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PubMedDate not supplied

Topological and segmental phylogenetic analyses of the anion exchanger (band 3) family of transporters.

Eleven sequenced anion exchanger (AE; band 3) proteins, including five AE1, four AE2 and two AE3 proteins, comprise the anion exchanger family (AEF) of homologous proteins. Eliminating the rat and rabbit proteins that are nearly identical to the corresponding mouse proteins, seven dissimilar members of this family were selected for study, divided into N-terminal, central and C-terminal segments (designated segments 0, 1 and 2, respectively) and analysed separately for sequence similarity and phylogenetic relatedness. Segments 0 are variable in length and sequence, are essentially lacking in some of the members of the AEF, and are not demonstrably homologous in other members of the family. All segments 1 and 2 are homologous, but they exhibit widely differing degrees of sequence divergence. Segments 2 are highly conserved in all AEF proteins. Segments 1 of the AE2 and AE3 proteins are as conserved as are segments 2, but segments 1 of the AE1 proteins have diverged from each other and from the AE2 and AE3 segments 1 much more than have segments 2 of these same proteins. The distributions of various types of amino acid residues in the putative transmembrane helical spanners of the seven dissimilar members of the AEF, based on a modification of the 14-spanner model of Wang et al. (1994) was determined, and this distribution was compared with those of other transmembrane transport proteins of known structure (bacterial rhodopsins, outer membrane porins of Gram-negative bacteria and bacterial photosynthetic reaction centres.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1986

Analysis of the primary structure and promoter function of a pyruvate decarboxylase gene (PDC1) from Saccharomyces cerevisiae.

The PDC1 gene of Saccharomyces cerevisiae, encoding pyruvate decarboxylase was sequenced. The gene contains an open reading frame of 1647 base pairs. The codon usage shows the same strong bias as found for some other glycolytic enzymes. Transcription starts mainly at -30 and terminates 100 base pairs downstream of the termination codon. In some strains a second termination site, 46 base pairs upstream of the stop codon was observed. The function of the promoter region was analyzed by fusion to the bacterial structural gene encoding beta-lactamase (bla). On multicopy plasmid or integrated in the genome, the expression of the bla gene showed the regulation of the authentic PDC1 gene.

Amino Acid Sequence↗
PubMed2006

Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments.

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.

Bacteria↗
PubMed1977

The capsular network of Klebsiella pneumoniae.

Attempts at improving chemical fixation for electron-microscopic observation of the capsule of Klebsiella pneumoniae were made. The capsule was preserved by using alcian blue - lanthanum and tris-(1-aziridinyl) phosphine oxide (TAPO) - aldehyde - osmium procedures. Despite the different retention of the overall capsular material and minor variations in morphological details, in both cases the interpretation of ultrastructural patterns suggested that the capsule be composed of a meshed network of thin polysaccharide fibrils radiating from the cell wall. This organization is in keeping with all recognized chemical properties of bacterial polysaccharide capsules or, at least, does not contradict them. Moreover, an effective preservation of bacterial structures other than capsule has been obtained, mostly in specimens fixed by the TAPO-aldehyde-osmium method, a fact which gives further reliability to the technical approach used for capsule visualization.

Bacteriological Techniques↗
PubMed2006

Lactobacillus paracasei A survives gastrointestinal passage and affects the fecal microbiota of healthy infants.

This study focuses on the potentiality of a putative probiotic strain, Lactobacillus paracasei A, to survive gastrointestinal (GI) passage and modulate the resident microbiota of healthy infants. In a placebo-controlled study, 26 children aged 12-24 months received 100 g/day of either fermented milk containing strain A or pasteurized yogurt for four weeks. Fecal samples were analyzed before starting the administration, after 1, 3 and 4 weeks of consumption and after washout. The fate of strain A was followed by means of a newly developed PCR targeting a strain-specific genomic marker. The composition and dynamics of fecal microbial communities during the study were analyzed by culturing on selective media and by the PCR-denaturing gradient gel electrophoresis (DGGE) technique using universal and group-specific (Lactobacillus and Bifidobacterium) primers. The variation in enzymatic activities in infant feces during probiotic consumption was also analyzed. Strain A survived in fecal samples in most (92%) of the infants examined after 1 week of consumption, and temporarily dominated the intestinal Lactobacillus community. The administration of L. paracasei A led to a significant increment in the Lactobacillus population, while a moderate effect upon the main bacterial groups in the GI ecosystem was observed. Strain A also affected the diversity of the Lactobacillus and Bifidobacterium populations. The fecal bacterial structure of 1 - 2-year-old infants seems to combine neonate and adult-like features. The microbiota of these subjects promptly responded to probiotic consumption, later restoring the endogenous equilibrium.

Cultured Milk Products↗
PubMed1990

Evidence that the capsule around mycobacteria grown in axenic media contains mycobacterial antigens: implications at the level of cell envelope architecture.

The intracellular growth of pathogenic mycobacteria has been linked to the presence of an electron transparent zone (ETZ or capsule), which surrounds the phagocytized bacteria and prevents the diffusion of lysosomal enzymes in infected macrophages. Recently, it was suggested that this capsule may be a bacterial structures, even being present in test tube-grown pathogenic mycobacteria (FEMS Microbiol. Lett. 1988, 56, 225-230). In the present paper, we show that under special fixation and embedding conditions, this capsule was clearly observed among 7 strains of mycobacteria grown in axenic media and also in M. leprae extracted and purified from experimentally infected armadillo or nude mice. In the case of bacteria treated likewise but subject to a prior dehydration step, this capsular structure disappeared suggesting its lipidic nature. Ultrathin sections of M. intracellular after immunolabelling showed for the first time that this capsule obtained mycobacterial antigens confirming its mycobacterial origin. It is suggested that the mycobacterial capsule may be formed of inert lipids, in which surface antigens are embedded.

Antigens, Bacterial↗
PubMed2003

Intracellular bacterial biofilm-like pods in urinary tract infections.

Escherichia coli entry into the bladder is met with potent innate defenses, including neutrophil influx and epithelial exfoliation. Bacterial subversion of innate responses involves invasion into bladder superficial cells. We discovered that the intracellular bacteria matured into biofilms, creating pod-like bulges on the bladder surface. Pods contained bacteria encased in a polysaccharide-rich matrix surrounded by a protective shell of uroplakin. Within the biofilm, bacterial structures interacted extensively with the surrounding matrix, and biofilm associated factors had regional variation in expression. The discovery of intracellular biofilm-like pods explains how bladder infections can persist in the face of robust host defenses.

Adhesins, Bacterial↗
PubMed1997

The limits of life on Earth and searching for life on Mars.

Considerations of basic properties of bacteria such as size, structure, and metabolic versatility allow one to understand how these remarkable life-forms are so adaptable to environments previously thought to be uninhabitable. It is now appreciated that bacteria on Earth can utilize almost any redox couple that yields energy, taking advantage of this energy, while transforming the elements during metabolism. The ability to grow at the expense of inorganic redox couples allows the microbes to occupy niches not available to the more metabolically constrained eukaryotes. Furthermore, the simplicity of the bacterial structure allows them considerably more resistance to environmental variables (pH, salinity, temperature) that are toxic or lethal to more complex organisms. This information can be used to explain the predominance of prokaryotes in extreme environments on Earth, and to speculate as to simple types of metabolism and biogeochemical cycles that may exist on this planet, Mars, and perhaps other non-Earth environments.

Adenosine Triphosphate↗
PubMed1998

Structure and function of bacterial cytochrome c oxidase.

The crystal structure of cytochrome c oxidase from the soil bacterium Paracoccus denitrificans has been reported. This structure has provided a basis for understanding the mechanism of the redox-coupled transmembrane proton pump which is the key component of the respiratory chain in most aerobic organism. Over the past ten years, there have been many site-directed mutagenesis studies performed on bacterial oxidases. Structural features of Paracoccus oxidase have been summarized in the light of these mutagenesis studies and other structural works.

Bacterial Proteins↗
PubMed1989

Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.

The structure of isocitrate dehydrogenase [threo-DS-isocitrate: NADP+ oxidoreductase (decarboxylating), EC 1.1.1.42] from Escherichia coli has been solved and refined at 2.5 A resolution and is topologically different from that of any other dehydrogenase. This enzyme, a dimer of identical 416-residue subunits, is inactivated by phosphorylation at Ser-113, which lies at the edge of an interdomain pocket that also contains many residues conserved between isocitrate dehydrogenase and isopropylmalate dehydrogenase. Isocitrate dehydrogenase contains an unusual clasp-like domain in which both polypeptide chains in the dimer interlock. Based on the structure of isocitrate dehydrogenase and conservation with isopropylmalate dehydrogenase, we suggest that the active site lies in an interdomain pocket close to the phosphorylation site.

3-Isopropylmalate Dehydrogenase↗
PubMed2003

Crystal structure of a bacterial endospore coat component. A laccase with enhanced thermostability properties.

Endospores produced by the Gram-positive soil bacterium Bacillus subtilis are shielded by a proteinaceous coat formed by over 30 structural components, which self-assemble into a lamellar inner coat and a thicker striated electrodense outer coat. The 65-kDa CotA protein is an abundant component of the outer coat layer. CotA is a highly thermostable laccase, assembly of which into the coat is required for spore resistance against hydrogen peroxide and UV light. Here, we report the structure of CotA at 1.7-A resolution, as determined by x-ray crystallography. This is the first structure of an endospore coat component, and also the first structure of a bacterial laccase. The overall fold of CotA comprises three cupredoxin-like domains and includes one mononuclear and one trinuclear copper center. This arrangement is similar to that of other multicopper oxidases and most similar to that of the copper tolerance protein CueO of Escherichia coli. However, the three cupredoxin domains in CotA are further linked by external interdomain loops, which increase the packing level of the structure. We propose that these interdomain loops contribute to the remarkable thermostability of the enzyme, but our results suggest that additional factors are likely to play a role. Comparisons with the structure of other monomeric multicopper oxidases containing four copper atoms suggest that CotA may accept the largest substrates of any known laccase. Moreover, and unlike other laccases, CotA appears to have a flexible lidlike region close to the substrate-binding site that may mediate substrate accessibility. The implications of these findings for the properties of CotA, its assembly and the properties of the bacterial spore coat structure are discussed.

Amino Acid Sequence↗
PubMed2003

Interaction of nutrient limitation and protozoan grazing determines the phenotypic structure of a bacterial community.

We examined the impact of nutrient conditions (carbon and phosphorus limitation) and grazing by protozoans on the phenotypic community structure of freshwater bacteria in continuous culture systems. Lakewater bacteria were grown on mineral medium, which was supplemented with glucose and amino acids and adjusted by different phosphorus concentrations to achieve either carbon or phosphorus limitation. Each nutrient treatment was inoculated with the same bacterial community and consisted of a nongrazing and a grazing treatment, to which the heterotrophic nanoflagellates Spumella sp. and Ochromonas sp. were added. We found that nutrient conditions alone resulted in differences in the phenotypic structure of the bacterial community: small and motile bacteria dominated under C limitation while large, elongated, and capsulated bacteria were characteristic for P limitation. The genotypic community composition as measured by T-RFLP (terminal restriction fragment length polymorphism) was not severely influenced by the two nutrient treatments. In the presence of flagellate predators, grazing-resistant bacteria developed under both nutrient conditions, but with different survival mechanisms: highly motile bacteria prevailed under C limitation, whereas the P-limited grazing treatment was dominated by filamentous forms. T-RFLP analysis revealed only moderate changes in bacterial community composition due to grazing, which were most pronounced under P limitation. Analysis by video microscopy revealed that high swimming speed is an efficient nonmorphological survival mechanism for bacteria to reduce the capture success of the flagellate predator. The rejection of optimal-sized, nonmotile bacteria under P limitation suggests the importance of other nonmorphological, surface-located cell properties. Our results illustrate that the realized mechanisms of grazing resistance are linked to the actual limitation conditions, and that the combined effects of nutrient limitation and grazing are major determinants of bacterial community structure.

Animals↗
PubMed2006

Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.

Construction and microscopic imaging of protein fusions to green fluorescent protein (GFP) have revolutionised our understanding of bacterial structure and function. We have undertaken a systematic study of the localisation of over 100 Bacillus subtilis proteins, following the development of high-throughput construction and analysis procedures. We focused on proteins linked in various ways to the DNA replication machinery, as well as on proteins exemplifying a range of other cellular functions and structures. The results validate the approach as a way of obtaining systematic protein localisation information. They also provide a range of novel biological insights, particularly through the identification of a number of proteins not previously known to be associated with the DNA replication factory.

Bacillus subtilis↗
PubMed2006

Codon usage domains over bacterial chromosomes.

The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context.

Amino Acids↗
PubMed2001

Structural basis of bacterial photosynthetic reaction centers.

The photosynthetic reaction center (RC) is the first membrane protein whose three-dimensional structure was revealed at the atomic level by X-ray crystallograph more than fifteen years ago. Structural information about RC made a great contribution to the understanding of the reaction mechanism of the complicated membrane protein complex. High-resolution structures of RCs from three photosynthetic bacteria are now available, namely, those from two mesophilic purple non-sulfur bacteria, Blastochloris viridis and Rhodobacter sphaeroides, and that from a thermophilic purple sulfur bacterium, Thermochromatium tepidum. In addition, a variety of structural studies, mainly by X-ray crystallography, are still being performed to give more detailed insight into the reaction mechanism of this membrane protein. This review deals with structural studies of bacterial RC complexes, and a discussion about the electron transfer reaction between RCs and electron donors is the main focus out of several topics addressed by these structural studies. The structural data from three RCs and their electron donors provided reliable models for molecular recognition in the primary step of bacterial photosynthesis.

Bacterial Proteins↗
PubMed1984

Pathogenic synergy: mixed intra-abdominal infections.

In this article we review our researches into the pathogenesis of mixed infections. These may conveniently be divided into in vitro and in vivo studies. In vitro we confirmed that interference with the killing of aerobes by polymorphonuclear leucocytes (PMN's) is a property of the Bacteroides strains tested and appears to depend on competition for opsonins i.e. complement factors. Further studies are in progress to define which complement factors and which bacterial structures are involved. The influence of B. fragilis on chemotaxis has also been studied. Our preliminary data suggest that B. fragilis is itself poorly chemotactic and reduces the chemoattractivity of Proteus mirabilis. This observation is surprising when we consider that abscess formation is the hall-mark of B. fragilis infections and needs clarification. In vivo we have developed a skin infection model in mice which is economical and gives reproducible and quantitative results. In this model we have demonstrated pathogenic synergy between Escherichia coli and B. fragilis. Further studies are planned to assess the role of complement and bacterial factors in this in vivo synergy.

Animals↗
PubMed1985

Mechanisms of bacterial virulence.

In this review the nature of prokaryotic parasites was first discussed with emphasis on the evolution of virulence. Subsequently, nonspecific mechanisms of host defense were considered with emphasis on recent findings relating to bacterial killing by serum and professional phagocytes. Based on this background, the nature of virulence factors required for growth of pathogens in the nonimmune host was considered. Strategies used by extracellular and intracellular parasites were compared. It is evident from the resulting overview of experimental findings that knowledge concerning virulence of extracellular parasites outweighs that collected for both facultative and obligate intracellular parasites. Remaining problems regarding extracellular parasitism include precise resolution of the nature of serum resistance, pilus-independent adhesion, tissue invasiveness, and resistance to phagocytosis. Solutions to these questions will probably arise during the course of studies primarily emphasizing bacterial structure and function. Unresolved problems concerning intracellular parasites include definition of regulatory changes involved in adaptation for intra- and extracellular growth, the nature of reactions preventing phagosome-lysosome fusion, mechanisms of survival within phagolysosomes, and explanations for host-cell dependence. These topics provide real problems in cellular and molecular biology, and they will probably be resolved by those familiar with these disciplines. The ability of parasitic prokaryotes to shut off otherwise effective specific immune responses was shown to cross phenotypic lines. Resolution of these somewhat sinister mechanisms of virulence will require an understanding of fundamental immune processes. Further study of bacterial virulence factors will probably provide an understanding of basic cellular processes relevant to other biological disciplines. Indeed, information of this nature may not be obtainable by any other experimental approach.

Adhesiveness↗
PubMed2002

Identification of Cardiobacterium hominis by broad-range bacterial polymerase chain reaction analysis in a case of culture-negative endocarditis.

Culture-negative bacterial endocarditis may be attributed to fastidious microorganisms, prior institution of antibiotic treatment, or both. We describe a case of culture-negative endocarditis in which a modified Steiner stain revealed bacterial structures in the resected heart valve material. Prompted by this finding, broad-range polymerase chain reaction (PCR) amplification of small-subunit ribosomal DNA (16S rDNA) was performed, and Cardiobacterium hominis sequences were detected. This case demonstrates the usefulness of both the Steiner stain and broad-range direct molecular amplification as supplemental diagnostic tools in identification of otherwise unexplained infections.

Coloring Agents↗