Identification of high affinity Tbf1p-binding sites within the budding yeast genome

The yeast TBF1 gene is essential for mitotic growth and encodes a protein that binds the human telomere repeats in vitro, although its cellular function is unknown. The sequence of the DNA-binding domain of Tbf1p is more closely related to that of the human telomeric proteins TRF1 and TRF2 than to any yeast protein sequence, yet the functional homologue of TRF1 and TRF2 is thought to be Rap1p. In this study we show that the Tbf1p DNA-binding domain can target the Gal4 transactivation domain to a (TTAGGG)_n sequence inserted in the yeast genome, supporting the model that Tbf1p binds this sub-telomeric repeat motif in vivo. Immunofluorescence of Tbf1p shows a spotty pattern throughout the interphase nucleus and along synapsed chromosomes in meiosis, suggesting that Tbf1p binds internal chromosomal sites in addition to sub-telomeric regions. PCR-assisted binding site selection was used to define a consensus for high affinity Tbf1p-binding sites. Compilation of 50 selected oligonucleotides identified the consensus TAGGGTTGG. Five potential Tbf1p-binding sites resulting from a search of the total yeast genome were tested directly in gel shift assays and shown to bind Tbf1p efficiently in vitro, thus confirming this as a valid consensus for Tbf1p recognition.     

In vitro binding of Helicobacter pylori to monohexosylceramides

H. pylori is the major cause of human gastritis, duodenal ulcer and thus gastric adenocarcinoma. Many glycosphingolipid species have been postulated as receptors for H. pylori and it is likely that H. pylori attachment requires multiple, perhaps sequential receptor/ligand interactions. In this study, the binding of a number of H. pylori clinical isolates, as well as stock strains, to acid and neutral glycosphingolipids separated on thin-layer chromatograms was characterized under microaerobic conditions. All H. pylori clinical isolates, laboratory strains and type culture collection strains recognized galactosylceramide (Gal1Cer) with ceramide containing sphingosine and hydroxylated fatty acid (type I), or non-hydroxylated fatty acid (type II), on thin-layer chromatograms and when incorporated into liposomes. The clinical isolates bound stronger to Gal1Cer (type II) than Gal1Cer (type I) on TLC, whereas lab and culture collection strains showed the opposite binding preference. A clear preference in binding to Gal1Cer (type I) incorporated into liposome was shown by most tested strains. Clinical isolates bound well to glucosylceramide (Glc1Cer) with hydroxylated fatty acid, whereas weak binding to this glycolipid was detected with the lab and type collection strains. None of the tested strains bound Glc1Cer with non-hydroxylated fatty acid on the solid surface, but some strains of both clinical or type collection origins showed weak or very weak binding in the liposome assay. A clear distinction between the binding specificity of living organisms (under microaerobic conditions) as opposed to dying organisms (under normoxic conditions) illustrates the importance of cellular physiology in this process.These studies illustrate lipid modulation of the potential receptor function of monohexosylceramides and the distinction between the receptor repertoire of H. pylori clinical isolates and cultured strains commonly used to study host-cell adhesion.     

In vitro inhibition of Helicobacter pylori by micromycetes

The anti-Helicobacter pylori effect of 22 micromycetes were studied against one standard strain and 11 clinical isolates of H. pylori. Penicillium ochlochloron and Penicillium funiculosum have been proven the most active fungi against this microorganism. Further bio-guided chemical analysis of P. funiculosum afforded an active component identified as (-) 2,3,4-trihydroxybutanamide.     

In vitro susceptibility of Helicobacter pylori to trifluoromethyl ketones

Heteroaromatic trifluoromethyl ketones (TFMK's) showed strong inhibitory activity against Helicobacter pylori. The MIC50 observed for 2-trifluoroacetonylbenzoxazole (1) is 20-fold more active than metronidazole and is only twice as high as that of clarithromycin. The inhibitory mode of TFMK's on Hp growth was not related to inhibition of urease.     

In vivo interactome of Helicobacter pylori urease revealed by tandem affinity purification

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.     

In vitro inhibition of Helicobacter pylori by extracts of thyme

Extracts of several plants were tested for inhibitory activity against Helicobacter pylori. Among these plants thyme (aqueous extract) and cinnamon (alcoholic extract) were the most effective. Since aqueous extract of thyme is easier to produce and consume, it was further investigated. Compared with several antibacterials, the thyme extract had a significant inhibitory effect on H. pylori , reducing both its growth and potent urease activity. From the results of this study, the aqueous extract of thyme possesses a therapeutic potential which merits validation by clinical studies.     

In vitro inhibitory activity of boropinic acid against Helicobacter pylori

In this study, we assessed in vitro minimum inhibitory concentration (MIC) values of some natural geranyloxycoumarins, geranyloxy- and isopentenyloxy acids against growth of Helicobacter pylori. Boropinic acid, active principle isolated from Boronia pinnata (Fam. Rutaceae), was seen to be the most effective compound with a MIC value of 1.62 microg/mL.     

In vitro selection of an RNA sequence that interacts with high affinity with thymidylate synthase

Previous studies have shown that the repressive effect of thymidylate synthase (TS) mRNA translation is mediated by direct binding of TS itself to two cis-acting elements on its cognate mRNA. To identify the optimal RNA nucleotides that interact with TS, we in vitro synthesized a completely degenerate, linear RNA pool of 25 nt and employed in vitro selection to isolate high affinity RNA ligands that bind human TS protein. After 10 rounds of selection and amplification, a single RNA molecule was selected that bound TS protein with nearly 20-fold greater affinity than native, wild-type TS RNA sequences. Secondary structure analysis of this RNA sequence predicted it to possess a stem–loop structure. Deletion and/or modification of the UGU loop element within the RNA sequence decreased binding to TS by up to 1000-fold. In vivo transfection experiments revealed that the presence of the selected RNA sequence resulted in a significant increase in the expression of a heterologous luciferase reporter construct in human colon cancer H630 and TS-overexpressing HCT-C:His-TS+ cells, but not in HCT-C18 cells expressing a functionally inactive TS. In addition, the presence of this element in H630 cells leads to induced expression of TS protein. An immunoprecipitation method using RT–PCR confirmed a direct interaction between human TS protein and the selected RNA sequence in transfected human cancer H630 cells. This study identified a novel RNA sequence from a degenerate RNA library that specifically interacts with TS.     

Comparative genome analysis of Helicobacter pylori strains

DNA macroarrays were used to characterize 17 Helicobacter pylori strains isolated in four geographic regions of Russia (Moscow, St. Petersburg, Kazan, and Novosibirsk). Of all genes, 1272 (81%) proved to occur in all strains and to constitute a functional core of the genome, and 293 (18.7%) were strain-specific and greatly varied among the H. pylori strains. Most (71%) of the latter had unknown functions; the remainder included restriction-modification genes (3-9%), transposition genes (2-4%), and genes coding for outer membrane proteins (2-4%). The Russian H. pylori strains did not differ in genome organization or in the number and distribution of strain-specific genes from strains isolated in other countries.     

Simple sequence repeats in the Helicobacter pylori genome

We describe an integrated system for the analysis of DNA sequence motifs within complete bacterial genome sequences. This system is based around ACeDB, a genome database with an integrated graphical user interface; we identify and display motifs in the context of genetic, sequence and bibliographic data. Tomb et al . (1997) previously reported the identification of contingency genes in Helicobacter pylori through their association with homopolymeric tracts and dinucleotide repeats. With this as a starting point, we validated the system by a search for this type of repeat and used the contextual information to assess the likelihood that they mediate phase variation in the associated open reading frames (ORFs). We found all of the repeats previously described, and identified 27 putative phase-variable genes (including 17 previously described). These could be divided into three groups: lipopolysaccharide (LPS) biosynthesis, cell-surface-associated proteins and DNA restriction/modification systems. Five of the putative genes did not have obvious homologues in any of the public domain sequence databases. The reading frame of some ORFs was disrupted by the presence of the repeats, including the alpha(1-2) fucosyltransferase gene, necessary for the synthesis of the Lewis Y epitope. An additional benefit of this approach is that the results of each search can be analysed further and compared with those from other genomes. This revealed that H . pylori has an unusually high frequency of homopurine:homopyrimidine repeats suggesting mechanistic biases that favour their presence and instability.     

In vitro antibacterial activity of Chilean red wines against Helicobacter pylori

The antibacterial activity of sixteen Chilean red wines (Cabernet Sauvignon, Cabernet Merlot, Cabernet Organic and Pinot Noir), and the active extracts of two randomly selected wines were assayed for their antibacterial activity on six strains of Helicobacter pylori isolated from gastric biopsies. The active fraction of the wines was obtained by dichloromethane extraction, and the antibacterial activity of the wines and extracts was evaluated by an agar diffusion method. All the red wines studied showed some antibacterial activity on the six strains of H. pylori, although the strains were heterogeneous in their susceptibility to each particular wine. The active fraction of the two wines selected also showed good activity against the strains tested. The main active compound was identified as resveratrol. The results presented indicate that Chilean red wines have antibacterial activity against H. pylori, which depends mainly on the presence of resveratrol.     

In vitro inhibition of Helicobacter pylori by Enterococcus faecium GM-1

A strain of Enterococcus faecium that exhibits antibacterial activity against Helicobacter pylori was isolated from the feces of newborn babies. This strain was selected for its ability to inhibit the growth of H. pylori and to withstand harsh environmental conditions, such as acidic pH and high bile concentration. Biochemical tests and 16S rRNA sequencing specific for Enterococcus faecium GM-1 were used to identify the isolated bacterial strain. In vitro studies were used to investigate the inhibitory effects of E. faecium GM-1 on H. pylori. These results showed that the culture supernatant of E. faecium GM-1 significantly decreased the viability and urease activity of H. pylori. This inhibitory activity remained after adjustment of pH of culture supernatant to neutral. However, treatment with proteolytic enzymes reduced the anti-H. pylori activity of GM-1. Therefore, some substance(s) of E. faecium GM-1 other than pH and lactic acid might be associated with this inhibitory activity. Analysis by electron microscopy also demonstrated that the addition of GM-1 destroyed the cell structure of H. pylori. Additional studies suggested that the binding of H. pylori to human colonial cells decreased in the presence of GM-1.     

Prevalence of Helicobacter pylori CagA-producing strains within families

During prophylactic examination of blood sera taken from the members of 59 families by the enzyme immunoassay, antibodies to H. pylori and CagA protein were determined. As shown in this study, the children of non-infected mothers proved to be infected in 6.3% of cases and the children of infected mothers, in 72.1% of cases (p < 0.001). The children of non-infected fathers were H. pylori-positive in 71.4% and those of infected fathers, in 58.4% of cases. The CagA status was found to coincide in mothers and their children (p = 0.01), but not in fathers and their children. These data indicate that children acquire H. pylori infection from the members of their family, mainly from their mothers.     

In vitro growth inhibition of Helicobacter pylori by lactobacilli belonging to the Lactobacillus plantarum group

AIMS: The aim of this study was to test and locate the in vitro anti-Helicobacter activity of seven Lactobacillus strains belonging to Lactobacillus plantarum group. METHODS AND RESULTS: Growth inhibition of H. pylori was tested using a well-plate assay. Of the strains displaying the strongest growth inhibition, a L. plantarum isolated from sauerkraut (MLBPL1) was chosen for further studies. The detected anti-Helicobacter activity of MLBPL1 was mainly associated with cell wall, and to a minor extent with the culture supernatant. The active component, which was determined to be between 3 and 10 kDa in size, retained its activity after 10 min treatment at 100 degrees C. The activity was present when MLBPL1 was cultivated in rich laboratory cultivation medium MRS and in different food matrices. CONCLUSIONS: The strains belonging to L. plantarum group showed anti-Helicobacter activity in vitro. The main activity seemed to be associated with cell wall rather than culture supernatant or intracellular fraction. SIGNIFICANCE AND IMPACT OF THE STUDY: In view of the rapid spread of resistant H. pylori strains caused by antibiotic therapy, addition of a fermented food containing L. plantarum to the conventional antibiotic treatment of Helicobacter infection could establish a potential complementary means to suppress the infection.     

Transchelation of 99mTc from low affinity sites to high affinity sites of antibody

An exclusive labeling of high affinity sites of IgG and its F(ab′)₂ fragments with ^99mTc was accomplished. Antibody was first labeled in 0.1 M acetate buffer at pH 4.5, using stannous chloride as a reducing agent. Thus, high capacity, low affinity sites and low capacity, high affinity sites were both labeled. These ^99mTc complexes were stable at pH 4.5 and 7.0; however, they became destabilized at pH 8.2 and 9.0. Transchelation of ^99mTc to DTPA took place at the higher pH values and leveled off at 54% ^99mTc-F(ab′)₂ and 73% ^99mTc-IgG. These results indicate that the majority of ^99mTc bound to the low affinity sites was transchelated to the high affinity sites rather than to DTPA since low affinity sites account for 84% of total F(ab′)₂ sites and 76% of IgG sites. Biodistribution data in mice at 2.5 h postinjection were consistent with this hypothesis in that tissue concentrations of ¹¹¹In-DTPA-F(ab′)₂ were similar to the reequilibrated ^99mTc-F(ab′)₂ but were much higher than that of the unequilibrated ^99mTc-F(ab′)₂.     

Complementary DNA display selection of high‐affinity peptides binding the vacuolating toxin (VacA) of Helicobacter pylori

Artificial peptides designed for molecular recognition of a bacterial toxin have been developed. Vacuolating cytotoxin A protein (VacA) is a major virulence factor of Helicobacter pylori, a gram‐negative microaerophilic bacterium inhabiting the upper gastrointestinal tract, particularly the stomach. This study attempted to identify specific peptide sequences with high affinity for VacA using systematic directed evolution in vitro, a cDNA display method. A surface plasmon resonance‐based biosensor and fluorescence correlation spectroscopy to examine binding of peptides with VacA identified a peptide (GRVNQRL) with high affinity. Cyclization of the peptide by attaching cysteine residues to both termini improved its binding affinity to VacA, with a dissociation constant (K_d) of 58 nm . This study describes a new strategy for the development of artificial functional peptides, which are promising materials in biochemical analyses and medical applications. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

In vitro selection of packaging sites in a double-stranded RNA virus.

The Saccharomyces cerevisiae double-stranded RNA virus ScVL1 recognizes a small sequence in the viral plus strand for both packaging and replication. Viral particles will bind to this viral binding sequence (VBS) with high affinity in vitro. An in vitro selection procedure has been used to optimize binding, and the sequences isolated have been analyzed for packaging and replication in vivo. The selected sequence consists of a stem with a bulged A residue topped by a loop of several bases. Four residues of the 18 bases are absolutely conserved for tight binding. These all fall in regions that appear to be single stranded. Eight more residues have preferred identities, and six of these are in the stem. The VBS is similar to the R17 bacteriophage coat protein binding site. Packaging and replication require tight binding to viral particles.