Of microbe and man: determinants ofHelicobacter pylori-related diseases

NO-dependent modifications of nucleic acids

This review is devoted to chemical transformations of nucleic acids and their components under the action of nitrogen oxide metabolites. The deamination reaction of bases is discussed in the context of possible competing transformations of its intermediates (nitrosamines, diazonium cations, diazotates, triazenes, and diazoanhydrides) and mechanisms of crosslink formation with proteins and nucleic acids. The oxidation and nitration of bases by NO2 is considered together with the possibility of radical transfer to domains from the base stacks in DNA. Reduction of redox potentials of bases as a result of stacking interactions explains the possibility of their reactions within nucleic acids with the oxidants whose redox potential is insufficient for the effective reactions with mononucleotides. Modifications of nucleic acids with peroxynitrite derivatives are discussed in the context of the effect of the DNA primary structure and the modification products formed on the reactivity of single bases. The possibility of reduction of nitro groups within modified bases to amino derivatives and their subsequent diazotation is considered. The substitution of oxoguanine for nitroguanine residues may result; the reductive diazotation can lead to undamaged guanine. The intermediate modified bases, e.g., 8-aminoguanine and 8-diazoguanine, were shown to participate in noncanonical base pairing, including the formation of more stable bonds with two bases, which is characteristic of the DNA Z-form. A higher sensitivity of RNA in comparison with DNA to NO-dependent modifications (NODMs) is predicted on the basis of the contribution of medium microheterogeneity and the known mechanisms of nitrosylation and nitration. The possible biological consequences of nucleic acids NODMs are briefly considered. It is shown that the NODMs under the action of nitrogen oxide metabolites generated by macrophages and similar cells in inflammations or infections should lead to a sharp increase in the number of mutations in the case of RNA-containing viruses. As a result, the defense mechanisms of the host organism may contribute to the appearance of new, including more dangerous, variants of infecting viruses.

Electrochemical DNA hybridization detection using peptide nucleic acids and [Ru(NH3)6]3+ on gold electrodes

An electrochemical DNA hybridization detection method based on the electrostatic interactions of [Ru(NH3)6]3+ cations with the anionic phosphate backbone of DNA is proposed. PNA molecules are immobilized as capture probes on the gold substrate. The cationic ruthenium complexes do not interact electrostatically with the PNA probes due to the absence of the anionic phosphate groups on the PNA probes. But after hybridization, [Ru(NH3)6]3+ is adsorbed on the DNA backbone, giving a clear hybridization detection signal in ac voltammetry. The analytical parameters (sensitivity, selectivity and reproducibility) are evaluated. Very good discrimination against the single-base mismatch A2143G, internal to the 23S rRNA gene of Helicobacter pylori, is observed. Moreover the system is successfully applied to the detection of complementary PCR amplicons.

Structure−Function Relationship of the Fifth Transmembrane Domain in the Na+/H+ Antiporter of Helicobacter pylori: Topology and Function of the Residues, Including Two Consecutive Essential Aspartate Residues

We examined the structure-function relationships of residues in the fifth transmembrane domain (TM5) of the Na+/H+ antiporter A (NhaA) from Helicobacter pylori (HP NhaA) by cysteine scanning mutagenesis. TM5 contains two aspartate residues, Asp-171 and Asp-172, which are essential for antiporter activity. Thirty-five residues spanning the putative TM5 and adjacent loop regions were replaced by cysteines. Cysteines replacing Val-162, Ile-165, and Asp-172 were labeled with NEM, suggesting that these three residues are exposed to a hydrophilic cavity within the membrane. Other residues in the putative TM domain, including Asp-171, were not labeled. Inhibition of NEM labeling by the membrane impermeable reagent AMS suggests that Val-162 and Ile-165 are exposed to a water filled channel open to the cytoplasmic space, whereas Asp-172 is exposed to the periplasmic space. D171C and D172C mutants completely lost Na+/H+ and Li+/H+ antiporter activities, whereas other Cys replacements did not result in a significant loss of these activities. These results suggest that Asp-171 and Asp-172 and the surrounding residues of TM5 provide an essential structure for H+ binding and Na+ or Li+ exchange. A168C and Y183C showed markedly decreased antiporter activities at acidic pH, whereas their activities were higher at alkaline pH, suggesting that the conformation of TM5 also plays a crucial role in the HP NhaA-specific acidic pH antiporter activity.

Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)

Background

The epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rRNA trees. No unique molecular or biochemical characteristics specific for this group are known.

Results

Comparative analyses of proteins in the genomes of Wolinella succinogenes DSM 1740 and Campylobacter jejuni RM1221 against all available sequences have identified a large number of proteins that are unique to various epsilon proteobacteria (Campylobacterales), but whose homologs are not detected in other organisms. Of these proteins, 49 are uniquely found in nearly all sequenced epsilon-proteobacteria (viz. Helicobacter pylori (26695 and J99), H. hepaticus, C. jejuni (NCTC 11168, RM1221, HB93-13, 84-25, CF93-6, 260.94, 11168 and 81-176), C. lari, C. coli, C. upsaliensis, C. fetus, W. succinogenes DSM 1740 and Thiomicrospira denitrificans ATCC 33889), 11 are unique for the Wolinella and Helicobacter species (i.e. Helicobacteraceae family) and many others are specific for either some or all of the species within the Campylobacter genus. The primary sequences of many of these proteins are highly conserved and provide novel resources for diagnostics and therapeutics. We also report four conserved indels (i.e. inserts or deletions) in widely distributed proteins (viz. B subunit of exinuclease ABC, phenylalanyl-tRNA synthetase, RNA polymerase β '-subunit and FtsH protein) that are specific for either all epsilon proteobacteria or different subgroups. In addition, a rare genetic event that caused fusion of the genes for the largest subunits of RNA polymerase (rpoB and rpoC) in Wolinella and Helicobacter is also described. The inter-relationships amongst Campylobacterales as deduced from these molecular signatures are in accordance with the phylogenetic trees based on the 16S rRNA and concatenated sequences for nine conserved proteins.

Conclusion

These molecular signatures provide novel tools for identifying and circumscribing species from the Campylobacterales order and its subgroups in molecular terms. Although sequence information for these signatures is presently limited to Campylobacterales species, it is likely that many of them will also be found in other epsilon proteobacteria. Functional studies on these proteins and conserved indels should reveal novel biochemical or physiological characteristics that are unique to these groups of epsilon proteobacteria.

PseG of pseudaminic acid biosynthesis: a UDP-sugar hydrolase as a masked glycosyltransferase

The flagellin proteins in pathogenic bacteria such as Campylobacter jejuni and Helicobacter pylori are heavily glycosylated with the nine-carbon alpha-keto acid, pseudaminic acid. The presence of this posttranslational modification is absolutely required for assembly of functional flagella. Since motility is required for colonization, pseudaminic acid biosynthesis represents a virulence factor in these bacteria. Pseudaminic acid is generated from UDP-N-acetylglucosamine in five biosynthetic steps. The final step has been shown to involve the condensation of 2,4-diacetamido-2,4,6-trideoxy-L-altrose (6-deoxy-Altdi-NAc) with phosphoenolpyruvate as catalyzed by the enzyme pseudaminic acid synthase, NeuB3. The 6-deoxy-AltdiNAc used in this process is generated from its nucleotide-linked form, UDP-6-deoxy-AltdiNAc, by the action of a hydrolase that cleaves the glycosidic bond and releases UDP. This manuscript describes the first characterization of a UDP-6-deoxy-AltdiNAc hydrolase, namely PseG (Cj1312) from C. jejuni. The activity of this enzyme is independent of the presence of divalent metal ions, and the values of the catalytic constants were found to be k(cat) = 27 s(-1) and K(m) = 174 microm. The enzyme was shown to hydrolyze the substrate with an overall inversion of stereochemistry at C-1 and to utilize a C-O bond cleavage mechanism during catalysis. These results, coupled with homology comparisons, suggest that the closest ancestors to the hydrolase are members of the metal-independent GT-B family of glycosyltransferases that include the enzyme MurG.