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PubMed2006

Microbial pattern recognition receptors mediate M-cell uptake of a gram-negative bacterium.

The receptors involved in the sampling of particulate microbial antigens by the gut are largely unknown. Here we demonstrate for the first time in an in vitro M-cell model and in situ in isolated murine intestinal segments that the receptors TLR-4, PAF-R, and alpha5beta1 integrin are all involved in mediating bacterial uptake associated with transcytosis. The pattern of expression of TLR-4 and alpha5beta1 integrin differed between M cells and enterocytes. There was increased apical expression of TLR-4 in M-cell cultures, and it was present on the apical surface of murine M cells but not enterocytes in situ. In contrast, PAF-R was expressed equally by both cell types in vitro and was abundantly expressed throughout the intestinal epithelium. Inhibition of TLR-4 and PAF-R, but not TLR-2, reduced gram-negative bacterial uptake by both cell types, whereas inhibition of the apically expressed alpha5beta1 integrin significantly reduced the ability of M cells to translocate bacteria. Hence, the involvement of each receptor was dependent not only on differences in the level of receptor expression but the cellular localization. Using bacteria that had mutations that affected the bacterial lipooligosaccharide structure indicated that the oligosaccharide moiety was important in bacterial uptake. Taken together, the data suggest that pathogen-associated molecular pattern interactions with pattern recognition receptors are key factors in M-cell recognition of intestinal antigens for mucosal immune priming.

Animals↗
PubMed1993

[Bacterial endotoxins: relationship between chemical structure and biological effect].

Gram-negative bacteria carry on their surface endotoxins, which are essential for bacterial growth and survival. If released from the bacterial cell, endotoxins induce in higher organisms a great variety of pathophysiological effects. Chemically, endotoxins constitute lipopolysaccharides (LPS), the lipid component (termed lipid A) of which is responsible for the induction of endotoxin effects. The structural and conformational parameters, endowing lipid A with its potent bioactivity, have been well characterized. The toxic effects of endotoxins are initiated by the specific interaction of lipid A with macrophages/monocytes resulting in the production of peptide or lipid mediators. This interaction is governed by a unique (toxic) conformation of lipid A on the one hand, and by specific cellular receptors on the other. The interaction and subsequent mediator production can be specifically and antagonistically inhibited by lipid A partial structures. A recently developed monoclonal anti-LPS-antibody cross-reacts with endotoxins of various bacterial origin, and it cross-protects against harmful endotoxin effects such as pyrogenicity and lethality.

Animals↗
PubMed1996

3D structure of ramoplanin: a potent inhibitor of bacterial cell wall synthesis.

The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study.

Amino Acid Sequence↗
PubMed1989

[Effect of beta-lactam antibiotics on lipid bilayer membranes. I. Penicillin antibiotics].

Interaction between penicillins and model membrane systems, flat black bilayer lipid membranes (BLM) composed of vegetable or bacterial phospholipids was studied with an account of the complicated structure of bacterial cell membranes and possible presence in them of "pure" bilayer lipid areas. By their effect on electroconductivity of the BLM the antibiotics could be divided into three groups: those having no effect on the BLM electroconductivity at the maximum concentrations i.e. benzylpenicillin, carbenicillin, piperacillin (at pH 6.0 and 7.0) and ampicillin (at pH 6.0), those insignificantly changing electroconductivity of the BLM i.e. carfecillin and azlocillin and those having a significant effect on the BLM electroconductivity i.e. ampicillin N-acyl derivatives and 6-APA. The effect of ampicillin on the BLM conductivity markedly depended on the electrolite pH. The penicillins bound to the bilayer and induced changes in the transmembrane potential (evident from the changes in the second harmonic of the capacitive current) and the BLM elasticity-capacitance parameters (evident from the changes in the ratio of the amplitudes of the first and third harmonics). It was shown that all the penicillins penetrated through the BLM composed of either vegetable or bacterial phospholipids. The capacity for the transmembrane transfer without changing of the bilayer conductivity must be connected with the fact that the penetrating antibiotics did not induce any changes in the BLM structure. The effect on the conductivity probably depended in its turn on the form of the molecule and the ratio of the hydrophilic and hydrophobic parts in it.

Electrolytes↗
PubMed1998

The 80S rat liver ribosome at 25 A resolution by electron cryomicroscopy and angular reconstitution.

BACKGROUND: The ribosome is central to protein synthesis in all living organisms. Single-particle electron cryomicroscopy has recently led to the determination of three-dimensional structures of bacterial ribosomes to approximately 20 A, which have since revolutionised our understanding of ribosomal function. The structure we present here of the 80S rat liver ribosome leads the way to similar progress for mammalian ribosomes. RESULTS: Among the new details revealed by our 25 A structure of the 80S rat liver ribosome are channels within the subunits, a large 'flat ribosomal surface' (FRS) on the outer surface of the large subunit and structural extensions of the mammalian compared to the bacterial ribosome. The main large subunit channel in both the bacterial and the mammalian species starts at the peptidyl transferase centre, below the central protuberance, and ends in the FRS, at the lower back of the large subunit. Structurally, the channels of both species can be directly superimposed. CONCLUSIONS: The mammalian structural extensions--none of which trespass the FRS--can be interpreted in terms of rRNA inserts and additional protein content over that of bacterial ribosomes. The main large subunit channel, which ends at the FRS, is the best candidate for the exit channel for proteins targeted for the endoplasmic reticulum.

Animals↗
PubMed2005

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life.

Although most globins, including the N-terminal domains within chimeric proteins such as flavohemoglobins and globin-coupled sensors, exhibit a 3/3 helical sandwich structure, many bacterial, plant, and ciliate globins have a 2/2 helical sandwich structure. We carried out a comprehensive survey of globins in the genomes from the three kingdoms of life. Bayesian phylogenetic trees based on manually aligned sequences indicate the possibility of past horizontal globin gene transfers from bacteria to eukaryotes. blastp searches revealed the presence of 3/3 single-domain globins related to the globin domains of the bacterial and fungal flavohemoglobins in many bacteria, a red alga, and a diatom. Iterated psi-blast searches based on groups of globin sequences found that only the single-domain globins and flavohemoglobins recognize the eukaryote 3/3 globins, including vertebrate neuroglobins, alpha- and beta-globins, and cytoglobins. The 2/2 globins recognize the flavohemoglobins, as do the globin coupled sensors and the closely related single-domain protoglobins. However, the 2/2 globins and the globin-coupled sensors do not recognize each other. Thus, all globins appear to be distributed among three lineages: (i) the 3/3 plant and metazoan globins, single-domain globins, and flavohemoglobins; (ii) the bacterial 3/3 globin-coupled sensors and protoglobins; and (iii) the bacterial, plant, and ciliate 2/2 globins. The three lineages may have evolved from an ancestral 3/3 or 2/2 globin. Furthermore, it appears likely that the predominant functions of globins are enzymatic and that oxygen transport is a specialized development that accompanied the evolution of metazoans.

Bayes Theorem↗
PubMed2005

Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase.

A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.

Aminoglycosides↗
PubMed2002

Ion channels: structural bioinformatics and modelling.

Ion channels are membrane proteins of key physiological and pharmacological importance. As is the case for many integral membrane proteins, X-ray structures are known for a few bacterial channels, yet structures of human homologues are required for analysis of channel-associated diseases and for drug design. Homology modelling can be used to help remedy this deficit. In combination with molecular dynamics simulations and associated calculations, modelling provides a powerful approach to understanding structure/function relationships in human ion channels. Modelling techniques have been applied to two classes of potassium channels: voltage-gated (Kv) and inward rectifier (Kir) channels. Kir channel models, based on the structure of the bacterial channel KcsA, have been used as a starting point for detailed simulation studies that have increased our understanding of ion permeation and selectivity mechanisms. The transmembrane domain of GluR0, a bacterial homologue of mammalian glutamate receptors, also may be modelled using the KcsA structure as a template. Models of the nicotinic acetylcholine receptor may be constructed in a modular fashion. The snail acetylcholine-binding protein provides a template for the extracellular ligand-binding domain. The transmembrane pore region can be modelled on the basis of NMR structures of the pore-lining M2 helix.

Amino Acid Sequence↗
PubMed2002

Structure-function relationship studies on the frog skin antimicrobial peptide tigerinin 1: design of analogs with improved activity and their action on clinical bacterial isolates.

Structure-function relationships in antimicrobial peptides have been extensively investigated in order to obtain improved analogs. Most of these studies have targeted either alpha-helical peptides or beta-sheet peptides with multiple disulfide bridges. Tigerinins are short, nonhelical antimicrobial peptides with a single disulfide bridge. In this study, we have synthesized several analogs of tigerinin 1 with an aim to understand the structural basis of activity as well as improve its activity. The studies demonstrate that the loop structure of tigerinin 1 is essential for its optimal activity. However, linearization with increased cationic charges can compensate for loss of loop structure to some extent. Morphology of the cells after treatment with the active analogs shows extensive leakage of cytoplasmic contents. Tigerinin 1 and two of its analogs exhibit impressive activity against a variety of clinical bacterial isolates.

Anti-Bacterial Agents↗
PubMed2004

X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts.

Ubihydroquinone: cytochrome (cyt)c oxidoreductase, or cyt bc (1), is a widespread, membrane integral enzyme that plays a crucial role during photosynthesis and respiration. It is one of the major contributors of the electrochemical proton gradient, which is subsequently used for ATP synthesis. The simplest form of the cyt bc (1) is found in bacteria, and it contains only the three ubiquitously conserved catalytic subunits: the Fe-S protein, cyt b and cyt c (1). Here we present a preliminary X-ray structure of Rhodobacter capsulatus cyt bc (1) at 3.8 A and compare it to the available structures of its homologues from mitochondria and chloroplast. Using the bacterial enzyme structure, we highlight the structural similarities and differences that are found among the three catalytic subunits between the members of this family of enzymes. In addition, we discuss the locations of currently known critical mutations, and their implications in terms of the cyt bc (1) catalysis.

Journal Article↗
PubMed2004

Intravital fluorescence microscopy: a novel tool for the study of the interaction of Staphylococcus aureus with the microvascular endothelium in vivo.

BACKGROUND: The ability of Staphylococcus aureus to adhere to endothelial cells is a major prerequisite for the tissue-invasive stage of bacterial infection. METHODS: To develop a model for the study of endothelial attachment and detachment kinetics of S. aureus within the host's microvasculature in vivo, we labeled inactivated staphylococci with fluorescein isothiocyanate and investigated their interaction with the vascular endothelium of arterioles, capillaries, and venules in the dorsal skin-fold chamber of untreated and tumor necrosis factor (TNF)-alpha-treated hamsters by use of intravital fluorescence microscopy. RESULTS: During the first 20 min after injection, >99% of the bacteria were removed from the microvascular bloodstream. In parallel, single bacteria and bacterial clusters adhered to the endothelial lining of postcapillary venules and to nutritive capillaries. Bacterial adherence to the endothelium of arterioles was only rarely observed. TNF-alpha treatment significantly accelerated bacterial clearance and resulted in a significant increase of venular, but not arteriolar and capillary, bacterial adherence, indicating the venular endothelium to be the target structure for bacterial recruitment. CONCLUSION: The insights into host-pathogen interaction gained with this new in vivo model offer highly promising novel aspects of the understanding of infections caused by S. aureus.

Animals↗
PubMed1996

Structural flexibility and functional versatility of mammalian P450 enzymes.

P450 enzymes have evolved into a large superfamily that displays great diversity in substrate and product specificities by fixing the natural amino acid substitutions with high frequency. Site-directed mutagenesis has been used to correlate the substitutions with the diverse specificities in various P450s. As a result, the common residues that determine the specificities of various mammalian P450s have been identified and aligned to the corresponding residues in the substrate-heme pocket of the 3-dimensional structures of bacterial P450s. The substrate-heme pocket appears to be structurally variable so that only a minor substitution (Ala -> -> Val, for example) at the critical positions is enough to define the altered specificity. Thus, the structural variability of the P450s provides the inherent versatility in acquiring a novel activity. Recent mutational studies indicate that the side chain size is the major determining factor of specificity, outweighing other factors such as polarity. Further understanding of the paradoxical characteristics observed may provide us with the underlying principles that determine P450 activities, and may lead to the ability to predict P450 activities based on the types of key amino acid residues.

Amino Acid Sequence↗
PubMed2004

Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability.

We investigated vertical distribution and depth-related patterns (from 670 to 2,570 metres) of bacterial diversity in sediment samples collected along a transect in the warm deep Mediterranean sea. Analyses of bacterial diversity were compared with the abundance of benthic bacteria, their metabolically active fraction and the substrates potentially available for their growth. The number of active bacteria was dependent upon the availability of organic substrate in the sediment deriving from phytopigment inputs from the photic layer. The T-RFLP analysis revealed that the surface layers of all sediments analysed were dominated by the same ribotypes, but clear shifts in bacterial community structure were observed in deeper sediment layers. High values of bacterial diversity (expressed as D, H') and evenness (as J) were observed at all stations (a total of 61 ribotypes was identified), and as a result of the large fraction of rare ribotypes (c. 35%), the overall bacterial diversity in the deep sea region investigated was among the highest reported so far in literature. Biodiversity parameters did not display any relationship with water depth, but ribotype richness was related with the number and percentage of active bacteria, suggesting a coupling between organic inputs stimulating bacterial growth and deep-sea bacterial diversity.

Bacteria↗
PubMed2004

[A new mechanosensitive channel SAKCA and a new MS channel blocker GsTMx-4].

Cells can respond to a variety of mechanical stimuli such as tension, pressure, and shear stress. However, the mechanisms of mechanotransduction are largely unknown. The major reason for this lies in the ambiguity of the molecular entity of cell mechanosensors. Currently only MS (mechanosensitive) channels conform to an established class of mechanosensors due to the firm and detailed analyses by electrophysiolgy. Although molecular structures of MS channels are known for limited members, higher order structures of bacterial MS channels have been resolved and their detailed structure-function studies are in progress. In contrast, molecular and biophysical analyses of eukaryote MS channels, which may attract much attention, are yet not well-studied. Although many candidate molecules have been proposed as the cell mechanosensor, currently only 2-pore-domain K channels (TREK/TRAAK) and SAKCA, a new class of MS channel introduced here, may be the subjects eligible for rigorous electrophysiological analyses. On the other hand, lack of specific blockers to MS channels is another reason why the progress in this field is slow. Gadolinium (Gd(3+)) has been extensively used as a potent blocker of MS channels, but its nonspecific actions have limited its usefulness. Very recently, a promising 35 mer peptide, which can be more specific for MS channels, named GsMTx-4 has been isolated from spider venom. This peptide is interesting because it inhibits stretch-induced atrial fibrillation, which may involve MS channel activation and thus can be used as a basis for developing a new class of drugs to cure heart failure. This short review deals with recent progresses in MS channel studies and the structure-function of SAKCA, a recently cloned MS channel from heart, as well as its interaction with the new MS channel blocker GsMTx-4.

Animals↗
PubMed1978

Dental plaque morphology as revealed by direct observation and by replicating techniques.

The ability of four elastomer impression materials to reproduce details of bacterial plaque structures was studied by comparing areas of the replica models with corresponding areas of the replicated plaque. Plaque was grown on hydroxyapatite splint segments for 48 hours and replica models were made from three different resins. One of the resins, a methacrylate material, was not suited for this purpose due to its content of spherical particles. The polysulfide and polyether impression materials reacted with the heat curing epoxy resin, and less satisfactory results were obtained with cold curing epoxy resin. Best results were obtained by a combined use of low viscosity silicone impression materials and cold or heat curing epoxy resins as model materials. However, a considerable loss of detail occurred in the replica models compared with observations of plaque directly on splint surfaces. Outlines of individual bacteria could sometimes be seen in the models, but generally several cells seemed to fuse, and appeared like small globular structures where cells and pellicle were difficult to distinguish. The bacterial colonization started near the gingival border of the surface, initiated by attachment of individual bacteria to the pellicle surface.

Dental Impression Materials↗
PubMed1986

Pathogenesis of urinary tract infections. Bacterial adherence, bladder defense mechanisms.

Bacterial virulence depends upon the ability of bacteria to adhere to mucosal cells. The risk of infection is increased by bacterial factors promoting this adherence and the fact that bacterial surface structures seek epithelial receptors. The host's ability to inactivate bacterial virulence factors and to "mask" its own cell receptors determines whether infections are to be warded off successfully. The current knowledge of these processes is reviewed in this article.

Adhesins, Escherichia coli↗
PubMed1992

Sexuality in a natural population of bacteria--Bacillus subtilis challenges the clonal paradigm.

Reproduction by binary fission necessarily establishes a clonal genotypic structure in bacterial populations unless a high rate of genetic recombination opposes it. Several genetic properties were examined for a wild population of Bacillus subtilis in the Sonoran Desert of Arizona to assess the extent of recombination in a natural population. These properties included allozyme variation revealed by multilocus enzyme electrophoresis, phage and antibiotic resistance, and restriction fragment length polymorphism with Southern hybridization. Evidence of extensive genetic recombination was found along with evidence of modest clonal structure. Recombination must be frequent relative to binary fission in this population. This mixed population structure provides broader options for bacterial evolution than would a purely clonal structure.

Bacillus subtilis↗
PubMed2005

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater.

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.

Adaptation, Physiological↗