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PubMed2000

Chitin is only a minor component of the peritrophic matrix from larvae of Lucilia cuprina.

The gut of most insects is lined with a peritrophic matrix that facilitates the digestive process and protects insects from invasion by micro-organisms and parasites. It is widely accepted that the matrix is composed of chitin, proteins and proteoglycans. Here we critically re-examine the chitin content of the typical type 2 peritrophic matrix from the larvae of the fly Lucilia cuprina using a range of techniques. Many of the histochemical and biochemical techniques indicate the presence of chitin, although they are often adversely influenced by the presence of highly glycosylated proteins, a principal component of the matrix. The alkali-stable fraction, which is used as an indicator of the maximum chitin content in a biological sample, is only 7.2% of the weight of the matrix. Larvae fed on the potent chitin synthase inhibitor polyoxin D or the chitin-binding agent Calcofluor White, showed strong concentration-dependent inhibition of larval weight and survival but no discernible effects on the matrix structure. A bacterial endochitinase fed to larvae had no effect on larval growth and no observable effect in vitro on the structure of isolated peritrophic matrix. RT-PCR did not detect a chitin synthase mRNA in cardia, the tissue from which PM originates. It is concluded that chitin is a minor structural component of the type 2 peritrophic matrix of this insect.

Animals↗
PubMed2005

Hydralysins, a new category of beta-pore-forming toxins in cnidaria.

Cnidaria are venomous animals that produce diverse protein and polypeptide toxins, stored and delivered into the prey through the stinging cells, the nematocytes. These include pore-forming cytolytic toxins such as well studied actinoporins. In this work, we have shown that the non-nematocystic paralytic toxins, hydralysins, from the green hydra Chlorohydra viridissima comprise a highly diverse group of beta-pore-forming proteins, distinct from other cnidarian toxins but similar in activity and structure to bacterial and fungal toxins. Functional characterization of hydralysins reveals that as soluble monomers they are rich in beta-structure, as revealed by far UV circular dichroism and computational analysis. Hydralysins bind erythrocyte membranes and form discrete pores with an internal diameter of approximately 1.2 nm. The cytolytic effect of hydralysin is cell type-selective, suggesting a specific receptor that is not a phospholipid or carbohydrate. Multiple sequence alignment reveals that hydralysins share a set of conserved sequence motifs with known pore-forming toxins such as aerolysin, epsilon-toxin, alpha-toxin, and LSL and that these sequence motifs are found in and around the poreforming domains of the toxins. The importance of these sequence motifs is revealed by the cloning, expression, and mutagenesis of three hydralysin isoforms that strongly differ in their hemolytic and paralytic activities. The correlation between the paralytic and cytolytic activities of hydralysin suggests that both are a consequence of receptor-mediated pore formation. Hydralysins and their homologues exemplify the wide distribution of beta-pore formers in biology and provide a useful model for the study of their molecular mode of action.

Amino Acid Motifs↗
PubMed2004

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L.

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.

Bacteria↗
PubMed2006

Antibacterial lysine analogs that target lysine riboswitches.

Lysine riboswitches are bacterial RNA structures that sense the concentration of lysine and regulate the expression of lysine biosynthesis and transport genes. Members of this riboswitch class are found in the 5' untranslated region of messenger RNAs, where they form highly selective receptors for lysine. Lysine binding to the receptor stabilizes an mRNA tertiary structure that, in most cases, causes transcription termination before the adjacent open reading frame can be expressed. A lysine riboswitch conceivably could be targeted for antibacterial therapy by designing new compounds that bind the riboswitch and suppress lysine biosynthesis and transport genes. As a test of this strategy, we have identified several lysine analogs that bind to riboswitches in vitro and inhibit Bacillus subtilis growth, probably through a mechanism of riboswitch-mediated repression of lysine biosynthesis. These results indicate that riboswitches could serve as new classes of antibacterial drug targets.

Anti-Bacterial Agents↗
PubMed2002

Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease.

Mitochondrial ribosomes comprise the most diverse group of ribosomes known. The mammalian mitochondrial ribosomes (55S) differ unexpectedly from bacterial (70S) and cytoplasmic ribosomes (80S), as well as other kinds of mitochondrial ribosomes. The bovine mitochondrial ribosome has been developed as a model system for the study of human mitochondrial ribosomes to address several questions related to the structure, function, biosynthesis and evolution of these interesting ribosomes. Bovine mitochondrial ribosomal proteins (MRPs) from each subunit have been identified and characterized with respect to individuality and electrophoretic properties, amino acid sequence, topographic disposition, RNA binding properties, evolutionary relationships and reaction with affinity probes of ribosomal functional domains. Several distinctive properties of these ribosomes are being elucidated, including their antibiotic susceptibility and composition. Mammalian mitochondrial ribosomes lack several of the major RNA stem structures of bacterial ribosomes but they contain a correspondingly higher protein content (as many as 80 proteins), suggesting a model where proteins have replaced RNA structural elements during the evolution of these ribosomes. Despite their lower RNA content they are physically larger than bacterial ribosomes, because of the 'extra' proteins they contain. The extra proteins in mitochondrial ribosomes are 'new' in the sense that they are not homologous to proteins in bacterial or cytoplasmic ribosomes. Some of the new proteins appear to be bifunctional. All of the mammalian MRPs are encoded in nuclear genes (a separate set from those encoding cytoplasmic ribosomal proteins) which are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. Interest is growing in the structure, organization, chromosomal location and expression of genes for human MRPs. Proteins which are essential for mitoribosome function are candidates for involvement in human genetic disease.

Animals↗
PubMed1985

Interaction of Salmonella telaviv with Maclura pomifera lectin.

Salmonella telaviv, Salmonella tranoroa, and Salmonella illinois were examined for their ability to interact with 15 purified lectins of known sugar specificity. The only interaction observed was between the lectin of Maclura pomifera and S. telaviv. M. pomifera lectin specifically agglutinated suspensions of S. telaviv and precipitated with its purified lipopolysaccharide and isolated lipid A free O polysaccharide. Quantitative inhibition assays showing methyl-alpha-D-galactopyranoside and N-acetyl-D-galactosamine to be potent inhibitors of Maclura lectin precipitation by S. telaviv O polysaccharide suggest that the interaction is mediated by D-galactose or N-acetyl-D-galactosamine units of bacterial polysaccharide structure, or both.

Agglutination↗
PubMed2006

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure-function relationships in sequence families and superfamilies.

Base Sequence↗
PubMed2003

A superfamily of voltage-gated sodium channels in bacteria.

NaChBac, a six-alpha-helical transmembrane-spanning protein cloned from Bacillus halodurans, is the first functionally characterized bacterial voltage-gated Na(+)-selective channel. As a highly expressing ion channel protein, NaChBac is an ideal candidate for high resolution structural determination and structure-function studies. The biological role of NaChBac, however, is still unknown. In this report, another 11 structurally related bacterial proteins are described. Two of these functionally expressed as voltage-dependent Na(+) channels (Na(V)PZ from Paracoccus zeaxanthinifaciens and Na(V)SP from Silicibacter pomeroyi). Na(V)PZ and Na(V)SP share approximately 40% amino acid sequence identity with NaChBac. When expressed in mammalian cell lines, both Na(V)PZ and Na(V)SP were Na(+)-selective and voltage-dependent. However, their kinetics and voltage dependence differ significantly. These single six-alpha-helical transmembrane-spanning subunits constitute a widely distributed superfamily (Na(V)Bac) of channels in bacteria, implying a fundamental prokaryotic function. The degree of sequence homology (22-54%) is optimal for future comparisons of Na(V)Bac structure and function of similarity and dissimilarity among Na(V)Bac proteins. Thus, the Na(V)Bac superfamily is fertile ground for crystallographic, electrophysiological, and microbiological studies.

Amino Acid Sequence↗
PubMed2005

New insights into the interaction of ribosomal protein L1 with RNA.

The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.

Amino Acid Sequence↗
PubMed2006

Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus.

The structures of two major phosphoglycolipids from the thermophilic bacteria Thermus oshimai NTU-063, Thermus thermophilus NTU-077, Meiothermus ruber NTU-124, and Meiothermus taiwanensis NTU-220 were determined using spectroscopic and chemical analyses to be 2'-O-(1,2-diacyl-sn-glycero-3-phospho) -3'-O-(alpha-N-acetyl-glucosaminyl)-N-glyceroyl alkylamine [PGL1 (1)] and the novel structure 2'-O-(2-acylalkyldio-1-O-phospho)-3'-O-(alpha-N-acetylglucosaminyl)-N-glyceroyl alkylamine [PGL2 (2)]. PGL2 (2) is the first phosphoglycolipid identified with a 2-acylalkyldio-1-O-phosphate moiety. The fatty acids of the phosphoglycolipids are mainly iso-C(15:0), -C(16:0), and -C(17:0) and anteiso-C(15:0) and -C(17:0). The ratios of PGL2 (2) to PGL1 (1) are significantly altered when grown at different temperatures for three strains, T. thermophilus NTU-077, M. ruber NTU-124, and M. taiwanensis NTU-220, but not for T. oshimai NTU-063. Accordingly, the ratios of iso- to anteiso-branched fatty acids increase when grown at the higher temperature.

Chromatography, High Pressure Liquid↗
PubMed1999

Oligomeric integrity--the structural key to thermal stability in bacterial alcohol dehydrogenases.

Principles of protein thermostability have been studied by comparing structures of thermostable proteins with mesophilic counterparts that have a high degree of sequence identity. Two tetrameric NADP(H)-dependent alcohol dehydrogenases, one from Clostridium beijerinckii (CBADH) and the other from Thermoanaerobacter brockii (TBADH), having exceptionally high (75%) sequence identity, differ by 30 degrees in their melting temperatures. The crystal structures of CBADH and TBADH in their holo-enzyme form have been determined at a resolution of 2.05 and 2.5 A, respectively. Comparison of these two very similar structures (RMS difference in Calpha = 0.8 A) revealed several features that can account for the higher thermal stability of TBADH. These include additional ion pairs, "charged-neutral" hydrogen bonds, and prolines as well as improved stability of alpha-helices and tighter molecular packing. However, a deeper structural insight, based on the location of stabilizing elements, suggests that enhanced thermal stability of TBADH is due mainly to the strategic placement of structural determinants at positions that strengthen the interface between its subunits. This is also supported by mutational analysis of structural elements at critical locations. Thus, it is the reinforcement of the quaternary structure that is most likely to be a primary factor in preserving enzymatic activity of this oligomeric bacterial ADH at elevated temperatures.

Alcohol Dehydrogenase↗
PubMed2002

Soil and plant effects on microbial community structure.

We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.

Bacteria↗
PubMed2006

Effect of introduced phthalate-degrading bacteria on the diversity of indigenous bacterial communities during di-(2-ethylhexyl) phthalate (DEHP) degradation in a soil microcosm.

Four previously isolated di-butyl-phthalate (DBP) degraders were tested for their abilities to degrade di-(2-ethylhexyl) phthalate (DEHP). In aqueous medium supplemented with 100mg/l of DEHP, both isolate G1 and Rhodococcus rhodochrous G2 showed excellent degradative activity; in three days they were able to degrade more than 97% of the added DEHP. Rhodococcus rhodochrous G7 degraded 32.5% of the added DEHP and Corynebacterium nitrilophilus G11 showed the least amount of DEHP degradation. The addition of surfactant Brij 30 at 0.1x critical micelle concentration (2mg/l) significantly improved DEHP degradation by Rhodococcus rhodochrous G2 (more than 90% of the added DEHP was degraded within 24 hours), but slightly inhibited the degradation of DEHP by the isolate G1 and Rhodococcus rhodochrous G7. Based on the 16S rDNA sequence data, isolate G1 was identified as Gordonia polyisoprenivorans. Soil inhibited DEHP degradation by G. polyisoprenivorans G1; fourteen days after a second addition of DEHP, 11.5% of the total added DEHP (i.e., 243.4 microg/g soil) remained detectable. Changes in the bacterial community were monitored using denaturing gradient gel electrophoresis (DGGE) and respective dendrogram analysis. It is clear that DEHP and DEHP plus G. polyisoprenivorans G1 substantially affected the bacterial community structure in the soils. However, as the population of indigenous DEHP degraders increased in the DEPH-treated soil, its bacterial communities resembled those in the DEHP plus G. polyisoprenivorans G1-inoculated soil by Day 17.

Biodegradation, Environmental↗
PubMed2006

Effect of cast molded rifampicin/silicone on Staphylococcus epidermidis biofilm formation.

Infection is one of the most common catheter-related complications, especially in shunt systems used to treat hydrocephalus. Staphylococcus epidermidis is directly related to biomaterial infections owing to its ability to form a biofilm on implanted materials. In this study, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were employed to investigate the effect of the antibiotic rifampicin on the colonization and growth of S. epidermidis 35984 on the surface of silicone. A cast molding method was used to load rifampicin into the silicone precursor before it was cured. Bacteria with a diameter of 800-1000 nm and height of 200-500 nm were found to be embedded in the biofilm. Compact multilayer biofilm structures were found on silicone surfaces upon incubation for 4 and 24 h. On the other hand, sparser biofilm structures were observed on rifampicin-loaded surfaces after incubation for the same duration. Deformation of bacteria was observed by AFM. Moreover, different bacterial colony structures on the surfaces of silicone and rifampicin-loaded silicone were observed by AFM and SEM.

Antibiotics, Antitubercular↗
PubMed2005

The Q-loop disengages from the first intracellular loop during the catalytic cycle of the multidrug ABC transporter BmrA.

The ATP-binding cassette is the most abundant family of transporters including many medically relevant members and gathers both importers and exporters involved in the transport of a wide variety of substrates. Although three high resolution three-dimensional structures have been obtained for a prototypic exporter, MsbA, two have been subjected to much criticism. Here, conformational changes of BmrA, a multidrug bacterial transporter structurally related to MsbA, have been studied. A three-dimensional model of BmrA, based on the "open" conformation of Escherichia coli MsbA, was probed by simultaneously introducing two cysteine residues, one in the first intracellular loop of the transmembrane domain and the other in the Q-loop of the nucleotide-binding domain (NBD). Intramolecular disulfide bonds could be created in the absence of any effectors, which prevented both drug transport and ATPase activity. Interestingly, addition of ATP/Mg plus vanadate strongly prevented this bond formation in a cysteine double mutant, whereas ATP/Mg alone was sufficient when the ATPase-inactive E504Q mutation was also introduced, in agreement with additional BmrA models where the ATP-binding sites are positioned at the NBD/NBD interface. Furthermore, cross-linking between the two cysteine residues could still be achieved in the presence of ATP/Mg plus vanadate when homobifunctional cross-linkers separated by more than 13 Angstrom were added. Altogether, these results give support to the existence, in the resting state, of a monomeric conformation of BmrA similar to that found within the open MsbA dimer and show that a large motion is required between intracellular loop 1 and the nucleotide-binding domain for the proper functioning of a multidrug ATP-binding cassette transporter.

ATP-Binding Cassette Transporters↗
PubMed2003

Structure elucidation of Sch 538415, a novel acyl carrier protein synthase inhibitor from a microorganism.

A novel acyl carrier protein synthase inhibitor, Sch 538415 (1), was isolated from an unidentified bacterial microbe. Structure elucidation of 1 was accomplished based on analysis of spectroscopic data including UV, MS and 2D-NMR spectra. Compound 1 exhibited inhibitory activity in the acyl carrier protein synthase (AcpS) assay with an IC(50) value of 4.19 microM and showed antibacterial activity against Staphylococcus aureus in the agar diffusion assay.

Aza Compounds↗
PubMed2003

Properties of human mitochondrial ribosomes.

Mammalian mitochondrial ribosomes (55S) differ unexpectedly from bacterial (70S) and cytoplasmic ribosomes (80S), as well as other kinds of mitochondrial ribosomes. Typical of mammalian mitochondrial ribosomes, the bovine mitochondrial ribosome has been developed as a model system for the study of human mitochondrial ribosomes, to address several questions related to the structure, function, biosynthesis and evolution of these interesting ribosomes. Bovine mitochondrial ribosomal proteins (MRPs) from each subunit have been identified and characterized with respect to individuality and electrophoretic properties, amino acid sequence, topographic disposition, RNA binding properties, evolutionary relationships and reaction with affinity probes of ribosomal functional domains. Several distinctive properties of these ribosomes are being elucidated, including their antibiotic susceptibility and composition. Human mitochondrial ribosomes lack several of the major RNA stem structures of bacterial ribosomes but they contain a correspondingly higher protein content (as many as 80 proteins), suggesting a model where proteins have replaced RNA structural elements during the evolution of these ribosomes. Despite their lower RNA content they are physically larger than bacterial ribosomes, because of the 'extra' proteins they contain. The extra proteins in mitochondrial ribosomes are 'new' in the sense that they are not homologous to proteins in bacterial or cytoplasmic ribosomes. Some of the new proteins appear to be bifunctional. All of the mammalian MRPs are encoded in nuclear genes (a separate set from those encoding cytoplasmic ribosomal proteins) which are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system.

Escherichia coli↗
PubMed1983

Adherence of gram-negative uropathogens to human uroepithelial cells.

The adherence of several gram-negative uropathogens to human uroepithelial cells was examined with scanning and transmission electron microscopy, and in vitro adhesion assays. The bacteria studied demonstrated different extracellular structures: fimbria and glycocalyx. Human uroepithelial cells were obtained from a bladder tumor cell line (T-24) and from different groups of patients, including those with no history of urinary tract infection (controls), recurrent urinary tract infection, acute cystitis and bladder tumors before and after bacillus Calmette-Guerin therapy. Results from these comparative studies showed that bacteria with extracellular structures adhered better than those bacteria without extracellular structures. It also was shown that uroepithelial cells obtained from patients with recurrent urinary tract infection and with acute cystitis were more susceptible to bacterial adherence than the uroepithelial cells of the controls (there were significant increases of 2 to 5-fold in mean adherence in the former 2 groups, p equals 0.015 and 0.002). There was no significant difference in bacterial adherence between the T-24 cells and the bladder tumor cells before bacillus Calmette-Guerin treatment. However, in both groups after treatment with bacillus Calmette-Guerin the mean adherence increased 2 to 4-fold (p equals 3 times 10(-5)). A survey of 29 bladder tumor patients also showed a 5-fold increase in the incidence of acquired urinary tract infection after bacillus Calmette-Guerin therapy. These results reveal a correlation between bacterial adherence and urinary tract infection, and suggest that bacterial adherence to uroepithelial cells depends upon the bacterial extracellular structures and the source of the uroepithelial cells.

BCG Vaccine↗