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At least 955 records · Page 53Linked to original sources
PubMed1999

Bacterial function and community structure in reactors treating biopolymers and surfactants at mesophilic and thermophilic temperatures.

Microbial communities capable of degrading biopolymers and surfactants typically found in graywater were selected in continuous-flow bioreactors operated at 30, 44, 53, or 62 degrees C. The effect of temperature upon microbial activity and community composition was determined. Microbial respiration of the organic components of the medium (including linear alkylbenzene sulfonate) was detected in samples from each reactor. The microbial community in each reactor was adapted to the operating temperature. Nucleic acid-based analyses of community composition showed that distinct consortia were present at each temperature. Community complexity was inversely related to temperature. The specific maintenance rate was twofold higher at 62 degrees C than at the lower temperatures. Under starvation conditions, microbes in the 62 degrees C system lost membrane integrity 30- to 100-fold faster than microbes at lower temperatures.

Journal Article↗
PubMedDate not supplied

Cereal supplementation modified the fibrolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta.

4 ruminally cannulated cows were fed a forage diet (93% hay + 7% straw) and a mixed diet (33 % hay + 7% straw + 40% barley) in a 2 x 2 crossover experimental design. In sacco degradation of forage, fibrolytic activities (polysaccharidases and glycosidases) of the solid-associated bacteria (SAB), and distribution of the 3 main cellulolytic bacterial species (Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens) were determined for both diets. Barley supplementation decreased the hay degradation rate and mainly the polysaccharidase activities of the SAB (30% on average). The sum of rRNA of the 3 cellulolytic bacterial species represented on average 17% of the total bacterial signal and R. albus was the dominant cellulolytic bacterial species of the 3 studied. Barley supplementation did not modify the proportion of the 3 cellulolytic bacteria attached to plant particles. The negative effect of barley on the ruminal hay degradation rate is due to a decrease in fibrolytic activity of the SAB, and not to a modification of the balance of the three cellulolytic bacterial species examined.

Animal Feed↗
PubMed2005

Mechanism of peptide bond synthesis on the ribosome.

With the emergence of atomic-resolution crystal structures of bacterial ribosomal subunits, major advances in eliciting structure-function relationships of the translation process are underway. Nevertheless, the detailed mechanism of peptide bond synthesis that occurs on the large ribosomal subunit remains unknown. Separate x-ray structures of aminoacyl-tRNA and peptidyl-tRNA analogues bound to the ribosomal A- and P-sites, however, allow for structural modeling of the active complex in catalysis. Here, we combine available structural data to construct such a model of the peptidyl transfer reaction center with bound substrates. Molecular dynamics and free energy perturbation simulations then are used in combination with an empirical valence bond description of the reaction energy surface to examine possible catalytic mechanisms. Already, simulations of the reactant and tetrahedral intermediate states reveal a stable, preorganized H-bond network poised for catalysis. The most favorable mechanism is found not to involve any general acid-base catalysis by ribosomal groups but an intra-reactant proton shuttling via the P-site adenine O2' oxygen, which follows the attack of the A-site alpha-amino group on the P-site ester. The calculated rate enhancement for this mechanism is approximately 10(5), and the catalytic effect is found to be entirely of entropic origin, in accordance with recent experimental data, and is associated with the reduction of solvent reorganization energy rather than with substrate alignment or proximity. This mechanism also explains the inability of 2'-deoxyadenine P-site substrates to promote peptidyl transfer. The observed H-bond network suggests an important structural role of several universally conserved rRNA residues.

Binding Sites↗
PubMed1970

Structure and function of bacterial ribosomes. XI. Dependence of 50S ribosomal assembly on simultaneous assembly of 30S subunits.

Some spectinomycin-resistant mutants of Escherichia coli are cold-sensitive. They are unable to assemble both 30S and 50S ribosomal subunits at low temperatures. They accumulate two kinds of incomplete particles, related to 30S and 50S subunits respectively. A single mutation, causing an alteration in a 30S ribosomal component, is responsible for these phenotypes. These results show that assembly of 50S subunits in vivo is dependent on simultaneous assembly of 30S subunits. On the other hand, the assembly of 30S subunits appears to be independent of 50S assembly.

Bacterial Proteins↗
PubMed1998

Visualization of a slow, ATP-induced structural transition in the bacterial molecular chaperone DnaK.

Recent reports have shown that the binding of ATP to a 70-kDa molecular chaperone induces a rapid global conformational transition from a "high affinity" state to a "low affinity" state, where these states are defined by tight and weak binding to (poly)peptides, respectively. To complete the activity cycle, a chaperone molecule must ultimately return to the high affinity state. In this report, this return to the high affinity state was studied using a chemical cross-linking assay in conjunction with SDS-polyacrylamide gel electrophoresis. The basis for this assay is that in the absence of nucleotide or in the presence of ADP, conditions that stabilize the high affinity state, cross-linking of the Escherichia coli molecular chaperone DnaK yielded two monomeric forms, with apparent molecular masses of 70 kDa (77%) and 90 kDa (23%), whereas cross-linking yielded only the 70-kDa monomeric form in the presence of ATP. This ATP-dependent difference in cross-linking was used to follow the kinetics of the low affinity to high affinity transition under single turnover conditions. The rate of this transition (kobs = 3.4 (+/-0.6) x 10(-4) s-1 at 25 degrees C) is almost identical to the reported rate of ATP hydrolysis (khy = 2.7 (+/-0.7) x 10(-4) s-1 at 22 degrees C). These results are consistent with a two-step sequential reaction where rate-limiting ATP hydrolysis precedes the conformational change. Models for the formation of two cross-linked DnaK monomers in the absence of ATP are discussed.

Adenosine Triphosphate↗
PubMed1999

Structural conservation of the pores of calcium-activated and voltage-gated potassium channels determined by a sea anemone toxin.

The structurally defined sea anemone peptide toxins ShK and BgK potently block the intermediate conductance, Ca(2+)-activated potassium channel IKCa1, a well recognized therapeutic target present in erythrocytes, human T-lymphocytes, and the colon. The well characterized voltage-gated Kv1.3 channel in human T-lymphocytes is also blocked by both peptides, although ShK has a approximately 1,000-fold greater affinity for Kv1.3 than IKCa1. To gain insight into the architecture of the toxin receptor in IKCa1, we used alanine-scanning in combination with mutant cycle analyses to map the ShK-IKCa1 interface, and compared it with the ShK-Kv1.3 interaction surface. ShK uses the same five core residues, all clustered around the critical Lys(22), to interact with IKCa1 and Kv1.3, although it relies on a larger number of contacts to stabilize its weaker interactions with IKCa1 than with Kv1.3. The toxin binds to IKCa1 in a region corresponding to the external vestibule of Kv1.3, and the turret and outer pore of the structurally defined bacterial potassium channel, KcsA. Based on the NMR structure of ShK, we deduce the toxin receptor in IKCa1 to have x-y dimensions of approximately 22 A, a diameter of approximately 31 A, and a depth of approximately 8 A; we estimate that the ion selectivity lies approximately 13 A below the outer lip of the toxin receptor. These dimensions are in good agreement with those of the KcsA channel determined from its crystal structure, and the inferred structure of Kv1.3 based on mapping with scorpion toxins. Thus, these distantly related channels exhibit architectural similarities in the outer pore region. This information could facilitate development of specific and potent modulators of the therapeutically important IKCa1 channel.

Amino Acid Sequence↗
PubMed2003

Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-A resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.

Amino Acid Sequence↗
PubMed1988

Reduction of yellow fever virus mouse neurovirulence by immunization with a bacterially synthesized non-structural protein (NS1) fragment.

Part of a yellow fever virus-specified non-structural protein (NS1) was expressed in Escherichia coli as a fusion protein with beta-galactosidase. Immunization of mice with this partially purified NS1-beta-galactosidase fusion protein induced yellow fever virus-specific antibodies and provided some protection against intracerebral challenge with the virus.

Animals↗
PubMed1976

Relationship of structure to function in bacterial endotoxins: serologically cross-reactive components and their effect on protection of mice against some gram-negative infections.

Rabbit antisera were prepared against the heptoseless Re mutants, Salmonella minnesota R595 and S. typhimurium SLI102, as well as against purified R595 glycolipid coated on autologous erythrocytes. The antisera cross-reacted with the endotoxic glycolipids extracted from Re mutants of various bacterial strains, including S. minnesota R595, S. typhimurium SLI102, Escherichia coli D3Im4, E. coli D2If2 and E. coli F515, as shown by passive haemagglutination and gel diffusion tests. The anti-Re sera also cross-reacted with the RESI preparations (a purified 'lipid A' fraction) from the endotoxic lipopolysaccharides of various heterologous smooth Gram-negative bacteria including Serratia marcescens. Psuedomonas fluorescens and E. coli 0127. However, the same antisera failed to protect mice against infection by Gram-negative bacteria such as Klebsiella pneumoniae type II, S. typhi 0901, P. aeruginosa 119 and E. coli. The results suggest that although the lipid moieties of the lipopolysaccharides in the cell wall of Gram-negative bacteria share cross-reactive immunodeterminant groups, these groups may not be accessible to antibody against them.

Animals↗
PubMed2006

Structure and function of bacterial communities emerging from different sources under identical conditions.

The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by "metacommunity processes." A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.

Agriculture↗