Hiroyuki Ashida

Molecular Characterization of a Novel Peroxidase from the Cyanobacterium Anabaena sp. Strain PCC 7120

ABSTRACT The open reading frame alr1585 of Anabaena sp. strain PCC 7120 encodes a heme-dependent peroxidase (Anabaena peroxidase [AnaPX]) belonging to the novel DyP-type peroxidase family (EC 1.11.1.X). We cloned and heterologously expressed the active form of the enzyme in Escherichia coli. The purified enzyme was a 53-kDa tetrameric protein with a pI of 3.68, a low pH optima (pH 4.0), and an optimum reaction temperature of 35°C. Biochemical characterization revealed an iron protoporphyrin-containing heme peroxidase with a broad specificity for aromatic substrates such as guaiacol, 4-aminoantipyrine and pyrogallol. The enzyme efficiently catalyzed the decolorization of anthraquinone dyes like Reactive Blue 5, Reactive Blue 4, Reactive Blue 114, Reactive Blue 119, and Acid Blue 45 with decolorization rates of 262, 167, 491, 401, and 256 μM·min−1, respectively. The apparent Km and kcat/Km values for Reactive Blue 5 were 3.6 μM and 1.2 × 107 M−1 s−1, respectively, while the apparent Km and kcat/Km values for H2O2 were 5.8 μM and 6.6 × 106 M−1 s−1, respectively. In contrast, the decolorization activity of AnaPX toward azo dyes was relatively low but was significantly enhanced 2- to ∼50-fold in the presence of the natural redox mediator syringaldehyde. The specificity and catalytic efficiency for hydrogen donors and synthetic dyes show the potential application of AnaPX as a useful alternative of horseradish peroxidase or fungal DyPs. To our knowledge, this study represents the only extensive report in which a bacterial DyP has been tested in the biotransformation of synthetic dyes.

Molecular Properties and Enhancement of Thermostability by Random Mutagenesis of Glutamate Dehydrogenase from Bacillus subtilis

The rocG gene encoding glutamate dehydrogenase from Bacillus subtilis (Bs-GluDH) was cloned, and expressed at considerable magnitude in Escherichia coli. The recombinant Bs-GluDH was purified to homogeneity and has been determined to have a hexameric structure (M r 270 kDa) with strict specificity for 2-oxoglutarate and L-glutamate, requiring NADH and NAD+ as cofactors respectively. The enzyme showed low thermostability with T m=41 °C due to dissociation of the hexamer. To improve the thermostability of this enzyme, we performed error-prone PCR, introducing random mutagenesis on cloned GluDH. Two single mutant enzymes, Q144R and E27F, were isolated from the final mutant library. Their T m values were 61 °C and 49 °C respectively. Furthermore, Q144R had a remarkably high k cat value (435 s−1) for amination reaction at 37 °C, 1.3 times higher than that of the wild-type. Thus, Q144R can be used as a template gene to modify the substrate specificity of Bs-GluDH for industrial use.

Effect of intracellular glutathione on heat-induced cell death in the cyanobacterium, Synechocystis PCC 6803

A correlation was found between the rate of cell death induced by heat and the GSH content of Synechocystis PCC 6803: cells accumulating GSH above the control level were more tolerant to heat than the control cells, and those containing a lower concentration of GSH were more sensitive. Lethal heating caused a decrease of GSH content, and a rapid intracellular oxidation in cells containing the decreased amount of GSH.

Altering the substrate specificity of glutamate dehydrogenase from Bacillus subtilis by site-directed mutagenesis.

The Lys80, Gly82 and Met101 residues of glutamate dehydrogenase from Bacillus subtilis were mutated into a series of single mutants. The wild-type enzyme was highly specific for 2-oxoglutarate, whereas G82K and M101S dramatically switched to increased specificity for oxaloacetate with k cat values 3.45 and 5.68 s−1, which were 265-fold and 473-fold higher respectively than those for 2-oxoglutarate.

A non-NadB type L-aspartate dehydrogenase from Ralstonia eutropha strain JMP134: molecular characterization and physiological functions.

We report the molecular characterization and physiological function of a novel L-aspartate dehydrogenase (AspDH). The purified enzyme was a 28-kDa dimeric protein, exhibiting high catalytic activity for L-aspartate (L-Asp) oxidation using NAD and/or NADP as cofactors. Quantitative real-time PCR analysis indicated that the genes involved in the AspDH gene cluster, poly-3-hydroxyalkanoate (PHA) biosynthesis, and the TCA cycle were substantially induced by L-Asp in wild-type cells. In contrast, expression of the aspartase and aspartate aminotransferase genes was substantially induced in the AspDH gene knockout mutant (ΔB3576) but not in the wild type. GC-MS analyses revealed that the wild-type strain synthesized poly-3-hydroxybutyrate from fructose or L-Asp, whereas the ΔB3576 mutant did not synthesize PHA from L-Asp. AspDH gene cluster products might be involved in the biosynthesis of the PHA precursor, revealing that AspDH was a non-NadB type enzyme, and thus entirely different from the previously reported NadB type enzymes working in NAD biosynthesis.

Cloning, structural analysis and expression of the gene encoding aspartate aminotransferase from the thermophilic cyanobacterium Phormidium lapideum.

The aspartate aminotransferase gene from the thermophilic cyanobacterium Phormidium lapideum was cloned and expressed in Escherichia coli. The ORF of 1167 nucleotides encodes a protein of 388 amino acids having a molecular weight of 42,099. A molecular model of PIAspAT shows structural features similar to those of the Thermus thermophilus AspAT.

Anabaena sp. DyP‐type peroxidase is a tetramer consisting of two asymmetric dimers

DyP‐type peroxidases are a newly discovered family of heme peroxidases distributed from prokaryotes to eukaryotes. Recently, using a structure‐based sequence alignment, we proposed the new classes, P, I and V, as substitutes for classes A, B, C, and D [Arch Biochem Biophys 2015;574:49–55]. Although many class V enzymes from eukaryotes have been characterized, only two from prokaryotes have been reported. Here, we show the crystal structure of one of these two enzymes, Anabaena sp. DyP‐type peroxidase (AnaPX). AnaPX is tetramer formed from Cys224‐Cys224 disulfide‐linked dimers. The tetramer of wild‐type AnaPX was stable at all salt concentrations tested. In contrast, the C224A mutant showed salt concentration‐dependent oligomeric states: in 600 mM NaCl, it maintained a tetrameric structure, whereas in the absence of salt, it dissociated into monomers, leading to a reduction in thermostability. Although the tetramer exhibits non‐crystallographic, 2‐fold symmetry in the asymmetric unit, two subunits forming the Cys224‐Cys224 disulfide‐linked dimer are related by 165° rotation. This asymmetry creates an opening to cavities facing the inside of the tetramer, providing a pathway for hydrogen peroxide access. Finally, a phylogenetic analysis using structure‐based sequence alignments showed that class V enzymes from prokaryotes, including AnaPX, are phylogenetically closely related to class V enzymes from eukaryotes. Proteins 2016; 84:31–42.

Explorations and Applications of Enzyme-linked Bioremediation of Synthetic Dyes

Extensive use of synthetic dyes and their subsequent release in industrial wastewater is a growing environmental problem. These dyes are recalcitrant in nature, and some dyes are also well established to be potentially carcinogenic and mutagenic as well as genotoxic. Research efforts have been devoted to develop new, low-cost, and ecofriendly treatments capable of reducing and even eliminating synthetic dye com‐ pounds from the environment. Enzymatic approach has attracted much interest recently in the decolorization of textile and other industrially important dyes from wastewater as an alternative strategy to conventional chemical, physical, and biological treatments, which pose serious limitations. In this chapter, the accumulated research data on the potential of the oxidoreductive enzymes—high redox potential peroxidases (lignin peroxidase [LiP], EC 1.11.1.14; manganese peroxidase [MnP], EC 1.11.1.13; dye decolorizing peroxidase [DyP], EC 1.11.1.19; and versatile peroxidases [VP], EC 1.11.1.16), laccases (benzenediol–oxygen oxidoreductase, EC 1.10.3.2), polyphenol oxidases (EC 1.14.18.1), and azoreductases (azobenzene reductases, EC 1.7.1.6)—that have been exploited in the decolorization and degradation of synthetic dyes are presented. An overview of enzyme technology, including the importance of redox mediators for enhanced range of substrates and efficiency of degradation, current biodegradation applications, and suggestions to overcome the limitations to these proteins’ large scale and efficient use, is made. Different strategies currently being used and future prospects for the potential use of genetic engineering techni‐ ques to improve the performance of these oxidoreductases in terms of stability, selectivity, and catalytic activity in dye bioremediation technologies are also explored.