Hepatitis C virus induces E6AP-dependent degradation of the retinoblastoma protein

Hepatitis C virus (HCV) is a positive-strand RNA virus that frequently causes persistent infections and is uniquely associated with the development of hepatocellular carcinoma. While the mechanism(s) by which the virus promotes cancer are poorly defined, previous studies indicate that the HCV RNA-dependent RNA polymerase, nonstructural protein 5B (NS5B), forms a complex with the retinoblastoma tumor suppressor protein (pRb), targeting it for degradation, activating E2F-responsive promoters, and stimulating cellular proliferation. Here, we describe the mechanism underlying pRb regulation by HCV and its relevance to HCV infection. We show that the abundance of pRb is strongly downregulated, and its normal nuclear localization altered to include a major cytoplasmic component, following infection of cultured hepatoma cells with either genotype 1a or 2a HCV. We further demonstrate that this is due to NS5B-dependent ubiquitination of pRb and its subsequent degradation via the proteasome. The NS5B-dependent ubiquitination of pRb requires the ubiquitin ligase activity of E6-associated protein (E6AP), as pRb abundance was restored by siRNA knockdown of E6AP or overexpression of a dominant-negative E6AP mutant in cells containing HCV RNA replicons. E6AP also forms a complex with pRb in an NS5B-dependent manner. These findings suggest a novel mechanism for the regulation of pRb in which the HCV NS5B protein traps pRb in the cytoplasm, and subsequently recruits E6AP to this complex in a process that leads to the ubiquitination of pRb. The disruption of pRb/E2F regulatory pathways in cells infected with HCV is likely to promote hepatocellular proliferation and chromosomal instability, factors important for the development of liver cancer.     

Mutation induction with UV- and X-radiations in spores and vegetative cells of Bacillus subtilis.

Spores and vegetative cells of Bacillus subtilis strains with various defects in DNA-repair capacities (hcr-, ssp-, hcr-ssp-) were irradiated with UV radiation or X-rays. Induced mutation frequency was determined from the observed frequency of prototrophic reversion of a suppressible auxotrophic mutation. At equal physical dose, after either UV- or X-irradiation, spores were more resistant to mutations as well as to killing than were vegetative cells. However, quantitative comparison revealed that, at equally lethal doses, spores and vegetative cells were almost equally mutable by X-rays whereas spores were considerably less mutable by UV than were vegetative cells. Thus, as judged from their mutagenic efficiency relative to the lethality, X-ray-induced damage in the spore DNA and the vegetative DNA were equally mutagenic, while UV-induced DNA photoproducts in the spore were less mutagenic than those in vegetative cells. Post-treatment of UV-irradiated cells with caffeine decreased the survival and the induced mutation frequency for either spores or vegetative cells for all the strains. In X-irradiated spores, however, a similar suppressing effect of caffeine was observed only for mutability of a strain lacking DNA polymerase I activity.     

Deoxyuridine residues in DNA of thymine-requiring Bacillus subtilis strains with defective N-glycosidase activity for uracil-containing DNA.

DNA extracted from exponentially growing cells of thymine-requiring Bacillus subtilis strains with defective N-glycosidase activity for deoxyuridine residues in DNA was subjected to the action of N-glycosidase in vitro and analyzed by sedimentation in alkaline sucrose gradients. The sites attacked by N-glycosidase occurred once per 6 X 10(6) to 7 X 10(6) daltons of DNA from cells cultured in the presence of growth-supporting concentrations of thymine. The number of N-glycosidase-susceptible sites increased when the thymine concentration in the medium was lowered. Parallel to this observation, the N-glycosidase-defective mutant cells were less apt to show the detrimental effect due to thymine depletion than were the parental cells. Such sites were not detected in DNA from cells with a normal N-glycosidase activity or with a "wild type" capacity for thymidylate synthesis. The results are interpreted to mean that cells defective for thymidylate synthesis incorporate dUTP in place of TTP in DNA and that the deoxyuridine residues, once incorporated, remain in the DNA in the absence of N-glycosidase activity.     

Can Systems Biology Understand Pathway Activation? Gene Expression Signatures as Surrogate Markers for Understanding the Complexity of Pathway Activation

Cancer is thought to be caused by a sequence of multiple genetic and epigenetic alterations which occur in one or more of the genes controlling cell cycle progression and signaling transduction. The complexity of carcinogenic mechanisms leads to heterogeneity in molecular phenotype, pathology, and prognosis of cancers.     

m6A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis

Alternative splicing of pre‐mRNAs can regulate gene expression levels by coupling with nonsense‐mediated mRNA decay (NMD). In order to elucidate a repertoire of mRNAs regulated by alternative splicing coupled with NMD (AS‐NMD) in an organism, we performed long‐read RNA sequencing of poly(A)⁺ RNAs from an NMD‐deficient mutant strain of Caenorhabditis elegans, and obtained full‐length sequences for mRNA isoforms from 259 high‐confidence AS‐NMD genes. Among them are the S‐adenosyl‐L‐methionine (SAM) synthetase (sams) genes sams‐3 and sams‐4. SAM synthetase activity autoregulates sams gene expression through AS‐NMD in a negative feedback loop. We furthermore find that METT‐10, the orthologue of human U6 snRNA methyltransferase METTL16, is required for the splicing regulation in␣vivo, and specifically methylates the invariant AG dinucleotide at the distal 3′ splice site (3′SS) in␣vitro. Direct RNA sequencing coupled with machine learning confirms m⁶A modification of endogenous sams mRNAs. Overall, these results indicate that homeostasis of SAM synthetase in C. elegans is maintained by alternative splicing regulation through m⁶A modification at the 3′SS of the sams genes.     

The Presence of Novel Plant Growth Regulators in Leaves of Distylium racemosum Sieb et Zucc

The scaling law derived from the percolation theory was applied to the concentration dependence of mechanical properties of polyacrylamide measured near the sol–gel transition point. The critical concentration of the sol–gel transition, ?_g, was estimated from the plot of concentration (?) vs. the reciprocal of viscosity (η) by extrapolating 1/η to zero. The critical exponent for the sol viscosity, s, which was estimated from the slope of the log(?_g–?) vs. log η plot was about 0.7. The estimated value of s was similar to the value predicted by the percolation theory based on the superconductor–normal conductor mixture model. The critical exponent for the gel elasticity, t, as estimated from the slope of the log(?–?_g) vs. log G′ plot, where G′ was the dynamic shear modulus of the gel at a frequency of 2Hz. The value of t was about 2, which was also similar to the value predicted by the percolation theory. These results indicated the at the concentration dependences of η and G′ of polyacrylamide near the sol–gel transition point were described by the percolation theory.     

Isolation of Nematicidal Polyacetylenes from Carthamus tinctorius L.

Two nematicidal polyacetylenes, 3-cis,11-trans- and 3-trans,11-trans-trideca-1,3,11-triene-5,7,9-triyne, were isolated from flowers of Carthamus tinctorius L., by column chromatography and high speed liquid chromatography under the dark condition.

The nematicidal activities of 3-cis,11-trans- and 3-trans,11-trans-isomer to Aphelenchoides besseyi were 80% at 10 ppm and 95% at 1 ppm, respectively.     

Pyrolysis of Chlorogenic Acid and Rutin

Chlorogenic acid and rutin, major polyphenols in tobacco, were pyrolysed with a furnace type pyrolyser connected directly to a gas Chromatograph and 22 compounds (including catechol, benzoic acid, 4-vinylcatechol and quinic acid γ-lactone) from chlorogenic acid and 24 compounds [including catechol, 5-methyl-2-furaldehyde, 4-methylcatechol and 1,6-anhydroglucopyranose (levoglucosan)] from rutin have been identified as pyrolysis products. The gas Chromatograph was also replaced by a capillary cold trap which allowed collection of the pyrolysis products prior to a quantitative determination using an internal standard. Comparison of the pyrolysis products produced from chlorogenic acid or rutin with those derived from tobacco and analysis of the pyrolysis products from a mixture of tobacco and chlorogenic acid or rutin indicated that fairly large proportions of catechol, 4-vinylcatechol and quinic acid γ-lactone produced by the pyrolysis of tobacco may originate from endogenous chlorogenic acid.