Kenji Miyamoto

A bacterium that degrades and assimilates poly(ethylene terephthalate)

Some bacteria think plastic is fantastic Bacteria isolated from outside a bottle-recycling facility can break down and metabolize plastic. The proliferation of plastics in consumer products, from bottles to clothing, has resulted in the release of countless tons of plastics into the environment. Yoshida et al. show how the biodegradation of plastics by specialized bacteria could be a viable bioremediation strategy (see the Perspective by Bornscheuer). The new species, Ideonella sakaiensis, breaks down the plastic by using two enzymes to hydrolyze PET and a primary reaction intermediate, eventually yielding basic building blocks for growth. Science, this issue p. 1196; see also p. 1154 Two specialized enzymes from a newly isolated bacterium break down plastic into its simplest building blocks. [Also see Perspective by Bornscheuer] Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol.

Dramatically improved catalytic activity of an artificial (S)-selective arylmalonate decarboxylase by structure-guided directed evolution

Using three rounds of structure-guided directed evolution, the catalytic activity of the (S)-selective arylmalonate decarboxylase variant G74C/C188S could be increased up to 920-fold. The best variant had a 220-fold improved activity in the production of (S)-naproxen with excellent enantioselectivity (>99% ee).

Arylmalonate Decarboxylase-Catalyzed Asymmetric Synthesis of Both Enantiomers of Optically Pure Flurbiprofen

The bacterial decarboxylase (AMDase) catalyzes the enantioselective decarboxylation of prochiral arylmalonates with high enantioselectivity. Although this reaction would provide a highly sustainable synthesis of active pharmaceutical compounds such as flurbiprofen or naproxen, competing spontaneous decarboxylation has so far prevented the catalytic application of AMDase. Here, we report on reaction engineering and an alternate protection group strategy for the synthesis of these compounds that successfully suppresses the side reaction and provides pure arylmalonic acids for subsequent enzymatic conversion. Protein engineering increased the activity of the synthesis of the (S)‐ and (R)‐enantiomers of flurbiprofen. These results demonstrated the importance of synergistic effects in the optimization of this decarboxylase. The asymmetric synthesis of both enantiomers in high optical purity (>99u2009%) and yield (>90u2009%) can be easily integrated into existing industrial syntheses of flurbiprofen, thus providing a sustainable method for the production of this important pharmaceutical ingredient.

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

Structure‐guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40‐fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation‐transfer‐difference NMR (STD‐NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD‐NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure‐guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD‐NMR as versatile tool for the analysis of enzyme–substrate interactions in catalytically competent systems and for the guidance of protein engineering.

Engineered hydrophobic pocket of (S)-selective arylmalonate decarboxylase variant by simultaneous saturation mutagenesis to improve catalytic performance

A bacterial arylmalonate decarboxylase (AMDase) catalyzes asymmetric decarboxylation of unnatural arylmalonates to produce optically pure (R)-arylcarboxylates without the addition of cofactors. Previously, we designed an AMDase variant G74C/C188S that displays totally inverted enantioselectivity. However, the variant showed a 20,000-fold reduction in activity compared with the wild-type AMDase. Further studies have demonstrated that iterative saturation mutagenesis targeting the active site residues in a hydrophobic pocket of G74C/C188S leads to considerable improvement in activity where all positive variants harbor only hydrophobic substitutions. In this study, simultaneous saturation mutagenesis with a restricted set of amino acids at each position was applied to further heighten the activity of the (S)-selective AMDase variant toward α-methyl-α-phenylmalonate. The best variant (V43I/G74C/A125P/V156L/M159L/C188G) showed 9,500-fold greater catalytic efficiency kcat/Km than that of G74C/C188S. Notably, a high level of decarboxylation of α-(4-isobutylphenyl)-α-methylmalonate by the sextuple variant produced optically pure (S)-ibuprofen, an analgesic compound which showed 2.5-fold greater activity than the (R)-selective wild-type AMDase. Graphical abstract Using structure-guided directed evolution, the catalytic efficiency of (S)-selective arylmalonate decarboxylase variant could be increased up to 9,500-fold.

Photosynthetic production of enantioselective biocatalysts.

BackgroundGlobal resource depletion poses a dramatic threat to our society and creates a strong demand for alternative resources that do not compete with the production of food. Meeting this challenge requires a thorough rethinking of all steps of the value chain regarding their sustainability resource demand and the possibility to substitute current, petrol-based supply-chains with renewable resources. This regards also the production of catalysts for chemical synthesis. Phototrophic microorganisms have attracted considerable attention as a biomanufacturing platform for the sustainable production of chemicals and biofuels. They allow the direct utilization of carbon dioxide and do not compete with food production. Photosynthetic enzyme production of catalysts would be a sustainable supply of these important components of the biotechnological and chemical industries. This paper focuses on the usefulness of recombinant cyanobacteria for the photosynthetic expression of enantioselective catalysts. As a proof of concept, we used the cyanobacterium Synechocystis sp. PCC 6803 for the heterologous expression of two highly enantioselective enzymes.ResultsWe investigated the expression yield and the usefulness of cyanobacterial cell extracts for conducting stereoselective reactions. The cyanobacterial enzyme expression achieved protein yields of 3% of total soluble protein (%TSP) while the expression in E. coli yielded 6-8% TSP. Cell-free extracts from a recombinant strain expressing the recombinant esterase ST0071 from the thermophilic organism Sulfolobus tokodai ST0071 and arylmalonate decarboxylase from Bordetella bronchiseptica showed excellent enantioselectivity (>99% ee) and yield (>91%) in the desymmetrisation of prochiral malonates.ConclusionsWe were able to present the proof-of-concept of photoautotrophic enzyme expression as a viable alternative to heterotrophic expression hosts. Our results show that the introduction of foreign genes is straightforward. Cell components from Synechocystis did not interfere with the stereoselective transformations, underlining the usability of photoautotrophic organisms for the production of enzymes. Given the considerable commercial value of recombinant biocatalysts, cyanobacterial enzyme expression has thus the potential to complement existing approaches to use phototrophic organisms for the production of chemicals and biofuels.

Semiempirical QM/MM calculations reveal a step-wise proton transfer and an unusual thiolate pocket in the mechanism of the unique arylpropionate racemase AMDase G74C

The mechanism of the unique arylpropionate racemase AMDase G74C was investigated by a QM/MM approach. Molecular dynamics simulations showed that the mechanism is initiated by a deprotonation of the catalytic cysteine. The simulations revealed two thiolate pockets. While the first plays a role in the natural decarboxylative activity of AMDase, the second stabilizes the artificially introduced thiolate group of C74. The presence of the two structural motifs is a prerequisite for the promiscuous racemization reaction of AMDase G74C. QM/MM simulations show that the deprotonation and reprotonation proceed in a stepwise fashion, in which a planar enedionate intermediate is stabilized by a delocalized π-electron system on a vinylic or aromatic substituent of the substrate. The artificial racemase is thus a typical case of substrate-assisted catalysis.

Draft genome sequence of Bordetella bronchiseptica KU1201, the first isolation source of arylmalonate decarboxylase

ABSTRACT The analysis of the 6.8-Mbp draft genome sequence of the phenylmalonate-assimilating bacterium Bordetella bronchiseptica KU1201 identified 6,358 protein-coding sequences. This will give us an insight into the catabolic variability of this strain for aromatic compounds, along with the roles of arylmalonate decarboxylases in nature.

Modulating the catalytic activity and the substrate specificity of alcohol dehydrogenases using cyclic ethers

The catalytic activities of alcohol dehydrogenases (ADHs) are investigated in the presence of 5% cyclic ethers. Although most cyclic ethers show an inhibitory effect on ADHs, we found that the catalytic rate constant of 2-butanol oxidation by Thermoanaerobacter brockii ADH was increased from 57 to 190 min−1 by the addition of 1,3-dioxolane, which altered the substrate specificity.

Cofactor Recycling Using a Thermostable NADH Oxidase

From the standpoint of enzymatic organic synthesis, NADH oxidase (NOX) will be a key enzyme that plays an essential role in the cofactor regeneration of NAD+ dependent enzymatic reactions. For example, enzymatic enantioselective oxidations of racemic secondary alcohols (Geueke et al., 2003; Riebel et al., 2003; Hummel & Riebel, 1996) and amino acids (Hummel et al., 2003a) have been reported as utilizing this enzyme (Fig. 1). The kinetic resolutions of secondary alcohols are important processes in cases where preparation of the corresponding ketones is difficult. In these reported reactions, NAD+ dependent enantioselective alcohol dehydrogenase (or amino acid dehydrogenase) was used with NOX for regeneration of the oxidized form of cofactor NAD+.