Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Bacterial Structures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2006

Evolution of structural shape in bacterial globin-related proteins.

The globin family of proteins has a characteristic structural pattern of helix interactions that nonetheless exhibits some variation. A simplified model for globin structural evolution was developed in which protein shape evolved by random change of contacts between helices. A conserved globin domain of 15 bacterial proteins representing four structural families was studied. Using a parsimony approach ancestral structural states could be reconstructed. The distribution of number of contact changes per site for a fixed topology tree fit a gamma distribution. Homoplasy was high, with multiple changes per site and no support for an invariant class of residue-residue contacts. Contacts changed more slowly than sequence. A phylogenetic reconstruction using a distance measure based on the proportion of shared contacts was generally consistent with a sequence-based phylogeny but not highly resolved. Contact pattern convergence between members of different globin family proteins could not be detected. Simulation studies indicated the convergence test was sensitive enough to have detected convergence involving only 10% of the contacts, suggesting a limit on the extent of selection for a specific contact pattern. Contact site methods may provide additional approaches to study the relationship between protein structure and sequence evolution.

Amino Acids↗
PubMed2004

The extracytoplasmic function sigma factors: role in bacterial pathogenesis.

Bacteria utilize a distinct subfamily of sigma factors to regulate extra cytoplasmic function (thus termed as ECF subfamily). Eubacteria appear to have evolved to incorporate extensive genetic diversity into their repertoire of ECF sigma factors (some species have more than 60 ECF sigma factors), while maintaining three major themes common to all members including: (1) they regulate and respond to extracytoplasmic functions; (2) they are themselves regulated by anti-sigma and/or anti-anti-sigma factors; and (3) most of them control a relatively small regulon. The cell wall is the first bacterial structure that comes in contact with the host during infection by pathogenic bacteria. The cell wall components are often associated with functions related to host cell invasion. It is therefore, likely that the ECF sigma factors regulate the bacterial response to host insult. Moreover, in some cases, virulence factors have been shown to be regulated directly by the ECF sigma factors. Unfortunately, this facet of the ECF sigma factors has not been an important area of study by researchers. The present review attempts to highlight the important role played by ECF sigma factors in bacterial pathogenesis and highlights several areas of future study involving the genetics of ECF sigma factors vis-à-vis bacterial pathogenesis.

Bacteria↗
PubMed2004

Bulking sludge in biological nutrient removal systems.

Bulking sludge problems are commonly reported in biological nutrient removal (BNR) systems. This has led to the general belief that intrinsic BNR conditions favor the growth of undesirable and excessive filamentous bacteria. The present study shows that other factors have a major role in bulking, and not the BNR conditions. These factors have been verified in well-controlled, strictly anoxic-aerobic and strictly anaerobic-aerobic sequencing batch reactor systems. The experimental results show that conditions known to be responsible for bulking sludge in aerobic systems (i.e., low concentration of electron donor and/or electron acceptor) did not lead to bulking. Even when acetate was present at very low concentrations in the aerobic stage of an anaerobic-aerobic bio-P system, the sludge settleability remained very good. This clearly demonstrates that good bio-P activity can stabilize and improve sludge settleability. The presence of microaerophilic conditions in the anoxic stage of the anoxic-aerobic system was the only factor leading to worsening sludge settling characteristics. The results are discussed in light of our previous hypothesis about the importance of diffusion-limited substrate uptake for the development of filamentous structures in biological flocs. The hypothesis is extended to anaerobic-aerobic and anoxic-aerobic conditions, typical of BNR-activated sludge systems. Taking into account the effect of feeding patterns on biochemical rates and on the development of filamentous bacterial structures, we recommend the adoption of plug-flow selector configurations, with strictly anaerobic and/or strictly anoxic conditions, wherein microaerophilic conditions are excluded, in order to maintain reliable and robust BNR performance.

Acetates↗
PubMed1998

Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase.

The pyridoxal-P binding sites of the two isoforms of human glutamate decarboxylase (GAD65 and GAD67) were modeled by using PROBE (a recently developed algorithm for multiple sequence alignment and database searching) to align the primary sequence of GAD with pyridoxal-P binding proteins of known structure. GAD's cofactor binding site is particularly interesting because GAD activity in the brain is controlled in part by a regulated interconversion of the apo- and holoenzymes. PROBE identified six motifs shared by the two GADs and four proteins of known structure: bacterial ornithine decarboxylase, dialkylglycine decarboxylase, aspartate aminotransferase, and tyrosine phenol-lyase. Five of the motifs corresponded to the alpha/beta elements and loops that form most of the conserved fold of the pyridoxal-P binding cleft of the four enzymes of known structure; the sixth motif corresponded to a helical element of the small domain that closes when the substrate binds. Eight residues that interact with pyridoxal-P and a ninth residue that lies at the interface of the large and small domains were also identified. Eleven additional conserved residues were identified and their functions were evaluated by examining the proteins of known structure. The key residues that interact directly with pyridoxal-P were identical in ornithine decarboxylase and the two GADs, thus allowing us to make a specific structural prediction of the cofactor binding site of GAD. The strong conservation of the cofactor binding site in GAD indicates that the highly regulated transition between apo- and holoGAD is accomplished by modifications in this basic fold rather than through a novel folding pattern.

Amino Acid Sequence↗
PubMed2002

The bacterial protein SipA polymerizes G-actin and mimics muscle nebulin.

SipA is a Salmonella protein delivered into host cells to promote efficient bacterial entry, which is essential for pathogenicity. SipA exerts its function by binding F-actin, resulting in the stabilization of F-actin and the stimulation of the bundling activity of fimbrin. Here we show that under low salt conditions where spontaneous nucleation and polymerization of actin do not occur, SipA induces extensive polymerization. We have used electron microscopy and a method for helical image analysis to visualize the complex of actin with the actin-binding fragment of SipA. The SipA fragment binds to actin as a tubular molecule extending approximately 95 A. The main sites of SipA binding on actin involve sequence insertions that are not present in the bacterial homolog of actin, MreB, suggesting a mechanism for preventing SipA from interacting with bacterial MreB filaments. Remarkably, the pattern of SipA binding, which connects subunits on opposite actin strands and explains the stabilization of F-actin, is similar to that shown for a fragment of the giant muscle protein nebulin. We suggest that SipA is a bacterial structural mimic of muscle nebulin and nebulin-like proteins in non-muscle cells that are involved in the regulation of the actin-based cytoskeleton.

Actins↗
PubMedDate not supplied

Bacterial infections: antibiotics and decontamination.

Infectious disease is caused by bacteria, viruses, fungi, protozoa and micro-organisms including the mycoplasmas, rickettsiae and chlamydiae. Most of the infections commonly encountered in the UK are caused either by bacteria or viruses. This article describes bacterial structure and function to explain how antibiotics work and the processes of decontamination such as cleaning, disinfection and sterilisation, which are important in infection control.

Anti-Bacterial Agents↗
PubMed2001

Antagonistic interactions among marine pelagic bacteria.

Recent studies suggest that bacterial abundance and species diversity in the ocean's water column are variable at the millimeter scale, apparently in response to the small-scale heterogeneity in the distribution of organic matter. We hypothesized that bacterium-bacterium antagonistic interactions may contribute to variations in community structure at the microscale. We examined each of the 86 isolates for their inhibition of growth of the remaining 85 isolates by the Burkholder agar diffusion assay. More than one-half of the isolates expressed antagonistic activity, and this trait was more common with particle-associated bacteria than with free-living bacteria. This was exemplified by members of the alpha subclass of the class Proteobacteria (alpha-proteobacteria), in which production of antagonistic molecules was dominated by attached bacteria. We found that gamma-proteobacteria (members of the orders Alteromonadales and Vibrionales) are the most prolific producers of inhibitory materials and also the most resilient to them, while members of the Bacteriodetes were the organisms that were least productive and most sensitive to antagonistic interactions. Widespread interspecies growth inhibition is consistent with the role of this phenomenon in structuring bacterial communities at the microscale. Furthermore, our results suggest that bacteria from pelagic marine particles may be an underutilized source of novel antibiotics.

Alphaproteobacteria↗
PubMed1984

Specific absorption with monoclonal antibodies to muramyl dipeptide of the pyrogenic and somnogenic activities of rabbit monokine.

It is well established that muramyl dipeptide (MDP) can induce fever and enhance slow-wave sleep. Recently, crude or purified supernatants of activated macrophages containing endogenous pyrogen (EP) were also shown to enhance slow-wave sleep. These similarities and the recent finding that a mammalian factor that enhances slow-wave sleep is a muramyl peptide triggered us to study the possibility of the presence of this bacterial structure in the EP molecule. In the present study, EP was produced by stimulation of rabbit peritoneal cells with a nonpyrogenic, nonsomnogenic analog of MDP. The EP-containing supernatant lost its pyrogenicity and somnogenicity after passage over an immunoadsorbent column of monoclonal anti-MDP but not of another monoclonal antibody of different specificity. High percentage of the EP was recovered by elution of the anti-MDP columns with HCl/glycine buffer. Results suggest that bacterial muramyl peptides may be incorporated by mammalian cells into substances that act in picomole quantities to mediate immunological and physiological processes. In addition, the technique may be useful to extract interleukin 1 for structural studies.

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed1998

Flow cytometric quantitation of human opsonin-dependent phagocytosis and oxidative burst responses to meningococcal antigens.

A one-step flow cytometric (FCM) assay has been developed to quantify both opsonin- and antigen-dependent phagocytosis and intraphagocyte oxidative burst responses. Meningococcal outer membrane structures (OMV) were adsorbed to fluorescent polystyrene beads, opsonized with serum, and exposed to leukocytes. FCM parameters of phagocytosis were evaluated in combinations with oxidative burst indicators. Rhodamine-123 was the most sensitive indicator and was compatible with quantitation of phagocytosis. The phagocytosis and oxidative burst responses induced by OMV beads were dependent on both antigens and opsonins. Increased human opsonic responses against OMV were induced during clinical meningococcal disease. A dissociation was noted between phagocytosis and oxidative burst in individual cells, indicating that functional opsonins against OMV components may differ in their ability to stimulate phagocytosis and oxidative burst responses. The method facilitates evaluation of purified bacterial structures as mediators of opsonin-dependent phagocytosis and intracellular oxidative microbicidal mechanisms, which is of interest in the complex process of selecting bacterial antigens as constituents of certain vaccines.

Adult↗
PubMed1996

The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution.

The structure of Salmonella typhimurium LT2 neuraminidase (STNA) is reported here to a resolution of 1.6 angstroms together with the structures of three complexes of STNA with different inhibitors. The first is 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (Neu5Ac2en or DANA), the second and third are phosphonate derivatives of N-acetyl-neuraminic acid (NANA) which have phosphonate groups at the C2 position equatorial (ePANA) and axial (aPANA) to the plane of the sugar ring. The complex structures are at resolutions of 1.6 angstroms, 1.6 angstroms and 1.9 angstroms, respectively. These analyses show the STNA active site to be topologically inflexible and the interactions to be dominated by the arginine triad, with the pyranose rings of the inhibitors undergoing distortion to occupy the space available. Solvent structure differs only around the third phosphonate oxygen, which attracts a potassium ion. The STNA structure is topologically identical to the previously reported influenza virus neuraminidase structures, although very different in detail; the root-mean-square (r.m.s) deviation for 210 C alpha positions considered equivalent is 2.28 angstroms (out of a total of 390 residues in influenza and 381 in STNA). The active site residues are more highly conserved, in that both the viral and bacterial structures contain an arginine triad, a hydrophobic pocket, a tyrosine and glutamic acid residue at the base of the site and a potential proton-donating aspartic acid. However, differences in binding to O4 and to the glycerol side-chain may reflect the different kinetics employed by the two enzymes.

Binding Sites↗
PubMed2004

Cross-reactivity of human immunoglobulin G2 recognizing phosphorylcholine and evidence for protection against major bacterial pathogens of the human respiratory tract.

Phosphorylcholine (ChoP) is an antigenic component on the cell surface of many commensal and pathogenic bacteria that reside in the upper airway. In the present study, human ChoP-specific antibody was affinity-purified from pooled serum gamma globulin. This naturally acquired antibody, which is primarily of the immunoglobulin (Ig) G2 subtype, recognized ChoP on the lipoteichoic acid of Streptococcus pneumoniae and on the lipopolysaccharide of Haemophilus influenzae, 2 of the leading etiologic agents of infection involving the human respiratory tract. In in vitro killing assays, anti-ChoP IgG2 was effective against some clinical isolates of nontypeable H. influenzae and against isolates of several common serotypes of S. pneumoniae. Moreover, passively administered human anti-ChoP antibody protected mice against lethal challenge with a transparent isolate of S. pneumoniae type 6A. The effectiveness of human antibody to this conserved bacterial structure suggests that, if it can be manipulated to broaden its activity, it could function as a single vaccine antigen that targets multiple pathogens.

Antibodies, Bacterial↗
PubMed1985

Binding of aggregated human serum albumin to M12 and some other types of group A streptococci.

In radiobinding tests many group A, C and G streptococci react with IgG and IgA, irrespective of the antigen-combining sites, as well as with various other serum proteins, e.g. human serum albumin (HSA). The present study demonstrated that glutaraldehyde-aggregated, radiolabelled HSA (a*HSA), in comparison to monomeric HSA, binds more avidly to streptococci. Of group A streptococci, strains representing types M6, M12, M18, M46, M55 and M57 displayed pronounced binding of a*HSA whereas a number of other serotypes were non-reactive. The streptococcal sites involved proved to be relatively heat-resistant and highly sensitive to trypsin treatment. Human fibrinogen counteracted the binding of a*HSA. The uptake by M12 was inhibited strongly by rabbit antiserum raised against M12, whereas other antisera were less active. The results suggest that the bacterial structure binding a*HSA is a protein and that, in at least one serotype, M12, the binding occurs to the M-protein.

Adhesiveness↗
PubMed1970

Studies on the ultrastructure of Bordetella pertussis. I. Morphology, origin, and biological activity of structures present in the extracellular fluid of liquid cultures of Bordetella pertussis.

Two distinct particles have been recognized in the extracellular fluid of B. pertussis cultures. Both appeared to arise from the surface (cell wall) of the organism. One of these, a membranous particle, seemed to derive from long projections on the organism composed of the outer membrane of the cell wall. The second particle, a fine filament, was not readily comparable with any previously described bacterial structure. The two particles could be separated from each other by gradient centrifugation in CsCl. Lymphocytosis-promoting factor and histamine-sensitizing activity were only associated with fractions containing the fine filaments.

Animals↗
PubMed1991

[The ultrastructure of plasmid-containing and plasmid-free Salmonella derby cells].

The comparative electron-microscopic study of S. derby plasmid-containing and plasmid-free cells has revealed certain differences in their structures: These structural differences are always accompanied by changes in the form and size of the cells, the form of the cell wall with the appearance of fimbria-like processes, depending on the presence or absence of S. derby R-plasmid in the cells. These differences in the morphology and ultrastructure of S. derby cells, associated with the R-plasmid, are of interest in the study of molecular mechanisms of plasmid action on the development of various forms of whole cells and individual bacterial structures, which play an important role in the cell function.

Cell Wall↗
PubMed2006

The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphate.

The homodimeric 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase contributes to the nonmevalonate pathway of isoprenoid biosynthesis. The crystal structure of the catalytic domain of the recombinant enzyme derived from the plant Arabidopsis thaliana has been solved by molecular replacement and refined to 2.0 A resolution. The structure contains cytidine monophosphate bound in the active site, a ligand that has been acquired from the bacterial expression system, and this observation suggests a mechanism for feedback regulation of enzyme activity. Comparisons with bacterial enzyme structures, in particular the enzyme from Escherichia coli, indicate that whilst individual subunits overlay well, the arrangement of subunits in each functional dimer is different. That distinct quaternary structures are available, in conjunction with the observation that the protein structure contains localized areas of disorder, suggests that conformational flexibility may contribute to the function of this enzyme.

Amino Acid Sequence↗
PubMed2004

Genetic evidence that the Vibrio cholerae monolayer is a distinct stage in biofilm development.

Biofilm development is conceived as a developmental process in which free swimming cells attach to a surface, first transiently and then permanently, as a single layer. This monolayer of immobilized cells gives rise to larger cell clusters that eventually develop into the biofilm, a three-dimensional structure consisting of large pillars of bacteria interspersed with water channels. Previous studies have shown that efficient development of the Vibrio cholerae biofilm requires a combination of pili, flagella and exopolysaccharide. Little is known, however, regarding the requirements for monolayer formation by wild-type V. cholerae. In this work, we have isolated the wild-type V. cholerae monolayer and demonstrated that the environmental signals, bacterial structures, and transcription profiles that induce and stabilize the monolayer state are unique. Cells in a monolayer are specialized to maintain their attachment to a surface. The surface itself activates mannose-sensitive haemagglutinin type IV pilus (MSHA)-mediated attachment, which is accompanied by repression of flagellar gene transcription. In contrast, cells in a biofilm are specialized to maintain intercellular contacts. Progression to this stage occurs when exopolysaccharide synthesis is induced by environmental monosaccharides. We propose a model for biofilm development in natural environments in which cells form a stable monolayer on a surface. As biotic surfaces are degraded with subsequent release of carbohydrates, the monolayer develops into a biofilm.

Bacterial Proteins↗
PubMed2003

Endothelium activation in the anti-phospholipid syndrome.

Anti-phospholipid syndrome is an autoimmune systemic disease characterized by the persistent presence of anti-phospholipid antibodies and by the occurrence of thrombosis, fetal loss and thrombocytopenia. Anti-phospholipid antibodies are widely accepted as pathogenic antibodies mainly directed against the phospholipid-binding protein beta 2 glycoprotein I. Beta 2 glycoprotein I can be expressed on the endothelial cell membranes of different anatomical localizations and recognized by the autoantibodies. The antibody binding might induce an endothelial activation both in vitro and in vivo experimental models, that was suggested to represent one of the pathogenic mechanisms leading to the prothrombotic state of the syndrome. Beta 2 glycoprotein I endothelial adhesion was found to take place through the interaction of the cationic phospholipid binding site of the molecule with anionic endothelial structures and through annexin II, the endothelial cell receptor for tissue plasminogen activator. Anti-beta 2 glycoprotein I antibodies can directly activate the cells via NF-kB translocation and the signaling cascade triggered by toll like receptors. It has been suggested that beta 2 glycoprotein I might be associated with toll like receptors because of its molecular mimicry with bacterial structures, the natural ligands of toll like receptors. The binding of the antibodies is thought to cross-link beta 2 glycoprotein I and the toll like receptors, eventually switching their signaling pathway.

Antibodies, Antiphospholipid↗
PubMed2003

Effect of feeding pattern and storage on the sludge settleability under aerobic conditions.

The selection of filamentous bacteria is often assumed to be associated with specific microbial properties such as growth rate, substrate uptake rate, substrate affinity and potential for substrate storage. In this study we aimed to verify some of these factors. Sequencing batch reactor (SBR) systems were used to scale-down aerobic activated sludge systems with an aerobic selector. Adding acetate in different aerobic feeding periods allowed us to simulate a variable relative size of aerobic selector with different bulk liquid substrate concentrations. The experiments showed that as expected, the aerobic fill time ratio (FTR(ox)) and the corresponding feast period, which can be assumed similar to contact time in an aerobic selector, had a strong effect on the sludge settleability. Promoting a strong substrate gradient in the SBR (FTR(ox)<5.4%) resulted in good sludge settleability (SVI<120mLg(-1)). Whenever acetate was added in a limiting rate (FTR(ox)>6.2%), a condition in which the acetate concentration in the reactor was always very low, the sludge settleability decreased (SVI>150mLg(-1)). Sludge settleability could be improved by changing the feeding strategy to a pulse feed. The maximum specific acetate uptake rate and poly beta-hydroxybutyrate (PHB) production rate of bad settling sludge, including bulking sludge, was similar to well-settling sludge, which is not in accordance with the general assumptions that well settling sludge have a higher maximal substrate uptake rate and better storage capacities. An alternative hypothesis for the development of filamentous structures in biological flocs has been formulated. It is hypothesized that bulking sludge originates from the presence of substrate gradients in sludge aggregates. Whereas at low bulk liquid substrate concentration filamentous bacteria give easier access to the substrate at the outside of the flocs and thereby proliferate, at high bulk liquid substrate concentration there is no substrate advantage for filamentous organisms and smooth bacterial structures predominate. In this hypothesis there is no need for an intrinsic difference in kinetic parameters between floc and filamentous bacteria. Where presence of filamentous bacteria is related to process conditions, the presence of a specific filament is likely due to presence of a specific limiting substrate.

Bacteria, Aerobic↗