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)

Two mRNA analogs, pUUCUAAA (with stop codon UAA) and pUUCUCAA (with Ser codon UCA) containing a perfluoroarylazido group at U4, were used to study the position relative to the 18S rRNA for the first nucleotide of the codon located in the A site of the human 80S ribosome. To place UAA or UCA in the A site, UCC-recognizing tRNAPhe was bound in the P site. With each analog, crosslinking was detected for highly conserved fragment 1816-1831, which contains invariant dinucleotide A1823/A1824 and is in helix 44 at the 3' end of the 18S rRNA. Since 18S rRNA modification did not depend on whether the U4 photoreactive group was in the sense or stop codon, it was assumed that polypeptide chain release factor 1 directly recognizes the trinucleotide of a stop codon located in the A site.
Mol Biol (Mosk)
PMID:[Highly conserved region 1816-1831 of the 18S ribosomal RNA is close to the first nucleotide of the A-site codon in elongation and termination of translation]. 1281 56

Soybean (Glycine max [L.] Merrill) mutant aj6 carries a single recessive lesion, aj6, that eliminates ubiquitous urease activity in leaves and callus while retaining normal embryo-specific urease activity. Consistently, aj6/aj6 plants accumulated urea in leaves. In crosses of aj6/aj6 by urease mutants at the Eu1, Eu2, and Eu3 loci, F(1) individuals exhibited wild-type leaf urease activity, and the F(2) segregated urease-negative individuals, demonstrating that aj6 is not an allele at these loci. F(2) of aj6/aj6 crossed with a null mutant lacking the Eu1-encoded embryo-specific urease showed that ubiquitous urease was also inactive in seeds of aj6/aj6. The cross of aj6/aj6 to eu4/eu4, a mutant previously assigned to the ubiquitous urease structural gene (R.S. Torisky, J.D. Griffin, R.L. Yenofsky, J.C. Polacco [1994] Mol Gen Genet 242: 404-414), yielded an F(1) having 22% +/- 11% of wild-type leaf urease activity. Coding sequences for ubiquitous urease were cloned by reverse transcriptase-polymerase chain reaction from wild-type, aj6/aj6, and eu4/eu4 leaf RNA. The ubiquitous urease had an 837-amino acid open reading frame (ORF), 87% identical to the embryo-specific urease. The aj6/aj6 ORF showed an R201C change that cosegregated with the lack of leaf urease activity in a cross against a urease-positive line, whereas the eu4/eu4 ORF showed a G468E change. Heteroallelic interaction in F(2) progeny of aj6/aj6 x eu4/eu4 resulted in partially restored leaf urease activity. These results confirm that aj6/aj6 and eu4/eu4 are mutants affected in the ubiquitous urease structural gene. They also indicate that radical amino acid changes in distinct domains can be partially compensated in the urease heterotrimer.
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PMID:Interallelic complementation at the ubiquitous urease coding locus of soybean. 1291 38

Ureaplasma urealyticum is a common inhabitant of mucosal surfaces but is also associated with a higher incidence of pneumonia and bronchopulmonary dysplasia in preterm infants. Culture and polymerase chain reaction demonstrate high isolation rates of ureaplasma in clinical specimens documenting their presence but do not associate the organism directly with the diseased tissue. In this study, lung tissue samples from newborn mice inoculated intranasally with U. urealyticum were used to develop an in situ hybridization (ISH) test for the organism. In situ hybridization allows the localization of gene expression for visualization within the context of tissue morphology. New techniques which use biotinyl-tyramide based signal amplification have been able to greatly enhance the sensitivity of ISH. Using the Dako GenPoint Catalyzed Signal Amplification system to detect a biotinylated DNA probe specific for an internal nucleotide sequence within the urease gene of U. urealyticum, the organism was detected within the infected murine lung tissues. Electron microscopy was used to verify the presence of the organisms in the positive ISH areas. The ISH procedure developed in this study can be used to analyze the presence of ureaplasma in human neonatal lung tissue with the corresponding histopathology.
Exp Mol Pathol 2003 Oct
PMID:Ureaplasma in lung. 1. Localization by in situ hybridization in a mouse model. 1451 80

The carbon-14 urea breath test (UBT) is a reliable and non-invasive technique for the diagnosis of Helicobacter pylori (HP) infection. In this study we evaluated the diagnostic performance of a new, practical and low-dose (14)C-UBT system for the diagnosis of HP and compared the results with those obtained using the standard method. Seventy-five patients (56 female, 19 male) with dyspepsia underwent (14)C-UBT and endoscopy with antral biopsies for histological analysis. The rapid urease test (CLO test) was applied to 50 of these patients. After a 6-h fasting period, a 37-kBq (14)C-urea capsule was swallowed for UBT. Breath samples were collected and counted using two different methods, the Heliprobe method and the standard method. In the Heliprobe method, patients exhaled into a special dry cartridge system (Heliprobe BreathCard) at 10 min. The activities of the cartridges were counted using a designated small GM counter system (Heliprobe analyser). Results were expressed both as counts per minute (HCPM) and as grade (0, not infected; 1, equivocal; 2, infected) according to the counts. In the standard method, breath samples were collected by trapping in a liquid CO(2) absorber. Radioactivity was counted as disintegrations per minute (SDPM) using a liquid scintillation counter after addition of a liquid scintillation cocktail. Histological examination was used as a gold standard. Two patients were excluded from the study because of inadequate biopsy sampling. Forty-eight patients (65%) were found to be HP positive on histology. The Heliprobe method correctly classified 48 of 48 HP-positive patients and 19 of 25 HP-negative patients (sensitivity 100%, specificity 76%, PPV 88%, NPV 100%, accuracy 91%). The standard method correctly classified 48 of 48 HP-positive patients and 20 of 25 HP-negative patients (sensitivity 100%, specificity 80%, PPV 90%, NPV 100%, accuracy 93%). On the other hand, the CLO test identified 26 of 32 HP-positive and 12 of 16 HP-negative patients (sensitivity 81%, specificity 75%, PPV 86%, NPV 66%, accuracy 79%). With the Heliprobe method, all of the positive results were grade 2, and all of the negative results were grade 0. No patients were defined as having grade 1 results. Counts allowed clear discrimination of HP-positive and -negative patients with both methods, the difference being statistically significant in each case ( P<0.001). A significant correlation was found between HCPM and SDPM ( r 0.863, P<0.001). According to the ROC analysis, the area under the curve was nearly the same with HCPM (AUC, 0.888; 95% CI, 0.785-0.992) and SDPM (AUC, 0.898; 95% CI, 0.802-0.994). In conclusion, the new (14)C-UBT system is a highly accurate method for the diagnosis of HP infection. It is rapid and practical, and therefore suitable for clinical and office practice.
Eur J Nucl Med Mol Imaging 2003 Nov
PMID:A new, practical, low-dose 14C-urea breath test for the diagnosis of Helicobacter pylori infection: clinical validation and comparison with the standard method. 1457 83

Although successful and persistent colonization of the gastric mucosa depends on the ability to respond to changing environmental conditions and co-ordinate the expression of virulence factors during the course of infection, Helicobacter pylori possesses relatively few transcriptional regulators. We therefore investigated the contribution of the regulatory protein CsrA to global gene regulation in this important human pathogen. CsrA was necessary for full motility and survival of H. pylori under conditions of oxidative stress. Loss of csrA expression deregulated the oxidant-induced transcriptional responses of napA and ahpC, the acid induction of napA, cagA, vacA, the urease operon, and fur, as well as the heat shock responses of napA, groESL and hspR. Although the level of napA transcript was higher in the csrA mutant, its stability was similar in the wild-type and mutant strains, and less NapA protein was produced in the mutant strain. Finally, H. pylori strains deficient in the production of CsrA were significantly attenuated for virulence in a mouse model of infection. This work provides evidence that CsrA has a broad role in regulating the physiology of H. pylori in response to environmental stimuli, and may be important in facilitating adaptation to the different environments encountered during colonization of the gastric mucosa. Furthermore, CsrA appears to mediate its effects in H. pylori at the post-transcriptional level by influencing the processing and translation of target transcripts, with minimal effect on the stability of the target mRNAs.
Mol Microbiol 2004 Jan
PMID:Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori. 1465 8

Helicobacter species can induce carcinoma in the liver of certain mice. Furthermore, Helicobacter pylori (H. pylori) exhibits hepatotoxicity in vitro. These reports indicate that H. pylori may play a role in hepatocarcinogenesis. The aim of this study was to assess the presence of H. pylori in human hepatocellular carcinoma (HCC) to determine if H. pylori may affect the development of this disease. Liver specimens from 15 HCC patients dissected into tumor and non-tumor tissues were examined for H. pylori by PCR using two sets of primers for 16S rRNA and urease B. DNA sequencing analysis was performed to confirm that PCR products with 16S rRNA primers were derived from H. pylori DNA. The specimens were also examined for H. pylori by immunohistochemistry using anti-H. pylori antibody. H. pylori was found in 13 of 15 tumor tissues, not in the non-tumor tissues. By contrast, Escherichia coli and Bacteroides fragilis, frequent colonizers of gut, were not detected by PCR in the HCC tumors. Ten cirrhotic liver tissue specimens and seven normal liver tissue specimens were also negative for H. pylori DNA by PCR. The nucleotide sequence of the amplified fragment shared 100% identity with the 16S rRNA gene of H. pylori. H. pylori was also detected in HCC tissue by immunohistochemical analysis. The presence of H. pylori in human HCC tissue was demonstrated by PCR and immunohistochemical analysis. These findings suggest that H. pylori might contribute to the development of HCC. Further study is needed to prove the pathogenetic role of H. pylori in the development of human HCC.
Int J Mol Med 2004 Feb
PMID:Potential role of Helicobacter pylori in hepatocarcinogenesis. 1471 27

Creatininase from Pseudomonas putida is a member of the urease-related amidohydrolase superfamily. The crystal structure of the Mn-activated enzyme has been solved by the single isomorphous replacement method at 1.8A resolution. The structures of the native creatininase and the Mn-activated creatininase-creatine complex have been determined by a difference Fourier method at 1.85 A and 1.6 A resolution, respectively. We found the disc-shaped hexamer to be roughly 100 A in diameter and 50 A in thickness and arranged as a trimer of dimers with 32 (D3) point group symmetry. The enzyme is a typical Zn2+ enzyme with a binuclear metal center (metal1 and metal2). Atomic absorption spectrometry and X-ray crystallography revealed that Zn2+ at metal1 (Zn1) was easily replaced with Mn2+ (Mn1). In the case of the Mn-activated enzyme, metal1 (Mn1) has a square-pyramidal geometry bound to three protein ligands of Glu34, Asp45, and His120 and two water molecules. Metal2 (Zn2) has a well-ordered tetrahedral geometry bound to the three protein ligands of His36, Asp45, and Glu183 and a water molecule. The crystal structure of the Mn-activated creatininase-creatine complex, which is the first structure as the enzyme-substrate/inhibitor complex of creatininase, reveals that significant conformation changes occur at the flap (between the alpha5 helix and the alpha6 helix) of the active site and the creatine is accommodated in a hydrophobic pocket consisting of Trp174, Trp154, Tyr121, Phe182, Tyr153, and Gly119. The high-resolution crystal structure of the creatininase-creatine complex enables us to identify two water molecules (Wat1 and Wat2) that are possibly essential for the catalytic mechanism of the enzyme. The structure and proposed catalytic mechanism of the creatininase are different from those of urease-related amidohydrolase superfamily enzymes. We propose a new two-step catalytic mechanism possibly common to creatininases in which the Wat1 acts as the attacking nucleophile in the water-adding step and the Wat2 acts as the catalytic acid in the ring-opening step.
J Mol Biol 2004 Mar 19
PMID:Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism. 1500 55

The virulence of pathogenic bacteria is dependent on their adaptation to and survival in the stressful conditions encountered in their hosts. Helicobacter pylori exclusively colonizes the acid stomach of primates, making it an ideal study model. Little is known about how H. pylori responds to the moderately acidic conditions encountered at its colonization site, the gastric mucus layer. Thus, we compared gene expression profiles of H. pylori 26695 grown at neutral and acidic pH, and validated the data for a selection of genes by real-time polymerase chain reaction, dot-blots or enzymatic assays. During growth in acidic conditions, 56 genes were upregulated and 45 genes downregulated. We found that acidity is a signal modulating the expression of several virulence factors. Regulation of genes related to metal ion homeostasis suggests protective mechanisms involving diminished transport and enhanced storage. Genes encoding subunits of the F0F1 ATPase and of a newly identified Na+/H+ antiporter (NhaC-HP0946) were downregulated, revealing that this bacterium uses original mechanisms to control proton entry. Five of the upregulated genes encoded proteins controlling intracellular ammonia synthesis, including urease, amidase and formamidase, underlining the major role of this buffering compound in the protection against acidity in H. pylori. Regulatory networks and transcriptome analysis as well as enzymatic assays implicated two metal-responsive transcriptional regulators (NikR and Fur) and an essential two-component response regulator (HP0166, OmpR-like) as effectors of the H. pylori acid response. Finally, a nikR-fur mutant is attenuated in the mouse model, emphasizing the link between response to acidity, metal metabolism and virulence in this gastric pathogen.
Mol Microbiol 2004 Jul
PMID:Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori. 1522 39

Helicobacter-induced gastritis is considered nowadays an epidemic, the prevalence of which is one of the highest world-wide (70%), with as much as 40% of the population in industrialized countries. Helicobacter pylori (H. pylori) antigens (Ag) capable to elicit a protective immune response in animal models have been identified, but these antigens have not been shown to be strongly immunogenic when administered to humans. Due to their stability in the gastric environment and avidity, passive administration of secretory immunoglobulin A (SIgA) antibodies (Ab) targeting protective Ag might be particularly relevant as a substitute or complement to current therapies. To this aim, we have designed expression vectors to convert a scFv polypeptide specific for H. pylori urease subunit A into human IgG, polymeric IgA (IgAp/d) and SIgA. Purified proteins show proper binding characteristics toward both the native and denatured forms of H. pylori urease. The direct comparison between different isotype and molecular forms, but of unique specificity, demonstrates that SIgA and IgAp/d are more efficient in blocking free and H. pylori-associated urease than IgG and scFv. We conclude that the expression system reported herein will represent a valuable tool to produce human SIgA Ab of multiple specificities against H. pylori antigens involved in colonization and persistence.
Mol Immunol 2004 Aug
PMID:Human polymeric IgA is superior to IgG and single-chain Fv of the same monoclonal specificity to inhibit urease activity associated with Helicobacter pylori. 1530 63

Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein P(II) is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence. The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.
Microbiol Mol Biol Rev 2004 Dec
PMID:Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments. 1559 Jul 77


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