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At least 1,063 records · Page 59Linked to original sources
PubMed2002

Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clusters.

Proteins containing Rieske-type [2Fe-2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe-2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X-ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron-histidine bond length of at least 0.1 A upon reduction of two distantly related Rieske-type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P-1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox-dependent structural change may fine tune the protein-protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske-type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells.

Acinetobacter↗
PubMed1988

Size of bacterial ice-nucleation sites measured in situ by radiation inactivation analysis.

Four bacterial species are known to catalyze ice formation at temperatures just below 0 degrees C. To better understand the relationship between the molecular structure of bacterial ice-nucleation site(s) and the quantitative and qualitative features of the ice-nucleation-active phenotype, we determined by gamma-radiation analysis the in situ size of ice-nucleation sites in strains of Pseudomonas syringae and Erwinia herbicola and in Escherichia coli HB101 carrying the plasmid pICE1.1 (containing a 4-kilobase DNA insert from P. syringae that confers ice-nucleation activity). Lyophilized cells of each bacterial strain were irradiated with a flux of gamma radiation from 0 to 10.2 Mrad (1 Mrad = 10(6) J/kg). Differential concentrations of active ice nuclei decreased as a first-order function of radiation dose in all strains as temperature was decreased from -2 degrees C to -14 degrees C in 1 degrees C intervals. Sizes of ice nuclei were calculated from the gamma-radiation flux at which 37% of initial ice nuclei active within each 1 degrees C temperature interval remained. The minimum mass of a functional ice nucleus, active only between -12 degrees C and -13 degrees C, was about 150 kDa for all strains. The size of ice nuclei increased logarithmically with increasing temperature from -12 degrees C to -2 degrees C, where the estimated nucleant mass was 19,000 kDa. The ice nucleant in these three bacterial species may represent an oligomeric structure, composed at least in part of an ice gene product that can self-associate to assume many possible sizes.

Journal Article↗
PubMed1984

Morphological examination of cell surface structures of enterotoxigenic strains of Escherichia coli.

The very fine sinuous K99 pili of enterotoxigenic strains of Escherichia coli can be visualized in shadowed and in negatively stained preparations, especially if the amorphous K30 glycocalyx is not produced, but these very delicate structures cannot be directly resolved in sectioned material. The K99 pili can, however, be thickened by the nonspecific accretion of K30 glycocalyx material, during its condensation as a result of dehydration, to the point where it can be resolved in sectioned material. This visualization is enhanced if the accreted and condensed glycocalyx is stained with ruthenium red. Alternatively and additionally, the K99 pilus can be thickened by the specific accretion of monoclonal antibodies so that it is made visible in sectioned material. The condensation of the hydrated K30 antigen glycocalyx of enterotoxigenic strains of Escherichia coli during dehydration can be prevented by stabilization using specific antibodies so that this capsular glycocalyx structure is identified in sectioned material and is seen in its correct distribution and dimensions. These methods allow the identification and visualization of bacterial surface structures, both in vitro and in vivo, and they provide a useful means of assessing the presence and distribution of these structures at all stages of the bacterial disease and a possible means of assessing their roles in the pathogenic process.

Cell Membrane↗
PubMed1998

Molecular Analysis of Bacterial Communities in a Three-Compartment Granular Activated Sludge System Indicates Community-Level Control by Incompatible Nitrification Processes.

Bacterial community structure and the predominant nitrifying activities and populations in each compartment of a three-compartment activated sludge system were determined. Each compartment was originally inoculated with the same activated sludge community entrapped in polyethylene glycol gel granules, and ammonium nitrogen was supplied to the system in an inorganic salts solution at a rate of 5.0 g of N liter of granular activated sludge-1 day-1. After 150 days of operation, the system was found to comprise a series of sequential nitrifying reactions (K. Noto, T. Ogasawara, Y. Suwa, and T. Sumino, Water Res. 32:769-773, 1998), presumably mediated by different bacterial populations. Activity data showed that all NH4-N was completely oxidized in compartments one and two (approximately half in each), but no significant nitrite oxidation was observed in these compartments. In contrast, all available nitrite was oxidized to nitrate in compartment three. To study the microbial populations and communities in this system, total bacterial DNA isolated from each compartment was analyzed for community structure based on the G+C contents of the component populations. Compartment one showed dominant populations having 50 and 67% G+C contents. Compartment two was similar in structure to compartment one. The bacterial community in compartment three had dominant populations with 62 and 67% G+C contents and retained the 50% G+C content population only at a greatly diminished level. The 50% G+C content population from compartment one hybridized strongly with amo (ammonia monooxygenase) and hao (hydroxylamine oxidoreductase) gene probes from Nitrosomonas europaea. However, the 50% G+C content population from compartment two hybridized strongly with the hao probe but only weakly with the amo probe, suggesting that the predominant ammonia-oxidizing populations in compartments one and two might be different. Since different activities and populations come to dominate in each compartment from an identical inoculum, it appears that the nitrification processes may be somewhat incompatible, resulting in a series of sequential reactions and different communities in this three-compartment system.

Journal Article↗
PubMed1998

Advances in the enzymology of glutamine synthesis.

Meister's proposal of a gamma-glutamyl-P intermediate in the glutamine synthetase reaction set the scene for understanding how the stepwise activation of the carboxyl group greatly increased its susceptibility toward nucleophilic attack and amide bond synthesis. Topics covered in this review include: the discovery of the enzymatic synthesis of glutamine; the role of glutamine synthetase in defining the thermodynamics of ATPases; early isotopic tracer studies of the synthetase reaction; the proposed intermediacy of gamma-glutamyl-phosphate; the mechanism of methionine sulfoximine inhibition; stereochemical mapping of the enzyme's active site; detection of enzyme reaction cycle intermediates; borohydride trapping of gamma-glutamyl-P; positional isotope exchanges catalyzed by glutamine synthetase; regulation of bacterial enzyme; and a brief account of how knowledge of the atomic structure of bacterial glutamine synthetase has clarified ligand binding interactions. Concluding remarks also address how the so-called "Protein Ligase Problem" may be solved by extending the catalytic versatility of carboxyl-group activating enzymes.

Binding Sites↗
PubMed1996

Tn7 transposition as a probe of cis interactions between widely separated (190 kilobases apart) DNA sites in the Escherichia coli chromosome.

We have used the bacterial transposon Tn7 to examine communication between widely separated DNA sites in the Escherichia coli chromosome. Using Tn7 target immunity, a regulatory feature of transposition which influences target selection, we have evaluated (i) how the presence of Tn7 sequences at one DNA site affects Tn7 insertion into another site in the same DNA molecule and (ii) the nucleotide distances over which the two sites are able to communicate. We demonstrate that Tn7 sequences at one chromosomal site act at a distance to inhibit insertion of Tn7 elsewhere in that DNA as far away as 190 kb, reflecting effective long-range cis interactions. We have found that while target immunity is effective over a substantial region of the chromosome, insertion of Tn7 into a more distant site 1.9 Mb away in the same DNA is not inhibited; this observation provides evidence that target immunity relies on DNA spacing. We also find that within the region of the chromosome affected by target immunity, the magnitude of the immune effect is greater at close DNA sites than DNA sites farther away, suggesting that target immunity is distance dependent. We also extend the characterization of the Tn7 end-sequences involved in transposition and target immunity and describe how Tn7 target immunity can be used as a tool for probing bacterial chromosome structure.

Chromosomes, Bacterial↗
PubMed2003

Role of peptidoglycan subtypes in the pathogenesis of bacterial cell wall arthritis.

BACKGROUND: Bacterial cell wall (CW) arthritis develops in susceptible strains of rats after a single intraperitoneal injection of the CW from certain bacterial species, both pathogenic and non-pathogenic. For the development of chronic bacterial CW arthritis, the structure of the bacterial peptidoglycan (PG) has been found to be decisive. OBJECTIVE: To define the role of PG subtypes in the pathogenesis of chronic bacterial CW arthritis. METHOD: Arthritis was induced with CWs of Lactobacillus plantarum, L casei B, L casei C, and L fermentum. Gas chromatography-mass spectrometry was used to measure the presence of CW derived muramic acid in the liver and to determine PG subtypes. CWs were also tested for their resistance to lysozyme in vitro. RESULTS: These results and those published previously indicate that PGs of CWs which induce chronic arthritis, no matter whether they were derived from strains of Streptococcus, Bifidobacterium, Collinsella, or Lactobacillus, all have lysine as the third amino acid of the PG stem peptide, representing PG subtypes A3alpha and A4alpha. Those strains which induce only transient acute arthritis or no arthritis at all do not have lysine in this position, resulting in different PG subtypes. CONCLUSIONS: In vivo degradation of only those PGs with the subtypes A3alpha and A4alpha leads to the occurrence of large CW fragments, which persist in tissue and have good proinflammatory ability. CWs with other PG subtypes, even if they are lysozyme resistant, do not cause chronic arthritis, because the released fragments are not phlogistic. It is emphasised that a variety of microbial components not causing inflammation have been found in animal and human synovial tissue.

Animals↗
PubMed1993

Characterization of a synthetic calmodulin-binding peptide derived from Bacillus anthracis adenylate cyclase.

A 34-amino acid peptide corresponding to residues 532-565 of Bacillus anthracis adenylate cyclase (P532-565), a calmodulin (CaM)-activated enzyme, was synthesized by solid phase method. Although not homologous to any known CaM binding sequence, P532-565 exhibits molecular features characteristic of this class of peptides: a higher proportion of basic and hydrophobic residues, segregated onto the two faces of the alpha-helical structure. Fluorescence measurements and gel retardation analysis showed that P532-565 binds CaM in a Ca(2+)-dependent manner, with a binding energy that represents 80% of the binding energy of the adenylate cyclase-CaM complex. Circular dichroism analysis showed that P532-565 exists in solution as a mixture of random-coil and alpha-helical structures and that trifluoroethanol increases the relative proportion of alpha-helical population. Analysis of proton NMR spectrum in H2O allowed identification of the different amino acid spin systems and complete spectral assignment. The pattern of nuclear Overhauser effect connectivities, intense NN(i,i + 1) and medium range alpha N(i,i + 3) and alpha beta (i,i + 3) indicate the presence of an alpha-helix in the carboxylterminal end (between residues 551 and 563) in fast exchange with extended structures. These data, together with CaM-binding properties of Bordetella pertussis adenylate cyclase, show that despite rather divergent primary structures, the two bacterial enzymes possess similar structural organization of their binding sites for activator protein.

Adenylyl Cyclases↗
PubMed2006

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

Escherichia coli↗
PubMed2003

The structure of the antigenic polysaccharide produced by Eubactrium saburreum T15.

The antigenic polysaccharide was obtained from the cell wall of Eubacterium saburreum strain T15 by trypsin digestion followed by gel permeation and ion-exchange chromatography. Its structure was determined using acid hydrolysis, methylation analysis, and 1D and 2D NMR spectroscopy. It contained L-threo-pent-2-ulose (Xul), D-fucose (Fuc), and D-glycero-D-galacto-heptose (Hep) in 2:3:3 ratio. Methylation analysis indicated an octasaccharide repeating-unit containing five branches. The 1H and 13C signals in NMR spectra of the sugar residues were assigned by COSY, HOHAHA, and HMQC 2D experiments, and the sequence of sugar residues in the repeating unit was determined by NOESY and HMBC experiments. The polysaccharide also contains two O-acetyl groups in the repeating unit, located on the Hep residue. The repeating structure can be written as: [see text for equation]. This is a novel structure in bacterial cell-wall polysaccharides from Gram-positive bacteria.

Carbohydrate Conformation↗
PubMed1996

Characterization of Bacterial Communities from Activated Sludge: Culture-Dependent Numerical Identification Versus In Situ Identification Using Group- and Genus-Specific rRNA-Targeted Oligonucleotide Probes

The structures of bacterial communities were studied in activated sludge samples obtained from the aerobic and anaerobic zones of a wastewater treatment plant showing enhanced phosphorous removal. Samples were analyzed by in situ hybridization with oligonucleotide probes complementary to selected regions of the 16S and 23S ribosomal RNA (rRNA) characteristic for defined phylogenetic entities (genera and larger groups). The microbial community structures revealed by molecular techniques were compared with the compositions of culturable bacterial communities, obtained from the characterization of 255 isolates from tryptone-soy (TS) agar and R2A agar. These isolates were characterized by 89 physiological tests and their cellular fatty acid patterns, and identified. Culture-dependent techniques indicated the following distribution: different Aeromonas spp. (2.7-8.3% on R2A agar; 45.0-63.7% on TS agar), Acinetobacter spp. (5.4-9.0% on R2A agar; 5.0-9.1% on TS agar), Pseudomonas spp. (up to 10% on R2A agar) and Shewanella putrefaciens (up to 3.0% on R2A agar), all members of the gamma subclass of Proteobacteria, were isolated most frequently. The relatively rare isolates of the beta subclass were identified as Acidovorax spp., Alcaligenes spp., and Comamonas spp.. The Gram-positive bacteria (high DNA G+C) were assigned mainly to Arthrobacter spp., Microbacterium spp., and Mycobacterium phlei. In order to assess the in situ abundance of the most frequently isolated genus, Aeromonas, two rRNA-targeted oligonucleotide probes were developed. The two gamma proteobacterial genera Aeromonas and Acinetobacter constituted less than 5% of all bacteria. In situ, Proteobacteria belonging to the beta subclass and high G+C Gram-positive bacteria were dominant. From filamentous bacteria, Sphaerotilus spp. and Leptothrix spp. could be detected occasionally. In addition, one sample contained a high proportion of the morphologically distinct filaments of Microthrix parvicella.

Journal Article↗
PubMed2004

Comparison of atomic force microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods.

Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanometer scale. For AFM, bacterial cells need to be firmly anchored to a substratum surface in order to withstand the friction forces from the silicon nitride tip. Different strategies for the immobilization of bacteria have been described in the literature. This paper compares AFM interaction forces obtained between Klebsiella terrigena and silicon nitride for three commonly used immobilization methods, i.e., mechanical trapping of bacteria in membrane filters, physical adsorption of negatively charged bacteria to a positively charged surface, and glutaraldehyde fixation of bacteria to the tip of the microscope. We have shown that different sample preparation techniques give rise to dissimilar interaction forces. Indeed, the physical adsorption of bacterial cells on modified substrata may promote structural rearrangements in bacterial cell surface structures, while glutaraldehyde treatment was shown to induce physicochemical and mechanical changes on bacterial cell surface properties. In general, mechanical trapping of single bacterial cells in filters appears to be the most reliable method for immobilization.

Bacteria↗
PubMed2000

Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family.

BACKGROUND: L1 is an important primary rRNA-binding protein, as well as a translational repressor that binds mRNA. It was shown that L1 proteins from some bacteria and archaea are functionally interchangeable within the ribosome and in the repression of translation. The crystal structure of bacterial L1 from Thermus thermophilus (TthL1) has previously been determined. RESULTS: We report here the first structure of a ribosomal protein from archaea, L1 from Methanococcus jannaschii (MjaL1). The overall shape of the two-domain molecule differs dramatically from that of its bacterial counterpart (TthL1) because of the different relative orientations of the domains. Two strictly conserved regions of the amino acid sequence, each belonging to one of the domains and positioned close to each other in the interdomain cavity of TthL1, are separated by about 25 A in MjaL1 owing to a significant opening of the structure. These regions are structurally highly conserved and are proposed to be the specific RNA-binding sites. CONCLUSIONS: The unusually high RNA-binding affinity of MjaL1 might be explained by the exposure of its highly conserved regions. The open conformation of MjaL1 is strongly stabilized by nonconserved interdomain interactions and suggests that the closed conformations of L1 (as in TthL1) open upon RNA binding. Comparison of the two L1 protein structures reveals a high conformational variability of this ribosomal protein. Determination of the MjaL1 structure offers an additional variant for fitting the L1 protein into electron-density maps of the 50S ribosomal subunit.

Amino Acid Sequence↗
PubMedDate not supplied

Bacterial active-site serine penicillin-interactive proteins and domains: mechanism, structure, and evolution.

The bacterial active-site serine penicillin-hydrolyzing and penicillin-binding proteins or domains operate by a serine-ester-linked acyl enzyme mechanism similar to that of the peptidases of the trypsin and subtilisin families. On the basis of known primary and tertiary structures, predictive studies support the view that these proteins or domains form a superfamily of evolutionarily related enzymes. Although--depending on the evolutionary distance--they may have very different amino acid sequences and distinct functional characteristics and specificities, they all would have conserved the same unprecedented type of polypeptide scaffolding. When obtained, complete structural information should provide the necessary tools for the rational design of novel types of inactivators of these important enzyme targets.

Acyltransferases↗
PubMed1989

[Three-dimensional reconstruction of bacterial viruses from electron microscopy data. Subjects and methods of study].

The review summarizes the results of the study of the spatial structure of bacterial viruses (phages) whose tails seem to be the most primitive contracting biological mechanism. Data on the spatial molecular rearrangement are important for understanding the processes of biological mobility. The computer and laser techniques used in order to obtain information on the three-dimensional structure of the object under study by its two-dimensional electron-microphotography are presented in the first part of the review. The second deals with application of the above mentioned techniques for the study of various bacterial viruses.

Bacteriophages↗
PubMed2000

Spectroscopic studies of inhibited alcohol dehydrogenase from Thermoanaerobacter brockii: proposed structure for the catalytic intermediate state.

Thermoanaerobacter brockii alcohol dehydrogenase (TbADH) catalyzes the reversible oxidation of secondary alcohols to the corresponding ketones using NADP(+) as the cofactor. The active site of the enzyme contains a zinc ion that is tetrahedrally coordinated by four protein residues. The enzymatic reaction leads to the formation of a ternary enzyme-cofactor-substrate complex; and catalytic hydride ion transfer is believed to take place directly between the substrate and cofactor at the ternary complex. Although crystallographic data of TbADH and other alcohol dehydrogenases as well as their complexes are available, their mode of action remains to be determined. It is firmly established that the zinc ion is essential for catalysis. However, there is no clear agreement about the coordination environment of the metal ion and the competent reaction intermediates during catalysis. We used a combination of X-ray absorption, circular dichroism (CD), and fluorescence spectroscopy, together with structural analysis and modeling studies, to investigate the ternary complexes of TbADH that are bound to a transition-state analogue inhibitor. Our structural and spectroscopic studies indicated that the coordination sphere of the catalytic zinc site in TbADH undergoes conformational changes when it binds the inhibitor and forms a pentacoordinated complex at the zinc ion. These studies provide the first active site structure of bacterial ADH bound to a substrate analogue. Here, we suggest the active site structure of the central intermediate complex and, more specifically, propose the substrate-binding site in TbADH.

Absorptiometry, Photon↗