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Many Bacteria (many + bacteria)
Selected AbstractsThe presence of conifer resin decreases the use of the immune system in wood antsECOLOGICAL ENTOMOLOGY, Issue 3 2008GRÉGOIRE CASTELLA Abstract 1.,Wood ants (Formica paralugubris) incorporate large amounts of solidified conifer resin into their nest, which reduces the density of many bacteria and fungi and protects the ants against some detrimental micro-organisms. By inducing an environment unfavourable to pathogens, the presence of resin may allow workers to reduce the use of their immune system. 2.,The present study tested the hypothesis that the presence of resin decreases the immune activity of wood ants. Specifically, three components of the humoral immune defences of workers kept in resin-rich and resin-free experimental nests (antibacterial, lytic, and prophenoloxidase activities) were compared. 3.,The presence of resin was associated with reduced bacterial and fungal densities in nest material and with a small decrease in worker antibacterial and lytic activities. The prophenoloxidase activity was very low in all workers and was not affected by the presence of resin. 4.,These results suggest that collective medication with resin reduces pathogen pressure, which in turn decreases the use of the inducible part of the immune system. More generally, the use of plant secondary compounds might be an efficient and economical way to fight pathogens. [source] Chemotaxis of Ralstonia sp.ENVIRONMENTAL MICROBIOLOGY, Issue 10 2006SJ98 towards p -nitrophenol in soil Summary Bioremediation of contaminated sites has been accepted as an efficient and cheaper alternative to physicochemical means of remediation in several cases. Although chemotactic behaviour of many bacteria has been studied earlier and assays have been developed to study bacterial chemotaxis in semi-solid media, this phenomenon has never been demonstrated in soil. For bioremediation application it is important to know whether bacteria actually migrate through the heterogenous soil medium towards a gradient of a particular chemoattractant. In the present study we have successfully demonstrated bacterial chemotaxis of a Ralstonia sp. SJ98 in soil microcosm using qualitative and quantitative plate and tray assays. The migration of bacteria has been established using several methods such as plate counting, vital staining and flow cytometry and slot blot hybridization. A non-chemotactic p- nitrophenol utilizing strain Burkholderia cepacia RKJ200 has been used as negative control. Our work clearly substantiates the hypothesis that chemotactic bacteria may enhance in situ bioremediation of toxic pollutants from soils and sediments. [source] pyr RNA binding to the Bacillus caldolyticus PyrR attenuation protein , characterization and regulation by uridine and guanosine nucleotidesFEBS JOURNAL, Issue 4 2008Casper M. Jørgensen The PyrR protein regulates expression of pyrimidine biosynthetic (pyr) genes in many bacteria. PyrR binds to specific sites in the 5, leader RNA of target operons and favors attenuation of transcription. Filter binding and gel mobility assays were used to characterize the binding of PyrR from Bacillus caldolyticus to RNA sequences (binding loops) from the three attenuation regions of the B. caldolyticus pyr operon. Binding of PyrR to the three binding loops and modulation of RNA binding by nucleotides was similar for all three RNAs. The apparent dissociation constants at 0 °C were in the range 0.13,0.87 nm in the absence of effectors; dissociation constants were decreased by three- to 12-fold by uridine nucleotides and increased by 40- to 200-fold by guanosine nucleotides. The binding data suggest that pyr operon expression is regulated by the ratio of intracellular uridine nucleotides to guanosine nucleotides; the effects of nucleoside addition to the growth medium on aspartate transcarbamylase (pyrB) levels in B. subtilis cells in vivo supported this conclusion. Analytical ultracentrifugation established that RNA binds to dimeric PyrR, even though the tetrameric form of unbound PyrR predominates in solution at the concentrations studied. [source] Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosaFEBS JOURNAL, Issue 8 2005Ronja Tasler Phytochromes are photochromic biliproteins found in plants as well as in some cyanotrophic, photoautotrophic and heterotrophic bacteria. In many bacteria, their function is largely unknown. Here we describe the biochemical and spectroscopic characterization of recombinant bacterial phytochrome from the opportunistic pathogen Pseudomonas aeruginosa (PaBphP). The recombinant protein displays all the characteristic features of a bonafide phytochrome. In contrast with cyanobacteria and plants, the chromophore of this bacterial phytochrome is biliverdin IX,, which is produced by the heme oxygenase BphO in P. aeruginosa. This chromophore was shown to be covalently attached via its A-ring endo-vinyl group to a cysteine residue outside the defined bilin lyase domain of plant and cyanobacterial phytochromes. Site-directed mutagenesis identified Cys12 and His247 as being important for chromophore binding and photoreversibility, respectively. PaBphP is synthesized in the dark in the red-light-absorbing Pr form and immediately converted into a far-red-light-absorbing Pfr-enriched form. It shows the characteristic red/far-red-light-induced photoreversibility of phytochromes. A chromophore analog that lacks the C15/16 double bond was used to show that this photoreversibility is due to a 15Z/15E isomerization of the biliverdin chromophore. Autophosphorylation of PaBphP was demonstrated, confirming its role as a sensor kinase of a bacterial two-component signaling system. [source] Bacterial quorum sensing and nitrogen cycling in rhizosphere soilFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Kristen M. DeAngelis Abstract Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N) mineralization. Most soil organic nitrogen is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate limiting for plant nitrogen accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease-specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared with bulk soil. Low-molecular-weight (MW) DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density-dependent group behavior. Because proteobacteria are considered major rhizosphere colonizers, we assayed the proteobacterial QS signals N -acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and nitrogen cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in seven of eight isolates disrupted enzyme activity. Many Alphaproteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of nitrogen-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere nitrogen mineralization. [source] RpoS involvement and requirement for exogenous nutrient for osmotically induced cross protection in Vibrio vulnificusFEMS MICROBIOLOGY ECOLOGY, Issue 3 2005Thomas M. Rosche Abstract Vibrio vulnificus is an opportunistic human pathogen which is the causative agent of food-borne disease and wound infections. V. vulnificus is able to adapt to a variety of potentially stressful environmental changes, such as osmotic, nutrient, and temperature variations in estuarine environments, as well as oxidative, osmotic, and acidity differences following infection of a human host. After exposure to sub-lethal levels of a particular environmental stress, many bacteria become resistant to unrelated stresses, a phenomenon termed cross protection. In this study, we examined the ability of osmotic shock to cross protect V. vulnificus to high temperature as well as oxidative stress. Log phase cells of V. vulnificus strain C7184o were cross protected by prior osmotic shock to both heat and oxidative challenge, but only when exogenous nutrient was present during the osmotic upshift. Further, and unlike other bacteria, nutrient starvation alone did not result in cross protection against either stress. When small amounts of nutrient were present during osmotic shock, cross protection to an otherwise lethal heat challenge developed extremely rapidly, with significant protection seen within 10 min. Cross protection to oxidative stress was slower to develop, requiring several hours. Although stationary phase alone conferred some cross protection to heat and oxidative stress, the alternate sigma factor RpoS was required for complete cross protection of log phase cells to oxidative stress but not for resistance to heat challenge. Together these findings suggest that the cross protective response in V. vulnificus is complex and appears to involve multiple mechanisms. [source] Agrobacterium type IV secretion is a two-step process in which export substrates associate with the virulence protein VirJ in the periplasmMOLECULAR MICROBIOLOGY, Issue 5 2002Mario Pantoja Summary Type IV secretion systems are virulence determinants in many bacteria and share extensive homology with many conjugal transfer systems. Although type IV systems and their homologues have been studied widely, the mechanism by which substrates are secreted remains unclear. In Agrobacterium, we show that type IV secretion substrates that lack signal peptides form a soluble complex in the periplasm with the virulence protein VirJ. Additionally, these proteins co-precipitate with constituents of the type IV transporter: the VirB pilus and the VirD4 protein. Our findings suggest that the substrate proteins localized to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium. Our analyses of protein,protein interactions in a variety of mutant backgrounds indicate that substrates are probably secreted independently of one another. [source] Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystalsPROTEIN SCIENCE, Issue 12 2009Kelly A. Dryden Abstract Bacterial microcompartments (BMCs) are large intracellular bodies that serve as simple organelles in many bacteria. They are proteinaceous structures composed of key enzymes encapsulated by a polyhedral protein shell. In previous studies, the organization of these large shells has been inferred from the conserved packing of the component shell proteins in two-dimensional (2D) layers within the context of three-dimensional (3D) crystals. Here, we show that well-ordered, 2D crystals of carboxysome shell proteins assemble spontaneously when His-tagged proteins bind to a monolayer of nickelated lipid molecules at an air,water interface. The molecular packing within the 2D crystals recapitulates the layered hexagonal sheets observed in 3D crystals. The results reinforce current models for the molecular design of BMC shells. [source] The 1.25,Å resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2008Farah Javid-Majd Phosphoribosyl-ATP pyrophosphohydrolase is the second enzyme in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP to phosphoribosyl-AMP and pyrophosphate. It is encoded by the hisE gene, which is present as a separate gene in many bacteria and archaea but is fused to hisI in other bacteria, fungi and plants. Because of its essentiality for growth in vitro, HisE is a potential drug target for tuberculosis. The crystal structures of two native (uncomplexed) forms of HisE from Mycobacterium tuberculosis have been determined to resolutions of 1.25 and 1.79,Å. The structure of the apoenzyme reveals that the protein is composed of five ,-helices with connecting loops and is a member of the ,-helical nucleoside-triphosphate pyrophosphatase superfamily. The biological unit of the protein is a homodimer, with an active site on each subunit composed of residues exclusively from that subunit. A comparison with the Campylobacter jejuni dUTPase active site allowed the identification of putative metal- and substrate-binding sites in HisE, including four conserved glutamate and glutamine residues in the sequence that are consistent with a motif for pyrophosphohydrolase activity. However, significant differences between family members are observed in the loop region between ,-helices H1 and H3. The crystal structure of M. tuberculosis HisE provides insights into possible mechanisms of substrate binding and the diversity of the nucleoside-triphosphate pyrophosphatase superfamily. [source] The 1.9,Å resolution structure of Mycobacterium tuberculosis 1-deoxy- d -xylulose 5-phosphate reductoisomerase, a potential drug targetACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Lena M. Henriksson 1-Deoxy- d -xylulose 5-phosphate reductoisomerase catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy- d -xylulose 5-phosphate to form 2- C -methyl- d -erythritol 4-phosphate, as the second step of the deoxyxylulose 5-phosphate/methylerythritol 4-phosphate pathway found in many bacteria and plants. The end product, isopentenyl diphosphate, is the precursor of various isoprenoids vital to all living organisms. The pathway is not found in humans; the mevalonate pathway is instead used for the formation of isopentenyl diphosphate. This difference, combined with its essentiality, makes the reductoisomerase an excellent drug target in a number of pathogenic organisms. The structure of 1-deoxy- d -xylulose 5-phosphate reductoisomerase from Mycobacterium tuberculosis (Rv2870c) was solved by molecular replacement and refined to a resolution of 1.9,Å. The enzyme exhibited an estimated kcat of 5.3,s,1 and Km and kcat/Km values of 7.2,µM and 7.4 × 105,M,1,s,1 for NADPH and 340,µM and 1.6 × 104,M,1,s,1 for 1-deoxy- d -xylulose 5-phosphate. In the structure, a sulfate is bound at the expected site of the phosphate moiety of the sugar substrate. The M. tuberculosis enzyme displays a similar fold to the previously published structures from Escherichia coli and Zymomonas mobilis. Comparisons offer suggestions for the design of specific drugs. Furthermore, the new structure represents an intermediate conformation between the open apo form and the closed holo form observed previously, giving insights into the conformational changes associated with catalysis. [source] Photodynamic therapy: a targeted therapy in periodonticsAUSTRALIAN DENTAL JOURNAL, Issue 2009M Raghavendra Abstract The oral cavity is colonized by a large number and highly diversified communities of micro-organisms. Bacterial biofilm present on tooth or root surface is a major cause of gingivitis and periodontitis. Chemical antimicrobial agents are widely used in prophylactic and therapeutic regimens for dental plaque related diseases, which are among the most common human infections. As these agents are difficult to maintain at therapeutic concentrations in the oral cavity and can be rendered ineffective by resistance development in target organisms, there is a need for an alternative antimicrobial approach. A novel approach, photodynamic therapy (PDT), could be a solution to these problems. Lethal photosensitization of many bacteria, both Gram positive and Gram negative was found in many studies. The advantage of this new approach includes rapid bacterial elimination, minimal chance of resistance development and safety of adjacent host tissue and normal microflora. Thus, the available knowledge of photodynamic therapy should encourage a more clinically oriented application of this technique. [source] Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001Winfried Meining Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C2221, with unit-cell parameters a = 50.3, b = 104.7, c = 85.3,Å, , = , = , = 90°, and diffract to 2.6,Å resolution. [source] Purification, crystallization and preliminary X-ray analysis of urease from jack bean (Canavalia ensiformis)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Anuradha Balasubramanian Plant urease is a seed protein that is common in most legumes. It is also common in many bacteria and fungi and several species of yeast. Urease allows organisms to use exogenous and internally generated urea as a nitrogen source by catalyzing the hydrolysis of urea to ammonia and carbon dioxide. Urease from jack bean meal was purified to electrophoretic homogeneity using a series of steps involving acetone precipitation and size-exclusion and ion-exchange chromatography. The jack bean urease was crystallized and the resulting crystals diffracted to 2.05,Å resolution using synchrotron radiation. The crystals belonged to the hexagonal space group P6322, with unit-cell parameters a = b = 138.57, c = 198.36,Å. [source] Purification, crystallization and preliminary X-ray analysis of urease from pigeon pea (Cajanus cajan)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2008Anuradha Balasubramanian Urease is a seed protein that is common to most Leguminosae. It also occurs in many bacteria, fungi and several species of yeast. Urease catalyzes the hydrolysis of urea to ammonia and carbon dioxide, thus allowing organisms to use exogenous and internally generated urea as a nitrogen source. Urease from pigeon pea seeds has been purified to electrophoretic homogeneity using a series of steps involving ammonium sulfate fractionation, acid precipitation, ion-exchange and size-exclusion chromatography techniques. The pigeon pea urease was crystallized and the resulting crystals diffracted to 2.5,Å resolution. The crystals belong to the rhombohedral space group R32, with unit-cell parameters a = b = 176.29, c = 346.44,Å. [source] Microreview: Type IV secretion systems: versatility and diversity in functionCELLULAR MICROBIOLOGY, Issue 9 2010Karin Wallden Summary Type IV secretion systems (T4SSs) are large protein complexes which traverse the cell envelope of many bacteria. They contain a channel through which proteins or protein,DNA complexes can be translocated. This translocation is driven by a number of cytoplasmic ATPases which might energize large conformational changes in the translocation complex. The family of T4SSs is very versatile, shown by the great variety of functions among family members. Some T4SSs are used by pathogenic Gram-negative bacteria to translocate a wide variety of virulence factors into the host cell. Other T4SSs are utilized to mediate horizontal gene transfer, an event that greatly facilitates the adaptation to environmental changes and is the basis for the spread of antibiotic resistance among bacteria. Here we review the recent advances in the characterization of the architecture and mechanism of substrate transfer in a few representative T4SSs with a particular focus on their diversity of structure and function. [source] IRG proteins: key mediators of interferon-regulated host resistance to intracellular pathogensCELLULAR MICROBIOLOGY, Issue 5 2007Gregory A. Taylor Summary Immunity-related GTPases (IRG) (also known as p47 GTPases) are a family of proteins found in vertebrates, which play critical roles in mediating innate resistance to intracellular pathogens. The proteins are expressed at high levels following infection with bacteria, protozoa or viruses, as a consequence of interferon-stimulated transcription. Their absence in gene-targeted mice leads to profoundly decreased resistance to many bacteria and protozoa that varies markedly with the particular IRG protein that has been targeted. The proteins are thought to function by localizing to pathogen-containing vacuoles in host cells, such as macrophages, and then regulating the processing of the vacuole and ultimately driving elimination of the pathogen. This review details current knowledge of IRG proteins and their key roles in host resistance. [source] Helicobacter pylori is invasive and it may be a facultative intracellular organismCELLULAR MICROBIOLOGY, Issue 5 2007Andre Dubois Summary The pathogenicity of many bacteria colonizing the gastrointestinal tract often depends on their ability to gain access to cells that are normally non-phagocytic. Helicobacter pylori colonizes the stomach of over half the world population and is the main cause of peptic ulcer disease and gastric cancer. It is generally considered to be a non-invasive pathogen present only in the lumen of the stomach and attached to gastric epithelial cells although a number of in vivo and in vitro studies have demonstrated that H. pylori is in fact invasive. In addition, H. pylori can repopulate the extracellular environment after complete elimination of extracellular bacteria with gentamicin, suggesting it may be considered a facultative intracellular bacterium. This review examines the validity of these observations and describes the evidence suggesting that the intracellular presence of H. pylori plays a role in the induction of diseases, in immune evasion, and in life-long persistence of the bacterium in the stomach of a majority of humans. [source] Sporeformers as Human Probiotics: Bacillus, Sporolactobacillus, and BrevibacillusCOMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY, Issue 3 2003M.E. Sanders ABSTRACT The value of exogenously supplied live bacteria for the maintenance of health in humans has been recognized both scientifically in the published literature and commercially in the availability of probiotic products. Although many bacteria characterized as probiotics are strains of Lactobacillus or Bifidobacterium, sporeforming bacteria, primarily of the genus Bacillus and related genera, have also been studied and commercialized as probiotics. This article reviews the characterization, efficacy, and safety of sporeformers used as probiotics. [source] | |||||||||||||