Payne rearrangement during analysis of epoxyalcohols of linoleic and alpha-linolenic acids by normal phase liquid chromatography with tandem mass spectrometry

Hydroperoxides of polyunsaturated fatty acids can be transformed to epoxyalcohols and keto fatty acids by metal enzymes, hematin, and various catalysts. In the current study, we used hematin to transform 9-hydroperoxy-10E,12Z-octadecadienoic acid and 13-hydroperoxy-9Z,11E-octadecadienoic acid to epoxyalcohols (with trans epoxide configuration) and to keto fatty acids. The products were separated by normal phase high-performance liquid chromatography (NP-HPLC) and analyzed using postcolumn addition of isopropanol/water and online negative ion electrospray ionization mass spectrometry (MS). The tandem MS (MS/MS) spectra were studied using analogs prepared from [9,10,12,13-²H₄]linoleic acid (18:2n−6) and from α-linolenic acid (18:3n−3). We also studied the MS/MS spectra of epoxyalcohols formed from 11-hydroperoxy- and 8-hydroperoxy-9Z,12Z-octadecadienoic acids. Results were confirmed by MS/MS analysis of a series of authentic standards. MS/MS ions of 9-keto-10E,12Z-octadecadienoic acid and 13-keto-9Z,11E-octadecadienoic acid could be explained by keto-enol tautomerism. MS/MS spectra of regioisomeric allylic epoxyalcohols differed in relative intensities of characteristic ions. The MS/MS spectra of the epoxyalcohols with 1-hydroxy-2,3-epoxy-4Z-pentene or 3-hydroxy-1,2-epoxy-4Z-pentene elements were virtually identical and showed two characteristic ions that differed by 30 in m/z values (CH(OH)). The results suggested that epoxide migration (Payne rearrangement) occurred during collision-induced dissociation. We conclude that regioisomeric allylic epoxyalcohols can be identified by their MS/MS spectra, whereas regioisomeric epoxyalcohols can be identified by MS/MS in combination with their retention times on NP-HPLC.     

Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection

The integration of proteomic methods to virology has facilitated a significant breadth of biological insight into mechanisms of virus replication, antiviral host responses and viral subversion of host defenses. Throughout the course of infection, these cellular mechanisms rely heavily on the formation of temporally and spatially regulated virus–host protein–protein interactions. Reviewed here are proteomic-based approaches that have been used to characterize this dynamic virus–host interplay. Specifically discussed are the contribution of integrative mass spectrometry, antibody-based affinity purification of protein complexes, cross-linking and protein array techniques for elucidating complex networks of virus–host protein associations during infection with a diverse range of RNA and DNA viruses. The benefits and limitations of applying proteomic methods to virology are explored, and the contribution of these approaches to important biological discoveries and to inspiring new tractable avenues for the design of antiviral therapeutics is highlighted.     

Dissection of splicing regulation at an endogenous locus by zinc-finger nuclease-mediated gene editing

Sequences governing RNA splicing are difficult to study in situ due to the great difficulty of traditional targeted mutagenesis. Zinc-finger nuclease (ZFN) technology allows for the rapid and efficient introduction of site-specific mutations into mammalian chromosomes. Using a ZFN pair along with a donor plasmid to manipulate the outcomes of DNA repair, we introduced several discrete, targeted mutations into the fourth intron of the endogenous BAX gene in Chinese hamster ovary cells. Putative lariat branch points, the polypyrimidine tract, and the splice acceptor site were targeted. We recovered numerous otherwise isogenic clones carrying the intended mutations and analyzed the effect of each on BAX pre-mRNA splicing. Mutation of one of three possible branch points, the polypyrimidine tract, and the splice acceptor site all caused exclusion of exon five from BAX mRNA. Interestingly, these exon-skipping mutations allowed usage of cryptic splice acceptor sites within intron four. These data demonstrate that ZFN-mediated gene editing is a highly effective tool for dissection of pre-mRNA splicing regulatory sequences in their endogenous context.     

Thiouracil Cross-Linking Mass Spectrometry: a Cell-Based Method To Identify Host Factors Involved in Viral Amplification

Eukaryotic RNA viruses are known to utilize host factors; however, the identity of these factors and their role in the virus life cycle remain largely undefined. Here, we report a method to identify proteins bound to the viral RNA during amplification in cell culture: thiouracil cross-linking mass spectrometry (TUX-MS). TUX-MS relies on incorporation of a zero-distance cross-linker into the viral RNA during infection. Proteins bound to viral RNA are cross-linked prior to cell lysis, purified, and identified using mass spectrometry. Using the TUX-MS method, an unbiased screen for poliovirus (PV) host factors was conducted. All host and viral proteins that are known to interact with the poliovirus RNA were identified. In addition, TUX-MS identified an additional 66 host proteins that have not been previously described in poliovirus amplification. From these candidates, eight were selected and validated. Furthermore, we demonstrate that small interfering RNA (siRNA)-mediated knockdown of two of these uncharacterized host factors results in either a decrease in copy number of positive-stranded RNA or a decrease in PV translation. These data demonstrate that TUX-MS is a robust, unbiased method to identify previously unknown host cell factors that influence virus growth. This method is broadly applicable to a range of RNA viruses, such as flaviviruses, alphaviruses, picornaviruses, bunyaviruses, and coronaviruses.     

Rapid large-scale purification of pig heart nucleoside diphosphate kinase by affinity chromatography on Cibacron Blue 3G-A Sepharose

A rapid procedure for the large-scale purification of pig heart nucleoside diphosphate kinase is described. The purification procedure involves extraction of the enzyme, absorption on cibacron Blue 3G-A Sepharose, elution with ATP, ammonium sulfate precipitation, heat treatment, and rechromatography on Cibacron Blue 3G-A Sepharose. Typically, 10–12 mg of pure nucleoside diphosphate kinase is obtained from 1 kg of heart muscle (50% yield), with a purification factor of 1200 over the extract. The specific activity is 1500 units/mg at 25°C with 8-bromoinosine 5′-diphosphate as acceptor nucleotide. This method may be easily scaled up.     

Eco-coenotic conditions and structure of Trollius europaeus L. populations in an extrazonal habitat complex (Transylvanian Carpathian foothills)

To estimate the importance of community structure and environmental factors for maintenance and in situ conservation of populations of European Globeflower (Trollius europaeus subsp. europaeus) in four sites (one within a natural reserve) in a low elevation but cool valley of the Transylvanian Carpathian foothills, an inventory of all globeflower individuals was performed and floristic relevés were recorded in different community types (meadow, fen and scrub). As a surrogate for habitat conditions, we used plant species indicator values for light, moisture and nitrogen. Globeflower density is highest in mesic habitats, the ecological optimum estimated (about 6 on Ellenberg's scale) being slightly lower than that indicated for Central Europe (7). The juvenile:fertile plants ratio (J:F) declines with increasing soil moisture. Larger flower production in hygrophilous communities does not result in a higher proportion of juveniles or J:F ratio. Despite the presumed strong competition determined by high species richness in some host communities, the most dynamic population (large proportion of juveniles) was found in mesophilous, mown meadows. A clumped distribution of fertile plants under the open scrub canopy seems to be responsible for the significantly larger number of flowers per individual observed, as compared with the relative amount of flowers produced in the adjacent sward. Irrespective of host community, the juveniles display an aggregated distribution with respect to fertile plants, which is probably related to short-distance dispersal of seeds. Our results reveal the importance of host community species richness and soil moisture for the target population stage structure and reproductive investment.     

Lamin B1 acetylation slows the G1 to S cell cycle transition through inhibition of DNA repair

The integrity and regulation of the nuclear lamina is essential for nuclear organization and chromatin stability, with its dysregulation being linked to laminopathy diseases and cancer. Although numerous posttranslational modifications have been identified on lamins, few have been ascribed a regulatory function. Here, we establish that lamin B1 (LMNB1) acetylation at K134 is a molecular toggle that controls nuclear periphery stability, cell cycle progression, and DNA repair. LMNB1 acetylation prevents lamina disruption during herpesvirus type 1 (HSV-1) infection, thereby inhibiting virus production. We also demonstrate the broad impact of this site on laminar processes in uninfected cells. LMNB1 acetylation negatively regulates canonical nonhomologous end joining by impairing the recruitment of 53BP1 to damaged DNA. This defect causes a delay in DNA damage resolution and a persistent activation of the G1/S checkpoint. Altogether, we reveal LMNB1 acetylation as a mechanism for controlling DNA repair pathway choice and stabilizing the nuclear periphery.