Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

<p>Abstract</p> <p>Background</p> <p>The addition of an acetyl group to protein N-termini is a widespread co-translational modification. NatB is one of the main N-acetyltransferases that targets a subset of proteins possessing an N-terminal methionine, but so far only a handful of substrates have been reported. Using a yeast <it>nat3Δ </it>strain, deficient for the catalytic subunit of NatB, we employed a quantitative proteomics strategy to identify NatB substrates and to characterize downstream effects in <it>nat3Δ</it>.</p> <p>Results</p> <p>Comparing by proteomics WT and <it>nat3Δ </it>strains, using metabolic ¹⁵N isotope labeling, we confidently identified 59 NatB substrates, out of a total of 756 detected acetylated protein N-termini. We acquired in-depth proteome wide measurements of expression levels of about 2580 proteins. Most remarkably, NatB deletion led to a very significant change in protein phosphorylation.</p> <p>Conclusions</p> <p>Protein expression levels change only marginally in between WT and <it>nat3Δ</it>. A comparison of the detected NatB substrates with their orthologous revealed remarkably little conservation throughout the phylogenetic tree. We further present evidence of post-translational N-acetylation on protein variants at non-annotated N-termini. Moreover, analysis of downstream effects in <it>nat3Δ </it>revealed elevated protein phosphorylation levels whereby the kinase Snf1p is likely a key element in this process.</p

Targeted amino-terminal acetylation of recombinant proteins in E. coli.

One major limitation in the expression of eukaryotic proteins in bacteria is an inability to post-translationally modify the expressed protein. Amino-terminal acetylation is one such modification that can be essential for protein function. By co- expressing the fission yeast NatB complex with the target protein in E.coli, we report a simple and widely applicable method for the expression and purification of functional N-terminally acetylated eukaryotic proteins

Quantum dot–antibody conjugates via carbodiimide-mediated coupling for cellular imaging

This chapter describes the processes of antibody (Ab) production, purification, conjugation to quantum dots (QDs), and the use of the conjugates produced in intracellular imaging of cell components and structures. Specifically, information is provided on the conjugation of carboxyl surface-terminated QDs to Abs via a one-step reaction using the water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). The chapter details the process of conjugate optimization in terms of its final fluorescence and biological activity. The method described should guarantee the production of QD–Ab conjugates, which outperform classic organic fluorophore–Ab conjugates in terms of both image definition produced and the longevity of the imaging agent

QD-antibody conjugates via carbodiimide-mediated coupling: a detailed study of the variables involved and a possible new mechanism for the coupling reaction under basic aqueous conditions

A detailed study into the optimization of carbodiimide-mediated coupling of antibodies (Ab) and quantum dots (QD) for use in cellular imaging has been undertaken. This involved the grafting of commercially available carboxyl-modified QDs (Evident Technologies “Lake Placid Blue” Evitag and eBioscience’s eflour nanocrystals) with anti-Cdc8 Abs to produce conjugates with specific affinity for fission yeast tropomyosin Cdc8 protein. The water-soluble carbodiimide 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) was used to activate the QDs prior to their incubation with antibody, and a range of QD-carboxyl/EDC/Ab mole ratios were used in the experiments in attempts to optimize fluorescence and bioaffinity of the conjugate products (EDC to QD-carboxyl-600 nmol/15pmol to 0.12 nmol/15 pmol and QD to Ab 120 pmol/24 pmol to 120 pmol/1.2 pmol). It was observed that a specific “optimum” ratio of the three reactants was required to produce the most fluorescent and biologically active product and that it was generated at alkaline pH 10.8. Increasing the ratio of Ab to QD produced conjugate which was less fluorescent while reducing the ratio of EDC to QD in the activation step led to increased fluorescence of product. Conjugates were tested for their possession of antibody by measurement of their absorption at OD280 nm and for their fluorescence by assay λmaxem at 495 nm. A quantitative assay of the bioactivity of the conjugates was developed whereby a standardized amount of Cdc8 antigen was spotted onto nylon membranes and reacted with products from conjugation reactions in a sandwich-type colormetric assay The “best” conjugate was used in intracellular imaging of yeast Cdc8 protein and produced brighter, higher definition images of fixed yeast cell actin structure than a fluorescein–Ab conjugate routinely produced in our laboratory. The QD–Ab conjugate was also significantly more resistant to photobleaching than the fluorescein–Ab conjugate. Results from other experiments involving EDC, the water-soluble carbodiimide 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulphonate (CMC), and EDC.HCl have suggested a new reaction mechanism for EDC coupling under basic aqueous conditions. In summary, a robust understanding of commercial QD-COOH surface chemistry and the variables involved in the materials’ efficient conjugation with a bioligand using carbidiimide has been obtained along with an optimized approach for Ab–QD conjugate production. A novel assay has been developed for bioassay of QD–Ab conjugates and a new mechanism for EDC coupling under basic aqueous conditions is proposed

Tropomyosin and Myosin-II Cellular Levels Promote Actomyosin Ring Assembly in Fission Yeast

A combination of in vivo and in vitro approaches were used to show how tropomyosin and myosin-II contribute to contractile ring assembly in fission yeast. Ring assembly is sensitive to changes in the cellular levels of myosin-II, and tropomyosin works to maximize myosin-II motor function during this process by stabilizing actomyosin interactions