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PubMed2005

Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis.

Kimchi is a traditional Korean food fermented from a variety of vegetables. We elucidated the microbial community structure of five commercially produced kimchis made from Chinese cabbage by examining culture-independent 16S rRNA gene clone libraries. Most of the clones (347 out of 348) belonged to lactic acid bacteria and included several species of the genera Lactobacillus, Leuconostoc and Weissella. Weissella koreensis was found in all the samples and predominated in three of them (42.6-82%). Leuconostoc gelidum, Leuconostoc gasicomitatum and Lactobacillus sakei were common in the remaining kimchi clone libraries (>34%). The composition of bacterial phylotypes in kimchi varied between samples. Our approach revealed different community structures from those reported in previous culture-dependent studies based on phenotypic identification methods. The culture-independent method used here proved to be efficient and accurate and showed that the bacterial communities in kimchi differ from those in other fermented vegetable foods.

Base Sequence↗
PubMed2001

Structures of bacterial flagellar motors from two FliF-FliG gene fusion mutants.

Flagella purified from Salmonella enterica serovar Typhimurium contain FliG, FliM, and FliN, cytoplasmic proteins that are important in torque generation and switching, and FliF, a transmembrane structural protein. The motor portion of the flagellum (the basal body complex) has a cytoplasmic C ring and a transmembrane M ring. Incubation of purified basal bodies at pH 4.5 removed FliM and FliN but not FliG or FliF. These basal bodies lacked C rings but had intact M rings, suggesting that FliM and FliN are part of the C ring but not a detectable part of the M ring. Incubation of basal bodies at pH 2.5 removed FliG, FliM, and FliN but not FliF. These basal bodies lacked the C ring, and the cytoplasmic face of the M ring was altered, suggesting that FliG makes up at least part of the cytoplasmic face of the M ring. Further insights into FliG were obtained from cells expressing a fusion protein of FliF and FliG. Flagella from these mutants still rotated but cells were not chemotactic. One mutant is a full-length fusion of FliF and FliG; the second mutant has a deletion lacking the last 56 residues of FliF and the first 94 residues of FliG. In the former, C rings appeared complete, but a portion of the M ring was shifted to higher radius. The C-ring-M-ring interaction appeared to be altered. In basal bodies with the fusion-deletion protein, the C ring was smaller in diameter, and one of its domains occupied space vacated by missing portions of FliF and FliG.

Artificial Gene Fusion↗
PubMed1963

The composition and structure of bacterial spores.

The composition of the insoluble "integuments" and soluble "contents" fractions of spores of four Bacillus species of widely differing heat resistance were compared. Electron microscopy of thin sections was also used to determine and compare the morphological structures in the integument preparations. The soluble fractions of the thermophiles, B. coagulans and B. stearothermophilus, had a higher content of hexose and dipicolinic acid. The hexose content of both fractions of the four species was related to heat resistance. Integument fractions consisted chiefly of protein together with variable amounts of the mucopeptide constituents, alpha, epsilon-diaminopimelic acid (DAP) and hexosamine. In the thermophiles the DAP and hexosamine were found chiefly in the insoluble integuments fractions, while in B. cereus and B. subtilis most of this material was soluble. Integument preparations, containing mainly protein with little mucopeptide, consisted chiefly of outer and inner spore coats, while preparations having more mucopeptide contained also residual cortical material and a cortical membrane (possibly the germ cell wall). The results suggest that spore integuments consist of mainly proteinaceous outer and inner coats together with variable amounts of residual cortex and cortical membrane which contain the mucopeptide material.

Amino Acids↗
PubMed1998

Recent Advances in the High Resolution Structures of Bacterial Channels: Gramicidin A.

Gramicidin is a polypeptide antibiotic which forms dimeric channels specific for the transport of monovalent cations across membranes. It adopts several different conformations, most notably double helical (pore) and helical dimer (channels) forms, which have very different structural and functional characteristics. This review focuses on recent high resolution structure determinations of both the pore and channel forms of the molecule by X-ray crystallographic and/or NMR spectroscopic techniques. It discusses the structural consequences of binding ions and the location of ion binding sites and how the structures are related to the conductance properties of the molecule. This relatively simple molecule is probably the best characterized ion channel (both structurally and functionally) and has, to date, been the principal proving-ground for many of our ideas about the molecular nature of ion conduction in membranes. Copyright 1998 Academic Press.

Journal Article↗
PubMed2002

The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.

The initiation of DNA replication is a key event in the cell cycle of all organisms. In bacteria, replication initiation occurs at specific origin sequences that are recognized and processed by an oligomeric complex of the initiator protein DnaA. We have determined the structure of the conserved core of the Aquifex aeolicus DnaA protein to 2.7 A resolution. The protein comprises an AAA+ nucleotide-binding fold linked through a long, helical connector to an all-helical DNA-binding domain. The structure serves as a template for understanding the physical consequences of a variety of DnaA mutations, and conserved motifs in the protein suggest how two critical aspects of origin processing, DNA binding and homo-oligomerization, are mediated. The spatial arrangement of these motifs in DnaA is similar to that of the eukaryotic-like archaeal replication initiation factor Cdc6/Orc1, demonstrating that mechanistic elements of origin processing may be conserved across bacterial, archaeal and eukaryotic domains of life.

Amino Acid Sequence↗
PubMed2005

Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis).

Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats - the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales-related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut.

Animals↗
PubMed2006

Variations of bacterial community structure in flooded paddy soil contaminated with herbicide quinclorac.

The denaturing gradient gel electrophoresis (DGGE) method was applied to determine the relative genetic complexity of microbial communities in flooded paddy soil treated with herbicide quinclorac (3,7-dichloro-8-quinoline-carboylic acid). The results obtained showed a significant effect of quinclorac on the development of bacterial populations in soils contaminated with different concentrations of the herbicide at the early time after application. In general, however, the number of populations of the same soil sample treated with the same concentration of the quinclorac differed obviously with increasing incubation time within the early 8 weeks. The scale of differences in banding patterns-showed that the microbial community structures of the quinclorac-treated and non-quinclorac-treated soils were not significantly different after 21 weeks of incubation. Quantification, as demonstrated in this paper, was studied by establishing dose-response relationships. Significant pattern variations were quantified. Prominent DGGE bands were excised, cloned and sequenced to gain insight into the identities of predominant bacterial populations. The majority of DGGE band sequences were related to bacterial genera Clostridium, Sphingobacterium, Xanthomonas and Rhodococcus.

Bacteria↗
PubMed1996

Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.

Chitin, the second most abundant polysaccharide on earth, is degraded by chitinases and chitobiases. The structure of Serratia marcescens chitobiase has been refined at 1.9 A resolution. The mature protein is folded into four domains and its active site is situated at the C-terminal end of the central (beta alpha)8-barrel. Based on the structure of the complex with the substrate disaccharide chitobiose, we propose an acid-base reaction mechanism, in which only one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction. The structural data lead to the hypothesis that the reaction proceeds with retention of anomeric configuration. The structure allows us to model the catalytic domain of the homologous hexosaminidases to give a structural rationale to pathogenic mutations that underlie Tay-Sachs and Sandhoff disease.

Acetylglucosaminidase↗
PubMed1995

Structure of bacterial flagellar filaments at 11 A resolution: packing of the alpha-helices.

Recent advances in the analysis of electron micrographs of frozen, hydrated bacterial filaments have allowed us to average data from more than 150 images and to reconstruct the bacterial flagellar filament of Salmonella typhimurium at a resolution of approximately 11 A. In addition to the outermost features seen in earlier lower resolution maps of the filament, we find a pair of concentric tubes which surround a approximately A diameter channel at the center of the structure. The walls of these tubes are composed of rod-like features which we have interpreted as columns of individual alpha-helices stacked end-to-end. Each column runs approximately parallel to the helix axis. The wall of the innermost tube, at a radius of approximately 20 A, is formed from 11 such columns. The wall of the second tube is formed from 22 columns which occur alternately at radii of approximately 43 and approximately 47 A. The two concentric tubes are held apart by spacers. These are short, rod-like features, which run approximately parallel to the helix axis. We have interpreted these as additional alpha-helices. By symmetry, each flagellin monomer contributes an alpha-helix to the inner tube, two alpha-helices to the outer tube and a fourth alpha-helix to the spacer. We have tentatively assigned one type of alpha-helix in the outer tube to the approximately 30 C-terminal residues of flagellin while the remaining three alpha-helices are assigned to the approximately 70 N-terminal residues. This interpretation of the reconstruction is consistent with available biochemical, biophysical and amino acid sequence information. We also present details of improved methodology to extract and evaluate the original data and also to assess the statistical significance of features in the three-dimensional map.

Bacterial Proteins↗
PubMed1989

Correlation of paramagnetic states and molecular structure in bacterial photosynthetic reaction centers: the symmetry of the primary electron donor in Rhodopseudomonas viridis and Rhodobacter sphaeroides R-26.

The orientation of the principal axes of the primary electron donor triplet state measured in single crystals of photosynthetic reaction centers is compared to the x-ray structures of the bacteria Rhodobacter (Rb.) sphaeroides R-26 and Rhodopseudomonas (Rps.) viridis. The primary donor of Rps. viridis is significantly different from that of Rb. sphaeroides. The measured directions of the axes indicate that triplet excitation is almost completely localized on the L-subunit half of the dimer in Rps. viridis but is more symmetrically distributed (approximately 63% on the L half of the special pair and approximately 37% on the M half) on the dimeric donor in Rb. sphaeroides R-26. The large reduction of the zero field splitting parameters relative to monomeric bacteriochlorophyll triplet in vitro suggests significant participation of asymmetrical charge transfer electronic configurations in the special pair triplet state of both organisms (approximately 23% in Rps. viridis and approximately 13% in Rb. sphaeroides).

Bacterial Proteins↗
PubMed1990

Layered structure of bacterial aggregates produced in an upflow anaerobic sludge bed and filter reactor.

The ultrastructure of bacterial granules that were maintained in an upflow anaerobic sludge bed and filter reactor was examined. The reactor was fed a sucrose medium, and it was operated at 35 degrees C. Scanning and transmission electron microscopy revealed that the granular aggregates were three-layered structures. The exterior layer of the granule contained a very heterogeneous population that included rods, cocci, and filaments of various sizes. The middle layer consisted of a slightly less heterogeneous population than the exterior layer. A more ordered arrangement, made up predominantly of bacterial rods, was evident in this second layer. The third layer formed the internal core of the granules. It consisted of large numbers of Methanothrix-like cells. Large cavities, indicative of vigorous gas production, were evident in the third layer. On the basis of these ultrastructural results, a model that presents a possible explanation of granule development is offered.

Bacteria↗
PubMed2001

The influence of curli, a MHC-I-binding bacterial surface structure, on macrophage-T cell interactions.

Escherichia coli express thin surface fimbriae called curli which bind soluble matrix proteins and major histocompatibility complex (MHC)-I molecules. The present study addressed the ability of purified curli or curliated E. coli to influence peptide presentation on MHC-I, T cell proliferation and bacterial uptake by macrophages. In vitro studies with curli-proficient E. coli YMel and the isogenic curli-deficient strain YMel-1, both expressing the model antigen Crl-OVA, showed that curli expression by E. coli does not appear to influence the efficiency by which the bacteria are processed by murine macrophages for OVA(257-264) presentation on K(b). Furthermore, curli expression by E. coli did not influence the binding of exogenously added OVA(257-264) peptide to K(b) on the surface of prefixed macrophages. In addition, neither curliated nor non-curliated heat-killed bacteria influenced proliferation of either murine or human T cells stimulated with anti-CD3. Finally, curliated E. coli adhered to and were internalized by macrophages from C57BL/6 and MHC-I-deficient TAP1(-/-) mice equally well. Together these studies show that curli expression by E. coli does not appear to influence phagocytic processing of bacteria expressing Crl-OVA for OVA(257-264)/K(b) presentation, the binding of exogenously added OVA(257-264) to K(b) or T cell proliferation. In addition, although curli expression by E. coli enhances bacterial interaction with macrophages, curli interaction with MHC-I does not significantly contribute to this adherence.

Animals↗
PubMed2002

Structure of bacterial 3beta/17beta-hydroxysteroid dehydrogenase at 1.2 A resolution: a model for multiple steroid recognition.

The enzyme 3beta/17beta-hydroxysteroid dehydrogenase (3beta/17beta-HSD) is a steroid-inducible component of the Gram-negative bacterium Comamonas testosteroni. It catalyzes the reversible reduction/dehydrogenation of the oxo/beta-hydroxy groups at positions 3 and 17 of steroid compounds, including hormones and isobile acids. Crystallographic analysis at 1.2 A resolution reveals the enzyme to have nearly identical subunits that form a tetramer with 222 symmetry. This is one of the largest oligomeric structures refined at this resolution. The subunit consists of a monomer with a single-domain structure built around a seven-stranded beta-sheet flanked by six alpha-helices. The active site contains a Ser-Tyr-Lys triad, typical for short-chain dehydrogenases/reductases (SDR). Despite their highly diverse substrate specificities, SDR members show a close to identical folding pattern architectures and a common catalytic mechanism. In contrast to other SDR apostructures determined, the substrate binding loop is well-defined. Analysis of structure-activity relationships of catalytic cleft residues, docking analysis of substrates and inhibitors, and accessible surface analysis explains how 3beta/17beta-HSD accommodates steroid substrates of different conformations.

17-Hydroxysteroid Dehydrogenases↗
PubMed2005

Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer.

alphabeta-Tubulin heterodimers, from which the microtubules of the cytoskeleton are built, have a complex chaperone-dependent folding pathway. They are thought to be unique to eukaryotes, whereas the homologue FtsZ can be found in bacteria. The exceptions are BtubA and BtubB from Prosthecobacter, which have higher sequence homology to eukaryotic tubulin than to FtsZ. Here we show that some of their properties are different from tubulin, such as weak dimerization and chaperone-independent folding. However, their structure is strikingly similar to tubulin including surface loops, and BtubA/B form tubulin-like protofilaments. Presumably, BtubA/B were transferred from a eukaryotic cell by horizontal gene transfer because their high degree of similarity to eukaryotic genes is unique within the Prosthecobacter genome.

Bacterial Proteins↗
PubMed2003

Crystal structures of bacterial lipoprotein localization factors, LolA and LolB.

Lipoproteins having a lipid-modified cysteine at the N-terminus are localized on either the inner or the outer membrane of Escherichia coli depending on the residue at position 2. Five Lol proteins involved in the sorting and membrane localization of lipoprotein are highly conserved in Gram-negative bacteria. We determined the crystal structures of a periplasmic chaperone, LolA, and an outer membrane lipoprotein receptor, LolB. Despite their dissimilar amino acid sequences, the structures of LolA and LolB are strikingly similar to each other. Both have a hydrophobic cavity consisting of an unclosed beta barrel and an alpha-helical lid. The cavity represents a possible binding site for the lipid moiety of lipoproteins. Detailed structural differences between the two proteins provide significant insights into the molecular mechanisms underlying the energy-independent transfer of lipoproteins from LolA to LolB and from LolB to the outer membrane. Furthermore, the structures of both LolA and LolB determined from different crystal forms revealed the distinct structural dynamics regarding the association and dissociation of lipoproteins. The results are discussed in the context of the current model for the lipoprotein transfer from the inner to the outer membrane through a hydrophilic environment.

Amino Acid Sequence↗
PubMed1985

Formation of HCN by human phagocytosing neutrophils--1. Chlorination of Staphylococcus epidermidis as a source of HCN.

Phagocytosis of Staphylococcus epidermidis by human neutrophils is accompanied by HCN liberation. The amount of HCN evolved is significantly higher when the bacteria are damaged by penicillin. One of the substrates yielding HCN during phagocytosis are N-dichloroglycyl residues of bacterial peptidoglycan formed by the chlorinating myeloperoxidase-H2O2-Cl- system of neutrophils. HCN deriving from the bacterial structures constitutes 6-12% of total HCN liberated during phagocytosis, which indicates that there are other substrates for HCN production. Chlorination process within phagocytosing neutrophils seems to be essential for formation of both, total HCN and that deriving from bacterial structures.

Chlorine↗