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PubMed2006

Methods for predicting bacterial protein subcellular localization.

The computational prediction of the subcellular localization of bacterial proteins is an important step in genome annotation and in the search for novel vaccine or drug targets. Since the 1991 release of PSORT I--the first comprehensive algorithm to predict bacterial protein localization--many other localization prediction tools have been developed. These methods offer significant improvements in predictive performance over PSORT I and the accuracy of some methods now rivals that of certain high-throughput laboratory methods for protein localization identification.

Amino Acid Sequence↗
PubMed1990

Determinants of membrane-targeting and transmembrane translocation during bacterial protein export.

We have separately analyzed membrane-targeting and membrane translocation of an exported bacterial protein. The precursor of the outer membrane protein LamB of Escherichia coli was synthesized in vitro and translocated into inverted plasma membrane vesicles under co- and post-translational conditions. The translation/translocation products of LamB were subsequently resolved into soluble and membrane-associated material. Dissipation of the H(+)-motive force, depletion of ATP and treatment of membranes with N-ethylmaleimide each inhibited processing and translocation of preLamB without preventing its binding to the membranes. Hence, all three conditions block transmembrane passage rather than membrane-targeting. The latter was abolished by pretreatment of salt-extracted membrane vesicles with trypsin. It was also drastically reduced when preLamB was synthesized in cell extracts derived from either a secA amber or a secB null mutant. Membrane-targeting of preLamB therefore requires soluble SecA and SecB as well as a protease-sensitive membrane receptor. The finding that SecA is involved in targeting whereas ATP is required for the transmembrane passage suggests that SecA, which harbors an ATPase activity [Lill et al. (1989), EMBO J., 8, 961-966], might have a dual function in bacterial protein export.

Adenosine Triphosphate↗
PubMed2002

Human neutrophils use the myeloperoxidase-hydrogen peroxide-chloride system to chlorinate but not nitrate bacterial proteins during phagocytosis.

The generation of extracellular oxidants by neutrophils has been widely investigated, but knowledge about the chemical reactions that occur in the phagolysosome, the cellular compartment that kills pathogens, is more limited. One important pathway may involve the production of potent halogenating agents such as hypochlorous acid (HOCl) by the myeloperoxidase-hydrogen peroxide-halide system. However, explorations of the oxidation chemistry of phagolysosomes have been hampered by the organelle's inaccessibility. To overcome this limitation, we recovered Escherichia coli that had been internalized by human neutrophils. We then analyzed the bacterial proteins for 3-chlorotyrosine, a stable marker of damage by HOCl. Mass spectrometric analysis revealed that levels of 3-chlorotyrosine in E. coli proteins increased markedly after the bacteria were internalized by human neutrophils. This increase failed to occur in E. coli exposed to neutrophils deficient in NADPH oxidase or myeloperoxidase, implicating H(2)O(2) and myeloperoxidase in the halogenation reaction. The extent of protein chlorination by normal neutrophils paralleled bacterial killing. Our observations support the view that the phagolysosome of human neutrophils uses the myeloperoxidase-hydrogen peroxide-chloride system to chlorinate bacterial proteins. In striking contrast, human neutrophils failed to nitrate bacterial proteins unless the medium was supplemented with 1 mm nitrite, and the level of nitration was low. Protein chlorination associated with bacterial killing was unaffected by the presence of nitrite in the medium. Nitration required NADPH oxidase but appeared to be independent of myeloperoxidase, suggesting that neutrophils can nitrate proteins through a pathway that requires nitrite but is independent of myeloperoxidase.

Bacterial Proteins↗
PubMed1993

Bacterial proteins binding to the mammalian extracellular matrix.

Pathogenic bacteria frequently express surface proteins with affinity for components of the mammalian extracellular matrix, i.e. collagens, laminin, fibronectin or proteoglycans. This review summarizes our current knowledge on the mechanisms of bacterial adherence to extracellular matrices and on the biological significance of these interactions. The best-characterized bacterial proteins active in these interactions are the mycobacterial fibronectin-binding proteins, the fibronectin- and the collagen-binding proteins of staphylococci and streptococci, specific enterobacterial fimbrial types, as well as the polymeric surface proteins YadA of yersinias and the A-protein of Aeromonas. Some of these bacterial proteins are highly specific for an extracellular matrix protein, some are multifunctional and express binding activities towards a number of target proteins. The interactions can be based on a protein-protein or on a protein-carbohydrate interaction, or on a bridging mechanism mediated by a bivalent soluble target protein. Many of the interactions have also been demonstrated on tissue sections or in vivo, and adherence to the extracellular matrix has been shown to promote bacterial colonization of damaged tissues.

Adhesins, Bacterial↗
PubMed1980

Rumen bacterial protein synthesis and the proportion of dietary protein escaping degradation in the rumen of sheep.

1. The effect of supplementing barley diets with urea (U), extracted, decorticated groundnut meal (GNM) or Peruvian fish meal (PFM) on rumen bacterial protein synthesis and the proportion of undegraded food protein passing to the duodenum of sheep has been examined. 2. Three wethers were given isonitrogenous, isoenergetic diets containing (g/kg dry matter (DM)): U 20, GNM 106 or PFM 78, the crude protein (nitrogen x 6.25) contents being 139, 145 and 148 respectively. The sheep were fed hourly, the mean daily intake of DM being 0.634 kg. 3. Rumen bacterial protein synthesis was determined using 35S and diaminopimelic acid (DAPA) as bacterial markers and polyethylene glycol (PEG) and chromic oxide as markers of digesta flow. Rumen volatile fatty acid (VFA) production rate was determined by a continuous infusion of [1-14C]acetate. 4. 35S and DAPA gave similar estimates of the proportion of bacterial N in the trichloroacetic acid-precipitable nitrogen of the rumen digesta, the mean value being 0.86. The VFA production rate did not vary significantly between diets, the mean being 5.8 mol/24 h. The flow of bacterial N from the rumen was calculated from the PEG and CR2O3 estimates of flow and the 35S and DAPA estimates of the proportion of bacterial N in the rumen. 35S and DAPA gave similar values (mean 12.5 g/24 h) and Cr2O3 gave a slightly lower value (11.5 g/24 h) than PEG (13.5 g/24 h). Dietary effects, averaged over the four methods, were not significant; the values were 13.0, 13.4 and 11.0 g/24 h for the U, GNM and PFM diets respectively. 5. Duodenal samples were taken from two 12 h continuous collections from re-entrant cannulas and the DM flow adjusted to total recovery of Cr2O3. The mean recovery Cr2O3 at the duodenum was 0.798. The rates of flow of DM were 0.296, 0.311 and 0.334 kg/24 h and of non-ammonia-N (NAN) 13.5, 15.2 and 15.4 g/24 h on the U, GNM and PFM diets respectively. 6. The concentrations of the essential amino acids in duodenal digesta were generally higher with the PFM diet than with either of the other two diets. The flow of most amino acids through the duodenum was generally higher on the PFM and GNM diets than on the U diet. 7. The energetic efficiency of bacterial protein synthesis was calculated to be 2.1 g bacterial N/mol VFA or 28 g bacterial N/kg organic matter fermented in the rumen. 8. From the estimates of bacterial N flow the rumen and NAN flow through the duodenum it was calculated that 0.22 and 0.69 of the supplemental N from GNM and PFM respectively passed through the rumen undegraded.

Amino Acids↗
PubMed1997

Structural and functional characterisation of two proteolytic fragments of the bacterial protein toxin, pneumolysin.

Proteolytic cleavage of the bacterial protein toxin pneumolysin with protease K creates two fragments of 37 and 15 kDa. This paper describes the purification of these two fragments and their subsequent physical and biological characterisation. The larger fragment is directly involved in the cytolytic mechanism of this pore-forming protein, via membrane binding and self-association. The smaller fragment lacks ordered structure or discernible activity.

Bacterial Proteins↗
PubMed1995

[Detection of bacterial protein toxins by a bead-ELISA].

A highly sensitive bead-enzyme-linked immunosorbent assay to detect bacterial protein toxins was developed. Fab' of anti-toxin IgG was conjugated with horseradish peroxidase by the maleimide method and tetramethylbenzidine was used as a substrate. As the solid phase, a 6.5 mm diameter polystyrene bead was used and this was coated with the anti-toxin IgG. The sensitivities of the bead-ELISA for various bacterial protein toxins were as follows: less than 40 pg/ml for cholera enterotoxin (CT), less than 20 pg/ml for VT1 and less than 6 pg/ml for VT2 of enterohemorrhagic Escherichia coli. The bead ELISA was evaluated for direct detection of CT from stool specimens of patients with acute secretory diarrhea. Of the 75 stool samples examined, 59 yielded biochemically and serologically confirmed strains of Vibrio cholerae O1. The bead ELISA was positive for CT in stool supernatants in 50 (84.7%) of the 59 samples from which V. cholerae O1 was isolated. In addition, the bead ELISA was positive for three stool specimens which were negative by culture. These data indicate that the bead ELISA is a sensitive and simple method for direct detection of CT in nonsterile stool samples.

Acute Disease↗
PubMed2000

Bacterial protein toxins targeting rho GTPases.

Several bacterial protein toxins target eukaryotic cells by modulating the functions of Rho GTPases that are involved in various signal processes and in the regulation of the actin cytoskeleton. The toxins inhibit Rho functions by ADP-ribosylation or glucosylation and activate them by deamidation and transglutamination. New findings indicate that the GTPases are also targeted by various 'injected' toxins which are introduced into the eukaryotic cells by the type-III secretion system. The injected toxins do not covalently modify Rho GTPases, but manipulate their regulatory GTPase cycle by acting as GTPase-activating proteins or guanine nucleotide exchange factors.

Bacteria↗
PubMedDate not supplied

Rho GTPases as targets of bacterial protein toxins.

Several bacterial toxins target Rho GTPases, which constitute molecular switches in several signaling processes and master regulators of the actin cytoskeleton. The biological activities of Rho GTPases are blocked by C3-like transferases, which ADP-ribosylate Rho at Asn41, but not Rac or Cdc42. Large clostridial cytotoxins (e. g., Clostridium difficile toxin A and B) glucosylate Rho GTPases at Thr37 (Rho) or Thr35 (Rac/Cdc42), thereby inhibiting Rho functions by preventing effector coupling. The 'injected' toxins ExoS, YopE and SptP from Pseudomonas aeruginosa, Yersinia and Salmonella ssp., respectively, which are transferred into the eukaryotic target cells by the type-III secretion system, inhibit Rho functions by acting as Rho GAP proteins. Rho GTPases are activated by the cytotoxic necrotizing factors CNF1 and CNF2 from Escherichia coli and by the dermonecrotizing toxin DNT from B. bronchiseptica. These toxins deamidate/transglutaminate Gln63 of Rho to block the intrinsic and GAP-stimulated GTP hydrolysis, thereby constitutively activating the GTPases. Rho GTPases are also activated by SopE, a type-III system injected protein from Salmonella ssp., that acts as a GEF protein.

Bacterial Toxins↗
PubMed2001

Specificity of signal peptide recognition in tat-dependent bacterial protein translocation.

The bacterial twin arginine translocation (Tat) pathway translocates across the cytoplasmic membrane folded proteins which, in most cases, contain a tightly bound cofactor. Specific amino-terminal signal peptides that exhibit a conserved amino acid consensus motif, S/T-R-R-X-F-L-K, direct these proteins to the Tat translocon. The glucose-fructose oxidoreductase (GFOR) of Zymomonas mobilis is a periplasmic enzyme with tightly bound NADP as a cofactor. It is synthesized as a cytoplasmic precursor with an amino-terminal signal peptide that shows all of the characteristics of a typical twin arginine signal peptide. However, GFOR is not exported to the periplasm when expressed in the heterologous host Escherichia coli, and enzymatically active pre-GFOR is found in the cytoplasm. A precise replacement of the pre-GFOR signal peptide by an authentic E. coli Tat signal peptide, which is derived from pre-trimethylamine N-oxide (TMAO) reductase (TorA), allowed export of GFOR, together with its bound cofactor, to the E. coli periplasm. This export was inhibited by carbonyl cyanide m-chlorophenylhydrazone, but not by sodium azide, and was blocked in E. coli tatC and tatAE mutant strains, showing that membrane translocation of the TorA-GFOR fusion protein occurred via the Tat pathway and not via the Sec pathway. Furthermore, tight cofactor binding (and therefore correct folding) was found to be a prerequisite for proper translocation of the fusion protein. These results strongly suggest that Tat signal peptides are not universally recognized by different Tat translocases, implying that the signal peptides of Tat-dependent precursor proteins are optimally adapted only to their cognate export apparatus. Such a situation is in marked contrast to the situation that is known to exist for Sec-dependent protein translocation.

Amino Acid Sequence↗
PubMed1986

Inhibition of K88-mediated adhesion of Escherichia coli to mammalian receptors by antibiotics that affect bacterial protein synthesis.

The ability of ten inhibitors of bacterial protein synthesis to decrease adhesion of Escherichia coli bearing K88ac fimbriae was examined. In the presence of the antibiotics at concentrations below the MIC values neomycin was the least effective inhibitor of adhesion and minocycline the most active. The effect of minocycline on the synthesis of individual polypeptides encoded by the K88ac determinant was examined in detail. The rate of synthesis of K88ac pilus protein in the presence of minocycline 0.75 mg/l (0.5 MIC) was less than that of total cell protein synthesis, suggesting that pilus protein becomes progressively 'diluted' in the outer membrane during exposure to this antibiotic concentration. Furthermore, the synthesis of two 'helper' polypeptides (molecular weights of 27.5 K and 27 K) which are probably involved in secretion of K88ac pilus protein through the cell envelope, was particularly sensitive to minocycline. Our observations suggest that the ability of translational inhibitors to decrease K88ac mediated adhesion probably results from direct inhibition of synthesis of fimbrial protein itself, together with inhibition of 'helper' polypeptide synthesis.

Animals↗
PubMed1992

How bacterial protein toxins enter cells; the role of partial unfolding in membrane translocation.

Bacterial protein toxins translocate across membranes by processes that are still mysterious. Studies on diphtheria toxin have shown that partial unfolding processes play a major role in toxin membrane insertion and translocation. Similar unfolding behaviour is seen with other bacterial toxins. The lessons gained from this behaviour allow us to propose novel mechanisms for toxin translocation.

Bacterial Proteins↗
PubMed2001

Effects of alimet on nutrient digestibility, bacterial protein synthesis, and ruminal disappearance during continuous culture.

A dual effluent continuous culture system was used to investigate the effects of inclusion of Alimet (Novus International, Inc., St. Louis, MO) feed supplement [an 88% aqueous solution of dl, 2-hydroxy-4-(methylthio) butanoic acid (HMB)] in the diet on nutrient digestibility, bacterial protein synthesis and ruminal disappearance of HMB. Four fermenters were fed three times daily a basal diet that consisted of 50% grain mixture and 50% forage for 9 d. In experiment 1, four concentrations of HMB (0, 0.20, 0.77, and 1.43% DM basis) were added to the diet and fed to the fermenters twice daily. In experiment 2, two concentrations of dietary HMB (0 and 0.88% DM basis) were fed twice daily and evaluated with two solids retention times (16.7 vs. 25.0 h) and two liquid dilution rates (0.15 vs. 0.125 h(-1)). Increasing the amount of HMB in the diet did not affect nutrient digestibility, volatile fatty acid concentrations, or ruminal escape of HMB. Bacterial protein synthesis was improved with the addition of HMB during high and low retention times. The extent of HMB escaping ruminal degradation ranged from 21.6 to 43.2% and was highest at the lower retention time. It can be concluded that a fraction of HMB survives rumen microbial degradation and, therefore, provides a rumen-protected form of methionine at the same time that it improves bacterial protein synthesis.

Ammonia↗
PubMed2006

Molecular imprinted polymer with cloned bacterial protein template enriches authentic target in cell extract.

Here we describe a new method for preparing a protein-imprinted polymer with a cloned bacterial protein template, which recognizes/adsorbs authentic target protein present at a relatively low level in cell extract. In this work, cloned pig cyclophilin 18 (pCyP18) was used as a template. The template protein was selectively assembled with memory molecules from their library, which consists of numerous limited length polymer chains with randomly distributed recognition sites and immobilizing sites. These assemblies of protein and memory molecules were adsorbed by porous polymeric beads and immobilized by cross-linking polymerization. After removing the template, binding sites that were complementary to the target protein in size, shape and the position of recognition groups were exposed, and their confirmation was preserved by the cross-linked structure. The synthesized imprinted polymer was used to adsorb authentic pCyP18 from cell extract, and its proportional content was enriched 300 times.

Bacterial Proteins↗
PubMed1976

A proposal for a uniform nomenclature for the genetics of bacterial protein synthesis.

A new genetic nomenclature for the macromolecules involved in bacterial protein synthesis is proposed and explained. Genes for ribosomal proteins are designated rsp, rpl and rpm while genes for ribosomal RNAs are rrs and rrl. Protein synthesis factors and ribosome assembly and modification activities are also consistantly named.

Bacterial Proteins↗
PubMed1989

Effects of a salivary stimulant, slaframine, on ruminal fermentation, bacterial protein synthesis and digestion in frequently fed steers.

Slaframine (SF), a parasympathomimetic salivary stimulant, was administered i.m. (10, 15 or 20 micrograms SF/kg BW) to ruminally and abomasally fistulated steers at 12-h intervals for 18-d periods in a latin square-designed experiment. Steers were fed semicontinuously (12 times daily) a 40:60 roughage:concentrate diet at twice their net energy requirement for maintenance. Ruminal digestion coefficients for DM, ADF and starch were 10 to 16% lower and linearly related in an inverse manner to the level of SF administered (P less than .05). Postruminal digestion of DM, ADF and starch increased as much as 46.7, 9.5 and 44.0%, respectively, in a fashion linearly related (P less than .05) to the level of SF administered. Total tract digestion of DM and ADF were not affected by SF; however, total tract starch digestion was increased as much as 5% and was related linearly (P less than .05) to SF treatment. With SF administration, as much as 13% more bacterial protein exited the rumen, resulting in a 16.5% linear improvement (P less than .1) in the efficiency of ruminal bacterial protein production per 100 g of OM fermented. Ruminal concentrations of VFA, ammonia and pH were not affected by SF. These results demonstrate a positive relationship between salivation and ruminal bacterial protein synthesis and suggest that feed utilization by ruminants may be improved by pharmacological stimulation of salivary secretions.

Abomasum↗
PubMed1993

Rendering a membrane protein soluble in water: a common packing motif in bacterial protein toxins.

The recently determined structures of three different protein toxins by X-ray crystallography has unexpectedly revealed a common membrane-insertion domain. This domain consists of an alpha-helical bundle of between seven and ten helices, some of which are hydrophobic. The three toxins, colicin, insecticidal delta-endotoxin and diphtheria toxin are directed towards different hosts, have different killing mechanisms and bear no sequence homology. The observation of a common membrane-insertion domain has implications for the design of therapeutic agents in combating disease.

Bacillus thuringiensis Toxins↗