Improvement of whole-cell transamination with Saccharomyces cerevisiae using metabolic engineering and cell pre-adaptation

Biological valorization of lignin-derived vanillin to vanillylamine by recombinant E. coli expressing ω-transaminase and alanine dehydrogenase in a petroleum ether-water system

Vanillylamine, as an important drug precursor and fine chemical intermediate, has great economic value. By constructing a strategy of double enzyme co-expression, one newly constructed recombinant E. coli HNIQLE-AlaDH expressing ω-transaminase from Aspergillus terreus and alanine dehydrogenase from Bacillus subtilis was firstly used aminate lignin-derived vanillin to vanillylamine by using a relatively low dosage of amine donors (vanillin:L-alanine:isopropylamine = 1:1:1, mol/mol/mol). In addition, in a two-phase system (water:petroleum ether = 80:20 v/v), the bioconversion of vanillin to vanillylamine was catalyzed by HNIQLE-AlaDH cell under the ambient condition, and the vanillylamine yield was 71.5%, respectively. This double-enzyme HNIQLE-AlaDH catalytic strategy was applied to catalyze the bioamination of furfural and 5-hydroxymethylfurfural with high amination efficiency. It showed that the double-enzyme catalytic strategy in this study promoted L-alanine to replace D-Alanine to participate in bioamination of vanillin and its derivatives, showing a great prospect in the green biosynthesis of biobased chemicals from biomass.

Recombinant yeast for production of the pain receptor modulator nonivamide from vanillin

We report on the development of a method based on recombinant yeast Saccharomyces cerevisiae to produce nonivamide, a capsaicinoid and potent agonist of the pain receptor TRPV1. Nonivamide was produced in a two-step batch process where yeast was i) grown aerobically on glucose and ii) used to produce nonivamide from vanillin and non-anoic acid by bioconversion. The yeast was engineered to express multiple copies of an amine transaminase from Chromobacterium violaceum (CvTA), along with an NADH-dependent alanine dehydrogenase from Bacillus subtilis (BsAlaDH) to enable efficient reductive amination of vanillin. Oxygen-limited conditions and the use of ethanol as a co-substrate to regenerate NADH were identified to favour amination over the formation of the by-products vanillic alcohol and vanillic acid. The native alcohol dehydrogenase ADH6 was deleted to further reduce the formation of vanillic alcohol. A two-enzyme system consisting of an N-acyltransferase from Capsicum annuum (CaAT), and a CoA ligase from Sphingomonas sp. Ibu-2 (IpfF) was co-expressed to produce the amide. This study provides proof of concept for yeast-based production of non-ivamide by combined transamination and amidation of vanillin.

Towards engineered yeast as production platform for capsaicinoids

Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.

Hydrogel-Based Enzyme and Cofactor Co-Immobilization for Efficient Continuous Transamination in a Microbioreactor

A microbioreactor was developed in which selected amine transaminase was immobilized together with the cofactor pyridoxal phosphate (PLP) to allow efficient continuous transamination. The enzyme and cofactor were retained in a porous copolymeric hydrogel matrix formed in a two-plate microreactor with an immobilization efficiency of over 97%. After 10 days of continuous operation, 92% of the initial productivity was retained and no leaching of PLP or enzyme from the hydrogel was observed. The microbioreactor with co-immobilized cofactor showed similar performance with and without the addition of exogenous PLP, suggesting that the addition of PLP is not required during the process. The space-time yield of the microbioreactor was 19.91 g L⁻¹ h⁻¹, while the highest achieved biocatalyst productivity was 5.4 mg mg_enzyme⁻¹ h⁻¹. The immobilized enzyme also showed better stability over a wider pH and temperature range than the free enzyme. Considering the time and cost efficiency of the immobilization process and the possibility of capacity expansion, such a system is of great potential for industrial application.

Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates

Whole-cell bioconversion of technical lignins using Pseudomonas putida strains overexpressing amine transaminases (ATAs) has the potential to become an eco-efficient route to produce phenolic amines. Here, a novel cell growth-based screening method to evaluate the in vivo activity of recombinant ATAs towards vanillylamine in P. putida KT2440 was developed. It allowed the identification of the native enzyme Pp-SpuC-II and ATA from Chromobacterium violaceum (Cv-ATA) as highly active towards vanillylamine in vivo. Overexpression of Pp-SpuC-II and Cv-ATA in the strain GN442ΔPP_2426, previously engineered for reduced vanillin assimilation, resulted in 94- and 92-fold increased specific transaminase activity, respectively. Whole-cell bioconversion of vanillin yielded 0.70 ± 0.20 mM and 0.92 ± 0.30 mM vanillylamine, for Pp-SpuC-II and Cv-ATA, respectively. Still, amine production was limited by a substantial re-assimilation of the product and formation of the by-products vanillic acid and vanillyl alcohol. Concomitant overexpression of Cv-ATA and alanine dehydrogenase from Bacillus subtilis increased the production of vanillylamine with ammonium as the only nitrogen source and a reduction in the amount of amine product re-assimilation. Identification and deletion of additional native genes encoding oxidoreductases acting on vanillin are crucial engineering targets for further improvement.

Advanced Strategies for Production of Natural Products in Yeast

Natural products account for more than 50% of all small-molecule pharmaceutical agents currently in clinical use. However, low availability often becomes problematic when a bioactive natural product is promising to become a pharmaceutical or leading compound. Advances in synthetic biology and metabolic engineering provide a feasible solution for sustainable supply of these compounds. In this review, we have summarized current progress in engineering yeast cell factories for production of natural products, including terpenoids, alkaloids, and phenylpropanoids. We then discuss advanced strategies in metabolic engineering at three different dimensions, including point, line, and plane (corresponding to the individual enzymes and cofactors, metabolic pathways, and the global cellular network). In particular, we comprehensively discuss how to engineer cofactor biosynthesis for enhancing the biosynthesis efficiency, other than the enzyme activity. Finally, current challenges and perspective are also discussed for future engineering direction.

Characterization of the stability of Vibrio fluvialis JS17 amine transaminase

The amine transaminase from Vibrio fluvialis (Vf-ATA) is an attractive enzyme with applications within Biocatalysis for the preparation of chiral amines. Various catalytic properties of Vf-ATA have been investigated, but a biophysical characterization of its stability has been lacking. Today, the industrial application of Vf-ATA is limited by its low operational stability. In order to enhance the knowledge regarding the structural stability of ATAs, general characterizations of different ATAs are required. In this work, the stability of Vf-ATA was explored. First, the affinity between enzyme and pyridoxal-5'-phosphate (PLP) (K_D value of 7.9 μM) was determined. Addition of PLP to enzyme preparations significantly improved the enzyme thermal stability by preventing enzyme unfolding. With the aim to understand if this was due to the PLP phosphate group coordination into the phosphate group binding cup, the effect of phosphate buffer on the enzyme stability was compared to HEPES buffer. Low concentrations of phosphate buffer showed a positive effect on the enzyme initial activity, while higher phosphate buffer concentrations prevented cofactor dissociation. Additionally, the effects of various amine or ketone substrates on the enzyme stability were explored. All tested amines caused a concentration dependent enzyme inactivation, while the corresponding ketones showed no or stabilizing effects. The enzyme inactivation due to the presence of amine can be connected to the formation of PMP, which forms in the presence of amines in the absence of ketone. Since PMP is not covalently bound to the enzyme, it could readily leave the enzyme upon formation. Exploring the different stability effects of cofactor, substrates, additives and buffer system on ATAs seems to be important in order to understand and improve the general performance of ATAs.

Amine transaminases in chiral amines synthesis: recent advances and challenges

Transaminases, which catalyze the stereoselective transfer of an amino group between an amino donor and a prochiral ketone substrate, are interesting biocatalytic tools for the generation of optically pure chiral amines. In particular, amine transaminases (ATAs) are of industrial interest because they are capable of performing reductive amination reactions using a broad range of amine donors and acceptors. The most remarkable example of ATAs industrial application is in the production process of the anti-hyperglycaemic drug sitagliptin (Januvia^®/Janumet^®), which generated around 6 billion U.S. dollars of revenue to Merck in 2016. In this review, an update about the availability of microbial ATAs, discovered by both screening and database-mining approaches, or obtained by protein engineering of wild-type enzymes, will be provided. Current challenges in ATAs application and possible solutions will be also discussed. In particular, innovative biocatalytic process strategies aimed at the improvement of ATAs performances in chiral amines synthesis, e.g., using in situ product removal process strategies or flow reactors, will be presented. The progress in the industrial exploitation of these enzymes will be highlighted by selected examples of large-scale ATA-catalyzed processes.

In vivo plug-and-play: a modular multi-enzyme single-cell catalyst for the asymmetric amination of ketoacids and ketones

Background

Transaminases have become a key tool in biocatalysis to introduce the amine functionality into a range of molecules like prochiral α-ketoacids and ketones. However, due to the necessity of shifting the equilibrium towards the product side (depending on the amine donor) an efficient amination system may require three enzymes. So far, this well-established transformation has mainly been performed in vitro by assembling all biocatalysts individually, which comes along with elaborate and costly preparation steps. We present the design and characterization of a flexible approach enabling a quick set-up of single-cell biocatalysts producing the desired enzymes. By choosing an appropriate co-expression strategy, a modular system was obtained, allowing for flexible plug-and-play combination of enzymes chosen from the toolbox of available transaminases and/or recycling enzymes tailored for the desired application.

Results

By using a two-plasmid strategy for the recycling enzyme and the transaminase together with chromosomal integration of an amino acid dehydrogenase, two enzyme modules could individually be selected and combined with specifically tailored E. coli strains. Various plug-and-play combinations of the enzymes led to the construction of a series of single-cell catalysts suitable for the amination of various types of substrates. On the one hand the fermentative amination of α-ketoacids coupled both with metabolic and non-metabolic cofactor regeneration was studied, giving access to the corresponding α-amino acids in up to 96% conversion. On the other hand, biocatalysts were employed in a non-metabolic, “in vitro-type” asymmetric reductive amination of the prochiral ketone 4-phenyl-2-butanone, yielding the amine in good conversion (77%) and excellent stereoselectivity (ee = 98%).

Conclusions

The described modularized concept enables the construction of tailored single-cell catalysts which provide all required enzymes for asymmetric reductive amination in a flexible fashion, representing a more efficient approach for the production of chiral amines and amino acids.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0750-5) contains supplementary material, which is available to authorized users.

Production of (S)-2-aminobutyric acid and (S)-2-aminobutanol in Saccharomyces cerevisiae

Background

Saccharomyces cerevisiae (baker’s yeast) has great potential as a whole-cell biocatalyst for multistep synthesis of various organic molecules. To date, however, few examples exist in the literature of the successful biosynthetic production of chemical compounds, in yeast, that do not exist in nature. Considering that more than 30% of all drugs on the market are purely chemical compounds, often produced by harsh synthetic chemistry or with very low yields, novel and environmentally sound production routes are highly desirable. Here, we explore the biosynthetic production of enantiomeric precursors of the anti-tuberculosis and anti-epilepsy drugs ethambutol, brivaracetam, and levetiracetam. To this end, we have generated heterologous biosynthetic pathways leading to the production of (S)-2-aminobutyric acid (ABA) and (S)-2-aminobutanol in baker’s yeast.

Results

We first designed a two-step heterologous pathway, starting with the endogenous amino acid l-threonine and leading to the production of enantiopure (S)-2-aminobutyric acid. The combination of Bacillus subtilis threonine deaminase and a mutated Escherichia coli glutamate dehydrogenase resulted in the intracellular accumulation of 0.40 mg/L of (S)-2-aminobutyric acid. The combination of a threonine deaminase from Solanum lycopersicum (tomato) with two copies of mutated glutamate dehydrogenase from E. coli resulted in the accumulation of comparable amounts of (S)-2-aminobutyric acid. Additional l-threonine feeding elevated (S)-2-aminobutyric acid production to more than 1.70 mg/L. Removing feedback inhibition of aspartate kinase HOM3, an enzyme involved in threonine biosynthesis in yeast, elevated (S)-2-aminobutyric acid biosynthesis to above 0.49 mg/L in cultures not receiving additional l-threonine. We ultimately extended the pathway from (S)-2-aminobutyric acid to (S)-2-aminobutanol by introducing two reductases and a phosphopantetheinyl transferase. The engineered strains produced up to 1.10 mg/L (S)-2-aminobutanol.

Conclusions

Our results demonstrate the biosynthesis of (S)-2-aminobutyric acid and (S)-2-aminobutanol in yeast. To our knowledge this is the first time that the purely synthetic compound (S)-2-aminobutanol has been produced in vivo. This work paves the way to greener and more sustainable production of chemical entities hitherto inaccessible to synthetic biology.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0667-z) contains supplementary material, which is available to authorized users.