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PubMed1987

[Antigenic bacterial polysaccharides. 23. The structure of the O-specific polysaccharide chain of Salmonella arizonae 059 lipopolysaccharide].

The O-specific polysaccharide of Salmonella arizonae O59 (Arizona 19) is composed of D-galactose, N-acetyl-D-glucosamine, and N-acetyl-L-fucosamine (FucNAc, 2-acetamido-2,6-dideoxy-L-galactose) in the ratio 1:1:1. The computerized calculation of the 13C NMR spectrum of the polysaccharide, based on the monosaccharide composition, spectra of the free monosaccharides and glycosydation effects, together with the chemical analysis (methylation and Smith degradation) showed that the polysaccharide is built up of trisaccharide repeating units of the following structure: ----3)-alpha-L-FucNAcp(1----3)-beta-D-GlcNAcp-(1----2)-beta- D-Galp-1(----. The molecular basis of serological interrelations between S. arizonae O59 and Pseudomonas aeruginosa O7 (Lányi) is discussed.

Antigens, Bacterial↗
PubMed2004

Novel inhibitors of bacterial protein synthesis: structure-activity relationships for 1,8-naphthyridine derivatives incorporating position 3 and 4 variants.

Structure-activity relationships for a recently discovered novel ribosome inhibitor (NRI) class of antibacterials were investigated. Preliminary efforts to optimize protein synthesis inhibitory activity of the series through modification of positions 3 and 4 of the naphthyridone lead template resulted in the identification of several biochemically potent analogues. A lack of corresponding whole cell antibacterial activity is thought to be a consequence of poor cellular penetration as evidenced by the enhancement of activity observed for a lead analogue tested in the presence of a cell permeabilizing agent.

Anti-Bacterial Agents↗
PubMed1993

Crystal structure of a flavoprotein related to the subunits of bacterial luciferase.

The molecular structure of the luxF protein from the bioluminescent bacterium Photobacterium leiognathi has been determined by X-ray diffraction techniques and refined to a conventional R-factor of 17.8% at 2.3 A resolution. The 228 amino acid polypeptide exists as a symmetrical homodimer and 33% of the monomer's solvent-accessible surface area is buried upon dimerization. The monomer displays a novel fold that contains a central seven-stranded beta-barrel. The solvent-exposed surface of the monomer is covered by seven alpha-helices, whereas the dimer interface is primarily a flat surface composed of beta-strands. The protein monomer binds two molecules of flavin mononucleotide, each of which has C6 of the flavin isoalloxazine moiety covalently attached to the C3' carbon atom of myristic acid. Both myristyl groups of these adducts are buried within the hydrophobic core of the protein. One of the cofactors contributes to interactions at the dimer interface. The luxF protein displays considerable amino acid sequence homology with both alpha- and beta-subunits of bacterial luciferase, especially the beta-subunit. Conserved amino acid residues shared between luxF and the luciferase subunits cluster predominantly in two distinct regions of the luxF protein molecule. These homologous regions in the luciferase subunits probably share a three-dimensional fold similar to that of the luxF protein.

Amino Acid Sequence↗
PubMed2006

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.

The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.

Amino Acid Sequence↗
PubMed1999

Bacterial mechanosensitive channels: integrating physiology, structure and function.

When confronted with hypo-osmotic stress, many bacterial species are able rapidly to adapt to the increase in cell turgor pressure by jettisoning cytoplasmic solutes into the medium through membrane-tension-gated channels. Physiological studies have confirmed the importance of these channels in osmoregulation. Mutagenesis of one of these channels, combined with structural information derived from X-ray crystallography, has given the first clues of how a mechanosensitive channel senses and responds to membrane tension.

Bacteria↗
PubMed2004

A trimeric quaternary structure is conserved in bacterial and human glutamate transporters.

Neuronal and glial glutamate transporters play a central role in the termination of synaptic transmission and in extracellular glutamate homeostasis in the mammalian central nervous system. They are known to be multimers; however, the number of subunits forming a functional transporter is controversial. We studied the subunit stoichiometry of two distantly related glutamate transporters, the human glial glutamate transporter hEAAT2 and a bacterial glutamate transporter from Escherichia coli, ecgltP. Using blue native polyacrylamide gel electrophoresis, analysis of concatenated transporters, and chemical cross-linking, we demonstrated that human and prokaryotic glutamate transporters expressed in Xenopus laevis oocytes or in mammalian cells are assembled as trimers composed of three identical subunits. In an inducible mammalian cell line expressing hEAAT2 the glutamate uptake currents correlate to the amount of trimeric transporters. Overexpression and purification of ecgltP in E. coli resulted in a homogenous population of trimeric transporters that were functional after reconstitution in lipid vesicles. Our results indicate that an evolutionarily conserved trimeric quaternary structure represents the sole native and functional state of glutamate transporters.

Amino Acid Sequence↗
PubMed2006

Hydrophobic cluster analysis and modeling of the human Rh protein three-dimensional structures.

Rh (Rhesus) is a major blood group system in man, which is clinically significant in transfusion medicine. Rh antigens are carried by an oligomer of two major erythroid specific polypeptides, the Rh (D and CcEe) proteins and the RhAG glycoprotein, that shared a common predicted structure with 12 transmembrane a-helices (M0 to M11). Non erythroid homologues of these proteins have been identified (RhBG and RhCG), notably in diverse organs specialized in ammonia production and excretion, such as kidney, liver and intestine. Phylogenetic studies and experimental evidence have shown that these proteins belong to the Amt/Mep/Rh protein superfamily of ammonium/methylammonium permease, but another view suggests that Rh proteins might function as CO2 gas channels. Until recently no information on the structure of these proteins were available. However, in the last two years, new insight has been gained into the structural features of Rh proteins (through the determination of the crystal structures of bacterial AmtB and archeaebacterial Amt-1. Here, models of the subunit and oligomeric architecture of human Rh proteins are proposed, based on a refined alignment with and crystal structure of the bacterial ammonia transporter AmtB, a member of the Amt/Mep/Rh superfamily. This alignment was performed considering invariant structural features, which were revealed through Hydrophobic Cluster Analysis, and led to propose alternative predictions for the less conserved regions, particularly in the N-terminal sequences. The Rh models, on which an additional Rh-specific, N-terminal helix M0 was tentatively positioned, were further assessed through the consideration of biochemical and immunochemical data, as well as of stereochemical and topological constraints. These models highlighted some Rh specific features that have not yet been reported. Among these, are the prediction of some critical residues, which may play a role in the channel function, but also in the stability of the subunit structure and oligomeric assembly. These results provide a basis to further understand the structure/function relationships of Rh proteins, and the alterations occurring in variant phenotypes.

Amino Acid Sequence↗
PubMed2005

Field studies on the environmental fate of the Cry1Ab Bt-toxin produced by transgenic maize (MON810) and its effect on bacterial communities in the maize rhizosphere.

Field studies were done to assess how much of the transgenic, insecticidal protein, Cry1Ab, encoded by a truncated cry1Ab gene from Bacillus thuringiensis (Bt), was released from Bt-maize MON810 into soil and whether bacterial communities inhabiting the rhizosphere of MON810 maize were different from those of the rhizosphere of nontransgenic maize cultivars. Bacterial community structure was investigated by SSCP (single-strand conformation polymorphism) of PCR-amplified 16S rRNA genes from community DNA. Using an improved extraction and detection protocol based on a commercially available ELISA, it was possible to detect Cry1Ab protein extracted from soils to a threshold concentration of 0.07 ng/g soil. From 100 ng of purified Cry1Ab protein added per gram of soil, only an average of 37% was extractable. At both field sites investigated, the amount of Cry1Ab protein in bulk soil of MON810 field plots was always lower than in the rhizosphere, the latter ranging from 0.1 to 10 ng/g soil. Immunoreactive Cry1Ab protein was also detected at 0.21 ng/g bulk soil 7 months after harvesting, i.e. in April of the following year. At this time, however, higher values were found in residues of leaves (21 ng/g) and of roots (183 ng/g), the latter corresponding to 12% of the Cry1Ab protein present in intact roots. A sampling 2 months later indicated further degradation of the protein. Despite the detection of Cry1Ab protein in the rhizosphere of MON810 maize, the bacterial community structure was less affected by the Cry1Ab protein than by other environmental factors, i.e. the age of the plants or field heterogeneities. The persistence of Cry1Ab protein emphasizes the importance of considering post-harvest effects on nontarget organisms.

Analysis of Variance↗
PubMed2003

Analysis of the structure of very large bacterial aggregates by small-angle multiple light scattering and confocal image analysis.

This work aims at developing a more accurate measurement of the physical parameters of fractal dimension and the size distribution of large fractal aggregates by small-angle light scattering. The theory of multiple scattering has been of particular interest in the case of fractal aggregates for which Rayleigh theory is no longer valid. The introduction of multiple scattering theory into the interpretation of scattering by large bacterial aggregates has been used to calculate the fractal dimension and size distribution. The fractal dimension is calculated from the form factor F(q) at large scattering angles. At large angles the fractal dimension can also be computed by considering only the influence of the very local environment on the optical contrast around a subunit. The fractal dimensions of E. coli strains flocculated with two different cationic polymers have been computed by two techniques: static light scattering and confocal image analysis. The fractal dimensions calculated with both techniques at different flocculation times are very similar: between 1.90 and 2.19. The comparison between two completely independent techniques confirms the theoretical approach of multiple scattering of large flocs using the Mie theory. Size distributions have been calculated from light-scattering data taking into account the linear independence of the structure factor S(q) relative to each size class and using the fractal dimension measured from F(q) in the large-angle range or from confocal image analysis. The results are very different from calculations made using hard-sphere particle models. The size distribution is displaced toward the larger sizes when multiple scattering is considered. Using this new approach to the analysis of very large fractal aggregates by static light multiple scattering, the fractal dimension and size distribution can be calculated using two independent parts of the scattering curve.

Bacteria↗
PubMed1976

Relationship of structure to function in bacterial endotoxins. IX. Differences in the lipid moiety of endotoxic glycolipids.

Chemical, immunochemical, chromatographic, and endotoxic properties of five chromatographically pure glycolipids were compared. The preparations were extracted by chloroform-methanol from three Escherichia coli, one Salmonella minnesota, and one S. typhimurium Re heptoseless mutant strains. The local Shwartzman skin assay, the nonspecific resistance-enhancing effect, and the Limulus assays could not distinguish among the five glycolipids, all five being active in all three assays. Significant differences could be seen when the tumor resistance-enhancing effect of the glycolipids in mice was compared with the nonspecific TA3-Ha murine mammary adenocarcinoma growing in ascites form. Even greater variation was observed in the capacity of the preparations to enhance the nonspecific resistance of mice to virulent S. typhi 0901 infections. The data show that the five glycolipids are quite dissimilar in their biological effects. Similarly, thin-layer chromatography and molecular ratio determinations showed that differences exist in the chemical structure of the glycolipids. Accordingly, we claim that not only the polysaccharide but the lipid moiety as well may vary in various gram-negative endotoxin preparations.

Animals↗
PubMed1998

The structural gene module in Streptococcus thermophilus bacteriophage phi Sfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts.

The structural gene cluster and the lysis module from lytic group II Streptococcus thermophilus bacteriophage phi Sfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. phi Sfi11 differed from the temperate S. thermophilus bacteriophage phi O1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, phi Sfi11 and the lytic group 1 S. thermophilus phi Sfi19 shared regions with variable degrees of similarity. Orf 1291 from phi Sfi19 was replaced by four genes in phi Sfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with phi Sfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between phi Sfi11 and phi Sfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of phi Sfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between phi Sfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G + C group of gram-positive bacteria is derived from a common ancestor.

Biological Evolution↗
PubMed2004

Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme.

The anisotropic network model (ANM), a coarse-grained normal mode analysis, is used to study the vibrational dynamics of RNA polymerases (RNAP) around the native states. The theoretical temperature factors obtained from ANM are in conformity with the experimental values for yeast and bacterial RNAP structures in free and complex forms. In the low-frequency collective modes that are related to biological function, both bacterial and yeast RNAPs with a crab claw shape display an opening/closing of the cleft due to the rigid-body motion of the clamp (bottom pincer), which has been also predicted by experiments, together with the motion of the top pincer. Even though slightly lower fluctuations are observed in the elongation complex of yeast RNAP, similar clamp motion still exists in collective modes, which should be concerted with the flexible switches and the bridge helix in driving the transcription process, pointing at the possibility of a ratchet-like mechanism. Two different bacterial holoenzyme (HE) structures are studied, which may have functional significance at different stages of transcription initiation. In a specific closed conformation of the HE, the clamp and top pincer are highly immobilized due to interactions with the sigma subunit. In contrast, the deformation of the top pincer is not inhibited in a relatively open conformation of another HE, which may help load the DNA into the cleft during transcription initiation, even though the clamp motion is still inhibited.

Anisotropy↗
PubMed1998

Unraveling the structures and modes of action of bacterial toxins.

The mechanism by which a soluble protein converts into a protein that spans a membrane remains a central question in understanding the molecular mechanism of toxicity of bacterial protein toxins. Using crystallographic structures of soluble toxins as templates, the past year has seen a number of experiments that are designed to probe the membrane state using other structural methods. In addition, crystallographic information concerning the clostridial neurotoxins has emerged, suggesting a novel mechanism of pore formation and new relationships between toxin binding domains.

Bacterial Toxins↗
PubMed1988

[Antigenic bacterial polysaccharides. 30. The structure of the polysaccharide chain of lipopolysaccharide of Pseudomonas syringae pv. syringae 281 (serogroup I)].

Anomeric methyl 3-O-(D-mannopyranosyl- and L-rhamnopyranosyl)-beta-D-talopyranosides were synthesised by the stereoselective 1,2-cis- and 1,2-trans manno- and rhamnosylation of methyl 2,4,6-tri-O-acetyl-beta-D-talopyranoside, which has been prepared from methyl beta-D-galactopyranoside by a synthetic scheme including conversion of the C2 configuration. From 13C-NMR spectra of the disaccharides obtained the spectral alpha- and beta-effects of O3-glycosylation of talopyranose were determined.

Antigens, Bacterial↗
PubMed1988

[Antigenic bacterial polysaccharides. 29. The structure of the polysaccharide chain of Pseudomonas holci 8300 (serogroup I) lipopolysaccharide].

The Pseudomonas holci 8300 lipopolysaccharide has an O-specific polysaccharide chain, containing L-rhamnose and 3-acetamido-3-deoxy-D-fucose residues in the ratio 4:1. On the basis of methylation, Smith degradation, and 1H- and 13C-NMR spectroscopy data, it was concluded that the polysaccharide is built up of pentasaccharide units of A and B types in the ratio approximately 2.5:1. In some stretches of the polysaccharide, minor B units form rather long chains, and in the others they alternate with predominant A units. (formula; see text)

Antigens, Bacterial↗
PubMed2005

Antibiotics GE23077, novel inhibitors of bacterial RNA polymerase. II. Structure elucidation.

During the screening program for new antibacterial agents produced by actinomycetes, GE23077 was isolated from fermentation broths of an Actinomadura sp. strain as a complex of factors A1, A2, B1, B2. NMR, MS and GC/MS analysis carried out on the isolated components led to the conclusion that GE23077 is a novel cyclic heptapeptide consisting of common and unusual amino acids. The chemical structures of the complex components were elucidated. Components A and B differ in the structure of the acyl group connected to a 2,3-diaminopropanoic acid moiety. A alpha-amino-malonic acid residue in the peptidic sequence is the origin of an isomerization process between A1 and A2 as well as B1 and B2. The chirality of the alpha-amino-malonic acid residue can be inverted easily via keto-enol tautomerism. Factors A2 and B2 should be considered as epimers of A1 and B1 respectively. By degradation studies the absolute configuration of some amino acids were determined. Chiral GC-MS and Micellar Electrokinetic Capillary Chromatography (MEKC) were used to define the absolute stereochemistries of five out of ten chiral centers.

Amino Acids↗
PubMed1996

Antibiotics A21459 A and B, new inhibitors of bacterial protein synthesis. II. Structure elucidation.

The structures of the antibiotics, active against a few Gram-negative bacteria and Clostridium difficile, were determined on the basis of physicochemical analyses on the intact molecules and on the acid hydrolysate of A21459 A. FAB-MS and 1H and 13C NMR investigations identified the amino acid units and determined their sequence. Antibiotics A21459 A and B are homodetic cyclic peptides constituted by eight amino acid units. They are glycine, methoxytryptophan, tryptophan, cysteine, alanine, sarcosine, dehydroalanine, and alpha-aminobutyric acid for A21459 A (alanine for A21459 B). Cysteine and alanine condensed to form a thiazole moiety, according to the biosynthesis of thiazole containing antibiotics.

Amino Acid Sequence↗