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PubMed2002

Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics.

The succession of bacterial communities inhabiting the forefield of the Dammaglacier (Switzerland) was investigated in soils ranging in successional age from 0 to 100 years since deglaciation. Overall activity per bacterial cell was estimated by the amount of fluorescein diacetate (FDA) hydrolyzed per DAPI-stained cell, and an index of "opportunism" was determined from the ratio of culturable to total cells (C:T ratio). Ribosomal intergenic spacer analysis (RISA) was used to estimate the richness of dominant phylotypes and to construct rank-abundance plots of the dominant populations. We observed a biphasic trend in specific cellular activity, which exhibited minima in the 0- and 100-year-old soils while a maximum activity per cell was reached in the 70-y soil. On average, the C:T ratio showed the same trend as the specific activity, although we observed some differences between the two sampling transects. RISA revealed a decrease in dominant phylotype richness as successional age increased, and rank-abundance plots indicated that the evenness of the dominant bacterial phylotypes significantly decreased with successional age. The combination of specific cellular activity and C:T ratio results suggested the presence of an r-K continuum of bacteria while RISA showed that richness and evenness of dominant phylotypes decreased with successional age. We conclude that bacterial succession in the glacier forefield was a dynamic process with adaptation to the differing stages of succession occurring on both the individual and community levels.

Bacteria↗
PubMed1990

Architecture of bacterial lipid A in solution. A neutron small-angle scattering study.

The phase structure of isolated bacterial lipid A, the lipid anchor of the lipopolysaccharides of the outer membrane of Gram-negative bacteria, has been investigated by neutron small-angle scattering. The shape of the scattering curves obtained at different H2O/2H2O ratios revealed a lamellar organisation of the lipid A at neutral pH both above and below its main phase temperature (approximately 40-45 degrees C). Analysis of the scattering curves and interpretation of the corresponding thickness distance distribution functions of the lamellar aggregates led to a model in which the lipid A molecules form a bilayer of about 5 nm in thickness. This value for the thickness of the bilayer, as well as the neutron-scattering density profile across the bilayer, can be explained by a molecular model which shows interdigitation of the fatty acid chains of the lipid A.

Hydrogen-Ion Concentration↗
PubMed2003

Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation.

Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.

Bacterial Proteins↗
PubMed2001

Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression.

Flagellin, the structural component of bacterial flagella, is secreted by pathogenic and commensal bacteria. Flagellin activates proinflammatory gene expression in intestinal epithelia. However, only flagellin that contacts basolateral epithelial surfaces is proinflammatory; apical flagellin has no effect. Pathogenic Salmonella, but not commensal Escherichia coli, translocate flagellin across epithelia, thus activating epithelial proinflammatory gene expression. Investigating how epithelia detect flagellin revealed that cell surface expression of Toll-like receptor 5 (TLR5) conferred NF-kappaB gene expression in response to flagellin. The response depended on both extracellular leucine-rich repeats and intracellular Toll/IL-1R homology region of TLR5 as well as the adaptor protein MyD88. Furthermore, immunolocalization and cell surface-selective biotinylation revealed that TLR5 is expressed exclusively on the basolateral surface of intestinal epithelia, thus providing a molecular basis for the polarity of this innate immune response. Thus, detection of flagellin by basolateral TLR5 mediates epithelial-driven inflammatory responses to Salmonella.

Animals↗
PubMed2005

Structure, surface interactions, and compressibility of bacterial S-layers through scanning force microscopy and the surface force apparatus.

Two-dimensional crystalline bacterial surface layers (S-layers) are found in a broad range of bacteria and archaea as the outermost cell envelope component. The self-assembling properties of the S-layers permit them to recrystallize on solid substrates. Beyond their biological interest as S-layers, they are currently used in nanotechnology to build supramolecular structures. Here, the structure of S-layers and the interactions between them are studied through surface force techniques. Scanning force microscopy has been used to study the structure of recrystallized S-layers from Bacillus sphaericus on mica at different 1:1 electrolyte concentrations. They give evidence of the two-dimensional organization of the proteins and reveal small corrugations of the S-layers formed on mica. The lattice parameters of the S-layers were a=b=14 nm, gamma=90 degrees and did not depend on the electrolyte concentration. The interaction forces between recrystallized S-layers on mica were studied with the surface force apparatus as a function of electrolyte concentration. Force measurements show that electrostatic and steric interactions are dominant at long distances. When the S-layers are compressed they exhibit elastic behavior. No adhesion between recrystallized layers takes place. We report for the first time, to our knowledge, the value of the compressibility modulus of the S-layer (0.6 MPa). The compressibility modulus is independent on the electrolyte concentration, although loads of 20 mN m-1 damage the layer locally. Control experiments with denatured S-proteins show similar elastic properties under compression but they exhibit adhesion forces between proteins, which were not observed in recrystallized S-layers.

Bacterial Proteins↗
PubMed1995

Carbohydrate specificity of the Escherichia coli P-pilus papG protein is mediated by its N-terminal part.

The adherence of pyelonephritic Escherichia coli isolates to mammalian host cells is mediated by the P-pili structures on the bacterial surface. The protein constituting the distal part of the pili structure, papG, interacts with glycan receptors on the host cell. Variation in specificity for different glycoconjugates between the isolates, that may reflect variation in host tropism, has been correlated to three different classes of papG. Truncated variants of the class I, II and III papG adhesins were produced as fusion protein in E. coli and analysed for carbohydrate binding. The results showed that both carbohydrate binding and specificity of the papG adhesin resided in a linear part of the N-terminus of the protein.

Adhesins, Escherichia coli↗
PubMed1991

The bacterial porin superfamily: sequence alignment and structure prediction.

The porins of Gram-negative bacteria are responsible for the 'molecular sieve' properties of the outer membrane. They form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Owing to the strong hydrophilicity of their amino acid sequence and the nature of their secondary structure (beta strands), conventional hydropathy methods for predicting membrane topology are useless for this class of protein. The large number of available porin amino acid sequences was exploited to improve the accuracy of the prediction in combination with tools detecting amphipathicity of secondary structure. Using the constraints of beta-sheet structure these porins are predicted to contain 16 membrane-spanning strands, 14 of which are common to the two (enteric and the neisserial) porin subfamilies.

Amino Acid Sequence↗
PubMed1976

Immunochemical studies on bacterial blood group substances. VIII. The structure of oligosaccharides from blood group H-active polysaccharide of Escherichia coli 2B-V.

Blood group H-active polysaccharide has been prepared from "smooth" strain Escherichia coli 2B-V by Freeman's method, alpha-Fucosidase derived from Bacillus fluminans caused the liberation of fucose from this polysaccharide, together with concomitant loss of blood group H activity. The results of quantitative microanalysis, borohydride reduction, the Morgan-Elson reaction and enzymic hydrolysis with betagalactosidase using isolated oligosaccharides obtained by partial acid hydrolysis indicated that the O-specific side chain of the polysaccharide has a pentassaccharide unit which is beta-D-Gal-(1 leads to 3)-D-GalNAc-(1 leads to 3)-D-GalNAc-Fuc with a D-glucose residue bound at some undetermined point on this structure. It was considered that terminal non-reducing fucose of the polysaccharide was liberated by partial acid hydrolysis.

Acetylgalactosamine↗
PubMed2000

Transfer of genetic information from agrobacteria to bacterial and plant cells: membrane and supramembrane structures involved in transfer.

The review deals with the supramembrane and membrane structures involved in the initial contact (attachment) of an agrobacterial cell with a bacterial or plant cell during the transfer of the agrobacterial genetic information. The relationships between the donor cell attachment to the recipient cell surface and the infection and conjugation processes are discussed. Experimental data on the recently found agrobacterial pili and surface protein rhicadhesin, which are involved in the conjugative transfer of the plasmid between agrobacteria, are considered. The role of adhesive and conjugative pili of E. coli in the initial and tight contacts is analyzed in the context of the recently proved similarity between the mechanisms of agrobacterial transformation in plants and conjugative transfer in bacteria. Possible involvement of the pilus in the conjugative transfer of agrobacterial DNA across the membranes of donor and recipient (bacterial and plant) cells is discussed.

Cell Membrane↗
PubMed2002

A proline-rich region with a highly periodic sequence in Streptococcal beta protein adopts the polyproline II structure and is exposed on the bacterial surface.

Proline-rich regions have been identified in many surface proteins of pathogenic streptococci and staphylococci. These regions have been suggested to be located in cell wall-spanning domains and/or to be required for surface expression of the protein. Because little is known about these regions, which are found in extensively studied and biologically important surface proteins, we characterized the proline-rich region in one such protein, the beta protein of group B streptococci. The proline-rich region in beta, designated the XPZ region, has a proline at every third position, and the sequence is highly periodic in other respects. Immunochemical analysis showed that the XPZ region was not associated with the cell wall but was exposed on the bacterial surface. Moreover, characterization of a beta mutant lacking the XPZ region demonstrated that this region was not required for surface expression of the beta protein. Comparison of the XPZ region in different beta proteins showed that it varied in size but always retained the typical sequence periodicity. Circular dichroism spectroscopy indicated that the XPZ region had the structure of a polyproline II helix, an extended and solvent-exposed structure with exactly three residues per turn. Because of the three-residue sequence periodicity in the XPZ region, it is expected to be amphipathic and to have distinct nonpolar and polar surfaces. This study identified a proline-rich structure with unique properties that is exposed on the surface of an important human pathogen.

Amino Acid Sequence↗
PubMed1992

Three-dimensional structure of catalase from Micrococcus lysodeikticus at 1.5 A resolution.

The three-dimensional crystal structure of catalase from Micrococcus lysodeikticus has been solved by multiple isomorphous replacement and refined at 1.5 A resolution. The subunit of the tetrameric molecule of 222 symmetry consists of a single polypeptide chain of about 500 amino acid residues and one haem group. The crystals belong to space group P4(2)2(1)2 with unit cell parameters a = b = 106.7 A, c = 106.3 A, and there is one subunit of the tetramer per asymmetric unit. The amino acid sequence has been tentatively determined by computer graphics model building and comparison with the known three-dimensional structure of beef liver catalase and sequences of several other catalases. The atomic model has been refined by Hendrickson and Konnert's least-squares minimisation against 94,315 reflections between 8 A and 1.5 A. The final model consists of 3,977 non-hydrogen atoms of the protein and haem group, 426 water molecules and one sulphate ion. The secondary and tertiary structures of the bacterial catalase have been analyzed and a comparison with the structure of beef liver catalase has been made.

Amino Acid Sequence↗
PubMed1995

Structural and functional homology between periplasmic bacterial molecular chaperones and small heat shock proteins.

The periplasmic Yersinia pestis molecular chaperone Caf1M belongs to a superfamily of bacterial proteins for one of which (PapD protein of Escherichia coli) the immunoglobulin-like fold was solved by X-ray analysis. The N-terminal domain of Caf1M was found to share a 20% amino acid sequence identity with an inclusion body-associated protein IbpB of Escherichia coli. One of the regions that was compared, was 32 amino acids long, and displayed more than 40% identity, probability of random coincidence was 1.2 x 10(-4). IbpB is involved in a superfamily of small heat shock proteins which fulfil the function of molecular chaperone. On the basis of the revealed homology, an immunoglobulin-like one-domain model of IbpB three-dimensional structure was designed which could be a prototype conformation of sHsp's. The structure suggested is in good agreement with the known experimental data obtained for different members of sHsp's superfamily.

Amino Acid Sequence↗
PubMed1993

Three-dimensional structures of the central regulatory proteins of the bacterial phosphotransferase system, HPr and enzyme IIAglc.

Enzyme IIA and HPr are central regulatory proteins of the bacterial phosphoenolpyruvate:sugar phosphotransferase (PTS) system. Three-dimensional structures of the glucose enzyme IIA domain (IIAglc) and HPr of Bacillus subtilis and Escherichia coli have been studied by both X-ray crystallography and Nuclear Magnetic Resonance (NMR) Spectroscopy. Phosphorylation of HPr of B. subtilis and IIAglc of E. coli have also been characterized by NMR spectroscopy. In addition, the binding interfaces of B. subtilis HPr and IIAglc have been identified from backbone chemical shift changes. This paper reviews these recent advances in the understanding of the three-dimensional structures of HPr and IIAglc and their interaction with each other.

Bacillus subtilis↗
PubMed2002

Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae.

The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

Animals↗
PubMed2005

Crystal structure of the RNA component of bacterial ribonuclease P.

Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 A resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

Catalytic Domain↗
PubMed1992

Zinc, a novel structural element found in the family of bacterial adenylate kinases.

The adk gene from Bacillus stearothermophilus was cloned and overexpressed in Escherichia coli under the control of the lac promoter. The primary structure of B. stearothermophilus adenylate kinase exhibited 76% identity with the enzyme from Bacillus subtilis, 60% identity with the enzyme from Lactococcus lactis, and 42% identity with the enzyme from E. coli. The most striking property of the adenylate kinase from B. stearothermophilus is the presence of a structural zinc atom bound to four cysteines in a zinc finger-like fashion. The ability to coordinate zinc is predicted also for a number of other isoforms of bacterial adenylate kinases. Furthermore, the tightly bound metal ion contributes to the high thermodynamic stability of adenylate kinase from B. stearothermophilus.

Adenylate Kinase↗
PubMed2004

A new form of bacterial movement, dragging of multicellular aggregate structures over solid surfaces, is powered by macrofiber supercoiling.

Growing Bacillus subtilis macrofibers use twist and supercoiling to: power their own self-assembly, join fibers together into multiclonal aggregates, move themselves over solid surfaces, and to drag other structures (cargo) over solid surfaces. The dragging of multiclonal aggregates attached to the ends of growing macrofibers is analyzed here. The linkage between fibers and cargo arose naturally in macrofiber cultures. Dragging was triggered when growing macrofibers became linked to cargo at both of their ends. Such macrofibers supercoiled, reduced their length, and dragged the cargo toward one another. In parallel experiments immobile wire was used in place of cargo at one end of macrofibers that were linked to cargo at the other. The cargo was dragged toward the wire when these fibers supercoiled. To estimate the force required for dragging we determined the dimensions of the cargo, the buoyant density of macrofibers in the growth medium where dragging occurred, the rate and distance over which the aggregate structures were dragged, and the viscosity of the growth medium. Friction resulting from contact with the solid surface over which the structures were dragged was estimated using the measured parameters. The results indicate that the supercoiling tension required to overcome limiting friction must have been approximately 10 nN, while that needed to overcome fluid drag was of the order of 1 nN. These values suggest that only a small fraction of the total power available from macrofiber supercoiling was needed to drive this new form of multicellular bacterial movement.

Bacillus subtilis↗