Wim Soetaert

Ghent University, Gand, Flemish, Belgium

Are you Wim Soetaert?

Claim your profile

Publications (166)394.78 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Imbalance in cofactors causing the accumulation of intermediates in biosynthesis pathways is a frequently occurring problem in metabolic engineering when optimizing a production pathway in a microorganism. In our previous study, a single knock-out Citrobacter werkmanii ∆dhaD was constructed for improved 1,3-propanediol (PDO) production. Instead of an enhanced PDO concentration on this strain, the gene knock-out led to the accumulation of the toxic intermediate 3-hydroxypropionaldehyde (3-HPA). The hypothesis was emerged that the accumulation of this toxic intermediate, 3-HPA, is due to a cofactor imbalance, i.e. to the limited supply of reducing equivalents (NADH). Here, this bottleneck is alleviated by rationally engineering cell metabolism to balance the cofactor supply. By eliminating non-essential NADH consuming enzymes (such as lactate dehydrogenase coded by ldhA, and ethanol dehydrogenase coded by adhE) or by increasing NADH producing enzymes, the accumulation of 3-HPA is minimized. Combining the above modifications in C. werkmanii ∆dhaD resulted in the strain C. werkmanii ∆dhaD∆ldhA∆adhE::ChlFRT which provided the maximum theoretical yield of 1.00 ± 0.03 mol PDO/mol glycerol when grown on glucose/glycerol (0.33 molar ratio) on flask scale under anaerobic conditions. On bioreactor scale, the yield decreased to 0.73 ± 0.01 mol PDO/mol glycerol although no 3-HPA could be measured, which indicates the existence of a sink of glycerol by a putative glycerol dehydrogenase, channeling glycerol to the central metabolism. In this study, a multiple knock-out was created in Citrobacter species for the first time. As a result, the concentration of the toxic intermediate 3-HPA was reduced to below the detection limit and the maximal theoretical PDO yield on glycerol was reached.
    Preview · Article · Dec 2016 · Microbial Cell Factories
  • [Show abstract] [Hide abstract]
    ABSTRACT: Although sophorolipids (SLs) produced by S. bombicola are a real showcase for the industrialization of microbial biosurfactants, some important drawbacks are associated with this efficient biological process, e.g. the simultaneous production of acidic and lactonic SLs. Depending on the application, there is a requirement for the naturally produced mixture to be manipulated to give defined ratios of the components. Recently, the enzyme responsible for the lactonization of SLs was discovered. The discovery of the gene encoding this lactone esterase (sble) enabled the development of promising S. bombicola strains producing either solely lactonic (using a sble overexpression strain described in this paper: oe sble) or solely acidic SLs (using a sble deletion strain, which was recently described, but not characterized yet: Δsble). The new S. bombicola strains were used to investigate the production processes (fermentation and purification) of either lactonic or acidic SLs. The strains maintain the high inherent productivities of the wild type or even perform slightly better and thus represent a realistic industrial opportunity. 100% acidic SLs with a mixed acetylation pattern were obtained for the Δsble strain, while the inherent capacity to selectively produce lactonic SLs was significantly increased (+ 42%) for the oe sble strain (99% lactonic SLs). Moreover, the regulatory effect of citrate on lactone SL formation for the wild type was absent in this new strain, which indicates that it is more robust and better suited for the industrial production of lactonic SLs. The final lactone content for the latter was increased to 99.5% using the developed purification process. Basic parameters were determined for the purified SLs, which confirm that the two new strains produce molecules with distinctive properties of which the application potential can now easily be investigated independently. This article is protected by copyright. All rights reserved
    No preview · Article · Aug 2015 · Biotechnology and Bioengineering
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Altering glycolipid structure by genetic engineering of S. bombicola is a recently started research topic and worthy alternative to the unsuccessful selective feeding strategies conventionally applied to reach this goal. One question to be addressed when expressing heterologous proteins in S. bombicola is the activity of the subsequent biosynthetic enzymes towards such modified substrates. In this scope, we studied the substrate specificity of the UDP-glucosyltransferases UgtA1 and UgtB1, responsible for the stepwise synthesis of sophorolipids from a hydroxylated fatty acid, and that of the acetyltransferase, responsible for acetylation of the sophorolipid molecule. All enzymes showed specificity towards a C18:1 chained acceptor and both glucosyltransferases were highly selective towards the UDP-glucose donor. Severe product inhibition of the glucosyltransferases explains the limited accumulation of sophorolipid intermediates by earlier created single deletion mutants of S. bombicola. Finally, a more detailed study of the acetylation of sophorolipid intermediates sheds light on the enzymatic cascade during synthesis. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
    Full-text · Article · Aug 2015 · FEMS Yeast Research
  • Koen Beerens · Wim Soetaert · Tom Desmet
    [Show abstract] [Hide abstract]
    ABSTRACT: UDP-sugar 4-epimerase (GalE) belongs to the short-chain dehydrogenase/reductase (SDR) superfamily of proteins and is one of enzymes in the Leloir pathway. They have been shown to be important virulence factors in a number of Gram-negative pathogens and to be involved in the biosynthesis of different polysaccharide structures. The metabolic disease type III galactosemia is caused by detrimental mutations in the human GalE. GalE and related enzymes display unusual enzymologic, chemical, and stereochemical properties; including irreversible binding of the cofactor NAD and uridine nucleotide-induced activation of this cofactor. These epimerases have been found active on UDP-hexoses, the N-acetylated and uronic acid forms thereof as well as UDP-pentoses. As they are involved in different pathways and functions, a deeper understanding of the enzymes, and their substrate promiscuity and/or selectivity, could lead to drug and vaccine design as well as antibiotic and probiotic development. This review summarizes the research performed on UDP-sugar 4-epimerases' structure, mechanism and substrate promiscuity. Copyright © 2015 Elsevier Ltd. All rights reserved. HIGHLIGHTS - GalEs display unusual enzymologic, chemical, and stereochemical properties - UDP-sugar 4-epimerases are important in Leloir and polysaccharide synthesis pathways - GalEs can be active on a broad range of UDP-sugars and derivatives - Understanding of human GalE important for type III galactosemia treatment - New insights could lead to drug and vaccine design and antibiotic development KEY WORDS: epimerase; uridine diphosphate galactose 4-epimerase; GalE; UDP-glucose; UDP-galactose; N-acetylated UDP-sugar Free access until August 26, 2015: http://authors.elsevier.com/a/1RKDk1zTQLj0F
    No preview · Article · Jun 2015 · Carbohydrate research
  • [Show abstract] [Hide abstract]
    ABSTRACT: Over the past decade, disaccharide phosphorylases have been successfully applied for the synthesis of numerous α-glucosides. In contrast, much less research has been done with respect to the production of β-glucosides. Although cellobiose phosphorylase was already successfully used for the synthesis of various disaccharides and branched trisaccharides, its glycosylation potential towards small organic compounds has not been explored to date. Unfortunately, disaccharide phosphorylases typically have a very low affinity for non-carbohydrate acceptors, which urges the addition of solvents. The ionic liquid AMMOENGTM 101 and ethyl acetate were identified as the most promising solvents, allowing the synthesis of various β-glucosides. Next to hexyl, heptyl, octyl, nonyl, decyl and undecyl β-D-glucopyranosides, also the formation of vanillyl 4-O-β-D-glucopyranoside, 2-phenylethyl β-D-glucopyranoside, β-citronellyl β-D-glucopyranoside and 1-O-β-D-glucopyranosyl hydroquinone was confirmed by nuclear magnetic resonance spectroscopy and mass spectrometry. Moreover, the stability of cellobiose phosphorylase could be drastically improved by creating cross-linked enzyme aggregates, while the efficiency of the biocatalyst for the synthesis of octyl β-D-glucopyranoside was doubled by imprinting with octanol. The usefulness of the latter system was illustrated by performing three consecutive batch conversions with octanol imprinted cross-linked enzyme aggregates, yielding roughly 2 g of octyl β-D-glucopyranoside.
    No preview · Article · May 2015 · Advanced Synthesis & Catalysis
  • [Show abstract] [Hide abstract]
    ABSTRACT: Glycosylation of small molecules like specialized (secondary) metabolites has a profound impact on their solubility, stability or bioactivity, making glycosides attractive compounds as food additives, therapeutics or nutraceuticals. The subsequently growing market demand has fuelled the development of various biotechnological processes, which can be divided in the in vitro (using enzymes) or in vivo (using whole cells) production of glycosides. In this context, uridine glycosyltransferases (UGTs) have emerged as promising catalysts for the regio- and stereoselective glycosylation of various small molecules, hereby using uridine diphosphate (UDP) sugars as activated glycosyldonors. This review gives an extensive overview of the recently developed in vivo production processes using UGTs and discusses the major routes towards UDP-sugar formation. Furthermore, the use of interconverting enzymes and glycorandomization is highlighted for the production of unusual or new-to-nature glycosides. Finally, the technological challenges and future trends in UDP-sugar based glycosylation are critically evaluated and summarized. Copyright © 2015. Published by Elsevier Inc.
    No preview · Article · Feb 2015 · Biotechnology Advances
  • I Van Bogaert · K Ciesielska · B Devreese · W Soetaert

    No preview · Chapter · Nov 2014
  • I. Van Bogaert · W. Soetaert

    No preview · Article · Sep 2014
  • Robin Geys · Wim Soetaert · Inge Van Bogaert
    [Show abstract] [Hide abstract]
    ABSTRACT: In the recent years, biosurfactants proved to be an interesting alternative to petrochemically derived surfactants. Two classes of biosurfactants, namely glycolipids and lipopeptides, have attracted significant commercial interest. Despite their environmental advantages and equal performance, commercialization of these molecules remains a challenge due to missing acquaintance of the applicants, higher price and lack of structural variation. The latter two issues can partially be tackled by screening for novel and better wild-type producers and optimizing the fermentation process. Yet, these traditional approaches cannot overcome all hurdles. In this review, an overview is given on how biotechnology offers opportunities for increased biosurfactant production and the creation of new types of molecules, in this way enhancing their commercial potential.
    No preview · Article · Jul 2014 · Current Opinion in Biotechnology
  • [Show abstract] [Hide abstract]
    ABSTRACT: A two-step process is reported for the anomeric phosphorylation of galactose, using trehalose phosphorylase as biocatalyst. The monosaccharide enters this process as acceptor but can subsequently be released from the donor side, thanks to the non-reducing nature of the disaccharide intermediate. A key development was the creation of an optimized enzyme variant that displays a strict specificity (99%) for β-galactose 1-phosphate as product.
    No preview · Article · Jun 2014 · Chemical Communications
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background 1,3-propanediol (PDO) is a substantially industrial metabolite used in the polymer industry. Although several natural PDO production hosts exist, e.g. Klebsiella sp., Citrobacter sp. and Clostridium sp., the PDO yield on glycerol is insufficient for an economically viable bio-process. Enhancing this yield via strain improvement can be achieved by disconnecting the production and growth pathways. In the case of PDO formation, this approach results in a microorganism metabolizing glycerol strictly for PDO production, while catabolizing a co-substrate for growth and maintenance. We applied this strategy to improve the PDO production with Citrobacter werkmanii DSM17579. Results Genetic tools were developed and used to create Citrobacter werkmanii DSM17579 ∆dhaD in which dhaD, encoding for glycerol dehydrogenase, was deleted. Since this strain was unable to grow on glycerol anaerobically, both pathways were disconnected. The knock-out strain was perturbed with 13 different co-substrates for growth and maintenance. Glucose was the most promising, although a competition between NADH-consuming enzymes and 1,3-propanediol dehydrogenase emerged. Conclusion Due to the deletion of dhaD in Citrobacter werkmanii DSM17579, the PDO production and growth pathway were split. As a consequence, the PDO yield on glycerol was improved 1,5 times, strengthening the idea that Citrobacter werkmanii DSM17579 could become an industrially interesting host for PDO production.
    Full-text · Article · May 2014 · Microbial Cell Factories
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In the present paper, we show that the saturated form of acidic sophorolipids, a family of industrially scaled bolaform microbial glycolipids, unexpectedly forms chiral nanofibers only at pH below 7.5. In particular, we illustrate that this phenomenon derives from a subtle cooperative effect of molecular chirality, hydrogen bonding, van der Waals forces and steric hindrance. The pH-responsive behaviour was shown by Dynamic Light Scattering (DLS), pH-titration and Field Emission Scanning Electron Microscopy (FE-SEM) while the nanoscale chirality was evidenced by Circular Dichroism (CD) and cryo Transmission Electron Microscopy (cryo-TEM). The packing of sophorolipids within the ribbons was studied using Small Angle Neutron Scattering (SANS), Wide Angle X-ray Scattering (WAXS) and 2D (1)H-(1)H through-space correlations via Nuclear Magnetic Resonance under very fast (67 kHz) Magic Angle Spinning (MAS-NMR).
    Full-text · Article · Apr 2014 · Soft Matter
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Sucrose phosphorylase is a promising biocatalyst for the glycosylation of a wide range of compounds, but its industrial application has been hampered by the low thermostability of known representatives. Hence, in this study, the putative sucrose phosphorylase from the thermophile Thermoanaerobacterium thermosaccharolyticum was recombinantly expressed and fully characterised. The enzyme showed significant activity on sucrose (optimum at 55 °C), and with a melting temperature of 79 °C and a half-life of 60 h at the industrially relevant temperature of 60 °C, it is far more stable than known sucrose phosphorylases. Substrate screening and detailed kinetic characterisation revealed however a preference for sucrose 6'-phosphate over sucrose. The enzyme can thus be considered as a sucrose 6'-phosphate phosphorylase, a specificity not yet reported to date. Homology modelling and mutagenesis pointed out particular residues (Arg134 and His344) accounting for the difference in specificity. Moreover, phylogenetic and sequence analysis suggest that glycoside hydrolase 13 subfamily 18 might harbour even more specificities. In addition, the second gene residing in the same operon as sucrose 6'-phosphate phosphorylase was identified as well, and found to be a phosphofructokinase. The concerted action of both these enzymes implies a new pathway for the breakdown of sucrose, in which the reaction products end up at different stages of the glycolysis.
    Preview · Article · Mar 2014 · Applied Microbiology and Biotechnology
  • Sofie Dobbelaere · Tom Anthonis · Wim Soetaert
    [Show abstract] [Hide abstract]
    ABSTRACT: Lignocellulosic biomass such as agricultural and forestry residues and herbaceous energy crops can serve as low-cost renewable feedstock for many, next-generation, bio-derived products. Over the years, numerous research and development efforts have been undertaken to develop and apply new cost-efficient conversion processes for lignocellulosic biomass. This chapter gives an overview of the conversion technologies for liquid fuels and biochemicals. Generally, two main routes for the conversion of lignocellulosic biomass can be distinguished, which can lead to the production of biofuels and other value-added commodity chemicals: the biochemical route and the thermochemical route. Biochemical conversion makes use of the enzymes of bacteria or other microorganisms to break down and convert the biomass. Thermochemical conversion includes processes in which heat and pressure are the dominant mechanisms to convert the biomass into another chemical form. Further research is needed to develop commercially viable processes utilizing the two technologies.
    No preview · Chapter · Mar 2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: Thanks to its broad acceptor specificity, sucrose phosphorylase (SP) has been exploited for the transfer of glucose to a wide variety of acceptor molecules. Unfortunately, the low affinity (Km > 1 M) of SP towards these acceptors typically urges the addition of cosolvents, which often either fail to dissolve sufficient substrate or progressively give rise to enzyme inhibition and denaturation. In this work, a buffer/ethyl acetate ratio of 5:3 was identified to be the optimal solvent system, allowing the use of SP in biphasic systems. Careful optimization of the reaction conditions enabled the synthesis of a range of α-d-glucosides, such as cinnamyl α-d-glucopyranoside, geranyl α-d-glucopyranoside, 2-O-α-d-glucopyranosyl pyrogallol, and series of alkyl gallyl 4-O-α-d-glucopyranosides. The usefulness of biphasic catalysis was further illustrated by comparing the glucosylation of pyrogallol in a cosolvent and biphasic reaction system. The acceptor yield for the former reached only 17.4%, whereas roughly 60% of the initial pyrogallol was converted when using biphasic catalysis.
    No preview · Article · Feb 2014 · Organic Process Research & Development
  • [Show abstract] [Hide abstract]
    ABSTRACT: Biosurfactants (BSs) are a class of secondary metabolites representing a wide variety of structures that can be produced from renewable feedstock by a wide variety of micro-organisms. They have (potential) applications in the medical world, personal care sector, mining processes, food industry, cosmetics, crop protection, pharmaceuticals, bio-remediation, household detergents, paper and pulp industry, textiles, paint industries, etc. Especially glycolipid BSs like sophorolipids (SLs), rhamnolipids (RLs), mannosylerythritol lipids (MELs) and cellobioselipids (CBLs) have been described to provide significant opportunities to (partially) replace chemical surfactants. The major two factors currently limiting the penetration of BSs into the market are firstly the limited structural variety and secondly the rather high production price linked with the productivity. One of the keys to resolve the abovementioned bottlenecks can be found in the genetic engineering of natural producers. This could not only result in more efficient (economical) recombinant producers, but also in a diversification of the spectrum of available BSs as such resolving both limiting factors at once. Unraveling the genetics behind the biosynthesis of these interesting biological compounds is indispensable for the tinkering, fine tuning and rearrangement of these biological pathways with the aim of obtaining higher yields and a more extensive structural variety. Therefore, this review focuses on recent developments in the investigation of the biosynthesis, genetics and regulation of some important members of the family of the eukaryotic glycolipid BSs (MELs, CBLs and SLs). Moreover, recent biotechnological achievements and the industrial potential of engineered strains are discussed.
    No preview · Article · Feb 2014 · Applied Microbiology and Biotechnology
  • [Show abstract] [Hide abstract]
    ABSTRACT: The yeast Starmerella bombicola secretes sophorolipids, a family of biosurfactants that find applications in green household products and cosmetics. Over the past years, a gene cluster was discovered that is responsible for the entire synthesis of the open (acidic) form of these molecules from glucose, fatty acids and acetyl-CoA building blocks. However, a significant fraction of the natural product is obtained as ring closed (lactonic). Both genetic and proteomic approaches hitherto failed to discover an enzyme responsible for the esterification reaction required for the ring closure step. We hypothesized that this enzyme is extracellular secreted. Therefore, we characterized the composition of the S. bombicola exoproteome at different time points of the growth and compared it with known yeast exoproteomes. We identified 44 proteins, many of them commonly found in other fungi. Curiously, we discovered an enzyme with homology to Pseudozyma antarctica lipase A. A deletion mutation of its gene resulted in complete abolishment of the sophorolipid lactonization providing evidence that this might be the missing enzyme in the sophorolipid biosynthetic pathway. Growing concern about the impact of chemical processes on the environment increases consumers' demand for bio-based products. Lately, the household care and personal care sectors show increasing interest in naturally occurring biosurfactants, which constitute environment-friendly alternatives for chemical surfactants, typically derived from mineral oils. A particular group of biosurfactants, sophorolipids, already found their way to the market, being used in a range of household detergent products and in cosmetics. This work describes how proteomic approaches have led to the completion of our knowledge on the biosynthetic pathway of sophorolipids as performed by Starmerella bombicola, a fungus used in the industrial production of these biosurfactants. Moreover, we proved that by creating a deletion mutant in the lactone esterase discovered in this study, we can shape the biosynthesis towards custom-made sophorolipids with desired functions. Herewith, we demonstrate the potential of proteomics in industrial biotechnology.
    No preview · Article · Jan 2014 · Journal of proteomics
  • Robin Geys · Wim Soetaert · Inge Van Bogaert

    No preview · Article · Jan 2014 · Current Opinion in Biotechnology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Lignin is one of the main factors determining recalcitrance to enzymatic processing of lignocellulosic biomass. Poplars (Populus tremula x Populus alba) down-regulated for cinnamoyl-CoA reductase (CCR), the enzyme catalyzing the first step in the monolignol-specific branch of the lignin biosynthetic pathway, were grown in field trials in Belgium and France under short-rotation coppice culture. Wood samples were classified according to the intensity of the red xylem coloration typically associated with CCR down-regulation. Saccharification assays under different pretreatment conditions (none, two alkaline, and one acid pretreatment) and simultaneous saccharification and fermentation assays showed that wood from the most affected transgenic trees had up to 161% increased ethanol yield. Fermentations of combined material from the complete set of 20-mo-old CCR-down-regulated trees, including bark and less efficiently down-regulated trees, still yielded ∼20% more ethanol on a weight basis. However, strong down-regulation of CCR also affected biomass yield. We conclude that CCR down-regulation may become a successful strategy to improve biomass processing if the variability in down-regulation and the yield penalty can be overcome.
    Full-text · Article · Dec 2013 · Proceedings of the National Academy of Sciences
  • [Show abstract] [Hide abstract]
    ABSTRACT: Sucrose phosphorylase (SP) is a promising biocatalyst for the production of special sugars and glycoconjugates, but its transglycosylation activity rarely exceeds the competing hydrolytic reaction. Knowing how specificity is controlled, would allow to optimise this activity in an efficient way by means of enzyme engineering. Therefore, in this study, a map of the acceptor site of the SP from Bifidobacterium adolescentis was created by substituting each residue by alanine and analysing the influence on the affinity for both the natural (inorganic phosphate and fructose) and alternative acceptors (D-arabitol and pyridoxine). All residues examined were found to contribute to the specificity for phosphate (Arg135, Leu343, Tyr344), fructose (Tyr132, Asp342) or both (Pro134, Tyr196, His234, Gln345). Alternative acceptors that are glycosylated rather efficiently (e.g. D-arabitol) were found to interact with the same residues as fructose, whereas poor acceptors like pyridoxine do not seem to make any specific interactions with the enzyme. Furthermore, it is shown here that SP is already optimised to outcompete water as an acceptor substrate, meaning that it will be very difficult to lower its hydrolytic activity any further. Consequently, increasing the transglycosylation activity towards alternative acceptors seems to be the best strategy, although that would probably require a drastic remodelling of the acceptor site in most cases.
    No preview · Article · Dec 2013 · Journal of Molecular Catalysis B Enzymatic

Publication Stats

2k Citations
394.78 Total Impact Points

Institutions

  • 1970-2015
    • Ghent University
      • • Department of Biochemical and Microbial Technology
      • • Faculty of Bioscience Engineering
      Gand, Flemish, Belgium
  • 2012
    • Institut Marqués, Spain, Barcelona
      Barcino, Catalonia, Spain