A Practical System for High-Throughput Screening of Mutants of Bacillus fastidiosus Uricase

Metabacillus kandeliae sp. nov., isolated from the rhizosphere soil of a decayed mangrove plant Kandelia candel

In this study, we isolated a novel Gram-stain-positive, aerobic, motile, rod-shaped bacterium, named GX 13764T, from the rhizosphere soil of a decayed mangrove plant Kandelia candel collected from Beihai, Guangxi, PR China, and characterized using a polyphasic taxonomic approach. The strain exhibited yellow-orange, round, convex, shiny, smooth, opaque and 2–3 mm diameter colonies on marine agar 2216 media after 3 days of incubation at 30 °C and was capable of growth at 4–45 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0) and 0–4 % NaCl (w/v; optimum, 2 %). The strain was positive for catalase and negative for the oxidase. The main cellular fatty acid was anteiso-C15:0, iso-C15:0, iso-C16:0 and iso-C14:0. The cell-wall peptidoglycan comprised meso-diaminopimelic acid and the main menaquinone was MK-7. The polar lipids included one diphosphatidylglycerol, one phosphatidylglycerol, two glycolipids, two unidentified phospholipids and three unidentified lipids. Based on 16S rRNA gene analysis, GX 13764T presented the highest sequence similarity to Metabacillus mangrovi KCTC 33872T (97.04 %). The DNA G+C content of the type strain was 44.2 mol%. The average nucleotide identity values between GX 13764T and M. mangrovi KCTC 33872T, Metabacillus idriensis DSM 19097T and Metabacillus indicus LMG 22858T were 69.39, 68.87 and 68.95 %, respectively, with digital DNA–DNA hybridization values of 19.9, 19.5 and 19.5 %, respectively. Based on the polyphasic data, strain GX 13764T should be nominated as a novel species of the genus Metabacillus , for which the name Metabacillus kandeliae sp. nov. is proposed. The type strain is GX 13764T (=MCCC 1K06654T=KCTC 43366T).

Design of Bacillus fastidious Uricase Mutants Bearing Long Lagging Phases Before Exponential Decreases of Activities Under Physiological Conditions

Under physiological conditions, Bacillus fastidious uricase (BFU) activity shows negligible lagging phase before the exponential decrease; mutants are thus designed for long lagging phases before exponential activity decreases. On homodimer surface of BFU (4R8X.pdb), the last fragment ANSEYVAL at the C-terminus forms a loop whose Y319 is H-bonded by the buried D257 in the same monomer. Within 1.5 nm from the α-carboxyl group of the last leucine (L322), E30, K26, D257, R258, E311, K312 and E318 from the same monomer plus D126 and K127 from a monomer of the other homodimer generate an electrostatic interaction network. Within 1.5 nm from Y319, D307 and R310 in the same monomer interact with ionized residues around the inter-chain β-sheet in the same homodimer. Mutagenesis of Y319R is designed to strengthen the original interactions and concomitantly generate new electrostatic attractions between homodimers. Under physiological conditions, the mutant V144A/Y319R showed an approximately 4 week lagging phase before the exponential activity decrease, an apparent half-life of activity nearly three folds of mutant V144A, but comparable activity. The introduction of ionizable residues into the C-terminus contacting the other homodimer for additional and/or stronger electrostatic attractions between homodimers may be a universal approach to thermostable mutants of uricases.

High-throughput screening of enzyme mutants by comparison of their activity ratios to an enzyme tag

With Escherichia coli alkaline phosphatase (ECAP) as the tag fused to the N-terminus of Pseudomonas Aeruginosa arylsulfatase (PAAS) and its mutants via a flexible linker, the comparison of the activity ratios of an applicable enzyme and its mutants to a suitable enzyme tag in cell lysates of their fused forms was tested for high-throughput (HTP) screening of mutants. After both the induced expression of a fused form and alkaline lysis of the transformed cells in microplate wells, HTP assay of the activities of ECAP and PAAS/mutant was realized via spectrophotometric-dual-enzyme-simultaneous-assay to derive their activity ratio. The successful induced expression of fused forms required ECAP activities higher than 5.3 U/L in cell lysates. Of three representative fused PAAS/mutants in cell lysates, there were similar proteolytic fragments and the comparison of their activity ratios greatly enhanced the recognition of weakly positive mutants. After saturation mutagenesis at M72 of the fused PAAS, the activity ratios of PAAS/mutants to ECAP in cell lysates of their fused forms were proportional to specific activities of their non-fused counterparts in cell lysates by an immunoturbidimetric assay. Therefore, the proposed strategy was absorbing for both HTP screening of mutants and HTP elucidation of sequence-activity relationship of applicable enzymes.

Data for high-throughput estimation of specific activities of enzyme/mutants in cell lysates through immunoturbidimetric assay of proteins

Data in this article are associated with the research article “Highthroughput estimation of specific activities of enzyme/mutants in cell lysates through immunoturbidimetric assay of proteins” (Yang et al., 2017) [1]. This article provided data on how to develop an immunoturbidimetric assay (ITA) of enzyme/mutants as proteins in cell lysates in high-throughput (HTP) mode together with HTP assay of their activities to derive their specific activities in cell lysates for comparison, with Pseudomonas aeruginosa arylsulfatase (PAAS) and Bacillus fastidious uricase (BFU) plus their mutants as models. Data were made publicly available for further analyses.

Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid

First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA^2-) during the catalytic reaction process; (2) proton transfer to the O₂^- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H₂O₂ to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.