Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Bacterial Structures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources
PubMed1989

Poly-beta-hydroxybutyrate/calcium polyphosphate complexes in eukaryotic membranes.

Poly-beta-hydroxybutyrate/calcium polyphosphate (PHB-CaPolyPi) complexes exist as labile quasi-crystalline structures in bacterial plasma membranes. The composition, structure, and distribution of the complex suggest it may play a role in the regulation of intracellular calcium and in calcium signaling. The importance of these functions led to this investigation of the occurrence of PHB-CaPolyPi complexes in eukaryotes. A variety of plant and animal systems were analyzed and all were found to contain PHB associated with CaPolyPi. The intracellular location of the complex in bovine liver was primarily the mitochondria and microsomes, with smaller amounts in the plasma membranes. Eukaryotic PHB had the same narrow range of chain lengths (120-200 subunits) as PHB in bacterial membranes, and was associated with PolyPi of somewhat greater length (170-220) than the bacterial counterpart (130-170).

Animals↗
PubMed1988

Structural homology between virulence-associated bacterial adenylate cyclases.

The primary structure of the calmodulin-sensitive adenylate cyclase toxin from Bacillus anthracis has been determined from the corresponding nucleotide sequence and compared to that of the homologous toxin secreted by Bordetella pertussis. The cya gene of Bacillus anthracis encodes an 800 amino acid (aa) protein beginning with an N-terminal signal peptide. The central part of the B. anthracis adenylate cyclase includes a region of striking homology with the N-terminal part of the B. pertussis enzyme. In this region a particularly well conserved 24-aa peptide and two other less homologous peptides have been identified. These data corroborate the immunological relatedness of the two enzymes and suggest that the two prokaryotic calmodulin-sensitive adenylate cyclases originate from a common ancestor.

Adenylyl Cyclases↗
PubMed2005

Soil bacterial and fungal community structure across a range of unimproved and semi-improved upland grasslands.

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.

Bacteria↗
PubMed2004

Structural insights into chloride and proton-mediated gating of CLC chloride channels.

CLC Cl(-) channels fulfill numerous physiological functions as demonstrated by their involvement in several human genetic diseases. They have an unusual homodimeric architecture in which each subunit forms an individual pore whose open probability is regulated by various physicochemical factors, including voltage, Cl(-) concentration, and pH. The voltage dependence of Torpedo channel CLC-0 is derived probably indirectly from the translocation of a Cl(-) ion through the pore during the opening step. Recent structure determinations of bacterial CLC homologues marked a breakthrough for the structure-function analysis of CLC channels. The structures revealed a complex fold with 18 alpha-helices and two Cl(-) ions per subunit bound in the center of the protein. The side chain of a highly conserved glutamate residue that resides in the putative permeation pathway appears to be a major component of the channel gate. First studies have begun to exploit the bacterial structures as guides for a rational structure-function analysis. These studies confirm that the overall structure seems to be conserved from bacteria to humans. A full understanding of the mechanisms of gating of eukaryotic CLC channels is, however, still lacking.

Animals↗
PubMed2001

Spatiotemporal Stability of an Ammonia-Oxidizing Community in a Nitrogen-Saturated Forest Soil.

Elevated levels of nitrogen input into various terrestrial environments in recent decades have led to increases in soil nitrate production and leaching. However, nitrifying potential and nitrifying activity tend to be highly variable over space and time, making broad-scale estimates of nitrate production difficult. This study investigates whether the high spatiotemporal variation in nitrate production might be explained by differences in the structure of ammonia-oxidizing bacterial communities in nitrogen-saturated coniferous forest soils. The diversity of ammonia-oxidizing bacteria of the b-subgroup Proteobacteria was therefore investigated using two different PCR-based approaches. The first targeted the 16S rRNA gene and involved temporal temperature gradient electrophoresis (TTGE) of specifically amplified PCR products, with subsequent band excision and nucleotide sequence determination. The second approach involved the cloning and sequencing of PCR-amplified amoA gene fragments. All recovered 16S rDNA sequences were closely related to the culture strain Nitrosospira sp. AHB1, which was isolated from an acid soil and is affiliated with Nitrosospira cluster 2, a sequence group previously shown to be associated with acid environments. All amoA-like sequences also showed a close affinity with this acid-tolerant Nitrosospira strain, although greater sequence variation could be detected in the amoA analysis. The ammonia-oxidizing bacterial community in the nitrogen-saturated coniferous forest soil was determined to be very stable, showing little variation between different organic layers and throughout the year, despite large differences in the total Bacterial community structure as determined by 16S rDNA DGGE community fingerprinting. These results suggest that environmental heterogeneity affecting ammonia oxidizer numbers and activity, and not ammonia oxidizer community structure, is chiefly responsible for spatial and temporal variation in nitrate production in these acid forest soils.

Journal Article↗
PubMed2003

Expression, purification, crystallization and preliminary crystallographic analysis of Trypanosoma brucei phosphofructokinase.

Phosphofructokinase from Trypanosoma brucei (TbPFK) was purified from a recombinant expression system in Escherichia coli by metal-affinity chromatography via its N-terminal His tag. The yield was 15-20 mg of pure enzyme per litre of culture. M(r) was shown to be 55 585 by mass spectrometry. Crystals suitable for X-ray diffraction analysis were obtained by the hanging-drop method of vapour diffusion with sodium formate as the precipitating agent. Monoclinic crystals of the apoenzyme grew within one week, as did orthorhombic crystals of PFK in the presence of enzymic reaction products or an active-site inhibitor. Initial attempts to solve the structure by molecular replacement with bacterial PFK structures as search models proved unrewarding, but a multiple-copy search with a polyalanine model was successful. In addition, heavy-atom soaking with platinum and mercury has yielded derivatives suitable for X-ray diffraction. A combination of the phase information from the molecular-replacement solution and the heavy-atom derivatives should allow structure solution of TbPFK. The availability of this first eukaryotic PFK structure will be of particular significance for structure-based drug design and will also provide important additional structural evidence for the allosteric control of PFK activity.

Animals↗
PubMed2006

Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy.

Cytidine triphosphate synthetase (CTPS) is a key enzyme in nucleic acid and phospholipid biosynthesis and its activity is increased in certain human cancers, making it a promising drug target. The crystal structure of the synthetase domain of human CTPS, which represents the first structure of a CTPS from an eukaryote, has been determined. The structure is homotetrameric and each active site is formed by three different subunits. Sulfate ions bound to the active sites indicate the positions of phosphate-binding sites for the substrates ATP and UTP and the feedback inhibitor CTP. Together with earlier structures of bacterial CTPS, the human CTPS structure provides an extended understanding of the structure-function relationship of CTPS-family members. The structure also serves as a basis for structure-based design of anti-proliferative inhibitors.

Amino Acid Sequence↗
PubMed1999

Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis.

Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the "microbial loop." To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.

Animals↗
PubMed1999

Structure-function relationships of bacterial endotoxins. Contribution to microbial sepsis.

A substantial body of knowledge has emerged over the past several decades concerning the primary and tertiary, and quaternary structure of endotoxic LPS and their contribution to the pathogenesis of gram-negative sepsis; however, important questions remain. Among them are the precise three-dimensional configuration of the LPS macromolecule and the contribution of the quaternary structure to the ability of these potent microbial factors to interact with host humoral and cellular inflammatory mediator systems. Also remaining to be sufficiently addressed is the relative contribution of endotoxin interactions with the host to the overall manifestation of disease and conditions under which such contributions serve as the pivotal event in determining outcome. The answers to these questions can be expected to provide valuable insights into potential novel therapeutic intervention strategies and approaches that will ultimately reduce both morbidity and mortality in infection from gram-negative microbes.

Animals↗
PubMed1993

Structural studies on the bacterial lyase-resistant tetrasaccharides derived from the antithrombin III-binding site of porcine intestinal heparin.

Three discrete tetrasaccharide structures which are resistant to Flavobacterium heparinase and heparitinases I and II were isolated from porcine intestinal heparin after exhaustive digestion with a mixture of all the above enzymes, and the tri-, tetra-, and penta-sulfated structures were determined by negative ion mode fast atom bombardment mass spectrometry and 500-MHz 1H NMR analysis as delta 4,5GlcA beta 1-4GlcNAc (6-sulfate)alpha 1-4GlcA beta 1-4GlcN(N,3-disulfate), delta 4,5 GlcA beta 1-4GlcNAc(6-sulfate)alpha 1-4GlcA beta 1-4GlcN (N,3,6-trisulfate), and delta 4,5GlcA beta 1-4GlcN (N,6-disulfate)alpha 1-4GlcA beta 1-4GlcN(N,3,6-trisulfate). The three components share the 3-O-sulfated reducing GlcN and the 6-O-sulfated internal GlcN, indicating that they are structural variants derived from the nonreducing portion of the minimal pentasaccharide sequence required for binding to antithrombin III. Isolation of the pentasulfated component has never been reported. Their unexpected resistance to heparitinases I and II indicates that 3-O-sulfation of the reducing GlcN contributes to the resistant nature of these tetrasaccharides to the enzymes. The present study demonstrates that the nonreducing trisaccharide portion of the structural variants of the antithrombin III-binding pentasaccharide sequence can be isolated in tetrasaccharides resistant to heparinase/heparitinases I and II, while the rest of the repeating region is degraded into disaccharide units. The lyase treatment is applicable to evaluation of heparin/heparan sulfate preparations in terms of the presence or absence of the specific structure containing the 3-O-sulfated GlcN representing biosynthetic precursors, intermediates or final products of the binding site.

Animals↗
PubMed1983

The influence of growth media on the morphology and in vitro adherence characteristics of gram-negative urinary pathogens.

We studied the adherence of 3 groups of gram-negative urinary pathogens, grown in different culture media, to human uroepithelial cells obtained from healthy females (controls) and from female patients with recurrent urinary tract infection, using an in vitro adhesion assay and electron microscopy. Morphologic examination and mannose sensitivity testing of the uropathogens grown in urine showed that they expressed extracellular structures similar to those found in infected urine in vivo. However, the production of various bacterial extracellular structures responsible for adhesion can be enhanced or decreased when the same uropathogens are grown in media other than urine, resulting in an alteration of the mean adherence of the uropathogens to uroepithelial cells. Brain Heart Infusion broth enhances the production of fimbriae, Modified Vogel and Bonner's Medium enhances the production of exopolysaccharides, and yeast nitrogen base decreases the production of both. These studies suggest that bacterial extracellular structures should be examined morphologically prior to in vitro adhesion assays and that urine is the medium of choice for studying the adherence characteristics of various urinary pathogens in vitro.

Adhesiveness↗
PubMed1991

Bacterial endotoxin: molecular relationships between structure and activity.

The significance of endotoxins in bacterial infection and their role as bacterial surface antigens (O antigens) have stimulated investigations into their chemical nature and the mechanisms of their biologic action during the last few decades. This article summarizes some of the recent results and emphasizes structure-activity relationships.

Animals↗
PubMed1995

Structure, function, and evolution of bacterial reverse transcriptase.

The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases. We first discuss a possible structure of bacterial reverse transcriptases on the basis of the known three-dimensional structure of HIV-1 reverse transcriptase, and how such a putative three-dimensional structure is able to recognize a single primer-template RNA molecule to initiate DNA chain elongation from the 2'-OH group of an internal G residue. This reaction leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded DNA) in which a single-stranded DNA branches out from an RNA molecule via a 2',5'-phosphodiester linkage. Second, the mobility of the bacterial retroelements called retrons, responsible for the production of msDNA, are discussed and compared with the mobility of group I and group II introns. Third, the original and evolution of bacterial reverse transcriptases are discussed in light of the question of whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases.

Amino Acid Sequence↗
PubMed1999

Bacterial phosphatidylinositol-specific phospholipase C: structure, function, and interaction with lipids.

The bacterial phosphatidylinositol-specific phospholipase C (PI-PLC) is a small, water-soluble enzyme that cleaves the natural membrane lipids PI, lyso-PI, and glycosyl-PI. The crystal structure, NMR and enzymatic mechanism of bacterial PI-PLCs are reviewed. These enzymes consist of a single domain folded as a (betaalpha)(8)-barrel (TIM barrel), are calcium-independent, and interact weakly with membranes. Sequence similarity among PI-PLCs from different bacterial species is extensive, and includes the residues involved in catalysis. Bacterial PI-PLCs are structurally similar to the catalytic domain of mammalian PI-PLCs. Comparative studies of both prokaryotic and eukaryotic isozymes have proved useful for the identification of distinct regions of the proteins that are structurally and functionally important.

Bacteria↗
PubMed2001

Formation of the glycan chains in the synthesis of bacterial peptidoglycan.

The main structural features of bacterial peptidoglycan are linear glycan chains interlinked by short peptides. The glycan chains are composed of alternating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), all linkages between sugars being beta,1-->4. On the outside of the cytoplasmic membrane, two types of activities are involved in the polymerization of the peptidoglycan monomer unit: glycosyltransferases that catalyze the formation of the linear glycan chains and transpeptidases that catalyze the formation of the peptide cross-bridges. Contrary to the transpeptidation step, for which there is an abundant literature that has been regularly reviewed, the transglycosylation step has been studied to a far lesser extent. The aim of the present review is to summarize and evaluate the molecular and cellullar data concerning the formation of the glycan chains in the synthesis of peptidoglycan. Early work concerned the use of various in vivo and in vitro systems for the study of the polymerization steps, the attachment of newly made material to preexisting peptidoglycan, and the mechanism of action of antibiotics. The synthesis of the glycan chains is catalyzed by the N-terminal glycosyltransferase module of class A high-molecular-mass penicillin-binding proteins and by nonpenicillin-binding monofunctional glycosyltransferases. The multiplicity of these activities in a given organism presumably reflects a variety of in vivo functions. The topological localization of the incorporation of nascent peptidoglycan into the cell wall has revealed that bacteria have at least two peptidoglycan-synthesizing systems: one for septation, the other one for elongation or cell wall thickening. Owing to its location on the outside of the cytoplasmic membrane and its specificity, the transglycosylation step is an interesting target for antibacterials. Glycopeptides and moenomycins are the best studied antibiotics known to interfere with this step. Their mode of action and structure-activity relationships have been extensively studied. Attempts to synthesize other specific transglycosylation inhibitors have recently been made.

Bacteria↗
PubMed2003

Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond.

The dehalogenases make use of fundamentally different strategies to cleave carbon-halogen bonds. The structurally characterized haloalkane dehalogenases, haloacid dehalogenases and 4-chlorobenzoate-coenzyme A dehalogenases use substitution mechanisms that proceed via a covalent aspartyl intermediate. Recent X-ray crystallographic analysis of a haloalcohol dehalogenase and a trans-3-chloroacrylic acid dehalogenase has provided detailed insight into a different intramolecular substitution mechanism and a hydratase-like mechanism, respectively. The available information on the various dehalogenases supports different views on the possible evolutionary origins of their activities.

Bacterial Proteins↗
PubMed1996

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I.

The three-dimensional structure of bacterial sphingomyelinase (SMase) was predicted using a protein fold recognition method; the search of a library of known structures showed that the SMase sequence is highly compatible with the mammalian DNase I structure, which suggested that SMase adopts a structure similar to that of DNase I. The amino acid sequence alignment based on the prediction revealed that, despite the lack of overall sequence similarity (less than 10% identity), those residues of DNase I that are involved in the hydrolysis of the phosphodiester bond, including two histidine residues (His 134 and His 252) of the active center, are conserved in SMase. In addition, a conserved pentapeptide sequence motif was found, which includes two catalytically critical residues, Asp 251 and His 252. A sequence database search showed that the motif is highly specific to mammalian DNase I and bacterial SMase. The functional roles of SMase residues identified by the sequence comparison were consistent with the results from mutant studies. Two Bacillus cereus SMase mutants (H134A and H252A) were constructed by site-directed mutagenesis. They completely abolished their catalytic activity. A model for the SMase-sphingomyelin complex structure was built to investigate how the SMase specifically recognizes its substrate. The model suggested that a set of residues conserved among bacterial SMases, including Trp 28 and Phe 55, might be important in the substrate recognition. The predicted structural similarity and the conservation of the functionally important residues strongly suggest a distant evolutionary relationship between bacterial SMase and mammalian DNase I. These two phosphodiesterases must have acquired the specificity for different substrates in the course of evolution.

Amino Acid Sequence↗
PubMed1994

Reduction of bacterial translocation and intestinal structural alterations by heparin in a murine burn injury model.

Burn injury produces acute gastrointestinal (GI) derangements that may predispose the burn victim to bacterial translocation (BT). We studied the effects of heparin on gastrointestinal (GI) anatomic alterations and BT after 25% and 32% total body surface area (TBSA), full-thickness murine burn injuries. Heparin (100 U/kg) was administered with 1 mL of normal saline (NS) resuscitation solution immediately postburn and 4 hours and 18 hours postburn in volumes of 0.5 mL NS. Mice with 25% TBSA burns treated with heparin maintained small intestine weight, measured 24 hours postburn, and ileal mucosal height was preserved, whereas burned, untreated mice lost organ weight and mucosal height. Bacterial translocation was decreased in mice with 25% TBSA burn injuries treated with heparin (35.0% vs. 10.7%, p < 0.025). After 32% TBSA burn injuries, BT was also decreased in heparin-treated animals (64.3% vs. 31.6%; p < 0.025). Analysis of mixed venous blood gases showed that heparin did not affect the severe metabolic acidosis that follows burn injury in this animal model, indicating that general tissue perfusion was not improved. Heparin administered in the acute postburn period ameliorates GI structural and functional damage in this murine burn model and decreases BT.

Acid-Base Imbalance↗