Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “microbial function”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,153 records · Page 64Linked to original sources
PubMed2005

Functional analysis of immune response genes in Drosophila identifies JNK pathway as a regulator of antimicrobial peptide gene expression in S2 cells.

The templates of innate immunity have ancient origins. Thus, such model animals as the fruit fly, Drosophila melanogaster, can be used to identify gene products that also play a key role in the innate immunity in mammals. We have used oligonucleotide microarrays to identify genes that are responsive to gram-negative bacteria in Drosophila macrophage-like S2 cells. In total, 53 genes were induced by greater than threefold in response to Escherichia coli. The induction of all these genes was peptidoglycan recognition protein LC (PGRP-LC) dependent. Twenty-two genes including 10 of the most strongly induced genes are also known to be up-regulated by septic injury in vivo. Importantly, we identified 31 genes that are not known to respond to bacterial challenge. We carried out targeted dsRNA treatments to assess the functional importance of these gene products for microbial recognition, phagocytosis and antimicrobial peptide release in Drosophila S2 cells in vitro. RNAi targeting three of these genes, CG7097, CG15678 and beta-Tubulin 60D, caused altered antimicrobial peptide release in vitro. Our results indicate that the JNK pathway is essential for normal antimicrobial peptide release in Drosophila in vitro.

Animals↗
PubMed2005

Nitrative stress through formation of 8-nitroguanosine: insights into microbial pathogenesis.

Reactive oxygen and nitrogen species, respectively, mediate oxidative and nitrative stresses by means of oxidation and nitration of various biomolecules including proteins, lipids, and nucleic acids. We have observed nitric oxide (NO)-dependent formation of 8-nitroguanosine and 3-nitrotyrosine during microbial infection, and we determined that both 8-nitroguanosine and 3-nitrotyrosine are useful biomarkers of nitrative stress. Of importance, however, is the great difference in biological characteristics of these two nitrated compounds. 8-Nitroguanosine has unique biochemical and pharmacological properties such as redox activity and mutagenic potential, which 3-nitrotyrosine does not. In this review, we discuss the mechanism of nitrative stress occurring during microbial infections, with special emphasis on biological functions of 8-nitroguanosine formed via NO during the host response to pathogens. These findings provide insights into NO-mediated pathogenesis not only of viral infections but also of many other diseases.

Animals↗
PubMed2001

Prophylactic and therapeutic uses of probiotics: a review.

Probiotics, live microbial food supplements that beneficially affect the host by improving its intestinal microbial balance, are quickly gaining interest as functional foods in the current era of self-care and complementary medicine. Microbes have been used for years in food and alcoholic fermentations and relatively recently have undergone scientific scrutiny to examine their purported health benefits. Some of the claims for which research supports a beneficial effect of probiotic consumption include: improving intestinal tract health, enhancing the immune system, synthesizing and enhancing the bioavailability of nutrients, reducing symptoms of lactose intolerance, decreasing the prevalence of allergy in susceptible individuals, and reducing risk of certain cancers. The mechanisms by which probiotics exert their effects are largely unknown, but may involve modifying gut pH, antagonizing pathogens through production of antimicrobial and antibacterial compounds, competing for pathogen binding and receptor sites as well as for available nutrients and growth factors, stimulating immunomodulatory cells, and producing lactase. Selection criteria, efficacy, food and supplement sources and safety issues around probiotics are reviewed. Nutrition professionals can provide a tremendous service by helping clients overcome negative perceptions of all bacteria and, when appropriate, by developing individualized dietary plans to take advantage of the benefits probiotics may confer.

Bifidobacterium↗
PubMed2002

Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE.

The stabilities of the bacterial community structures supported by seven full-scale biological reactors treating pharmaceutical wastewater were investigated by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA gene fragments. Effluent quality from this treatment process was consistently high with respect to BOD5 (<30 mgl(-1)), soluble COD (<500 mgl(-1)), and total ammonia (< 5 mgl(-1) as N) concentrations. Long-term community structure stability was studied by comparing the similarity of PCR-DGGE fingerprints from samples collected 87 days apart between which the influent wastewater characteristics were relatively stable. The Dice index (Cs) of similarity was moderately high for the first four reactors (Cs = 0.61-0.77) and very high for the last three reactors (Cs = 0.89-0.91). Short-term community structure stability was studied by comparing PCR-DGGE fingerprints from samples collected 15 days apart between which the influent wastewater characteristics changed significantly, while the effluent quality remained consistently high. The bacterial community composition of each of the seven bioreactors showed a moderate community shift (Cs = 0.70-0.76). Short-term variability in influent wastewater composition, therefore, affected a greater community shift than did long-term operation treating a wastewater of relatively consistent composition. These results indicate that functionally stable wastewater treatment bioreactors have stable microbial community structures under normal operating conditions but are able to adapt in response to perturbations to sustain high effluent quality.

Ammonia↗
PubMed2003

The Tat protein translocation pathway and its role in microbial physiology.

The Tat (twin arginine translocation) protein transport system functions to export folded protein substrates across the bacterial cytoplasmic membrane and to insert certain integral membrane proteins into that membrane. It is entirely distinct from the Sec pathway. Here, we describe our current knowledge of the molecular features of the Tat transport system. In addition, we discuss the roles that the Tat pathway plays in the bacterial cell, paying particular attention to the involvement of the Tat pathway in the biogenesis of cofactor-containing proteins, in cell wall biosynthesis and in bacterial pathogenicity.

Amino Acid Sequence↗
PubMed2002

Molecular characterization of the insect immune protein hemolin and its high induction during embryonic diapause in the gypsy moth, Lymantria dispar.

During the embryonic (pharate first instar) diapause of the gypsy moth, Lymantria dispar, a 55 kDa protein is highly up-regulated in the gut. We now identify that protein as hemolin, an immune protein in the immunoglobulin superfamily. We isolated a gypsy moth hemolin cDNA and demonstrated a high degree of similarity with hemolins from three other moth species. Hemolin mRNA levels increased at the time of diapause initiation and remained high throughout the mandatory period of chilling required to terminate diapause in this species, and then dropped in late diapause. This mRNA pattern reflects the pattern of protein synthesis. These results suggest that hemolin is developmentally up-regulated in the gut during diapause. Diapause in this species can be prevented using KK-42, an imidazole derivative known to inhibit ecdysteroid biosynthesis, and gypsy moths treated in this manner failed to elevate hemolin mRNA. Conversely, this diapause appears to be initiated and maintained by the steroid hormone, 20-hydroxyecdysone, and the addition of 20-hydroxyecdysone to the culture medium elevated hemolin mRNA in the gut. Our results thus indicate a role for 20-hydroxyecdysone in the elevation of hemolin mRNA during diapause. Presumably, hemolin functions to protect the gypsy moth from microbial infection during its long, overwintering diapause.

Amino Acid Sequence↗
PubMed2000

The role of the interleukin-1/Toll-like receptor superfamily in inflammation and host defence.

The IL-1 receptor/Toll-like receptor superfamily comprises a diverse family of cell surface receptors defined by a characteristic conserved sequence in their cytosolic regions, termed the Toll/IL-1 receptor domain, which function in inflammation and host defence against microbial pathogens. Members include receptors for the proinflammatory cytokines IL-1 and IL-18 and Toll-like receptors 2 and 4, which are involved in host responses to Gram-positive and Gram-negative bacteria, respectively. Signalling pathways activated by these receptors are conserved and the superfamily represents a pan-genomic system involved in the host response to infection and injury.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Modification of polysaccharides and plant cell wall by endo-1,4-beta-glucanase and cellulose-binding domains.

Cellulose is one of the most abundant polymers in nature. Different living systems evolved simultaneously, using structurally similar proteins to synthesize and metabolize polysaccharides. In the growing plant, cell wall loosening, together with cellulose biosynthesis, enables turgor-driven cell expansion. It has been postulated that endo-1,4-beta-glucanases (EGases) play a central role in these complex activities. Similarly, microorganisms use a consortium of lytic enzymes to convert cellulose into soluble sugars. Most, if not all, cellulases have a modular structure with two or more separate independent functional domains. Binding to cellulose is mediated by a cellulose-binding domain (CBD), whereas the catalytic domain mediates hydrolysis. Today, EGases and CBDs are known to exist in a wide range of species and it is evident that both possess immense potential in modifying polysaccharide materials in-vivo and in-vitro. The hydrolytic function is utilized for polysaccharide degradation in microbial systems and cell wall biogenesis in plants. The CBDs exerts activity that can be utilized for effective degradation of crystalline cellulose, plant cell wall relaxation, expansion and cell wall biosynthesis. Applications range from modulating the architecture of individual cells to an entire organism. These genes, when expressed under specific promoters and appropriate trafficking signals can be used to alter the nutritional value and texture of agricultural crop and their final products. EGases and CBDs may also find applications in the modification of physical and chemical properties of composite materials to create new materials possessing improved properties.

Bacterial Proteins↗
PubMed2002

Probiotics and atopic dermatitis. A new strategy in atopic dermatitis.

Over the last few decades, the prevalence of atopic dermatitis has been increasing from 2% to 100%, with 90% of cases within 5 years of age versus 6% between 6 and 10 years and 2% after 10 years, and environmental factors may possibly play an important role in this increase as in other atopic diseases. Many findings suggest an important role of atopy in atopic dermatitis; moreover, 40% of children with atopic dermatitis have food allergy and the removal of the food allergen from the patient's diet leads to a significant clinical improvement. In a possible scenario, IgE-bearing dendritic cells are likely to process allergens acquired in the gastrointestinal tract, circulate to the skin and activate local T cells. Cultures of beneficial live microorganisms characteristic of the commensal microflora are administered with probiotic functional foods in order to provide a microbial challenge for the maturation of gut-associated lymphoid tissue, which the infant often lacks. The probiotic effects are attributed to normalisation of the increased intestinal permeability and balancing gut microecology, improvement of the immunological defence barrier (IgA) of the intestine, alleviation of the intestinal inflammatory response, and downregulation of proinflammatory cytokines characteristic of local and systemic allergic inflammation.

Child↗
PubMed2002

Physicochemical and structural properties of oat globulin polymers formed by a microbial transglutaminase.

Oat globulin was polymerized by a microbial transglutaminase (TG), and some physicochemical and functional properties of polymers were studied. Reversed-phase HPLC revealed that the number of epsilon-(gamma-glutamyl) lysine isopeptide bonds formed after 4 h of enzyme incubation was 2.21 micromol/g of protein. SDS-PAGE showed that the oat globulin acidic polypeptides (AP) were more susceptible to polymerization than the basic polypeptides (BP), and the reactivities of both AP and BP were enhanced by the addition of other substrate proteins. Differential scanning calorimetry showed that both the denaturation temperature and denaturation enthalpy were decreased after TG treatment. Fourier transform infrared spectroscopy revealed marked increases in the intensity of two intermolecular beta-sheet bands associated with aggregate formation but little conformational changes in the polymerized protein. TG incubation led to progressive changes in flow properties of oat globulin dispersions, indicating enhanced pseudoplasticity and increased viscosity and yield stress.

Avena↗
PubMed2002

Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system.

An increasing number of microbial genomes have been completely sequenced, and functional analyses of these genomic sequences are under way. To facilitate these analyses, we have developed a genome-engineering tool for determining essential genes and minimizing bacterial genomes. We made two large pools of independent transposon mutants in Escherichia coli using modified Tn5 transposons with two different selection markers and precisely mapped the chromosomal location of 800 of these transposons. By combining a mapped transposon mutation from each of the mutant pools into the same chromosome using phage P1 transduction and then excising the flanked genomic segment by Cre-mediated loxP recombination, we obtained E. coli strains in which large genomic fragments (59-117 kilobases) were deleted. Some of these individual deletions were then combined into a single "cumulative deletion strain" that lacked 287 open reading frames (313.1 kilobases) but that nevertheless exhibited normal growth under standard laboratory conditions.

Bacteriophage P1↗
PubMed1999

Identification of target promoters for the Bacillus subtilis extracytoplasmic function sigma factor, sigma W.

The Bacillus subtilis sigW gene encodes an extracytoplasmic function (ECF) sigma factor that is expressed in early stationary phase from a sigW-dependent autoregulatory promoter, PW. Using a consensus-based search procedure, we have identified 15 operons preceded by promoters similar in sequence to PW. At least 14 of these promoters are dependent on sigma W both in vivo and in vitro as judged by lacZ reporter fusions, run-off transcription assays and nucleotide resolution start site mapping. We conclude that sigma W controls a regulon of more than 30 genes, many of which encode membrane proteins of unknown function. The sigma W regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides. We suggest that sigma W activates a large stationary-phase regulon that functions in detoxification, production of anti-microbial compounds or both.

Bacillus subtilis↗
PubMed2002

The multicopper oxidase of Pseudomonas aeruginosa is a ferroxidase with a central role in iron acquisition.

Recently it has been observed that multicopper oxidases are present in a number of microbial genomes, raising the question of their function in prokaryotes. Here we describe the analysis of an mco mutant from the opportunistic pathogen Pseudomonas aeruginosa. Unlike wild-type Pseudomonas aeruginosa, the mco mutant was unable to grow aerobically on minimal media with Fe(II) as sole iron source. In contrast, both the wild-type and mutant strain were able to grow either anaerobically via denitrification with Fe(II) or aerobically with Fe(III). Analysis of iron uptake showed that the mco mutant was impaired in Fe(II) uptake but unaffected in Fe(III) uptake. Purification and analysis of the MCO protein confirmed ferroxidase activity. Taken together, these data show that the mco gene encodes a multicopper oxidase that is involved in the oxidation of Fe(II) to Fe(III) subsequent to its acquisition by the cell. In view of the widespread distribution of the mco gene in bacteria, it is suggested that an iron acquisition mechanism involving multicopper oxidases may be an important and hitherto unrecognized feature of bacterial pathogenicity.

Aerobiosis↗
PubMed1999

Bacteriologic and immunologic aspects of gram-negative folliculitis: a study of 46 patients.

BACKGROUND: Gram-negative folliculitis is an infection with gram-negative rods that most often occurs as a complication of prolonged broad-spectrum antibiotic therapy in patients suffering from acne and rosacea. METHODS: The bacteriologic and immunologic findings are reported in 46 patients, 39 men and 7 women, aged 16-79 (median, 28) years, with gram-negative folliculitis. Hypersensitivity reactions to various microbial recall antigens as well as granulocyte functions were evaluated. Quantitative measurements of serum levels of immunoglobulin M, G, A, and E, total complement activity, complement factors C3 and C4, and alpha-1-antitrypsin were performed. RESULTS: The gram-negative organisms most frequently cultivated from nares, facial skin, and pustules were Klebsiella spp., Escherichia coli, Enterobacter spp., and Proteus spp. In all patients, deviations of one or more immune parameters were detected, including lowered serum concentrations of immunoglobulin M and alpha-1-antitrypsin, and elevated levels of immunoglobulin E. The humoral and cellular parameters were not influenced by isotretinoin therapy of gram-negative folliculitis. CONCLUSIONS: These findings suggest that gram-negative folliculitis is not only a complication of long-lasting antibiotic treatment of acne and rosacea, but might be an entity of its own. Immunologic factors may play a critical role in the pathogenesis of gram-negative folliculitis.

Adolescent↗
PubMed2000

Transfer of palmitate from phospholipids to lipid A in outer membranes of gram-negative bacteria.

Regulated covalent modifications of lipid A are implicated in virulence of pathogenic Gram-negative bacteria. The Salmonella typhimurium PhoP/PhoQ-activated gene pagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic anti-microbial peptides. Palmitoylated lipid A can also function as an endotoxin antagonist. We now show that pagP and its Escherichia coli homolog (crcA) encode an unusual enzyme of lipid A biosynthesis localized in the outer membrane. PagP transfers a palmitate residue from the sn-1 position of a phospholipid to the N-linked hydroxymyristate on the proximal unit of lipid A (or its precursors). PagP bearing a C-terminal His(6)-tag accumulated in outer membranes during overproduction, was purified with full activity and was shown by cross-linking to behave as a homodimer. PagP is the first example of an outer membrane enzyme involved in lipid A biosynthesis. Additional pagP homologs are encoded in the genomes of Yersinia and Bordetella species. PagP may provide an adaptive response toward both Mg(2+) limitation and host innate immune defenses.

Acylation↗
PubMed2002

Comparative study of the reaction mechanism of family 18 chitinases from plants and microbes.

Hydrolytic mechanisms of family 18 chitinases from rice (Oryza sativa L.) and Bacillus circulans WL-12 were comparatively studied by a combination of HPLC analysis of the reaction products and theoretical calculation of reaction time-courses. All of the enzymes tested produced beta-anomers from chitin hexasaccharide [(GlcNAc)(6)], indicating that they catalyze the hydrolysis through a retaining mechanism. The rice chitinases hydrolyzed predominantly the fourth and fifth glycosidic linkages from the nonreducing end of (GlcNAc)(6), whereas B. circulans chitinase A1 hydrolyzed the second linkage from the nonreducing end. In addition, the Bacillus enzyme efficiently catalyzed transglycosylation, producing significant amounts of chitin oligomers larger than the initial substrate, but the rice chitinases did not. The time-courses of (GlcNAc)(6) degradation obtained by HPLC were analyzed by theoretical calculation, and the subsite structures of the rice chitinases were identified to be (-4)(-3)(-2)(-1)(+1)(+2). From the HPLC profile of the reaction products previously reported [Terwisscha van Scheltinga et al. (1995) Biochemistry 34, 15619-15623], family 18 chitinase from rubber tree (Hevea brasiliensis) was estimated to have the same type of subsite structure. Theoretical analysis of the reaction time-course for the Bacillus enzyme revealed that the enzyme has (-2)(-1) (+1)(+2)(+3)(+4)-type subsite structure, which is identical to that of fungal chitinase from Coccidioides immitis [Fukamizo et al. (2001) Biochemistry 40, 2448-2454]. The Bacillus enzyme also resembled the fungal chitinase in its transglycosylation activity. Minor structural differences between plant and microbial enzymes appear to result in such functional variations, even though all of these chitinases are classified into the identical family of glycosyl hydrolases.

Chitinases↗
PubMed2005

Apoptosis signal-regulating kinase 1-mediated sustained p38 mitogen-activated protein kinase activation regulates mycoplasmal lipoprotein- and staphylococcal peptidoglycan-triggered Toll-like receptor 2 signalling pathways.

Toll-like receptor (TLR) 2 functions as a sensor for detecting various microbial components conserved in bacteria or fungi in innate immunity. TLR2 induces several signalling pathways linking to activation of the transcriptional factors NF-kappaB and AP-1 as well as induction of cell death. In human embryonic kidney 293 cells expressed human TLR2, mycoplasmal lipoproteins (MLP) or staphylococcal peptidoglycans (PGN) induced sustained phosphorylation of p38 mitogen-activated protein kinase (MAPK), accompanied by generation of reactive oxygen species. This observation encouraged us to examine roles of apoptosis signal-regulating kinase 1 (ASK1) in TLR2 signalling, because ASK1 is an upstream activator of p38 MAPK during exposure to oxidative stress and other stressful stimuli. A kinase-inactive mutant of ASK1 greatly impaired the sustained phosphorylation of p38 MAPK induced by MLP or PGN. This mutant also attenuated MLP- or PGN-induced transcriptional activities of NF-kappaB and AP-1 via inhibition of p38 MAPK activation. MLP- or PGN-induced cell death reactions, including DNA fragmentation and caspase-3/7 activation, were also down-regulated by the ASK1 mutant via p38 MAPK inhibition. Furthermore, TLR2 signalling had a potential to phosphorylate and dephosphorylate ASK1 at Ser83 residue. Thus, MLP and PGN have capabilities to induce ASK1-dependent signalling pathways which regulate p38 MAPK activation through TLR2, leading to activation of NF-kappaB and AP-1 as well as induction of cell death.

Apoptosis↗
PubMed1996

Entry of pathogens into the central nervous system.

The blood-brain barrier (BBB) is formed by the tight junctions of the cerebral capillary endothelium and the choroid plexus epithelium. The molecular anatomy of the tight junction resembles that of a polarized, transporting epithelium, suggesting some model cell culture systems can provide insight into traffic into the central nervous system. Pathogens target both the endothelium, causing encephalitis, and the choroid plexus, leading to meningitis. Routes of entry are diverse including paracellular and transcellular penetration. In addition, circulating microbial products can induce loss of BBB function. Understanding the heterogeneous molecular interactions between pathogens and the BBB may provide avenues to interrupt the devastating neurological sequelae that accompany central nervous system infections.

Bacteria↗