Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities

Human APOBEC3F and APOBEC3G are double-domained deaminases that can catalyze dC→dU deamination in HIV-1 and MLV retroviral DNA replication intermediates, targeting T–C or C–C dinucleotides, respectively. HIV-1 antagonizes their action through its vif gene product, which has been shown (at least in the case of APOBEC3G) to interact with the N-terminal domain of the deaminase, triggering its degradation. Here, we compare APOBEC3F and APOBEC3G to APOBEC3C, a single-domained deaminase that can also act on both HIV-1 and MLV. We find that whereas APOBEC3C contains all the information necessary for both Vif-binding and cytidine deaminase activity in a single domain, it is the C-terminal domain of APOBEC3F and APOBEC3G that confer their target site specificity for cytidine deamination. We have exploited the fact that APOBEC3C, whilst highly homologous to the C-terminal domain of APOBEC3F, exhibits a distinct target site specificity (preferring Y–C dinucleotides) in order to identify residues in APOBEC3F that might affect its target site specificity. We find that this specificity can be altered by single amino acid substitutions at several distinct positions, suggesting that the strong dependence of APOBEC3-mediated deoxycytidine deamination on the 5′-flanking nucleotide is sensitive to relatively subtle changes in the APOBEC3 structure. The approach has allowed the isolation of APOBEC3 DNA mutators that exhibit novel target site preferences

CD95/CD95L interactions and their role in autoimmunity

CD95 (Fas/Apo-1) is a broadly expressed death receptor involved in a variety of physiological and pathological apoptotic processes. Since its discovery, defects in CD95/CD95L system have been proposed as major pathogenic factors responsible for impaired immunological tolerance to self antigens and autoimmunity. Later, analysis of altered sensitivity to CD95-induced apoptosis in cells targeted by the immune response has revealed an unexpected role for CD95 and CD95L in organ-specific autoimmunity. CD95 has been shown to be expressed and functional in virtually all cell types that are target of the organ-specific autoimmune response. Here we review some of the major findings concerning the role of CD95 in autoimmunity, in dysfunctions due to increased or decreased CD95-induced apoptosis

Death in 2000 ways

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Transition-metal-catalyzed polymerization of heteroatom-functionalized cyclohexadienes: stereoregular precursors to poly(p-phenylene)

Poly(p-phenylene) (PPP) is an insoluble rigid-rod polymer that possesses remarkable thermal stability, chemical resistance, and electrical conductivity when doped. The structural properties that make PPP such an attractive engineering material also make it difficult to synthesize and process. Direct synthetic approaches have given either ill-defined material with a mixture of para, meta, and ortho linkages and crosslink or insoluble oligomers. Precursor strategies to PPP have been devised in which the synthetic and processing difficulties of the direct methods have been overcome through the use of a soluble intermediate polymer. The most successful of the precursor strategies was developed at ICI by Ballard et al. This process involves the radical polymerization of the bis(acetyl) or bis(methoxycarbonyl) derivatives of cis-5,ddihydroxy- 1,3-cyclohexadiene (l), a microbial oxidation product of benzene. The resulting polymers are subsequently aromatized to yield PPP by thermally induced acid elimination. This process, however, yields only phenylene oligomers due to fracturing of the precursors during pyrolysis. Fracturing is believed to arise from the 90% 1,4-linkages, 10% 1,2-linkages, and random stereochemistry along the precursor backbones which result from the nonstereospecific nature of the radical polymerization. A route to 100% 1,4-linked PPP precursors with the correct stereochemistry for facile cis-pyrolytic elimination of the pendant groups has been developed which combines the efficiency and processability of the ICI process with the regio- and stereochemical control possible through transition-metal catalysts (Scheme I)

Transition-metal-catalyzed polymerization of heteroatom-functionalized cyclohexadienes: stereoregular precursors to poly(p-phenylene)

Poly(p-phenylene) (PPP) is an insoluble rigid-rod polymer that possesses remarkable thermal stability, chemical resistance, and electrical conductivity when doped. The structural properties that make PPP such an attractive engineering material also make it difficult to synthesize and process. Direct synthetic approaches have given either ill-defined material with a mixture of para, meta, and ortho linkages and crosslink or insoluble oligomers. Precursor strategies to PPP have been devised in which the synthetic and processing difficulties of the direct methods have been overcome through the use of a soluble intermediate polymer. The most successful of the precursor strategies was developed at ICI by Ballard et al. This process involves the radical polymerization of the bis(acetyl) or bis(methoxycarbonyl) derivatives of cis-5,ddihydroxy- 1,3-cyclohexadiene (l), a microbial oxidation product of benzene. The resulting polymers are subsequently aromatized to yield PPP by thermally induced acid elimination. This process, however, yields only phenylene oligomers due to fracturing of the precursors during pyrolysis. Fracturing is believed to arise from the 90% 1,4-linkages, 10% 1,2-linkages, and random stereochemistry along the precursor backbones which result from the nonstereospecific nature of the radical polymerization. A route to 100% 1,4-linked PPP precursors with the correct stereochemistry for facile cis-pyrolytic elimination of the pendant groups has been developed which combines the efficiency and processability of the ICI process with the regio- and stereochemical control possible through transition-metal catalysts (Scheme I)

Ring-opening metathesis polymerization of substituted bicyclo[2.2.2]octadienes: a new precursor route to poly(1,4-phenylenevinylene)

Poly(1,4-phenylenevinylene) (PPV), a perfectly alternating copolymer of p-phenylene and trans-vinylene units, possesses attractive material properties. Thin films of PPV display high electrical conductivity when doped (σ = 5000 S/cm), a large, third-order nonlinear optical response (χ^3 = 1.5 X 10^(-10) esu), and photo- and electroluminescence in the visible region. However, the extended planar topology of the PPV backbone, which renders it infusible and insoluble in nonreactive media, limits the capacity for post-synthesis fabrication of the material. A convenient method to circumvent this problem consists of a two-step synthesis via a processable intermediate polymer. This precursor polymer can be fabricated into the desired form and subsequently converted to the target polymer by a clean, intramolecular chemical reaction. Wessling and Zimmerman have reported the synthesis of a processable, water-soluble poly(l,4-xylylenesulfonium salt) that undergoes a thermally-induced elimination to PPV under mild conditions

Ring-opening metathesis polymerization of substituted bicyclo[2.2.2]octadienes: a new precursor route to poly(1,4-phenylenevinylene)

Poly(1,4-phenylenevinylene) (PPV), a perfectly alternating copolymer of p-phenylene and trans-vinylene units, possesses attractive material properties. Thin films of PPV display high electrical conductivity when doped (σ = 5000 S/cm), a large, third-order nonlinear optical response (χ^3 = 1.5 X 10^(-10) esu), and photo- and electroluminescence in the visible region. However, the extended planar topology of the PPV backbone, which renders it infusible and insoluble in nonreactive media, limits the capacity for post-synthesis fabrication of the material. A convenient method to circumvent this problem consists of a two-step synthesis via a processable intermediate polymer. This precursor polymer can be fabricated into the desired form and subsequently converted to the target polymer by a clean, intramolecular chemical reaction. Wessling and Zimmerman have reported the synthesis of a processable, water-soluble poly(l,4-xylylenesulfonium salt) that undergoes a thermally-induced elimination to PPV under mild conditions

Bortezomib modulates CHIT1 and YKL40 in monocyte-derived osteoclast and in myeloma cells

Osteolytic bone disease is a common manifestation of multiple myeloma (MM) that leads to progressive skeleton destruction and is the most severe cause of morbidity in MM patients.It results from increased osteolytic activity and decrease osteoblastic function. Activation of mammalian chitinases CHIT1 and YKL40 is associated with osteoclast (OCs) differentiation and bone digestion. In the current study, we investigated the effect of two Bortezomib’s concentration (BO) (2.5 nM and 5nM) on osteoclastogenesis by analyzing regulation of chitinase expression. OCs exposition to BO was able to inhibit the expression of different OCs markers such as RANK, CTSK, TRAP and MMP9. In addition BO-treatment reduced CHIT1 enzymatic activity and both CHIT1 and YKL40 mRNA expression levels and cytoplasmatic and secreted protein. Moreover, immunofluorescence evaluation of mature OCs showed that BO was able to translocate YKL40 into the nucleus, while CHIT1 remained into the cytoplasm. Since MM cell lines such as U266, SKM-M1 and MM1 showed high levels of CHIT1 activity, we analyzed bone resorption ability of U266 using dentin disc assay resorption pits. Silencing chitinase proteins in U266 cell line with specific siRNAs, resulted in pits number reduction on dentine discs. In conclusion, we showed that BO decreases osteoclastogenesis and reduces bone resorption in OCs and U266 cell line by modulating the chitinases CHIT1 and YKL40. These results indicate that chitinases may be a therapeutic target for bone disease in MM patients

Interactions in vivo between the Vif protein of HIV-1 and the precursor (Pr55GAG) of the virion nucleocapsid proteins

The abnormality of viral core structure seen in vif-defective HIV-1 grown in PBMCs has suggested a role for Vif in viral morphogenesis. Using an in vivo mammalian two-hybrid assay, the interaction between Vif and the precursor (Pr55GAG) of the virion nucleocapsid proteins has been analysed. This revealed the amino-terminal (aa 1–22) and central (aa 70–100) regions of Vif to be essential for its interaction with Pr55GAG, but deletion of the carboxy-terminal (aa 158–192) region of the protein had only a minor effect on its interaction. Initial deletion studies carried out on Pr55GAG showed that a 35-amino-acid region of the protein bridging the MA(p17)–CA(p24) junction was essential for its ability to interact with Vif. Site-directed mutagenesis of a conserved tryptophan (Trp21) near the amino terminus of Vif showed it to be important for the interaction with Pr55GAG. By contrast, mutagenesis of the highly conserved YLAL residues forming part of the BC-box motif, shown to be important in Vif promoting degradation of APOBEC3G/3F, had little or no effect on the Vif–Pr55GAG interaction

ATDB: a uni-database platform for animal toxins

Venomous animals possess an arsenal of toxins for predation and defense. These toxins have great diversity in function and structure as well as evolution and therefore are of value in both basic and applied research. Recently, toxinomics researches using cDNA library sequencing and proteomics profiling have revealed a large number of new toxins. Although several previous groups have attempted to manage these data, most of them are restricted to certain taxonomic groups and/or lack effective systems for data query and access. In addition, the description of the function and the classification of toxins is rather inconsistent resulting in a barrier against exchanging and comparing the data. Here, we report the ATDB database and website which contains more than 3235 animal toxins from UniProtKB/Swiss-Prot and TrEMBL and related toxin databases as well as published literature. A new ontology (Toxin Ontology) was constructed to standardize the toxin annotations, which includes 745 distinct terms within four term spaces. Furthermore, more than 8423 TO terms have been manually assigned to 2132 toxins by trained biologists. Queries to the database can be conducted via a user-friendly web interface at http://protchem.hunnu.edu.cn/toxin