Characterization of DNA polymerase β from Danio rerio by overexpression in E. coli using the in vivo/in vitro compatible pIVEX plasmid

Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion

Almost all DNA polymerases (pols) exhibit bell-shaped activity curves as a function of both pH and Mg²⁺ concentration. The pol activity is reduced when the pH deviates from the optimal value. When the pH is too low the concentration of a deprotonated general base (namely, the attacking 3′-hydroxyl of the 3′ terminal residue of the primer strand) is reduced exponentially. When the pH is too high the concentration of a protonated general acid (i.e., the leaving pyrophosphate group) is reduced. Similarly, the pol activity also decreases when the concentration of the divalent metal ions deviates from its optimal value: when it is too low, the binding of the two catalytic divalent metal ions required for the full activity is incomplete, and when it is too high a third divalent metal ion binds to pyrophosphate, keeping it in the replication complex longer and serving as a substrate for pyrophosphorylysis within the complex. Currently, there is a controversy about the role of the third metal ion which we will address in this review.

An expression tag toolbox for microbial production of membrane bound plant cytochromes P450

Membrane-associated Cytochromes P450 (P450s) are one of the most important enzyme families for biosynthesis of plant-derived medicinal compounds. However, the hydrophobic nature of P450s makes their use in robust cell factories a challenge. Here, we explore a small library of N-terminal expression tag chimeras of the model plant P450 CYP79A1 in different Escherichia coli strains. Using a high-throughput screening platform based on C-terminal GFP fusions, we identify several highly expressing and robustly performing chimeric designs. Analysis of long-term cultures by flow cytometry showed homogeneous populations for some of the conditions. Three chimeric designs were chosen for a more complex combinatorial assembly of a multigene pathway consisting of two P450s and a redox partner. Cells expressing these recombinant enzymes catalyzed the conversion of the substrate to highly different ratios of the intermediate and the final product of the pathway. Finally, the effect of a robustly performing expression tag was explored with a library of 49 different P450s from medicinal plants and nearly half of these were improved in expression by more than twofold. The developed toolbox serves as a platform to tune P450 performance in microbial cells, thereby facilitating recombinant production of complex plant P450-derived biochemicals. Biotechnol. Bioeng. 2017;114: 751-760. © 2016 Wiley Periodicals, Inc.

Zebrafish as a model system to study DNA damage and repair

Zebrafish (Danio rerio) have become a popular vertebrate model to study embryological development, because of unique advantages not found in other model systems. Zebrafish share many gene functions with other vertebrates including humans, making zebrafish a useful system for studying cancer etiology. However, systematic studies of DNA damage and repair pathways using adult or embryonic zebrafish have not been extensively reported. The zebrafish genome contains nearly all the genes involved in different DNA repair pathways in eukaryotes, including direct reversal (DR), mismatch repair (MMR) nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR), non-homologous end joining (NHEJ) and translesion synthesis (TLS). It also includes the genes of the p53-mediated damage recognition pathway. Therefore, zebrafish provide an ideal model for gaining fundamental insights into mechanisms of DNA damage and repair, especially during embryological development. This review introduces recent work on different DNA damage and repair studies in zebrafish, with special emphasis on the role of BER in zebrafish early embryological development. AP endonuclease 1 (Apex1), a critical protein in the BER pathway, not only regulates BER but also controls cyclic AMP response binding protein (Creb1), which itself regulates ∼25% of eukaryotic coding sequences. In addition, Apex1 indirectly regulates levels of p53. As these findings also occur in murine B cells, they illustrate the usefulness of the zebrafish system in elucidating fundamental mechanisms.