Structure of the peptidogylcan of bacterial cell walls. I.
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Bacteria↗
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Mechanism for transcriptional action of cyclic AMP in Escherichia coli: entry into DNA to disrupt DNA secondary structure.
Binding analysis with purified bacterial receptor distinguishes two structural domains in cyclic AMP (cAMP). The first, the cyclic phosphate and furanose, constitutes a binding domain. This region is bound tightly to the receptor. The rest of cAMP is not bound; the adenine moiety of cAMP is exposed. Unlike binding, activity of cAMP requires the adenine moiety. To be active, cAMP must have in domain II the base adenine--specifically, its Watson--Crick atoms N-1 and N-6. Analysis of indoleacetic acid, a compound able to replace cAMP at the L-arabinose operon, indicates a similar distinction between binding and active domains. To be active, the indole must have substitution (carboxyl or amide) electronically comparable to the cAMP N-1 and N-6. On this basis, we propose a detailed mechanism for action of cAMP (or indoleacetic acid) in Escherichia coli. We propose that the exposed adenine of cAMP enters into the DNA. The adenine's N-1 and N-6 form hydrogen bonds to a thymine in DNA. This interaction destabilizes the DNA. It enhances transcription. Marked similarities indicate an identical mechanism for the steroid hormones in eukaryotes.
Cyclic AMP↗
Expression, purification, and initial structural characterization of YadQ, a bacterial homolog of mammalian ClC chloride channel proteins.
YadQ of Escherichia coli is a homolog of the mammalian chloride channels of the ClC family. The yadQ gene was cloned as a fusion protein with a hexahistidine tag and tobacco etch virus protease site for the removal of the tag. The protein was expressed in the membrane of E. coli and extracted with decylmaltoside. Purification was achieved by metal affinity chromatography followed by cation exchange. Circular dichroism revealed a high alpha-helical content. Size exclusion chromatography suggests that YadQ forms dimers. The similarity in primary, secondary, and quaternary structure and the ability to recombinantly express YadQ in the cell membrane make the protein a good candidate for the structural study of ClC chloride channels.
Amino Acid Sequence↗
Inhibition of the respiratory-linked membrane potential in E. coli membrane vesicles by octapeptin.
Octapeptin is a peptide antibiotic which affects bacterial membrane structure and selective membrane permeability for protons and potassium. The influence of octapeptin on the formation of a membrane potential generated across bacterial vesicles was monitored using the Rb+-valinomycin transport system. Octapeptin inhibited the respiratory-linked generation of membrane potentials formed in the presence of succinate or Asc/PMS. In addition, the antibiotic inhibited [3H]-leucine transport driven either by succinate or Asc/PMS. These studies support the proposal that the antimicrobial activity of octapeptin is due to inhibition of the formation of a membrane potential generated in the presence of appropriate respiratory substrates.
Anti-Bacterial Agents↗
Processing of the AIDA-I precursor: removal of AIDAc and evidence for the outer membrane anchoring as a beta-barrel structure.
The AIDA-I adhesin known to be responsible for the diffuse adherence (DA) phenotype of the diarrhoeagenic Escherichia coli (DAEC) strain 2787 has been shown previously to be synthesized as a precursor protein and to undergo additional C-terminal processing. Here, the C-terminal processing of the AIDA-I precursor and the outer membrane topology of the cleaved C-terminal fragment, AIDAc, were investigated. By isolation of the cleaved AIDAc fragment and N-terminal sequencing, the C-terminal cleavage site was identified between Ser-846 and Ala-847 thereby indicating a molecular mass of 47.5 kDa for AIDAc. The correct processing to AIDA-I and AIDAc in OmpT, OmpP and DegP protease-deficient E. coli strains as well as in avirulent salmonellae and shigellae points to an autocatalytic cleavage mechanism. The cleaved AIDAc was localized in the outer membrane. A leader sequence-AIDAc fusion was efficiently routed to the outer membrane. Analysis by protease digestion, secondary-structure prediction and modelling, by comparison with structurally related bacterial proteins like the IgA1 protease from neisseria, the vacuolating toxin from Helicobacter pylori, and the VirG protein of Shigella flexneri, strongly indicates that AIDAc is present in the outer membrane as a beta-barrel structure.
Adhesins, Escherichia coli↗
Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia.
Application of DNA fingerprinting methods enables the detection of diverse members of soil bacterial consortia, even including those bacteria not yet cultivated. However, extraction and purification of DNA from soil samples without bias is difficult. We compared five different DNA isolation methods and three purification methods for rhizosphere soil samples. Purified DNA extracts were amplified in PCR using universal bacterial primers and the PCR products were analysed with denaturing gradient gel electrophoresis (DGGE) for the visualisation of DNA bands representing dominant bacterial species. Both the isolation and purification methods affected the apparent bacterial community structure of the samples.
Bacteria↗
Potassium channels: structures, models, simulations.
Potassium channels have been studied intensively in terms of the relationship between molecular structure and physiological function. They provide an opportunity to integrate structural and computational studies in order to arrive at an atomic resolution description of mechanism. We review recent progress in K channel structural studies, focussing on the bacterial channel KcsA. Structural studies can be extended via use of computational (i.e. molecular simulation) approaches in order to provide a perspective on aspects of channel function such as permeation, selectivity, block and gating. Results from molecular dynamics simulations are shown to be in good agreement with recent structural studies of KcsA in terms of the interactions of K(+) ions with binding sites within the selectivity filter of the channel, and in revealing the importance of filter flexibility in channel function. We discuss how the KcsA structure may be used as a template for developing structural models of other families of K channels. Progress in this area is explored via two examples: inward rectifier (Kir) and voltage-gated (Kv) potassium channels. A brief account of structural studies of ancillary domains and subunits of K channels is provided.
Amino Acid Sequence↗
Structure, function and evolution of bacterial ferredoxins.
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Amino Acid Sequence↗
Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy.
Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.
Amino Acid Motifs↗
Automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of Lumbricus terrestris L.
An image analysis procedure was developed for bacterial cells after staining with the DNA-intercalating dye 4'-6-diamidino-2-phenylindole (DAPI), and after in situ hybridization with Cy3-labeled, rRNA-targeted oligonucleotide probes. DAPI- and Cy3-images were captured separately from the same scenery with a cooled digital video camera with three CCD chips for the basic colors red (R), green (G) and blue (B). Using the appropriate filter sets, images of DAPI-stained cells were captured with the red channel shut down, while Cy3-stained cells were captured with the green and blue channels shut down. DAPI images and Cy3 images were subsequently merged to produce virtual color (RGB)-images. Processing of all color channels allowed to specifically enumerate DAPI-stained and hybridized bacteria, to measure their cell sizes, to subsequently calculate their biovolumes and to estimate their biomass. Using this procedure, significant differences were detected in bacterial populations in food resources, digestive tract and cast of the earthworm L. terrestris L. In leaves, bacteria were on average ten times more abundant and two times larger than in soil. In the digestive tract of L. terrestris, however, numbers and volumes of bacteria were comparable to those in soil indicating the disruption of cells originating from leaves before arriving in the foregut. Passage through the digestive tract of L. terrestris significantly reduced bacterial populations belonging to the alpha-, beta- and gamma-subdivisions of Proteobacteria. While these populations did not recover during incubation of cast, populations of the delta-subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster of the CFB phylum increased in cast. These results suggest a large impact of passage through the digestive tract of L. terrestris on bacterial community structure and demonstrate the usefulness of our image analysis procedure for the determination of cell sizes and biovolumes and thus biomass of specific bacterial populations in different terrestrial habitats.
Animals↗
A probable new adhesive factor (F42) produced by enterotoxigenic Escherichia coli isolated from pigs.
Three enterotoxigenic Escherichia coli (ETEC) strains (coded 62, 104, and 567/7) isolated from piglets with neonatal diarrhea produced only a thermostable enterotoxin. Although these strains showed mannose-resistant microhemagglutination (MRMH), the responsible factor was serologically different from the known hemagglutinating colonization factors from porcine strains (K88, K99, and F41). Bacterial cells from these strains adhered to HeLa cells and pig brush borders. Electron microscope studies revealed the presence of fimbria-like structures on bacterial cells grown at 37 C but not on cells grown at 18 C. The antiserum prepared from partially purified fimbrial antigen (provisionally called F42) inhibited chicken erythrocyte MRMH caused by these strains as well as adherence of strain 567/7 to HeLa cells and to pig brush borders. These data taken together suggest the existence of a new hemagglutinating adhesin that is different from those so far described for porcine ETEC.
Adhesins, Escherichia coli↗
[Biocenosis of the natural foci of sapronotic infections (the results of 15-year observations)].
The summarized results of original studies, carried out in 1988-2003 by scientists of the Gamaleya Research Institute of Epidemiology and Microbiology, are discussed. The part dealing with the regularity and mechanisms of the circulation of pathogenic bacteria in the biocenosis of soil and water reservoirs includes the following subjects: population and intracellular interactions with protozoa; the evaluation of different representatives of hydrobios as hosts and the transmission along trophic biocenotic chains; the effect of algae and their metabolic products on bacterial populations; the possibility of the colonization of higher plants from the soil and the subsequent infection of rodents; the variability and clonal structure of bacterial population in its interaction with protozoa and plants; the chain of Yersinia circulation in agrocenosis. The part dealing with the mechanisms of the prolonged reservation of causative agents includes such subjects as the reversible transition of bacteria into the latent (uncultivable) state in soils and water reservoirs, as well as the biological inductors of this process; the prolonged preservation of latent bacteria in the cysts of protozoa and blue-green algae; the indication of causative agents in the natural foci of plague and pseudotuberculosis. On the basis of the original investigations and the data of literature new theoretical review in the field of the natural foci and the epidemiology of sapronotic infections have been formulated.
Adaptation, Physiological↗
[Effect of ionizing radiation on the structural and ultrastructural organization of Mycobacterium rubrum].
The structural and ultrastructural organization of Mycobacterium rubrum cells was studied in the course of normal growth and in the conditions of irradiation. The cytomorphological differentiation of the bacterial membrane structure was shown as well as their functional role. Ionizing radiation was used as a tool for revealing the role of the membrane structures; the latter were found to be related to a certain cellular function. Damages of various, individually functioning membrane systems upon the action of ionizing radiation on the cell are described. Mesosomes are absent from the cells if the synthesis of peptidoglycan is inhibited, whereas hypersynthesis of the cell wall material is observed upon their hypertrophy. The content of mitochondrial analogs in the cell increases with the rate of metabolic processes. The function of cellular division is disturbed as a result of damages in the nucleoid DNA structure and degradation of nucleoidosomes. Changes in carbohydrate and lipid metabolism are also observed.
Cell Membrane↗
Genotoxicity of the food colours red 2G and brown FK in bacterial systems; use of structurally-related dyes and azo-reduction.
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Animals↗
Structural flexibility and functional versatility of cytochrome P450 and rapid evolution.
P450 represents a large group of heme-thiolate enzymes that exhibit remarkably diverse activities for the metabolism of numerous endogenous and exogenous chemicals. Recent site-directed mutagenesis studies indicate that a single mutation at any of the key residues can be enough to alter the substrate and/or product specificities in the P450 activities. Molecular modeling predicts that these key residues are located within the substrate heme pocket. Structural elements involved in diversifying P450 activity appear to correspond to the B' helix, the F helix and the F/G interhelical loop in the bacterial P450s. Structures represented by these regions are extremely variable despite the fact that the core of the P450 substrate pocket is well conserved. A mutation within these regions may result in a significant geometrical alteration of the pocket and lead to diversify the P450 activity. Phylogenetical analysis shows a relatively high rate of nonsynonymous substitution within these substrate binding regions. The functional versatility of P450 can thus be largely accounted for in terms of pocket change brought about by rapid mutations.
Animals↗
Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil.
Hydrocarbonoclastic bacterial communities inhabiting mangrove sediments were characterized by combining molecular and culture-dependent approaches. Surface sediments were collected at two sampling sites in Guanabara Bay (Rio de Janeiro, Brazil) and used to inoculate in vitro enrichment cultures containing crude oil to obtain hydrocarbonoclastic bacterial consortia. In parallel, in situ mesocosms (located in the Guapimirim mangrove) were contaminated with petroleum. Comparison of bacterial community structures of the different incubations by T-RFLP analyses showed lower diversity for the enrichment cultures than for mesocosms. To further characterize the bacterial communities, bacterial strains were isolated in media containing hydrocarbon compounds. Analysis of 16S rRNA encoding sequences showed that the isolates were distributed within 12 distinct genera. Some of them were related to bacterial groups already known for their capacity to degrade hydrocarbons (such as Pseudomonas, Marinobacter, Alcanivorax, Microbulbifer, Sphingomonas, Micrococcus, Cellulomonas, Dietzia, and Gordonia groups). Other strains, with high capacity for degrading hydrocarbons (aliphatic or aromatic), were related to isolates from hydrothermal vents that have not been thus far detected in hydrocarbon-contaminated sites, nor described for their ability to grow or degrade petroleum hydrocarbons. Degradation studies showed the ability of Marinobacter, Alcanivorax and Sphingomonas isolates to degrade both PAH and alkane compounds. Our results point out the rich microbial diversity of the mangroves, whose potential for hydrocarbon degradation is promising for future studies on pollutant bioremediation.
Alcanivoraceae↗
Structural mechanism for rifampicin inhibition of bacterial rna polymerase.
Rifampicin (Rif) is one of the most potent and broad spectrum antibiotics against bacterial pathogens and is a key component of anti-tuberculosis therapy, stemming from its inhibition of the bacterial RNA polymerase (RNAP). We determined the crystal structure of Thermus aquaticus core RNAP complexed with Rif. The inhibitor binds in a pocket of the RNAP beta subunit deep within the DNA/RNA channel, but more than 12 A away from the active site. The structure, combined with biochemical results, explains the effects of Rif on RNAP function and indicates that the inhibitor acts by directly blocking the path of the elongating RNA when the transcript becomes 2 to 3 nt in length.
Amino Acid Sequence↗
My daily constitutional in martinsried.
The three-dimensional structures of bacterial reaction centers have served as the framework for much of our understanding of anoxygenic photosynthesis. A key step in the determination of the structure of the reaction center from Rhodobacter sphaeroides was the use the molecular replacement technique. For this technique, we made use of two sets of data. First, X-ray diffraction data had been measured from crystals of the reaction center from R. sphaeroides by our research group in California, led by George Feher and Douglas Rees. The second data set consisted of the coordinates of the three-dimensional structure of the reaction center from Rhodopseudomonas (now Blastochloris) viridis, which had been solved in the pioneering efforts of a group in Martinsried, led by Johann Deisenhofer, Robert Huber and Hartmut Michel. The collaborative efforts of these two groups to determine the structure of the reaction center from R. sphaeroides is described.
Journal Article↗