H7 is an important food-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans. Recently, we reported that the pO157 ecf (E. coli attaching and effacing gene-positive conserved fragments) operon is thermoregulated by an intrinsically curved DNA and contains the genes for bacterial surface-associated proteins, including a second copy of lipid A myristoyl transferase, whose chromosomal copy is the lpxM gene product. E. coli O157:H7 survives and persists well in diverse environments from the human and bovine gastrointestinal tracts (GIT) to nutrient-dilute farm water troughs. Transcriptional regulation of the ecf operon by intrinsic DNA curvature and the genetic redundancy of lpxM that is associated with lipid A modification led us to hypothesize that the pO157 ecf operon and lpxM are associated with bacterial survival and persistence in various in vivo and ex vivo environments by optimizing bacterial membrane structure and/or integrity. To test this hypothesis, three isogenic ecf operon and/or lpxM deletion mutants of E. coli O157:H7 ATCC 43894 were constructed and analyzed in vitro and in vivo. The results showed that a double mutant carrying deletions in the ecf and lpxM genes had an altered lipid A structure and membrane fatty acid composition, did not survive passage through the bovine GIT, did not persist well in farm water troughs, had increased susceptibility to a broad spectrum of antibiotics and detergents, and had impaired motility. Electron microscopic analyses showed gross changes in bacterial membrane structure.

Acyltransferases↗
PubMed2002

Structural identification of a bacterial quorum-sensing signal containing boron.

Cell-cell communication in bacteria is accomplished through the exchange of extracellular signalling molecules called autoinducers. This process, termed quorum sensing, allows bacterial populations to coordinate gene expression. Community cooperation probably enhances the effectiveness of processes such as bioluminescence, virulence factor expression, antibiotic production and biofilm development. Unlike other autoinducers, which are specific to a particular species of bacteria, a recently discovered autoinducer (AI-2) is produced by a large number of bacterial species. AI-2 has been proposed to serve as a 'universal' signal for inter-species communication. The chemical identity of AI-2 has, however, proved elusive. Here we present the crystal structure of an AI-2 sensor protein, LuxP, in a complex with autoinducer. The bound ligand is a furanosyl borate diester that bears no resemblance to previously characterized autoinducers. Our findings suggest that addition of naturally occurring borate to an AI-2 precursor generates active AI-2. Furthermore, they indicate a potential biological role for boron, an element required by a number of organisms but for unknown reasons.

Bacterial Proteins↗
PubMed2004

Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil.

A field-scale experiment with a complete randomized block design was performed to study the degradation of buried oil on a shoreline over a period of almost 1 year. The following four treatments were examined in three replicate blocks: two levels of fertilizer treatment of oil-treated plots, one receiving a weekly application of liquid fertilizer and the other treated with a slow-release fertilizer; and two controls, one not treated with oil and the other treated with oil but not with fertilizer. Oil degradation was monitored by measuring carbon dioxide evolution and by chemical analysis of the oil. Buried oil was degraded to a significantly greater extent in fertilized plots, but no differences in oil chemistry were observed between the two different fertilizer treatments, although carbon dioxide production was significantly higher in the oil-treated plots that were treated with slow-release fertilizer during the first 14 days of the experiment. Bacterial communities present in the beach sediments were profiled by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments and 16S rRNA amplified by reverse transcriptase PCR. Similarities between the DGGE profiles were calculated, and similarity matrices were subjected to statistical analysis. These analyses showed that although significant hydrocarbon degradation occurred both in plots treated with oil alone and in the plots treated with oil and liquid fertilizer, the bacterial community structure in these plots was, in general, not significantly different from that in the control plots that were not treated with oil and did not change over time. In contrast, the bacterial community structure in the plots treated with oil and slow-release fertilizer changed rapidly, and there were significant differences over time, as well as between blocks and even within plots. The differences were probably related to the higher concentrations of nutrients measured in interstitial water from the plots treated with slow-release fertilizer. Bacteria with 16S rRNA sequences closely related (>99.7% identity) to Alcanivorax borkumensis and Pseudomonas stutzeri sequences dominated during the initial phase of oil degradation in the plots treated with slow-release fertilizer. Field data were compared to the results of previous laboratory microcosm experiments, which revealed significant differences.

Bacteria↗
PubMed1996

[Bacterial endotoxins--methods of structural analysis].

The modern structural methods used in the determination of lipopolysaccharides chemical structures were described. The combination of nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MALDI-TOF, FAB and EI) applied to structural analysis of lipopolysaccharides, with a few chosen examples of characteristic original spectra were presented.

Bacterial Toxins↗
PubMed2005

Structural characterization of complex bacterial glycolipids by Fourier transform mass spectrometry.

Bacterial glycolipids are complex amphiphilic molecules which are on the one hand of utmost importance for the organization and function of bacterial membranes, and which on the other hand play a major role in the activation of cells of the innate and adaptive immune system of the host. Already small alterations of their chemical structure may influence the biological activity tremendously. Due to their intrinsic biological heterogeneity [number and type of fatty acids, saccharide structures, and substitution with e.g. phosphate (P), 2-aminoethyl- (pyro)phosphate groups (P-Etn) or 4-amino-4-deoxyarabinose (Ara4N)], separation of the different components are a prerequisite for unequivocal chemical and NMR structural analyses. In this contribution the structural information which can be obtained from heterogeneous samples of glycolipids by Fourier transform (FT) ion cyclotron resonance mass spectrometric methods is described. By means of recently analysed complex biological samples the possibilities of high resolution electrospray ionization FT-MS are demonstrated. Capillary skimmer dissociation, as well as tandem mass spectrometry MS/MS analysis utilizing collision-induced dissociation and infrared multiphoton dissociation, are compared and their advantages to provide structural information of diagnostic importance are discussed.

Carbohydrate Sequence↗
PubMed2000

Structure and function of bacterial outer membrane proteins: barrels in a nutshell.

The outer membrane protects Gram-negative bacteria against a harsh environment. At the same time, the embedded proteins fulfil a number of tasks that are crucial to the bacterial cell, such as solute and protein translocation, as well as signal transduction. Unlike membrane proteins from all other sources, integral outer membrane proteins do not consist of transmembrane alpha-helices, but instead fold into antiparallel beta-barrels. Over recent years, the atomic structures of several outer membrane proteins, belonging to six families, have been determined. They include the OmpA membrane domain, the OmpX protein, phospholipase A, general porins (OmpF, PhoE), substrate-specific porins (LamB, ScrY) and the TonB-dependent iron siderophore transporters FhuA and FepA. These crystallographic studies have yielded invaluable insight into and decisively advanced the understanding of the functions of these intriguing proteins. Our review is aimed at discussing their common principles and peculiarities as well as open questions associated with them.

Bacterial Outer Membrane Proteins↗
PubMed1988

Structure and mechanism of bacterial periplasmic transport systems.

Bacterial periplasmic transport systems are complex, multicomponent permeases, present in Gram-negative bacteria. Many such permeases have been analyzed to various levels of detail. A generalized picture has emerged indicating that their overall structure consists of four proteins, one of which is a soluble periplasmic protein that binds the substrate and the other three are membrane bound. The liganded periplasmic protein interacts with the membrane components, which presumably form a complex, and which by a series of conformational changes allow the formation of an entry pathway for the substrate. The two extreme alternatives for such pathway involve either the formation of a nonspecific hydrophilic pore or the development of a ligand-binding site(s) on the membrane-bound complex. One of the membrane-bound components from each system constitutes a family of highly homologous proteins containing sequence domains characteristic of nucleotide-binding sites. Indeed, in several cases, they have been shown to bind ATP, which is thus postulated to be involved in the energy-coupling mechanism. Interestingly, eukaryotic proteins homologous to this family of proteins have been identified (mammalian mdr genes and Drosophila white locus), thus indicating that they perform a universal function, presumably related to energy coupling in membrane-related processes. The mechanism of energy coupling in periplasmic permeases is discussed.

Cell Membrane↗