Interactive sites in the MyD88 Toll/interleukin (IL) 1 receptor domain responsible for coupling to the IL1beta signaling pathway

Myeloid differentiation factor MyD88 is the essential adaptor protein that integrates and transduces intracellular signals generated by multiple Toll-like receptors including receptor complex for interleukin (IL) 1beta, a key inflammatory cytokine. IL1beta receptor complex interacts with MyD88 via the Toll/IL1 receptor (TIR) domain. Here we report structure-function studies that help define the MyD88 TIR domain binding sites involved in IL1beta-induced protein-protein interactions. The MyD88 TIR domain, employed as a dominant negative inhibitor of IL1beta signaling to screen MyD88 TIR mutants, lost its suppressing activity upon truncation of its Box 3. Accordingly, mutations of Box 3 residues 285-286 reversed the dominant negative effect of the MyD88 TIR domain on IL1beta-induced and NFkappaB-dependent reporter gene activity and IL6 production. Moreover, mutations of residues 171 in helix alphaA, 195-197 in Box 2, and 275 in betaE-strand had similar functional effects. Strikingly, only mutations of residues 195-197 eliminated the TIR-TIR interaction of MyD88 and IL1 receptor accessory protein (IL1RAcP), whereas substitution of neighboring canonical Pro200 by His was without effect. Mutations in Box 2 and 3 prevented homotypic MyD88 oligomerization via TIR domain. Based on this structure-function analysis, a three-dimensional docking model of TIR-TIR interaction between MyD88 and IL1RAcP was developed.     

Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges.

The crystal structure of a quinohemoprotein amine dehydrogenase from Pseudomonas putida has been determined at 1.9-A resolution. The enzyme comprises three non-identical subunits: a four-domain alpha-subunit that harbors a di-heme cytochrome c, a seven-bladed beta-propeller beta-subunit that provides part of the active site, and a small gamma-subunit that contains a novel cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone. More surprisingly, the catalytic gamma-subunit contains three additional chemical cross-links that encage the cysteine tryptophylquinone cofactor, involving a cysteine side chain bridged to either an Asp or Glu residue all in a hitherto unknown thioether bonding with a methylene carbon atom of acidic amino acid side chains. Thus, the structure of the 79-residue gamma-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure.     

Ischemia-Induced Mitochondrial Apoptosis is Significantly Attenuated by Ischemic Preconditioning

Ischemic preconditioning (IPC) represents an important adaptation of CNS to sub-lethal ischemia, which results in increased tolerance of CNS to the lethal ischemia. Ischemia-induced mitochondrial apoptosis is considered to be an important event leading to neuronal cell death after cerebral blood flow arrest. In presented study, we have determined the effect of IPC on ischemia/reperfusion-induced mitochondrial apoptosis. Global brain ischemia was induced by permanent occlusion of vertebral arteries and temporal occlusion of carotid arteries for 15 min. Rats were preconditioned by 5 min of sub-lethal ischemia and 2 days later 15 min of lethal ischemia was induced. With respect to mitochondrial apoptosis initiation, translocation of p53 to mitochondria was observed in hippocampus but not in cerebral cortex. However, level of both apoptotic bax and anti-apoptotic bcl-xl in both hippocampal and cortical mitochondria was unchanged after global brain ischemia. Detection of genomic DNA fragmentation as well as Fluoro-Jade C staining showed that ischemia induces apoptosis in vulnerable CA1 layer of rat hippocampus. IPC abolished completely ischemia-induced translocation of p53 to mitochondria and had significant protective effect on ischemia-induced DNA fragmentation. In addition, significant decrease of Fluoro-Jade C positive cells was observed as well. Our results indicate that IPC abolished almost completely both initiation and execution of mitochondrial apoptosis induced by global brain ischemia.     

Tight linkage between myotonic dystrophy and apolipoprotein E genes revealed with allele-specific oligonucleotides

Summary The X chromosomes of individuals with isolated steroid sulphatase deficiency (X-linked ichthyosis) from ten families were studied by flow karyotype analysis. In four of the families, a small but significant reduction in the relative fluorescence of the X chromosome was detected consistent with a deletion ranging from 1.2%–3.4% of the X and amounting to a DNA loss of 1.9–5.2 million base pairs. In the remaining six families, three of which demonstrated a molecular deletion of the DNA sequence GMGX9 (DXS237), the relative fluorescence of the X chromosomes was indistinguishable from normal. The phenotypes of those with X deletions detectable by flow cytometry were similar to those of patients without such deletions.     

Experience with using Ellenberg’s <Emphasis Type="Italic">R</Emphasis> indicator values in Slovakia: Oligotrophic and mesotrophic submontane broad-leaved forests

Ellenberg’s indicator values have been suggested as useful method of estimating site conditions using plants. We examined whether Ellenberg’s R values are suitable for indicating soil reaction and if calibration to physical pH measurements can improve bioindication in oligotrophic and mesotrophic submontane broad-leaved forests in Slovakia. Vegetation relevés and pH-H₂O and pH-CaCl₂ soil reaction were recorded for this purpose. Ellenberg’s R values (R _e) were compared to Jurko’s indicator values (R _j) and a set of species R values and tolerances (T), which were calibrated with physical pH data using the weighted averaging (R _w, T _w) and Huisman-Olff-Fresco modelling (R _h, T _h). Original R _e values were then recalibrated with measured pH data to establish new, adjusted set of scores (R _c, T _c) at Ellenberg’s scale. The Re values are significantly correlated with the other R values, and they demonstrate similar frequency distribution to R _j and R _w values for the studied species pool. The frequency distribution becomes similar across all the R values when indifferent species were excluded. The performance of all the indicator values in terms of bioindication was tested. Relevé means of the R values were regressed on the field pH measurements. The performance of bioindication varied from 36% to 49% of the explained variance for pH-CaCl₂, with the R _e and R _c values yielding 46% and 49% respectively. The bioindication slightly improved for all calibrated methods (R _w, R _h and R _c) when species were weighted inversely with their tolerances — the performance varied from 42% to 51%, and the R _c values performed most effectively. We concluded that Ellenberg’s R values represent a powerful system for bioindicating soil acidity when compared to the other alternatives, with pH-CaCl₂ showing better results than pH-H₂O. Recalibration of Ellenberg’s values to the measured data improved the indicator system.     

Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.