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PubMed2001

Characterization of flagellum gene families of methanogenic archaea and localization of novel flagellum accessory proteins.

Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species suggests that archaeal flagellar biogenesis is likely mediated by novel components. In this study, a conserved flagellar gene family from each of Methanococcus voltae, Methanococcus maripaludis, Methanococcus thermolithotrophicus, and Methanococcus jannaschii has been characterized. These species possess multiple flagellin genes followed immediately by eight known and supposed flagellar accessory genes, flaCDEFGHIJ. Sequence analyses identified a conserved Walker box A motif in the putative nucleotide binding proteins FlaH and FlaI that may be involved in energy production for flagellin secretion or assembly. Northern blotting studies demonstrated that all the species have abundant polycistronic mRNAs corresponding to some of the structural flagellin genes, and in some cases several flagellar accessory genes were shown to be cotranscribed with the flagellin genes. Cloned flagellar accessory genes of M. voltae were successfully overexpressed as His-tagged proteins in Escherichia coli. These recombinant flagellar accessory proteins were affinity purified and used as antigens to raise polyclonal antibodies for localization studies. Immunoblotting of fractionated M. voltae cells demonstrated that FlaC, FlaD, FlaE, FlaH, and FlaI are all present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. These protein expression data indicate for the first time that the putative flagellar accessory genes of M. voltae, and likely those of other archaeal species, do encode proteins that can be detected in the cell.

Amino Acid Sequence↗
PubMed2006

Three-dimensional structure of the bacterial cell wall peptidoglycan.

The 3D structure of the bacterial peptidoglycan, the major constituent of the cell wall, is one of the most important, yet still unsolved, structural problems in biochemistry. The peptidoglycan comprises alternating N-acetylglucosamine (NAG) and N-acetylmuramic disaccharide (NAM) saccharides, the latter of which has a peptide stem. Adjacent peptide stems are cross-linked by the transpeptidase enzymes of cell wall biosynthesis to provide the cell wall polymer with the structural integrity required by the bacterium. The cell wall and its biosynthetic enzymes are targets of antibiotics. The 3D structure of the cell wall has been elusive because of its complexity and the lack of pure samples. Herein we report the 3D solution structure as determined by NMR of the 2-kDa NAG-NAM(pentapeptide)-NAG-NAM(pentapeptide) synthetic fragment of the cell wall. The glycan backbone of this peptidoglycan forms a right-handed helix with a periodicity of three for the NAG-NAM repeat (per turn of the helix). The first two amino acids of the pentapeptide adopt a limited number of conformations. Based on this structure a model for the bacterial cell wall is proposed.

Amino Acid Sequence↗
PubMed1990

The three-dimensional structure of the bacterial virus MS2.

The structure of the icosahedral bacteriophage MS2 has been determined to 3.3 A resolution by X-ray crystallography. The phase determination involved both molecular replacement at low resolution using a known structure and heavy-atom substitution. The coat protein has no structural similarity to that of any other known RNA virus.

Capsid↗
PubMed2005

Effect of natamycin on the enumeration, genetic structure and composition of bacterial community isolated from soils and soybean rhizosphere.

Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 degrees C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l(-1). Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming units. A natamycin concentration of 50-200 mg l(-1) is required for an efficient control of fungal growth on media in our experimental conditions depending on the soil type. Bacterial community structure was assessed on culturable cells (cells washed from enumeration plates: plate-wash approach) obtained at 12 degrees C from soybean rhizosphere soil by performing Ribosomal Intergenic Spacer Analysis (RISA) fingerprinting. We demonstrate that all natamycin concentrations used alter the structure of the recovered, culturable bacterial community, compared to control without natamycin. Using ARDRA (amplification of the 16S rDNA gene and restriction analysis) genotyping of individual isolates, some differences were observed between the bacterial isolates obtained in the presence or absence of natamycin. Bacterial isolates recovered in the presence of natamycin are more tolerant (maximal growth rate and lag phase) to this compound than those isolated without natamycin, indicating a possible selection of resistant strains. Therefore, high concentration of natamycin cannot be used for isolation of bacterial strains with the aim of studying biodiversity and could bias a selection of strains for practical applications.

Antifungal Agents↗
PubMed2005

Lactoferrin: an important host defence against microbial and viral attack.

The first function attributed to lactoferrin (Lf), an iron binding protein belonging to the non-immune natural defences, was antimicrobial activity that depended on its capacity to sequester iron. Iron-independent microbicidal activities, requiring direct interaction between this cationic protein and microbial surface components, were later demonstrated. Many other anti-microbial and anti-viral functions have since been ascribed to Lf. In mucosal secretions, iron and Lf modulate the motility and aggregation of pathogenic bacteria. Lf inhibits bacterial adhesion on abiotic surfaces through ionic binding to biomaterials, or specific binding to bacterial structures or both. Lf inhibition of bacterial adhesion to host cells requires Lf binding to bacteria and/or host cells. Lf hinders microbial internalization by binding to both glycosaminoglycans and bacterial proteins which can be degraded by Lf-mediated proteolysis. Moreover, Lf internalisation and localisation to the host cell nuclei could modulate bacterial entry into cells through gene regulation. Finally, the capability of Lf to exert antiviral activity, through its binding to host cells and/or viral particles, strengthens the idea that it is an important brick in the mucosal wall, effective against both microbial and viral attacks.

Animals↗
PubMed2001

Bacterial ion channels and their eukaryotic homologues.

Due to the relative ease of obtaining their crystal structures, bacterial ion channels provide a unique opportunity to analyse structure and function of their eukaryotic homologues. This review describes prokaryotic channels whose structures have been determined. These channels are KcsA, a bacterial homologue of eukaryotic potassium channels, MscL, a bacterial mechanosensitive ion channel and ClC0, a prokaryotic homologue of the eukaryotic ClC family of anion-selective channels. General features of their structure and function are described with a special emphasis on the advantages that these channels offer for understanding the properties of their eukaryotic homologues. We present amino-acid sequences of eukaryotic proteins related in their primary sequences to bacterial mechanosensitive channels. The usefulness of bacterial mechanosensitive channels for the studies on general principles of mechanosensation is discussed.

Amino Acid Sequence↗
PubMed1999

Bacterial phylogenetic clusters revealed by genome structure.

Current bacterial taxonomy is mostly based on phenotypic criteria, which may yield misleading interpretations in classification and identification. As a result, bacteria not closely related may be grouped together as a genus or species. For pathogenic bacteria, incorrect classification or misidentification could be disastrous. There is therefore an urgent need for appropriate methodologies to classify bacteria according to phylogeny and corresponding new approaches that permit their rapid and accurate identification. For this purpose, we have devised a strategy enabling us to resolve phylogenetic clusters of bacteria by comparing their genome structures. These structures were revealed by cleaving genomic DNA with the endonuclease I-CeuI, which cuts within the 23S ribosomal DNA (rDNA) sequences, and by mapping the resulting large DNA fragments with pulsed-field gel electrophoresis. We tested this experimental system on two representative bacterial genera: Salmonella and Pasteurella. Among Salmonella spp., I-CeuI mapping revealed virtually indistinguishable genome structures, demonstrating a high degree of structural conservation. Consistent with this, 16S rDNA sequences are also highly conserved among the Salmonella spp. In marked contrast, the Pasteurella strains have very different genome structures among and even within individual species. The divergence of Pasteurella was also reflected in 16S rDNA sequences and far exceeded that seen between Escherichia and Salmonella. Based on this diversity, the Pasteurella haemolytica strains we analyzed could be divided into 14 phylogenetic groups and the Pasteurella multocida strains could be divided into 9 groups. If criteria for defining bacterial species or genera similar to those used for Salmonella and Escherichia coli were applied, the striking phylogenetic diversity would allow bacteria in the currently recognized species of P. multocida and P. haemolytica to be divided into different species, genera, or even higher ranks. On the other hand, strains of Pasteurella ureae and Pasteurella pneumotropica are very similar to those of P. multocida in both genome structure and 16S rDNA sequence and should be regarded as strains within this species. We conclude that large-scale genome structure can be a sensitive indicator of phylogenetic relationships and that, therefore, I-CeuI-based genomic mapping is an efficient tool for probing the phylogenetic status of bacteria.

Base Sequence↗
PubMed2006

Aerobic biological treatment of low-strength synthetic wastewater in membrane-coupled bioreactors: the structure and function of bacterial enrichment cultures as the net growth rate approaches zero.

The goal of the current research was to determine if the stringent nutrient limitation imposed by membrane-coupled bioreactors (MBRs) could be used to force mixed bacterial communities to exhibit a zero net growth rate over an extended time period. Mechanistically, this zero net growth rate could be achieved when the amount of energy available for growth is balanced by the maintenance requirements of the bacterial community. Bench-scale MBRs were fed synthetic feed medium containing gelatin as the major organic substrate. Biomass concentrations initially increased rapidly, but subsequently declined until an asymptote was reached. Leucine aminopeptidase activities concomitantly increased by at least 10-fold, suggesting that bacterial catabolic activity remained high even while growth rates became negligible. In contrast, alpha-glucosidase and heptanoate esterase activities decreased, indicating that the bacterial community specifically adapted to the carbon source in the feed medium. Bacterial community analysis by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments (PCR-DGGE) suggested that the bacterial community structure completely changed from the beginning to the end of each MBR. Excision and nucleotide sequence analysis of prominent PCR-DGGE bands suggested that many of the dominant populations were similar to novel bacterial strains that were previously uncultivated or recently cultivated during studies specifically targeting these novel populations. This research demonstrates that MBRs have substantial practical applications for biological wastewater treatment; in addition, MBRs are a useful tool to study the ecology of slow-growing bacteria.

Bacteria, Aerobic↗
PubMed1998

[Structure of the bacterial cell wall].

The fine structure of the cell walls of Gram-positive and -negative bacteria were determined by electron microscopy with the new technique of freeze substitution method, and analysed the cell wall structure of Staphylococcus aureus in detail. The surface of Staphylococcal cell wall was covered with a fuzzy coat consisting of fine fibers or electron-dence mass. This coat was completely removed after extraction of teichoic acid from the cell wall with trichloroacetic acid treatment, but was not affected by sodium dodecyl sulfate or trypsin treatment. It was suggested that many amount of teichoic acid was located on the surface of the cell wall and less inside the cell wall. The capsule of strain Smith diffuse was assumed to play the role as the barrier protected from the penetration of antibody against teichoic acid.

Cell Wall↗
PubMed2002

Dynamic and clustering model of bacterial chemotaxis receptors: structural basis for signaling and high sensitivity.

Bacterial chemotaxis receptors can detect a small concentration gradient of attractants and repellents in the environment over a wide range of background concentration. The clustering of these receptors to form patches observed in vivo and in vitro has been suspected as a reason for the high sensitivity, and such wide dynamic range is thought to be due to the resetting of the receptor sensitivity threshold by methylation/demethylation of the receptors. However, the mechanisms by which such high sensitivity is achieved and how the methylation/demethylation resets the sensitivity are not well understood. A molecular modeling of an intact bacterial chemotaxis receptor based on the crystal structures of a cytoplasmic domain and a periplasmic domain suggests an interesting clustering of three dimeric receptors and a two-dimensional, close-packed lattice formation of the clusters, where each receptor dimer contacts two other receptor dimers at the cytoplasmic domain and two yet different receptor dimers at the periplasmic domain. This interconnection of the receptors to form a patch of receptor clusters suggests a structural basis for the high sensitivity of the bacterial chemotaxis receptors. Furthermore, we present crystallographic data suggesting that, in contrast to most molecular signaling by conformational changes and/or oligomerization of the signaling molecules, the changes in dynamic property of the receptors on ligand binding or methylation may be the language of the signaling by the chemotaxis receptors. Taken together, the changes of the dynamic property of one receptor propagating mechanically to many others in the receptor patch provides a plausible, simple mechanism for the high sensitivity and the dynamic range of the receptors.

Bacteria↗
PubMed1975

The structure of anaerobic bacterial communities in the hypolimnia of several Michigan lakes.

The structure of bacterial communities, the distribution of sulfide and oxygen, bacteriochlorophyll concentrations, and the temperature profile were determined for the anaerobic hypolimnia of two lakes in southern Michigan. Information from these studies, plus qualitative observations of two other lakes and two ponds over a 4-year period were used to correlate the spatial distribution of the populations, cell size, arrangement of photosynthetic vesicles or lamellae, presence of gas vacuoles or flagella, sulfur deposition, and environmental factors. On the basis of these results, three communities designated as A, B, and C were defined. The upper (A) community consisted of sequentially layered purple sulfur bacteria including two or more of the following genera: Thiopedia, Thiospirillum, Thiocystis, or Chromatium. The middle (B) community consisted of sequential layers of green bacteria from one or more of the following genera: Pelodictyon, Clathrochloris, Chlorochromatium, or Prosthecochloris. The lowest (C)community contained previously unreported gas-vacuolate colorless bacteria 0 to 0.7 m above the sediment. Microstratification (0.1- to 0.2-m layers) of populations was observed within the A and B communities.

Anaerobiosis↗
PubMedDate not supplied

[Structure of an Escherichia coli bacterial suspension].

The structure of bacterial suspensions of Escherichia coli M-17 at the counting concentrations of the cells 10(7), 10(8), 10(9) i/ml and in the temperature range of (18-50) degrees C has been investigated by means of orientational conductometric, electron microscopic and UV-spectroscopic methods. On the basis of experimental relationships of the anisotropy of suspensions electric conductivity upon the intensity of a sinusoidal electric field and relaxation of anisotropy after switching off the field the function of the distribution of bacteria with respect to their sizes was evaluated at different temperatures and concentrations. The conductometric function of bacteria distribution is in a good agreement with the analogous function obtained with the help of the electron microscope. In accordance with the functions the suspension of E. coli contained three kinds of cells: high electronic density, low electronic density bacteria and bacteria aggregates. Relative amounts of every kind of bacteria depended on temperature and concentration of cells. The minimum of bacteria aggregates and maximum of low electronic density cells were obtained in the temperature range of (32-42) degrees C. This fact could be explained by the activation of the transport membrane systems in this temperature range. This hypothesis was confirmed by the UV-spectroscopic method.

Conductometry↗
PubMed2004

Structural biology of bacterial pathogenesis.

Recent years have seen a rapid increase in structural information on proteins implicated in bacterial pathogenesis. The different modes by which bacteria establish contact with their host tissues are exemplified by the structures of bacterial adhesins in complex with their cognate host receptor. A more detailed structural understanding of the various Gram-negative secretion systems has emerged with the determination of the structures of type I and type IV secretion system components, and with the elucidation of the mechanism of fibre formation in the chaperone-usher pathway of pilus biogenesis. Finally, the structures of complexes of secreted virulence factors bound to their host targets have unravelled the mechanisms by which bacterial pathogens exploit cellular processes to their advantage.

Adhesins, Bacterial↗
PubMed2002

Differential recognition of structural details of bacterial lipopeptides by toll-like receptors.

The question which detailed structures of bacterial modulins determine their relative biological activity and respective host cell receptors was examined with synthetic variants of mycoplasmal lipopeptides as model compounds, as well as recombinant outer surface protein A (OspA) of Borrelia burgdorferi and lipoteichoic acid. Mouse fibroblasts bearing genetic deletions of various toll-like receptors (TLR) were the indicator cells to study receptor requirements, primary macrophages served to measure dose response. The following results were obtained: (i) the TLR system discriminates between modulins with three and those with two long-chain fatty acids in their lipid moiety, in that lipopeptides with three fatty acids were recognized by TLR2, whereas those with two long-chain fatty acids and lipoteichoic acid required the additional cooperation with TLR6; (ii) substitution of the free N terminus of mycoplasmal lipopeptides with an acetyl or palmitoyl group decreased the specific activity; (iii) removal of one or both ester-bound fatty acids lowered the specific activity by five orders of magnitude or deleted biological activity; (iv) oxidation of the thioether group lowered the specific activity by at least four orders of magnitude. The implications of these findings for physiological inactivation of lipopeptides and host-bacteria interactions in general are discussed.

Amino Acid Sequence↗
PubMed1994

[Mechanisms of antimicrobial resistance].

Most fundamental differences in the bacterial structure between the gram positive and negative bacteria are whether the organism has the outer membrane. The most essential mechanism of antimicrobial resistance in the gram negative bacteria are the alteration of membrane permeability to antibiotics. The outer membrane can perform as the barrier to prevent the cells from being exposed to antibiotics. On the other hand, the gram positive bacteria need to alternate the antimicrobial targets for reducing their binding affinity with antibiotics, because of defect of the outer membrane. On the basis of the structural difference between gram positive and negative bacteria, the mechanisms of bacterial resistance to beta-lactams, amino glycosides, macrolides, newer quinolones and vancomycin are discussed.

Aminoglycosides↗
PubMed2002

Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates.

Structure determination of bacterial homologues of human disease-related proteins provides an efficient path to understanding the three-dimensional fold of proteins that are associated with human diseases. However, the precise locations of active-site residues are often quite different between bacterial and human versions of an enzyme, creating significant differences in the biological understanding of enzyme homologs. To study this hypothesis, phenylalanine hydroxylase from a bacterial source has been structurally characterized at high resolution and comparison is made to the human analog. The enzyme phenylalanine hydroxylase (PheOH) catalyzes the hydroxylation of l-phenylalanine into l-tyrosine utilizing the cofactors (6R)-l-erythro-5,6,7,8 tetrahydrobiopterin (BH(4)) and molecular oxygen. Previously determined X-ray structures of human and rat PheOH, with a sequence identity of more than 93%, show that these two structures are practically identical. It is thus of interest to compare the structure of the divergent Chromobacterium violaceum phenylalanine hydroxylase (CvPheOH) ( approximately 24% sequence identity overall) to the related human and rat PheOH structures. We have determined crystal structures of CvPheOH to high resolution in the apo-form (no Fe-added), Fe(III)-bound form, and 7,8-dihydro-l-biopterin (7,8-BH(2)) plus Fe(III)-bound form. The bacterial enzyme displays higher activity and thermal melting temperature, and structurally, differences are observed in the N and C termini, and in a loop close to the active-site iron atom.

Amino Acid Sequence↗