Characterization of Helicobacter pylori HP0231 (DsbK): role in disulfide bond formation,redox homeostasis and production of Helicobacter cystein‐rich protein HcpE

Helicobacter pylori is a human gastric pathogen that colonizes ～ 50% of the world's population. It can cause gastritis, gastric or duodenal ulcers and also gastric cancer. The numerous side effects of available treatments and the emergence of antibiotic resistant strains are severe concerns that justify further research into H. pylori's pathogenic mechanisms. H. pylori produces secreted proteins that may play a role in virulence, including the Helicobacter cysteine‐rich protein HcpE (aka HP0235). We demonstrate herein that HcpE is secreted in the culture supernatant both as a soluble protein and in association with outer membrane vesicles. We show that the structure of HcpE comprises an organized array of disulfide bonds. We identify DsbK (aka HP0231) as a folding factor necessary for HcpE production and secretion in H. pylori and show that recombinant DsbK can interact with and refold unprocessed, reduced HcpE in vitro. These experiments highlight the first biologically relevant substrate for DsbK. Furthermore, we show that DsbK has disulfide bond (Dsb) forming activity on reduced lysozyme and demonstrate a DsbA‐type of activity for DsbK upon expression in E. coli, despite its similarity with DsbG. Finally, we show a role of DsbK in maintaining redox homeostasis in H. pylori.     

Group A streptococcal surface GAPDH, SDH, recognizes uPAR/CD87 as its receptor on the human pharyngeal cell and mediates bacterial adherence to host cells

Streptococcal surface dehydrogenase (SDH) is a multifunctional, anchorless protein present on the surface of group A Streptococcus (GAS). It plays a regulatory role in GAS-mediated intracellular signaling events in human pharyngeal cells. Using ligand-binding assays, we have identified an approximately 55 kDa protein as an SDH-specific receptor protein on the surface of Detroit human pharyngeal cells. LC-MS/MS analyses identified this SDH-binding pharyngeal cell-surface-exposed membrane-bound protein as uPAR (urokinase plasminogen activator receptor)/CD87. Ligand-binding assays also revealed that only the N-terminal domain (D1) of uPAR bound to SDH. uPAR-D1 more specifically bound to the C-terminal alpha-helix and two immediate flanking regions of the S-loop of the SDH molecule. Site-directed mutagenesis in GAS resulting in SDH with altered C-terminal ends, and the removal of uPAR from pharyngeal cells by phosphatidylinositol-phopsholipase C treatment decreased GAS ability to adhere to pharyngeal cells. When compared to uninfected Detroit pharyngeal cells, GAS-infected pharyngeal cells showed a transient but a significant increase in the expression of uPAR-specific mRNA, and a prolonged recycling process of uPAR on the cell surface. Together, these results indicate that the specific streptococcal surface protein-pharyngeal cell receptor interaction mediated by SDH and uPAR is modulated during GAS infection of human pharyngeal cells. This interaction significantly contributes to bacterial adherence and thus may play a significant role in GAS pathogenesis by regulating intracellular signaling events in pharyngeal cells.     

Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.     

piRNAs, transposon silencing, and Drosophila germline development

Transposons are prominent features of most eukaryotic genomes and mobilization of these elements triggers genetic instability. Transposon silencing is particularly critical in the germline, which maintains the heritable genetic complement. Piwi-interacting RNAs (piRNAs) have emerged as central players in transposon silencing and genome maintenance during germline development. In particular, research on Drosophila oogenesis has provided critical insights into piRNA biogenesis and transposon silencing. In this system, the ability to place piRNA mutant phenotypes within a well-defined developmental framework has been instrumental in elucidating the molecular mechanisms underlying the connection between piRNAs and transposon control.     

Physico-chemical and morphological characteristics of New Zealand Taewa (Maori potato) starches

The physico-chemical, morphological, thermal, pasting, textural, and retrogradation properties of the starches isolated from four traditional Taewa (Maori potato) cultivars (Karuparera, Tutaekuri, Huakaroro, Moemoe) of New Zealand were studied and compared with starch properties of a modern potato cultivar (Nadine). The relationships between the different starch characteristics were quantified using Pearson correlation and principal component analysis. Significant differences were observed among physico-chemical properties such as phosphorus content, amylose content, swelling power, solubility and light transmittance of starches from the different potato cultivars. The starch granule morphology (size and shape) for all the potato cultivars showed considerable variation when studied by scanning electron microscopy and particle size analysis. Starch granules from Nadine and Moemoe cultivars showed the presence of large and irregular or cuboid granules in fairly high number compared with the starches from the other cultivars. The transition temperatures (T_o; T_p; T_c) and the enthalpies (ΔH_gel) associated with gelatinization suggested differences in the stability of the crystalline structures among these potato starches. The Moemoe starch showed the lowest T_o, while it was higher for Tutaekuri and Karuparera starches. Pasting properties such as peak, final and breakdown viscosity and texture profile analysis (TPA) parameters of starch gels such as hardness and fracturability were found to be higher for Nadine and Huakaroro starches. The Nadine and Huakaroro starch gels also had lower tendency towards retrogradation as evidenced by their lower syneresis (%) during storage at 4 °C. Principal component analysis showed that the Tutaekuri and Nadine cultivars differed to the greatest degree in terms of the properties of their starches.     

Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium

Sphingobium indicum B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India. Here we report the draft genome sequence of this bacterium, which has now become a model system for understanding the genetics, biochemistry, and physiology of HCH degradation.     

Plasmalogen deficiency in cerebral adrenoleukodystrophy and its modulation by lovastatin

In cerebral adrenoleukodystrophy (cALD), an accumulation of very long chain fatty acids stems from a defect of the peroxisomal ALD protein (ALDP) and results in the loss of myelin/oligodendrocytes, induction of inflammatory disease and mental deterioration. In brain white matter of cALD patients, we observed not only increased levels of very long chain fatty acid but also reduced levels of plasmenylethanolamine (PlsEtn) and increased levels of reactive oxygen species (ROS). The loss of PlsEtn was greatest in the plaque area and lesser but significant at histologically normal-looking areas of the cALD brain. The reduction in PlsEtn was related to oxidative stress, as supported by increased levels of reactive lipid aldehydes (4-hydroxynonenal and acrolein) and deleterious oxidized proteins (protein carbonyl) in all areas of the cALD brain. This inverse relationship between the levels of PlsEtn and reactive oxygen species (ROS) was further supported in an in vitro study using gene-silencing for dihydroxyacetone phosphate-acyl transferase, a key enzyme for PlsEtn biosynthesis. Levels of PlsEtn were also found decreased in vitro following gene-silencing for the ALDP/ALD-related protein. Furthermore, low levels of PlsEtn were detected in brain white matter of ALDP knock out (KO) mice. A treatment of ALDP KO mice with lovastatin increased PlsEtn levels in the brain. Further, in an in vitro study, lovastatin treatment of rat C6 glial cells increased PlsEtn biosynthesis and reduced the cytokine-induced ROS accumulation. In summary, this study reports that altered metabolism of PlsEtn and ROS in cALD may be corrected by lovastatin treatment.