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PubMed2002

Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation.

A detailed structural analysis has been performed of the outer bacterial membrane of Pseudomonas aeruginosa using a parameterized classical simulation model (R. D. Lins and T. P. Straatsma, Biophysical Journal, 2001, Vol. 81, pp. 1037-1046) with modest modifications. The structural analysis of the membrane is presented and newly discovered characteristics of the membrane are discussed. Simulations indicate that the relative contribution of different ligands to calcium ion coordination varies across the membrane, while maintaining a constant average coordination number of 6.1. Water penetrates the surface of the membrane to a depth of about 30 A. The hydration of ions and phosphate groups is shown to depend on location within the membrane. A measure of saccharide residue orientation is defined and average orientations are presented. Saccharide residues possess varying degrees of motion with a trend of greater mobility at the membrane surface. However, their motion is limited and even in the membrane outer core region the average structure appears fairly rigid over a period of 1 ns.

Calcium↗
PubMed2005

Structure and function of clc channels.

The CLC family comprises a group of integral membrane proteins whose major action is to translocate chloride (Cl-) ions across the cell membranes. Recently, the structures of CLC orthologues from two bacterial species, Salmonella typhimurium and Escherichia coli, were solved, providing the first framework for understanding the operating mechanisms of these molecules. However, most of the previous mechanistic understanding of CLC channels came from electrophysiological studies of a branch of the channel family, the muscle-type CLC channels in vertebrate species. These vertebrate CLC channels were predicted to contain two identical but independent pores, and this hypothesis was confirmed by the solved bacterial CLC structures. The opening and closing of the vertebrate CLC channels are also known to couple to the permeant ions via their binding sites in the ion-permeation pathway. The bacterial CLC structures can probably serve as a structural model to explain the gating-permeation coupling mechanism. However, the CLC-ec1 protein in E. coli was most recently shown to be a Cl- -H+ antiporter, but not an ion channel. The molecular basis to explain the difference between vertebrate and bacterial CLCs, especially the distinction between an ion channel and a transporter, remains a challenge in the structure/function studies for the CLC family.

Animals↗
PubMed1992

Structural relatedness of enteric bacterial porins assessed with monoclonal antibodies to Salmonella typhimurium OmpD and OmpC.

The immunochemistry and structure of enteric bacterial porins are critical to the understanding of the immune response to bacterial infection. We raised 41 monoclonal antibodies (MAbs) to Salmonella typhimurium OmpD and OmpC porin trimers and monomers. Enzyme-linked immunosorbent assays, immunoprecipitations, and/or Western immunoblot techniques indicated that 39 MAbs (11 anti-trimer and 28 anti-monomer) in the panel are porin specific and one binds to the lipopolysaccharide; the specificity of the remaining MAb probably lies in the porin-lipopolysaccharide complex. Among the porin-specific MAbs, 10 bound cell-surface-exposed epitopes, one reacted with a periplasmic epitope, and the remaining 28 recognized determinants that are buried within the outer membrane bilayer. Many of the MAbs reacting with surface-exposed epitopes were highly specific, recognizing only the homologous porin trimers; this suggests that the cell-surface-exposed regions of porins tends to be quite different among S. typhimurium OmpF, OmpC, and OmpD porins. Immunological cross-reaction showed that S. typhimurium OmpD was very closely related to Escherichia coli NmpC and to the Lc porin of bacteriophage PA-2. Immunologically, E. coli OmpG and protein K also appear to belong to the family of closely related porins including E. coli OmpF, OmpC, PhoE, and NmpC and S. typhimurium OmpF, OmpC, and OmpD. It appears, however, that S. typhimurium "PhoE" is not closely related to this group. Finally, about one-third of the MAbs that presumably recognize buried epitopes reacted with porin domains that are widely conserved in 13 species of the family Enterobacteriaceae, but apparently not in the seven nonenterobacterial species tested. These data are evaluated in relation to host immune response to infection by gram-negative bacteria.

Antibodies, Monoclonal↗
PubMed2005

The bacterial nucleoid: a highly organized and dynamic structure.

Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

Bacteria↗
PubMed2026

Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.

Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.

Soil Microbiology↗
PubMed2005

Brood size modifications affect plumage bacterial assemblages of European starlings.

During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

Age Factors↗
PubMed2001

A corrected quaternary arrangement of the peptidase HslV and atpase HslU in a cocrystal structure.

The bacterial heat shock locus HslU ATPase and HslV peptidase together form an ATP-dependent HslVU protease. Crystal structures show that HslU forms a hexamer with a pore at one end and HslV forms a dodecamer with translocation pores at both ends of two back-to-back stacked hexameric rings. Consistent with three electron microscopic studies and one small-angle X-ray scattering study, three crystal structures show that the nucleotide-binding domains of HslU bind to HslV and that the pores of the peptidase and ATPase are next to each other and aligned. A fourth crystal structure shows a radically different quaternary arrangement. Here I present a crystallographic analysis of the fourth structure to show that it contained a crystallographic origin shift and a mistake in space group assignment. Once these errors are corrected, a quaternary arrangement that is similar to those observed in the other structures emerges.

ATP-Dependent Proteases↗
PubMed2002

Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria.

Predation is a major mortality factor of planktonic bacteria and an important shaping force for the phenotypic and taxonomic structure of bacterial communities. In this paper we: (1) summarise current knowledge on bacterial phenotypic properties which affect their vulnerability towards grazers, and (2) review experimental evidence demonstrating that this phenotypic heterogeneity results in shifts of bacterial community composition during enhanced protist grazing pressure. Size-structured interactions are especially important in planktonic systems and bacterial cell size influences the mortality rate and the type of grazer to which bacteria are most susceptible. When protists are the major bacterivores, both very small and large bacterial cells gain some size refuge. Recent studies have revealed that also various non-morphological traits such as motility, physicochemical surface characters and toxicity affect bacterial vulnerability and protist feeding success. These properties are effective at different stages during the feeding process of interception feeding flagellates (encounter, capture, ingestion, digestion). Grazing-resistant bacteria in natural communities can account for a substantial portion of the total bacterial biomass at least in more productive aquatic systems. In field and laboratory experiments it has been demonstrated that increased protozoan grazing results in shifts in the phenotypic and genotypic composition of the bacterial assemblage. The importance of this shaping force for the bacterial community structure depends, however, on the overall food web structure, especially on the composition of the metazooplankton. Whereas the structuring impact of bacterial grazers is well documented, relatively little is known about how grazing-mediated changes in bacterial communities influence microbially mediated processes and biogeochemically important transformations.

Animals↗
PubMed1992

The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication.

Mutants in bacterial topoisomerase (topo) IV are deficient in chromosomal partitioning. To investigate the basis of this phenotype, we examined plasmid DNA topology in conditionally lethal topo IV mutants. We found that dimeric catenated plasmids accumulated in vivo after topo IV inhibition. The catenanes were supercoiled, contained from 2 to > 32 nodes, and were the products of DNA synthesis. Electron microscopy and recombination tests proved that the catenanes have the unique structure predicted for replication intermediates. These data provide strong evidence for a model in which unlinking of the double helix can occur in two stages during DNA replication and for the critical role of topo IV in the second stage. The interlocks in the catenanes appear to be sequestered from DNA gyrase, perhaps by compartmentalization in an enzyme complex dedicated to partitioning.

Cell Compartmentation↗
PubMed1993

Principles of functional and structural organization in the bacterial cell: 'compartments' and their enzymes.

Most bacteria lack obvious compartmentation, i.e., structural partition of the cell into functional entities (organelles) formed by a closed biological membrane. Nevertheless, these organisms exhibit sophisticated regulation and interactions of their catabolic and anabolic pathways; they are able to exploit a great variety of carbon and energy sources, and they conserve and transform energy in an efficient manner. In a less stringent sense, 'compartments' are also present in bacteria if one accepts that bacterial 'compartments' are not necessarily surrounded by a membrane, but are rather defined as mere functional entities characterized by their structural components, their enzymes and other functional proteins such as binding proteins. This view would mean that the bacterial cell can be described as a highly organized structured system comprised of these functional entities. Regulated transport processes within 'compartments' and across boundaries involving low and high molecular mass compounds, solutes, and ions take place within the 'framework' constituted by this structured system. Special emphasis is given to the fact that many of the transport processes take place involving the functional entity 'energized membrane'. This 'framework', the structural basis for the functional potential of a bacterial cell, can be studied by electron microscopy. Advanced sample preparation techniques and imaging modes are available which keep the danger of artefact formation low; they can be applied at cellular and macromolecular levels. Recent developments in immunoelectron microscopy and affinity labelling techniques provide tools which allow to unequivocally locate enzymes and other antigens in the cell and to identify polypeptide chains in enzyme complexes. Application of these approaches in studies on cellular and macromolecular organization of bacteria and their enzyme systems confirmed some old views but also extended our knowledge. This is exemplified by a description of selected enzyme complexes located in the bacterial cytoplasm, in the cytoplasmic membrane or attached to it, in the periplasmic space, and attached to the cell wall or set free into the surrounding medium.

Aldehyde Oxidoreductases↗
PubMed2001

Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses.

AIMS: The objective of this study was to investigate the changes in the indigenous bacterial community structure for assessing the impact of biostimulation on spilled oil. METHODS AND RESULTS: Changes in the bacterial community structure were monitored by denaturing gradient gel electrophoresis (DGGE) and clone library methods based on 16S rRNA gene (rDNA) sequences. The results of DGGE, coupled with the use of the Shannon index and principal component analysis (PCA) and clone library analyses, were consistent. In the treated (fertilized) area, one operational taxonomic unit (OTU) became dominant during the fertilization period, and it was most closely related to Pseudomonas putida. CONCLUSIONS: The bacterial community structure in the treated area was markedly different from that in the control (non-fertilized) area during the fertilization period, but in the two areas it became similar at 14 weeks after the end of fertilization. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the bacterial community structure was disrupted by the biostimulation treatment, but that it recovered immediately after the end of fertilization.

Bacteria↗
PubMed2004

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

Acridine Orange↗
PubMed1997

Primary structure of the novel bacterial rhodopsin from extremely halophilic archaeon Haloarcula japonica strain TR-1.

A novel bacterial rhodopsin was identified in Haloarcula japonica strain TR-1. The gene encoding the bacterial rhodopsin was cloned and sequenced. The structural gene consisted of an open reading frame of 750 nucleotides encoding 250 amino acids. The deduced amino acid sequence of the Ha. japonica bacterial rhodopsin showed the highest homology to those of cruxrhodopsins.

Amino Acid Sequence↗
PubMed1997

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.

Representative genomes from each of the three kingdoms of life are compared in terms of protein structure, in particular, those of Haemophilus influenzae (a bacteria), Methanococcus jannaschii (an archaeon), and yeast (a eukaryote). The comparison is in the form of a census (or comprehensive accounting) of the relative occurrence of secondary and tertiary structures in the genomes, which particular emphasis on patterns of supersecondary structure. Comparison of secondary structure shows that the three genomes have nearly the same overall secondary-structure content, although they differ markedly in amino acid composition. Comparison of super-secondary structure, using a novel "frequent-words" approach, shows that yeast has a preponderance of consecutive strands (e.g. beta-beta-beta patterns), Haemophilus, consecutive helices (alpha-alpha-alpha), and Methanococcus, alternating helix-strand structures (beta-alpha-beta). Yeast also has significantly more helical membrane proteins than the other two genomes, with most of the differences concentrated in proteins containing two transmembrane segments. Comparison of tertiary structure (by sequence matching and domain-level clustering) highlights the substantial duplication in each genome (approximately 30% to 50%), with the degree of duplication following similar patterns in all three. Many sequence families are shared among the genomes, with the degree of overlap between any two genomes being roughly similar. In total, the three genomes contain 148 of the approximately 300 known protein folds. Forty-five of these 148 that are present in all three genomes are especially enriched in mixed super-secondary structures (alpha/beta). Moreover, the five most common of these 45 (the "top-5") have a remarkably similar super-secondary structure architecture, containing a central sheet of parallel strands with helices packed onto at least one face and beta-alpha-beta connections between adjacent strands. These most basic molecular parts, which, presumably, were present in the last common ancestor to the three Kingdoms, include the TIM-barrel, Rossmann, flavodoxin, thiamin-binding, and P-loop-hydrolase folds.

Archaea↗
PubMedDate not supplied

[Bacterial cis-regulatory RNA structures].

The review considers mechanism of bacterial gene expression based on formation of alternative RNA structures, such as riboswitches, attenuators, T-boxes, etc. These structures are classified by mechanism of action. Evolution and interaction of regulatory systems are discussed.

Aptamers, Nucleotide↗
PubMed1990

Association of type 1 blood group antigens with urinary tract infections in children with genitourinary structural abnormalities.

Bacterial adherence to carbohydrate receptors on the surface of urothelial cells is important in the pathogenesis of urinary tract infections. Blood group-related antigens, genetically determined carbohydrate structures found on the urothelial cell surface, may influence the availability of these receptors thereby affecting bacterial adherence and the susceptibility to urinary tract infections. Recent evidence indicates that the immunoanatomical distribution of type 1 blood group-related antigens in urothelium is influenced by ABO, Lewis and secretor phenotypes, women with Le(a-b-) and Le(a+b-) blood phenotypes have more than a 3-fold greater risk of recurrent urinary tract infections compared to Le(a-b+) women and epithelial cells from nonsecretors have more bacterial receptors than cells from secretors. To determine the relation between the expression of type 1 blood group-related antigens and urinary tract infections we performed an immunohistochemical analysis using a well characterized panel of monoclonal antibodies on 72 surgical specimens obtained from children who underwent correction of a structural genitourinary anomaly at the University of Rochester Medical Center from December 1983 to May 1988. Of 72 children 48 had a history of at least 1 documented urinary tract infection. The differences in the distribution of children by type 1 blood group immunophenotype in the infection and noninfection groups were highly significant (p = 0.003, Fisher's exact test). There is an increased frequency of urinary tract infections in children with genitourinary structural anomalies whose urothelium reflects the nonsecretor phenotype, that is they have minimal or undetectable levels of ABO and Leb reactivity compared to those with intense ABO and/or Leb immunoreactivity. Of 17 children with minimal or no ABO or Leb immunoreactivity 16 (94.1%) belonged to the infection group. Furthermore, 23 of 24 patients (95.8%) without a history of urinary tract infection expressed intense ABO and/or Leb immunoreactivity. It appears that the type 1 blood group-related antigen profile of urothelium influences susceptibility to urinary tract infection and it may be important in identifying patients who would benefit from prophylactic antibiotic therapy or earlier surgical intervention.

ABO Blood-Group System↗