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PubMed2003

Molecular mechanisms of mechanosensation: big lessons from small cells.

Little is known of molecular mechanisms of human mechanosensation. Only now are candidate eukaryotic sensors being identified. In contrast, bacterial sensors, including mechanosensitive channels, have been cloned, sequenced, reconstituted, and functional mutants characterized. Moreover, crystal structures for bacterial mechanosensitive channels have been resolved and structural gating transitions predicted. These studies give clues to general principles underlying the ability of a membrane protein to sense and respond to perturbations of its lipid environment that may be conserved between bacteria and humans.

Animals↗
PubMedDate not supplied

[Characteristics of the interaction of Klebsiella rhinoscleromatis DNA with the sera from patient with systemic lupus erythematos].

In blood sera of patients with systemic red lupus there were observed antibodies, which interacted in reaction of indirect hemagglutination and in complement fixation test with DNA of scleromic bacteria and did not react with the other structures of bacterial cell: with Buaven antigen, detergent and capsular polysaccharides. Reaction of indirect hemagglutination of scleromic DNA with the sera was inhibited by DNA preparations of animal origin. The serological activity of DNA from scleromic bacteria depended upon its secondary structure and did not correlate with polymeric state and nucleotide composition of the biopolymer.

Antibodies, Bacterial↗
PubMed2004

The high-resolution architecture and structural dynamics of Bacillus spores.

The capability to image single microbial cell surfaces at nanometer scale under native conditions would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, environmental resistance, and biotransformation. Here, using in vitro atomic force microscopy, we have directly visualized high-resolution native structures of bacterial endospores, including the exosporium and spore coats of four Bacillus species in air and water environments. Our results demonstrate that the mechanisms of spore coat self-assembly are similar to those described for inorganic and macromolecular crystallization. The dimensions of individual Bacillus atrophaeus spores decrease reversibly by 12% in response to a change in the environment from fully hydrated to air-dried state, establishing that the dormant spore is a dynamic physical structure. The interspecies distributions of spore length and width were determined for four species of Bacillus spores in water and air environments. The dimensions of individual spores differ significantly depending upon species, growth regimes, and environmental conditions. These findings may be useful in the reconstruction of environmental and physiological conditions during spore formation and for modeling the inhalation and dispersal of spores. This study provides a direct insight into molecular architecture and structural variability of bacterial endospores as a function of spatial and developmental organizational scales.

Bacillus↗
PubMed2006

Community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms.

The bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16S rRNA gene clone analysis, fluorescence in situ hybridization (FISH) and microelectrodes. These results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (IWTP). Both nitrification and denitrification occurred in the primary denitrification (PD) tank and denitrification occurred in the secondary denitrification (SD) tank. In contrast, nitrification and denitrification rates were very low in the nitrification (N) tank. 16S rRNA gene clone sequence analysis revealed that the bacteria affiliated with Alphaproteobacteria, followed by Betaproteobacteria, were numerically important microbial groups in three tanks. The many clones affiliated with Alphaproteobacteria were closely related to the denitrifying bacteria (e.g., Hyphomicrobium spp., Rhodopseudomonas palustris, and Rhodobacter spp.). In addition, Methylophilus leisingeri affiliated with Betaproteobacteria, which favorably utilized methanol, was detected only in the SD-tank to which methanol was added. Nitrosomonas europaea and Nitrosomonas marina were detected as the ammonia-oxidizing bacteria affiliated with Betaproteobacteria throughout this plant, although the dominant species of them was different among three tanks. Nitrifying bacteria were mainly detected in the upper parts of the PD-biofilm whereas their populations were low in the upper parts of the N-biofilm. The presence of denitrifying bacteria affiliated with Hyphomicrobium spp. in SD- and N-biofilms was verified by FISH analysis. Microelectrode measurements showed that the nitrifying bacteria present in the N- and PD-biofilms were active and the bacteria present in the SD-biofilm could denitrify.

Bacteria↗
PubMed2002

Multilocus restriction typing: a novel tool for studying global epidemiology of Burkholderia cepacia complex infection in cystic fibrosis.

Burkholderia cepacia complex infections contribute significantly to mortality and morbidity in persons with cystic fibrosis (CF). The aim of this study was to evaluate the use of a novel typing method, multilocus restriction typing (MLRT), for investigation of the global epidemiology of B. cepacia complex genomovar III, the species most commonly encountered in CF. In the MLRT method, variation at several loci is indexed by restriction analysis of polymerase chain reaction-amplified genes. Data obtained by MLRT and pulsed-field gel electrophoresis analysis of a large number of B. cepacia genomovar III isolates (including isolates belonging to epidemic lineages and environmental isolates) show a strong correlation. MLRT extends the utility of isolate genotyping by allowing comparisons of isolates collected in studies of larger scale (both temporal and spatial). The portability of MLRT data will facilitate comparison of data obtained in different laboratories. In addition, data obtained with MLRT can be used in studies of bacterial population structure.

Australia↗
PubMed1988

Multiple isoelectric forms of bacterial penicillin-binding proteins: artefacts or genuine cellular components?

Some bacterial penicillin-binding proteins (PBPs) are reported to exist as multiple isoelectric forms. Other PBPs were examined by two-dimensional electrophoresis to establish whether multiple isoelectric forms are widespread amongst PBPs. Bacillus subtilis PBPs 3 and 5 and Escherichia coli PBPs 1b alpha and 1b gamma focussed as discrete spots with no evidence of multiple isoforms. However, E. coli PBPs 1b beta and 4 displayed isoelectric variants. The results are discussed in relation to current models of bacterial peptidoglycan structure.

Bacillus subtilis↗
PubMed2026

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics↗
PubMed2002

Effects of two different application methods of Burkholderia ambifaria MCI 7 on plant growth and rhizospheric bacterial diversity.

In order to acquire a better understanding of the effects of the different delivery modes of bacterial inoculants on plant growth and on the community structure of rhizosphere bacterial populations, Burkholderia ambifaria MCI 7 (formerly B. cepacia MCI 7) was inoculated into the rhizosphere of maize plants by either seed adhesion or incorporation into soil. Plant growth was evaluated at different inoculum concentrations. The community structure of rhizosphere bacterial populations was evaluated by analysing the restriction patterns of the DNA coding for 16S rRNA amplified by polymerase chain reaction (PCR) (ARDRA) of 745 bacterial isolates. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from control and treated plants according to the concept of the r/K strategy. Moreover, the analysis of molecular variance (AMOVA) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that the method of application can be an essential element in determining the effects of the inoculant on plant growth. In fact, when applied as a maize seed treatment, B. ambifaria MCI 7 promoted plant growth significantly; on the contrary, when incorporated into soil, the same strain reduced plant growth markedly. As far as the bacterial community structure is concerned, B. ambifaria MCI 7 affected the indigenous microflora of treated plants according to the application method: seed treatment brought about an abrupt decrease in bacterial diversity, whereas incorporation into soil increased bacterial diversity. Moreover, changes in bacterial diversity were limited to r-strategist bacteria. In conclusion, B. ambifaria MCI 7 can act as both a plant growth-promoting rhizobacterium and a deleterious rhizobacterium depending on the inoculation method.

Burkholderia↗
PubMed1995

Loss of porins following carbapenem-resistance selection and adherence modification in enterobacteria.

The acquired resistance to the carbapenems is frequently joined to modified expression of porins or other outer membrane (OM) structures, thus bacterial adherence, that also depends on the presence of peculiar surface structures, might theoretically be influenced. In this study the ability to adhere to Hep-2 and I-407 eukaryotic cell monolayers was assayed for two susceptible strains of Serratia marcescens, one strain of Enterobacter cloacae and one of Providencia rettgeri in comparison with that of isogenic resistant mutants selected either by carbapenems or by cephalosporins. The mutants appeared slightly less adherent than the wild type strains, however, due to the high variability of this kind of assay, the differences observed in most cases could not be considered statistically significant. The data suggest that adherence, among the factors affecting the pathogenicity of the strains, remains probably unmodified in the resistant bacterial population possibly selected by a carbapenem treatment.

Bacterial Adhesion↗
PubMed2004

Structure of the O-polysaccharide of Providencia stuartii O4 containing 4-(N-acetyl-L-aspart-4-yl)amino-4,6-dideoxy-D-glucose.

The O-polysaccharide of Providencia stuartii O4 was obtained by mild acid degradation of the lipopolysaccharide, and the following structure of the pentasaccharide repeating unit was established: [structure: see text] where D-Qui4N(L-AspAc) is 4-(N-acetyl-L-aspart-4-yl)amino-4,6-dideoxy-D-glucose, which has not been hitherto found in bacterial polysaccharides. Structural studies were performed using sugar and methylation analyses, Smith degradation and NMR spectroscopy, including conventional 2D 1H,1H COSY, TOCSY, NOESY and 1H,13C HSQC experiments as well as COSY and NOESY experiments run in an H(2)O-D(2)O mixture to reveal correlations for NH protons.

Aspartic Acid↗
PubMed2000

Re-emerging structures: continuing crystallography of the bacterial reaction centre.

The reaction centre is nature's solar battery, and is found in a number of variations on a common theme in plants, algae and photosynthetic bacteria. During the last 20 years, a combination of X-ray crystallography, spectroscopy and mutagenesis has provided increasingly detailed insights into the mechanism of light energy transduction in the bacterial reaction centre. This mini-review looks at the application of X-ray crystallography to the bacterial reaction centre, focussing in particular on recent information on the structural consequences of site-directed mutagenesis, the roles played by water molecules in the reaction centre, the mechanism of ubiquinone reduction, and studies of the phospholipid environment of the protein.

Crystallography, X-Ray↗
PubMed2001

G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin.

G protein-coupled receptors (GPCRs) are a functionally diverse group of membrane proteins that play a critical role in signal transduction. Because of the lack of a high-resolution structure, the heptahelical transmembrane bundle within the N-terminal extracellular and C-terminal intracellular region of these receptors has initially been modeled based on the high-resolution structure of bacterial retinal-binding protein, bacteriorhodopsin. However, the low-resolution structure of rhodopsin, a prototypical GPCR, revealed that there is a minor relationship between GPCRs and bacteriorhodopsins. The high-resolution crystal structure of the rhodopsin ground state and further refinements of the model provide the first structural information about the entire organization of the polypeptide chain and post-translational moieties. These studies provide a structural template for Family 1 GPCRs that has the potential to significantly improve structure-based approaches to GPCR drug discovery.

Amino Acid Sequence↗
PubMed1996

Blocking adhesion of cancer cells to endothelial cell types by S. agalactiae type-specific polysaccharides.

By using immortalized and normal endothelial cells, we were able to detect inhibitory effects of type specific polysaccharides from Streptococcus agalactiae on adhesion of cancer cells to endothelial cells, which is an essential step of cancer metastatis. The inhibition was probably due to specific structures of the bacterial polysaccharides, since the structures of the saccharides are very similar to those of cancer specific sialyl Lewis carbohydrates (sialyl Le(a) and Le(x)) which bind to ELAM-1 of endothelial cells. This result indicated that the bacterial polysaccharides from S. agalactiae could be very useful and hopeful as cancer metastasis inhibitors.

Antineoplastic Agents↗
PubMed2002

Mutations that change the position of the putative gamma-phosphate linker in the nucleotide binding domains of CFTR alter channel gating.

The cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel is an ATP-binding cassette transporter that contains conserved nucleotide-binding domains (NBDs). In CFTR, the NBDs bind and hydrolyze ATP to open and close the channel. Crystal structures of related NBDs suggest a structural model with an important signaling role for a gamma-phosphate linker peptide that couples bound nucleotide to movement of an alpha-helical subdomain. We mutated two residues in CFTR that the structural model predicts will uncouple effects of nucleotide binding from movement of the alpha-helical subdomain. These residues are Gln-493 and Gln-1291, which may directly connect the ATP gamma-phosphate to the gamma-phosphate linker, and residues Asn-505 and Asn-1303, which may form hydrogen bonds that stabilize the linker. In NBD1, Q493A reduced the frequency of channel opening, suggesting a role for this residue in coupling ATP binding to channel opening. In contrast, N505C increased the frequency of channel opening, consistent with a role for Asn-505 in stabilizing the inactive state of the NBD. In NBD2, Q1291A decreased the effects of pyrophosphate without altering other functions. Mutations of Asn-1303 decreased the rate of channel opening and closing, suggesting an important role for NBD2 in controlling channel burst duration. These findings are consistent with both the bacterial NBD structural model and gating models for CFTR. Our results extend models of nucleotide-induced structural changes from bacterial NBDs to a functional mammalian ATP-binding cassette transporter.

Adenosine Diphosphate↗
PubMed2005

Inoculation with the plant-growth-promoting rhizobacterium Azospirillum brasilense causes little disturbance in the rhizosphere and rhizoplane of maize (Zea mays).

Inoculation with Azospirillum brasilense exerts beneficial effects on plant growth and crop yields. In this study, a comparative analysis of maize (Zea mays) root inoculated or not inoculated with A. brasilense strains was performed in two soils. Colonization dynamics of the rhizobacteria were tracked in various root compartments using 16S rRNA-targeted probes and 4',6'diamidino-2-phenylindole staining, and the structure of bacterial populations in the same samples was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction products of the 16S rRNA gene. Based on whole cell hybridization, a large fraction of the bacterial community was found to be active in both the rhizoplane-endorhizosphere and rhizosphere soil compartments, in both soil types. A DGGE fingerprint analysis revealed that plant inoculation with A. brasilense had no effect on the structural composition of the bacterial communities, which were also found to be very similar at the root tip and at zones of root branching. However, rhizobacterial populations were strongly influenced by plant age, and their complexity decreased in the rhizoplane-endorhizosphere in comparison to rhizosphere soil. A clone library generated from rhizosphere DNA revealed a highly diverse community of soil and rhizosphere bacteria, including an indigenous Azospirillum-like organism. A large proportion of these clones was only distantly related to known species.

Azospirillum brasilense↗
PubMed2006

GTPase activity, structure, and mechanical properties of filaments assembled from bacterial cytoskeleton protein MreB.

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.

Actins↗
PubMed1998

Structure and functional characteristics of bacterial biofilms in fluid processing operations.

Bacterial biofilms create a number of serious problems for industrial fluid processing operations. Mechanical blockages, impedance of heat transfer processes, and biodeterioration of the components of metallic and polymeric systems result in billions of dollars in losses each year. Product spoilage and possible risks to public health are also consequences of biofilm-mediated contamination. Fundamentally, these biofouling activities can be described in terms of the physicochemical properties that are associated with bacterial metabolism and biofilm development. Treatment of biofouling is also complicated by the unique structural attributes of biofilms: extracellular polymeric substances create diffusional barriers to antimicrobial agents, protecting labile cellular targets from both oxidizing and nonoxidizing compounds. The mechanisms associated with the initial events of bacterial adhesion to engineered surfaces and subsequent fouling of biofilm formation are poorly understood. However, studies of bacterial biofilm architecture have been greatly facilitated by the application of confocal laser microscopy, scanning or transmission electron microscopy, and Fourier transform infrared spectroscopy. This paper reviews the genesis of biofilm formation and describes the influence of structure on biofouling activities in industrial fluid handling systems.

Animals↗