Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Nickel is a cofactor for various microbial enzymes, yet as a trace element, its scavenging is challenging. In the case of the pathogen Helicobacter pylori, nickel is essential for the survival in the human stomach, because it is the cofactor of the important virulence factor urease. While nickel transport across the cytoplasmic membrane is accomplished by the nickel permease NixA, the mechanism by which nickel traverses the outer membrane (OM) of this Gram-negative bacterium is unknown. Import of iron-siderophores and cobalamin through the bacterial OM is carried out by specific receptors energized by the TonB/ExbB/ExbD machinery. In this study, we show for the first time that H. pylori utilizes TonB/ExbB/ExbD for nickel uptake in addition to iron acquisition. We have identified the nickel-regulated protein FrpB4, homologous to TonB-dependent proteins, as an OM receptor involved in nickel uptake. We demonstrate that ExbB/ExbD/TonB and FrpB4 deficient bacteria are unable to efficiently scavenge nickel at low pH. This condition mimics those encountered by H. pylori during stomach colonization, under which nickel supply and full urease activity are essential to combat acidity. We anticipate that this nickel scavenging system is not restricted to H. pylori, but will be represented more largely among Gram-negative bacteria.
Mol Microbiol 2007 Feb
PMID:Novel nickel transport mechanism across the bacterial outer membrane energized by the TonB/ExbB/ExbD machinery. 1723 22

Helicobacter pylori is an important risk factor of duodenal ulcer (DU). Although many virulence factors of H. pylori have been identified, few have been reported to show an association with the pathogenesis of DU. The aims of this study were to identify H. pylori antigens showing a high seropositivity in DU and to develop a platform for rapid and easy diagnosis for DU. Because DU and gastric cancer (GC) are considered clinical divergent gastroduodenal diseases, we compared two-dimensional immunoblots of an acid-glycine extract of an H. pylori strain from a patient with DU probed with serum samples from 10 patients with DU and 10 with GC to identify DU-related antigens. Of the 11 proteins that were strongly recognized by serum IgG from DU patients, translation elongation factor EF-G (FusA), catalase (KatA), and urease alpha subunit (UreA) were identified as DU-related antigens, showing a higher seropositivity in DU samples (n = 124) than in GC samples (n = 95) (FusA, 70.2 versus 45.3%; KatA, 50.8 versus 41.1%; UreA, 44.4 versus 27.4%). In addition, we found that the use of multiple antigens improved the discrimination between patients with DU and those with GC as the odds ratios increased from 1.82 (95% confidence interval (CI), 0.79-4.21; p = 0.1607) for seropositivity for FusA, KatA, or UreA alone to 4.95 (95% CI, 2.05-12.0; p = 0.0004) for two of the three antigens and to 5.71 (95% CI, 1.86-17.6; p = 0.0024) for all three antigens. Moreover a protein array containing the three DU-related antigens was developed to test the idea of using multiple biomarkers in diagnosis. We conclude that FusA, KatA, and UreA are DU-related antigens of H. pylori, and the combination of these on a protein array provided a rapid and convenient method for detecting serum antibody patterns of DU patients.
Mol Cell Proteomics 2007 Jun
PMID:Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches. 1731 59

Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.
Nat Struct Mol Biol 2007 Apr
PMID:Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. 1735 29

The dose effects of pectic polysaccharide-rich extract from the food spice cardamom (Amomum villosum Lour.) on intestinal environment were investigated. The results showed that pectic polysaccharides and hemicellulose were the major polysaccharides in the cardamom extract. The administration of cardamom extract (0.5 and 1.5 g/100 g diet) effectively (p < 0.05) shortened hamster gastrointestinal transit time by approximately 58%, increased fecal moisture contents (148-174%), increased SCFA concentrations in hindgut (4.0- to 7.8-fold), decreased the activities of beta-D-glucuronidase (by 71.4-85.7%), beta-D-glucosidase (by 24.3-51.5%), mucinase (by 63.6-72.7%), and urease (by 88.8-90.4%) in feces, and reduced the production of toxic ammonia (by 16.1-64.5%). These findings suggested that the consumption of cardamom extract (at least 0.5 g/100 g diet or 40 mg/day) might exert a favorable effect on improving the gastrointestinal milieu, and also provide a clue to substantiate its traditional therapeutic uses and dosage for intestinal health improvement.
Mol Nutr Food Res 2007 May
PMID:Dose effects of the food spice cardamom on aspects of hamster gut physiology. 1744 Sep 96

Azure A and methylene blue ("Diff-Quik," DQ) and tissue urease (U) tests are popular methods to diagnose Helicobacter pylori. These tests usually correlate well but sometimes produce discordant results. This study evaluates the DQ and U tests by comparing them with the immunoperoxidase reference method to resolve discordant results. DQ and U tests were performed on gastric biopsies. Results were tabulated as DQ(+)/U(+), DQ(+)/U(-), DQ(-)/U(+), and DQ(-)/U(-). Cases that were DQ(+)/U(+) were recorded as positive and not tested with immunoperoxidase. Cases that had discordant DQ/U results were tested by immunoperoxidase to resolve the discordance. Cases which were negative for both DQ/U were evaluated by immunoperoxidase to confirm the validity of DQ(1-)/U(-). The groups were compared with concordant results (DQ(1-)/U(-) group) and immunoperoxidase versus discordant DQ/U results and immunoperoxidase. There were 56 gastric biopsy specimens. Among all cases, 6 were DQ(+)/U(+). Of the remaining 50 cases, 38 were concordant DQ(-)/U(-), whereas 12 showed discordant DQ/U results. All 38 concordant DQ(-)/U(-) specimens were confirmed negative, 11 discordant DQ/U cases were confirmed negative, and 1 DQ(+)/U(-) specimen was confirmed positive by immunoperoxidase. Comparison of concordant versus discordant results was not statistically significant (P=0.10). Among all discordant DQ and U, 11/12 (92%) were confirmed negative by immunoperoxidase. Thus, both concordant negative results and discordant results can be considered negative. Such interpretation of discordant results might prevent unnecessary additional procedures or treatment.
Appl Immunohistochem Mol Morphol 2007 Jun
PMID:Immunoperoxidase in the interpretation of discordant histologic and urease findings for Helicobacter pylori. 1752 34

Conjugation of enzymes to antibodies involves the formation of a stable, covalent linkage between an enzyme [e.g., horseradish peroxidase (HRPO), urease, or alkaline phosphatase] and an antigen-specific monoclonal or polyclonal antibody in which neither the antigen-combining site of the antibody nor the active site of the enzyme is functionally altered. This unit describes procedures for cross-linking HRPO, urease or alkaline phosphatase to immunoaffinity-purified monoclonal or polyclonal antibodies (IgG).
Curr Protoc Mol Biol 2001 May
PMID:Conjugation of enzymes to antibodies. 1826 67

Mycoplasmas are parasitic bacteria with small genomes. Since parasitic bacteria need to adapt themselves to their hosts, there is a possibility that some genes evolved under species-specific constraint. We assume that Ureaplasma parvum has candidate genes that evolved in a species-specific manner in its genome. Here we examined synonymous-to-nonsynonymous substitution ratios (omega) of the 143 mycoplasma-orthologous genes of Ureaplasma and other mycoplasmas using branch models. As a result, the model allowing for Ureaplasma branch-specific omega in addition to omega of other mycoplasmas was significantly supported in 16 genes. First, the Ureaplasma-specific model was significantly supported in the genes encoding a transcription elongation factor and a transcription terminator factor, suggesting that transcription-related genes of Ureaplasma have evolved in a unique manner compared to those of other mycoplasmas. Second, the Ureaplasma-specific model was significantly supported in the gene encoding uracil-DNA glycosylase. In addition, the omega value of the gene in the Ureaplasma lineage was approximately 30-fold lower than those of other lineages, suggesting that uracil-DNA glycosylase of Ureaplasma evolved under stronger functional constraint than those of other mycoplasmas. Finally, three glycolytic genes of Ureaplasma were suggested to have evolved under relaxed selection. Among mycoplasmas, only Ureaplasma has urease and synthesizes ATPs via hydrolysis of urea. This raises the possibility that Ureaplasma does not need a glycolysis pathway for ATP synthesis. This unique energy-producing system may be related to the Ureaplasma-specific evolution of the glycolytic genes.
J Mol Evol 2008 May
PMID:Detection of the genes evolving under Ureaplasma-specific selection. 1841 24

One of the six predicted Proteus mirabilis autotransporters (ATs), ORF c2341, is predicted to contain a serine protease motif and was earlier identified as an immunogenic outer membrane protein in P. mirabilis. The 3.2 kb gene encodes a 117 kDa protein with a 58-amino-acid-long signal peptide, a 75-kDa-long N-terminal passenger domain and a 30-kDa-long C-terminal translocator. Affinity-purified 110 kDa AT exhibited chymotrypsin-like activity and hydrolysed N-Suc-Ala-Ala-Pro-Phe-pNa and N-Suc-Ala-Ala-Pro-Leu-pNa with a K(M) of 22 muM and 31 muM, respectively, under optimal pH of 8.5-9.0 in a Ca(2+)-dependent manner. Activity was inhibited by subtilase-specific inhibitors leupeptin and chymostatin. Both the cell-associated and purified form elicited cytopathic effects on cultured kidney and bladder epithelial cells. Substrate hydrolysis as well as cytotoxicity was associated with the passenger domain and was compromised upon mutation of any of the catalytic residues (Ser366, His147 and Asp533). At alkaline pH and optimal cell density, the AT also promoted autoaggregation of P. mirabilis and this function was independent of its protease activity. Cytotoxicity, autoaggregation and virulence were significantly reduced in an isogenic pta mutant of P. mirabilis. Proteus toxic agglutinin (Pta) represents a novel autotransported cytotoxin with no bacterial homologues that works optimally in the alkalinized urinary tract, a characteristic of urease-mediated urea hydrolysis during P. mirabilis infection.
Mol Microbiol 2008 May
PMID:A novel autotransporter of uropathogenic Proteus mirabilis is both a cytotoxin and an agglutinin. 1843 84

Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyveri, we show that during degradation, uracil is not reduced to dihydrouracil. Six loci, named URC1-6 (for uracil catabolism), are involved in the novel catabolic pathway. Four of them, URC3,5, URC6, and URC2 encode urea amidolyase, uracil phosphoribosyltransferase, and a putative transcription factor, respectively. The gene products of URC1 and URC4 are highly conserved proteins with so far unknown functions and they are present in a variety of prokaryotes and fungi. In bacteria and in some fungi, URC1 and URC4 are linked on the genome together with the gene for uracil phosphoribosyltransferase (URC6). Urc1p and Urc4p are therefore likely the core components of this novel biochemical pathway. A combination of genetic and analytical chemistry methods demonstrates that uridine monophosphate and urea are intermediates, and 3-hydroxypropionic acid, ammonia and carbon dioxide the final products of degradation. The URC pathway does not require the presence of an active respiratory chain and is therefore different from the oxidative and rut pathways described in prokaryotes, although the latter also gives 3-hydroxypropionic acid as the end product. The genes of the URC pathway are not homologous to any of the eukaryotic or prokaryotic genes involved in pyrimidine degradation described to date.
J Mol Biol 2008 Jul 18
PMID:A second pathway to degrade pyrimidine nucleic acid precursors in eukaryotes. 1855 80

In the human gastric bacterium Helicobacter pylori, two metalloenzymes, hydrogenase and urease, are essential for in vivo colonization, the latter being a major virulence factor. The UreA and UreB structural subunits of urease and UreG, one of the accessory proteins for Ni(2+) incorporation into apourease, were taken as baits for tandem affinity purification. The method allows the purification of protein complexes under native conditions and physiological expression levels of the bait protein. Furthermore the tandem affinity purification technology was combined with in vivo cross-link to capture transient interactions. The results revealed different populations of urease complexes: (i) urease captured during activation by Ni(2+) ions comprising all the accessory proteins and (ii) urease in association with metabolic proteins involved e.g. in ammonium incorporation and the cytoskeleton. Using UreG as a bait protein, we copurified HypB, the accessory protein for Ni(2+) incorporation into hydrogenase, that is reported to play a role in urease activation. The interactome of HypB partially overlapped with that of urease and revealed interactions with SlyD, which is known to be involved in hydrogenase maturation as well as with proteins implicated in the formation of [Fe-S] clusters present in the small subunit of hydrogenase. In conclusion, this study provides new insight into coupling of ammonium production and assimilation in the gastric pathogen and the intimate link between urease and hydrogenase maturation.
Mol Cell Proteomics 2008 Dec
PMID:In vivo interactome of Helicobacter pylori urease revealed by tandem affinity purification. 1868 79


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