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PubMed1992

Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters.

In this paper we describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light, stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. In weeks 3 and 4, small differences were detectable in the nutrient level, community structure of heterotrophic bacteria, and thymidine incorporation rate. However, the photosynthetic potential, depth profiles of heterotrophic bacterial community structure, and oxygen microgradients were maintained throughout the incubation period and did not differ between laboratory microcosms and the source ecosystem. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) that had been constructed to degrade mixtures of halo- and alkylbenzoates and -phenols. The GEM survived in the surface sediment at densities of 5 x 10(4) to 5 x 10(5)/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment.

Bacteria↗
PubMed1982

Purification and characterization of a protein from Escherichia coli which forms complexes with superhelical and single-stranded DNAs.

From the cells of an Escherichia coli K-12 strain, a 22,000-dalton protein which has an affinity for the superhelical DNA molecule was purified to apparent homogeneity by monitoring the DNA-binding activity using the filter binding assay. In the sedimentation analysis of the DNA-protein complex, the protein has an affinity for the superhelical or single-stranded DNA molecule but neither for the open-circular nor for the linear DNA molecule. The amino acid composition of the protein resembled those of the other prokaryotic histone-like proteins and also to eukaryotic histones H2A and H2B. The protein precipitated upon heating, which is in contrast to the heat-stable feature of the other histone-like proteins. Furthermore, DNA and RNA syntheses in vitro were not affected by the presence of the protein. In view of these characteristics, this protein may play a role in maintaining the bacterial nucleoid structure.

Bacterial Proteins↗
PubMed1991

Phytochromes and bacterial sensor proteins are related by structural and functional homologies. Hypothesis on phytochrome-mediated signal-transduction.

Phytochrome and bacterial sensor proteins are related by functional and structural homologies. They are both sensors of environmental stimuli and share structural homologies which comprise a domain of about 250 amino acids (about 28 kg.mol-1). This domain is C-terminal in phytochromes and in several bacterial sensor proteins. In both groups of sensors this domain undergoes conformational changes which are caused by the N-terminal part sensing the stimulus. In the case of bacterial sensors, the conformational alteration is, regulated by additional proteins, conferred to a corresponding regulator protein which then acts on transcription. The coincidences between the two groups of sensors are striking enough to assume phytochrome to transduce signals in a way comparable to the bacterial two-component systems.

Amino Acid Sequence↗
PubMed1985

Newer aspects of the chemical structure and biological activity of bacterial endotoxins.

Gram-negative bacteria express at their surface various amphiphiles among which the lipopolysaccharides (endotoxins, O-antigens) have been studied most intensively. Lipopolysaccharides consist of a heteropolysaccharide portion (O-specific chain and core) which is responsible for the O- (and R-) antigenic properties and a covalently bound lipid component, termed lipid A, which contains the endotoxic principle of lipopolysaccharides. The detailed chemical structure of a large number of O-chains and the general architecture of the core oligosaccharide has been established. Recent analyses of the enterobacterial inner core region indicate the presence of a linear trisaccharide of alpha 2.4-linked 3-deoxy-D-manno-2-octulosonic acid (KDO) residues of which only the reducing group is believed to be located in the main core chain. This KDO residue which provides the link between the polysaccharide and the lipid A component appears to be involved in a recently detected ubiquitous immunodeterminant expressed by lipopolysaccharides of various origin. The chemical structure of enterobacterial lipid A's is now known in some detail. Lipid A of Salmonella, Escherichia coli and Proteus consists of a beta 1.6-linked D-glucosamine disaccharide which carries four (R)-3-hydroxytetradecanoyl groups in positions 2, 3, 2' and 3' and two phosphoryl residues in positions 1 and 4'. Up to three of the hydroxy fatty acids (positions 2, 2' and 3') are, at their 3-hydroxyl groups, acylated by non-hydroxylated acyl residues, and to phosphoryl groups non-acylated, nitrogen-containing residues such as 4-amino-4-deoxy-L-arabinopyranose and phosphorylethanolamine may be bound. The hydroxyl group in position 4 of the glucosamine disaccharide is free and that in position 6' serves as the attachment site for KDO (i.e. the polysaccharide component) in lipopolysaccharide. Based on this structure lipid A analogues have been chemically synthesized and analysed for endotoxic activity in vivo and in vitro. In two test systems (pyrogenicity, local Shwartzman reaction) the synthetic part structures exhibited weak or no endotoxic activity, as did a precursor of lipid A biosynthesis which is structurally identical to one of the analogues. In many other systems, however, including lethal toxicity, B-lymphocyte mitogenicity, macrophage activation, induction of cross tolerance, expression of lipid A antigenicity, the synthetic materials were of comparable activity as bacterial free lipid A. These findings support the structural proposals made for lipid A and they prove the previous hypothesis that the endotoxic principle is embedded in lipid A.(ABSTRACT TRUNCATED AT 400 WORDS)

Endotoxins↗
PubMed1997

Interaction of Bartonella henselae with endothelial cells results in bacterial aggregation on the cell surface and the subsequent engulfment and internalisation of the bacterial aggregate by a unique structure, the invasome.

Vascular colonisation by Bartonella henselae may cause vaso-proliferative tumour growth with clumps of bacteria found in close association with proliferating endothelial cells. By using B. henselae-infected human umbilical vein endothelial cells as an in vitro model for endothelial colonisation, we report here on a novel mechanism of cellular invasion by bacteria. First, the leading lamella of endothelial cells establishes cellular contact to sedimented bacteria and mediates bacterial aggregation by rearward transport on the cell surface. Subsequently, the formed bacterial aggregate is engulfed and internalised by a unique host cellular structure, the invasome. Completion of this sequence of events requires 24 hours. Cortical F-actin, intercellular adhesion molecule-1 and phosphotyrosine are highly enriched in the membrane protrusions entrapping the bacterial aggregate. Actin stress fibres, which are anchored to the numerous focal adhesion plaques associated with the invasome structure, are typically found to be twisted around its basal part. The formation of invasomes was found to be inhibited by cytochalasin D but virtually unaffected by nocodazole, colchicine or taxol, indicating that invasome-mediated invasion is an actin-dependent and microtubuli-independent process. Bacterial internalisation via the invasome was consistently observed with several clinical isolates of B. henselae, while a spontaneous mutant obtained from one of these isolates was impaired in invasome-mediated invasion. Instead, this mutant showed increased uptake of bacteria into perinuclear localising phagosomes, suggesting that invasome-formation may interfere with this alternative mechanism of bacterial internalisation. Internalisation via the invasome represents a novel paradigm for the invasion of bacteria into host cells which may serve as a cellular colonisation mechanism in vivo, e.g. on proliferating and migrating endothelial cells during Bartonella-induced vaso-proliferative tumour growth.

Actins↗
PubMed1994

Characterization of the diversity of sulfate-reducing bacteria in soil and mining waste water environments by nucleic acid hybridization techniques.

Nucleic acid hybridization techniques were used to characterize the sulfate-reducing bacterial communities at seven waste water and two soil sites in Canada. Genomic DNA was obtained from liquid enrichment cultures of samples taken from these nine sites. The liquid enrichment protocol favored growth of the sulfate-reducing bacterial component of the communities at these sites. The genomic DNA preparations were analyzed with (i) a specific gene probe aimed at a single genus (Desulfovibrio), (ii) a general 16S rRNA gene probe aimed at all genera of sulfate-reducing bacteria and other bacteria, and (iii) whole genome probes aimed at specific bacteria. This three-pronged approach provided information on the sulfate-reducing bacterial community structures for the nine sites. These were compared with each other and with the sulfate-reducing bacterial communities of western Canadian oil field production waters, studied previously. It was found that there is considerable diversity in the sulfate-reducing bacterial community at each site. Most sulfate-reducing bacteria isolated from distinct sites are genomically different and differ also from sulfate-reducing bacteria found in oil field production waters.

Bacteria↗
PubMed1999

Bacterial meningitis in adults: demonstration of inner ear involvement using high-resolution MRI.

OBJECTIVE: To visualize the sites involved in audiovestibular dysfunction during bacterial meningitis in adults and to relate these findings to the extent of hearing impairment and vestibular dysfunction. BACKGROUND: Hearing impairment is among the most frequent complications of bacterial meningitis. METHODS: High-resolution MRI (HR-MRI) of the inner ear was performed in seven adult patients with hearing loss as a complication of bacterial meningitis. RESULTS: Five patients had unilateral (n = 1) or bilateral (n = 4) contrast enhancement of vestibulocochlear structures. The structures most frequently involved were the cochlear nerve (n = 9), the first cochlear turn (n = 9), the vestibulum (n = 9), and the semicircular canals (n = 7). There was a significant correlation between clinical and MRI findings: all nine ears with cochlear enhancement were deaf (hearing loss >90 dB), whereas none of the five ears with normal MRI findings had hearing losses of more than 90 dB (range, 30 to 70 dB; p = 0.0005). Vestibular dysfunction as revealed clinically and by quantitative vestibular function testing was found in six of seven patients (11 of 14 ears). Five of these patients (nine ears) also demonstrated enhancement of the vestibular organ on high-resolution MRI of the inner ear. CONCLUSIONS: High-resolution MRI can visualize the involvement of vestibulocochlear structures in bacterial meningitis in both cooperative and consciously impaired patients. These findings suggest a correlation between abnormalities on MRI and the extent of cochlear dysfunction.

Adolescent↗
PubMed1982

Lipid A, the lipid component of bacterial lipopolysaccharides: relation of chemical structure to biological activity.

Lipopolysaccharides are integral components of the outer membrane of Gram-negative bacteria and they participate in various membrane functions essential for bacterial growth and survival. Lipopolysaccharides also represent the endotoxins of Gram-negative bacteria and possibly play a role for the pathogenesis and manifestations of bacterial infections. These biological activities are mediated mainly by the lipid component of lipopolysaccharides, termed lipid A. Chemically, lipid A consists of a beta 1, 6-linked D-glucosamine disaccharide which carries substituted phosphoryl groups and a range of D-3-hydroxy and D-3-acyloxyacyl residues, the latter being arranged in a hexagonal dense packing. A number of experimental data allow the conclusion that the highly ordered and compact lipid A structure confers stability to the outer membrane, renders it less permeable to lipophilic molecules and by providing a proper fluidity stabilizes the conformation of biologically active membrane proteins. For endotoxic activities of lipid A the polar substituents of phosphate residues are dispensable. The presence of D-3-hydroxy (or acyloxy) acyl-groups, linked to the glucosamine disaccharide, however, seems to be of importance. Analyses of now available synthetic lipid A analogues are expected to allow a more precise characterization of substructures and conformations required for the expression of physiological functions and endotoxic activities of lipid A.

Chemical Phenomena↗
PubMed2002

X-ray analysis of ribosomes: the static of the dynamic.

This review considers a brief history, comments, and consequences of recent remarkable achievements: X-ray analysis on the level of atomic resolution of structures of bacterial ribosomes, their subunits, and functional complexes.

Bacterial Proteins↗
PubMed2006

Structure of full-length bacterial chitinase containing two fibronectin type III domains revealed by small angle X-ray scattering.

Chitinase A1 (ChiA1) from Bacillus circulans WL-12 consists of an N-terminal catalytic domain, two fibronectin type III domains (FnIIIDs), and a C-terminal chitin-binding domain. The full-length structure of ChiA1 was studied by small angle X-ray scattering. The obtained low-resolution structure showed that ChiA1 is an elongated molecule with a length of approximately 145 A composed of a large globular head and a rod-like tail. Combination with known high-resolution structures of individual ChiA1 domains provided a model of the domain arrangement. In this model, two FnIIIDs connect to each other in an extended rod-like shape without large bending between the FnIIIDs, and contribute largely to the length of ChiA1.

Bacillus↗
PubMed2005

Redox fluctuation structures microbial communities in a wet tropical soil.

Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), "Bacilli," "Clostridia," and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.

Aerobiosis↗
PubMed1984

Three-dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin.

The three-dimensional structure of the fungal serine protease proteinase K has been determined at 3.3 A resolution by single crystal X-ray diffraction analysis. The enzyme crystallizes in the tetragonal space group P4(3)2(1)2 with cell constants a = b = 68.3 A, c = 108.5 A. The asymmetric unit consists of one monomer of 27 000 daltons mol. wt., approximately 50% higher than the so far assumed value of 18 500 daltons. The main chain fold of proteinase K shows a high degree of tertiary homology with the corresponding bacterial subtilisin BPN'. Proteinase K is the second enzyme in this family of serine proteases to be studied by X-ray diffraction, thus confirming the existence of two unrelated families of serine proteases in pro-and eukaryotes.

Bacteria↗
PubMed2002

Biotransformation of phenylurea herbicides by a soil bacterial strain, Arthrobacter sp. N2: structure, ecotoxicity and fate of diuron metabolite with soil fungi.

In order to assess the influence of the aromatic substitution on the ability of a soil bacterial strain, Arthrobacter sp. N2, to degrade phenylurea herbicides, biotransformation assays were performed in mineral medium with resting cells of this soil bacterial strain on three phenylurea herbicides (diuron, chlorotoluron and isoproturon). Each herbicide considered, led to the formation of only one metabolite detected by HPLC analysis. After isolation, the metabolites were identified by NMR and MS, as the corresponding substituted anilines. According to the Microtox test (realized on the bacterium Vibrio fischeri), these metabolites presented non-target toxicity far more important (up to 600 times higher for 4-isopropylaniline) than the parent molecule. For isoproturon and chlorotoluron, the amount of substituted anilines obtained at the end of the biotransformation was very low, whereas the biotransformation of diuron into 3,4-dichloroaniline was almost quantitative. In this last case, the degradation product accumulated in the medium. In soil, other microorganisms are present that might degrade it. So the biotransformation of 3,4-dichloroaniline was then tested with four fungal strains: Aspergillus niger, Beauveria bassiana, Cunninghamella echinulata var. elegans and Mortierella isabellina. The aniline was further transformed with all the microorganisms tested. Only one metabolite was detected by HPLC analysis and after isolation, it was identified to be 3,4-dichloroacetanilide. This acetylated compound led to biological effects less important on V. fischeri than 3,4-dichloroaniline. These results stress the importance of identifying the degradation products to assess the impact of a polluting agent. Indeed, the pollutant may undergo transformation yielding compounds more toxic than the parent molecule.

Arthrobacter↗
PubMed2006

Single plasma membrane K+ channel detection by using dual-color quantum dot labeling.

K+ channels are widely expressed in eukaryotic and prokaryotic cells, where one of their key functions is to set the membrane potential. Many K+ channels are tetramers that share common architectural properties. The crystal structure of bacterial and mammalian K+ channels has been resolved and provides the basis for modeling their three-dimensional structure in different functional states. This wealth of information on K+ channel structure contrasts with the difficulties to visualize single K+ channel proteins in their physiological environment. We describe a method to identify single Ca2+-activated K+ channel molecules in the plasma membrane of migrating cells. Our method is based on dual-color labeling with quantum dots. We show that >90% of the observed quantum dots correspond to single K+ channel proteins. We anticipate that our method can be adopted to label any other ion channel in the plasma membrane on the single molecule level.

Animals↗
PubMed2000

Binding of von Willebrand factor by coagulase-negative staphylococci.

Coagulase-negative staphylococci (CNS) are the most common infectious micro-organisms isolated from prosthetic devices. To determine whether von Willebrand factor (vWF) acts as an adhesin in bacterial recognition, bacterial binding of recombinant vWF (rvWF) was studied. Eleven CNS strains, belonging to S. epidermidis, S. haemolyticus and S. hominis species, bound soluble rvWF, but to a lesser extent than S. aureus. S. epidermidis strain H2-W bound 125I-labelled rvWF in a dose-dependent manner. The binding could be inhibited by unlabelled rvWF and thrombospondin, but not by fibrinogen, vitronectin or the carbohydrates N-acetylgalactoseamine, D-galactose, D-glucose, and D-fucose. Pre-incubation of rvWF with type I collagen and Arg-Gly-Asp-Ser (RGDS) peptides did not inhibit binding, whereas pre-incubation of rvWF with heparin decreased binding significantly. The interaction between CNS and rvWF was sensitive to proteinase treatment of bacterial cells. CNS strains bound to immobilised rvWF an extent greater or equal to the positive control strain S. aureus Cowan I. rvWF binding structures from bacterial cell wall were detected by immunoblot. Cowan I strain had 140-, 90- and 38-kDa binding molecules. S. haemolyticus strain SM131 and S. epidermidis strain H2-W had two (120 and 60 kDa) and five (120, 90, 60, 52 and 38 kDa) binding molecules, respectively. Similar binding structures were formed when cell wall extracts from these strains were incubated with thrombospondin. These results indicate that specific ligand-receptor interaction between CNS and rvWF may contribute to bacterial adhesion and colonisation on biomaterial surfaces. Heparin-binding domains of rvWF might be the crucial regions for bacterial attachment. rvWF and thrombospondin may recognise similar molecules in staphylococcal cell wall extracts.

Bacterial Adhesion↗
PubMed2003

Widespread selection for local RNA secondary structure in coding regions of bacterial genes.

Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5' to the 3' end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.

Computational Biology↗
PubMed2003

Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations.

Batch cultures of aquatic bacteria and dissolved organic matter were used to examine the impact of carbon source concentration on bacterial growth, biomass, growth efficiency, and community composition. An aged concentrate of dissolved organic matter from a humic lake was diluted with organic compound-free artificial lake water to obtain concentrations of dissolved organic carbon (DOC) ranging from 0.04 to 2.53 mM. The bacterial biomass produced in the cultures increased linearly with the DOC concentration, indicating that bacterial biomass production was limited by the supply of carbon. The bacterial growth rate in the exponential growth phase exhibited a hyperbolic response to the DOC concentration, suggesting that the maximum growth rate was constrained by the substrate concentration at low DOC concentrations. Likewise, the bacterial growth efficiency calculated from the production of biomass and CO(2) increased asymptotically from 0.4 to 10.4% with increasing DOC concentration. The compositions of the microbial communities that emerged in the cultures were assessed by separation of PCR-amplified 16S rRNA fragments by denaturing gradient gel electrophoresis. Nonmetric multidimensional scaling of the gel profiles showed that there was a gradual change in the community composition along the DOC gradient; members of the beta subclass of the class Proteobacteria and members of the Cytophaga-Flavobacterium group were well represented at all concentrations, whereas members of the alpha subclass of the Proteobacteria were found exclusively at the lowest carbon concentration. The shift in community composition along the DOC gradient was similar to the patterns of growth efficiency and growth rate. The results suggest that the bacterial growth efficiencies, the rates of bacterial growth, and the compositions of bacterial communities are not constrained by substrate concentrations in most natural waters, with the possible exception of the most oligotrophic environments.

Biomass↗
PubMed1995

Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the GAL1 promoter.

Deletion of the histone H4 N-terminal residues 4-23 decreases activation of the GAL1 promoter as much as 20-fold, while deletion of histone H3 N-terminal residues 4-15 hyperactivates GAL1 approximately 3-fold. In an attempt to understand the mechanisms by which these two different events take place, we have examined the effects of the H4 and H3 lesions on GAL1 chromatin structure. The bacterial dam methylase, which methylates adenine residues of GATC sequences, was used as an in vivo probe for chromatin structure and both indirect end-labeling and ligation mediated PCR (LMPCR) analysis of micrococcal nuclease digestions were used to analyze chromatin in isolated nuclei. We show that while deletions of the H4 and H3 N-termini have similar effects on dam methylase access in the GAL1 coding region, the H4 N-terminal deletion uniquely alters dam access at a region near the TATA element. This change is independent of the transcriptional state of GAL1. In addition, LMPCR analysis of micrococcal nuclease digests of yeast nuclei demonstrate that H4 N-terminal deletion has unique effects on nuclease accessibility in the nucleosomal region upstream of the TATA element. Our results are consistent with the H4 N-terminus mediating activation of GAL1 through its effect on the proximal promoter region near the TATA box. These data also suggest that the H3 N-terminus affects GAL1 hyperactivation through a different promoter element than that affected by H4.

Base Sequence↗