Wim Soetaert

Ghent University, Merelbeke, VLG, Belgium

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Publications (138)313.54 Total impact

  • Robin Geys, Wim Soetaert, Inge Van Bogaert
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    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.
    Current opinion in biotechnology. 07/2014; 30C:66-72.
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    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.
    Chemical communications (Cambridge, England). 06/2014;
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    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 ΔdhaD 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.
    Microbial Cell Factories 05/2014; 13(1). · 3.31 Impact Factor
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    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).
    Soft Matter 04/2014; · 3.91 Impact Factor
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    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.
    Applied Microbiology and Biotechnology 03/2014; · 3.69 Impact Factor
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    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.
    Organic Process Research & Development 02/2014; 18(6):781–787. · 2.74 Impact Factor
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    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.
    Applied Microbiology and Biotechnology 02/2014; · 3.69 Impact Factor
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    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.
    Journal of proteomics 01/2014; · 5.07 Impact Factor
  • Robin Geys, Wim Soetaert, Inge Van Bogaert
    Current Opinion in Biotechnology. 01/2014; 30:66–72.
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    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.
    Proceedings of the National Academy of Sciences 12/2013; · 9.81 Impact Factor
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    ABSTRACT: The GNB/LNB (galacto-N-biose/lacto-N-biose) pathway plays a crucial role in bifidobacteria during growth on human milk or mucin from epithelial cells. It is thought to be the major route for galactose utilization in Bifidobacterium longum as it is an energy-saving variant of the Leloir pathway. Both pathways are present in B. bifidum and galactose 1-phosphate (gal1P) is considered to play a key role. Due to its toxic nature, gal1P is further converted into its activated uridine diphosphate (UDP) sugar through the action of poorly characterized uridylyltransferases. In this study, three uridylyltransferases (galT1, galT2 and ugpA) from Bifidobacterium bifidum were cloned in an Escherichia coli mutant and screened for activity on the key intermediate gal1P. GalT1 and GalT2 showed UDP-glucose-hexose-1-phosphate uridylyltransferase activity (EC 2.7.7.12), whereas UgpA showed promiscuous UTP-hexose-1-phosphate uridylyltransferase activity (EC 2.7.7.10). The activity of UgpA towards glucose 1-phosphate was about 33-fold higher than towards gal1P. GalT1, as part of the bifidobacterial Leloir pathway, was about 357-fold more active than GalT2, the functional analog in the GNB/LNB pathway. These results suggest that GalT1 plays a more significant role than previously thought and predominates when B. bifidum grows on lactose and human milk oligosaccharides. GalT2 activity is only required during growth on substrates with a GNB core such as mucin glycans.
    Applied and Environmental Microbiology 09/2013; · 3.95 Impact Factor
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    ABSTRACT: In natural 1,3-propanediol (PDO) producing microorganisms such as Klebsiella pneumoniae, Citrobacter freundii and Clostridium sp., the genes coding for PDO producing enzymes are grouped in a dha cluster. This article describes the dha cluster of a novel candidate for PDO production, Citrobacter werkmanii DSM17579 and compares the cluster to the currently known PDO clusters of Enterobacteriaceae and Clostridiaceae. Moreover, we attribute a putative function to two previously unannotated ORFs, OrfW and OrfY, both in C. freundii and in C. werkmanii: both proteins might form a complex and support the glycerol dehydratase by converting cob(I)alamin to the glycerol dehydratase cofactor coenzyme B12. Unraveling this biosynthesis cluster revealed high homology between the deduced amino acid sequence of the open reading frames of C. werkmanii DSM17579 and those of C. freundii DSM30040 and K. pneumoniae MGH78578, i.e., 96 and 87.5 % identity, respectively. On the other hand, major differences between the clusters have also been discovered. For example, only one dihydroxyacetone kinase (DHAK) is present in the dha cluster of C. werkmanii DSM17579, while two DHAK enzymes are present in the cluster of K. pneumoniae MGH78578 and Clostridium butyricum VPI1718.
    Bioprocess and Biosystems Engineering 09/2013; · 1.87 Impact Factor
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    ABSTRACT: This study describes an efficient, large scale fermentation of a recombinant α-l-rhamnosidase originating from Aspergillus terreus. High-cell-density Pichia pastoris fermentation resulted in yields up to 627U/L/h. The recombinant enzyme was used for the reverse rhamnosylation of various small organic compounds. A full factorial experimental design setup was applied to identify the importance of temperature, substrate concentrations, solvent type and concentration as well as the acidity of the reaction mixture. Careful optimization of these parameters allowed the synthesis of a range of α-l-rhamnosides among which cyclohexyl α-l-rhamnopyranoside, anisyl α-l-rhamnopyranoside and 2-phenylethyl α-l-rhamnopyranoside. In addition, α-l-rhamnosylation of phenolic hydroxyls in phenols such as hydroquinone, resorcinol, catechol and phenol was observed, which is a rather unique reaction catalyzed by glycosidases.
    Bioresource Technology 08/2013; · 5.04 Impact Factor
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    ABSTRACT: Starmerella (Candida) bombicola is the biosurfactant-producing species that caught the greatest deal of attention in the academic and industrial world due to its ability of producing large amounts of sophorolipids. Despite its high economic potential, the biochemistry behind the sophorolipid biosynthesis is still poorly understood. Here we present the first proteomic characterization of S. bombicola for which we created a lys1∆ mutant to allow the use of SILAC for quantitative analysis. In order to characterize the processes behind the production of these biosurfactants, the proteome of sophorolipid producing (early stationary phase) and non-producing cells (exponential phase) was compared. We report the simultaneous production of all known enzymes involved in sophorolipid biosynthesis including a predicted sophorolipid transporter. In addition, we identified the heme binding protein Dap1 as a possible regulator for Cyp52M1. Our results further indicate that ammonium and phosphate limitation are not the sole limiting factors inducing sophorolipid biosynthesis.
    Journal of Proteome Research 08/2013; · 5.06 Impact Factor
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    ABSTRACT: Over the past decade, disaccharide phosphorylases have received increasing attention as promising biocatalysts for glycoside synthesis. Unfortunately, these enzymes typically have a very low affinity for non-carbohydrate acceptors, which urges the addition of cosolvents to increase the dissolved concentration of these acceptors. However, commonly applied solvents such as methanol and dimethyl sulfoxide (DMSO) are not compatible with many intended applications of carbohydrate-derived products. In this work, the solubility of a wide range of relevant acceptors was assessed in the presence of ionic liquids (ILs) as alternative and ‘green’ solvents. The IL AMMOENG 101 was found to be the most effective cosolvent for compounds as diverse as medium- and long-chain alcohols, flavonoids, alkaloids, phenolics and terpenes. Moreover, this IL was shown to be less deleterious to the stability and activity of sucrose phosphorylase than the commonly used dimethyl sulfoxide. To demonstrate the usefulness of this solvent system, a process for the resveratrol glycosylation was established in a buffer containing 20% AMMOENG 101, 1 M sucrose and saturated amounts of the acceptor. A single regioisomer 3-O-α-D-glucopyranosyl-(E)-resveratrol was obtained as proven by NMR spectroscopy.
    Green Chemistry 05/2013; · 6.83 Impact Factor
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    ABSTRACT: Consensus engineering, i.e. replacing amino acids by the most frequently occurring one at their positions in a multiple sequence alignment (MSA), is a known strategy to increase the stability of a protein. The application of this concept to the entire sequence of an enzyme, however, has been tried only a few times mainly because of the problems determining the consensus in highly variable regions. We show that this problem can be solved by replacing such problematic regions by the corresponding sequence of the natural homologue closest to the consensus. When one or a few sub-families are overrepresented in the MSA the consensus sequence is a biased representation of the sequence space. We examine the influence of this bias by constructing three consensus sequences using different MSAs of sucrose phosphorylase (SP). Each consensus enzyme contained about 70 mutations compared to its closest natural homologue and folded correctly and displayed activity on sucrose. Correlation analysis revealed that the family's co-evolution network was kept intact, which is one of the main advantages of full-length consensus design. The consensus enzymes displayed an 'average' thermostability, i.e. one that is higher than some but not all known representatives. We cautiously present practical rules for the design of consensus sequences, but warn that the measure of success depends on which natural enzyme is used as point of comparison. Biotechnol. Bioeng. © 2013 Wiley Periodicals, Inc.
    Biotechnology and Bioengineering 04/2013; · 4.16 Impact Factor
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    ABSTRACT: Sophorolipids are promising biological derived surfactants or detergents which find application in household cleaning, personal care and cosmetics. They are produced by specific yeast species and among those, Starmerella bombicola (former Candida bombicola) is the most widely used and studied one. Despite the commercial interest in sophorolipids, the biosynthetic pathway of these secondary metabolites remained hitherto partially unsolved. In this manuscript we present the sophorolipid gene cluster consisting of five genes directly involved in sophorolipid synthesis: a cytochrome P450 monooxygenase, two glucosyltransferases, an acetyltransferase and a transporter. It was demonstrated that disabling the first step of the pathway - cytochrome P450 monooxygenase mediated terminal or subterminal hydroxylation of a common fatty acid - results in complete abolishment of sophorolipid production. This phenotype could be complemented by supplying the yeast with hydroxylated fatty acids. On the other hand, knocking out the transporter gene yields mutants still able to secrete sophorolipids, though only at levels of 10% as compared with the wild type, suggesting alternative routes for secretion. Finally, it was proved that hampering sophorolipid production does not affect cell growth or cell viability in laboratory conditions, as can be expected for secondary metabolites.
    Molecular Microbiology 03/2013; · 4.96 Impact Factor
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    ABSTRACT: The yeast Candida bombicola is capable of producing high amounts (400 g/L) of the biosurfactant sophorolipids. The genetic makeup of this industrially important yeast has recently been uncovered and molecular manipulation techniques have been developed. Hence, all tools for the development of new bioprocesses with Candida bombicola are now available. As a proof of concept, the production of two totally different molecules was aimed for: the bioplastic polyhydroxyalkanoate (PHA) and a new-to-nature cellobioselipid -biosurfactant. Integration of the new functionalities at genomic loci necessary for sophorolipid production safeguards the new biomolecules from sophorolipid contamination, while taking advantage of the regulation of the sophorolipid gene cluster. A maximum yield of 2.0% wt/dwt PHA was obtained; furthermore, this is the first time cellobioselipid synthesis by a non-natural producer is reported. We here provided proof of concept that Candida bombicola can be transformed into a platform organism for the production of tailor-made biomolecules. Biotechnol. Bioeng. © 2013 Wiley Periodicals, Inc.
    Biotechnology and Bioengineering 03/2013; · 4.16 Impact Factor
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    ABSTRACT: The bio-based economy relies on sustainable, plant-derived resources for fuels, chemicals, materials, food and feed rather than on the evanescent usage of fossil resources. The cornerstone of this economy is the biorefinery, in which renewable resources are intelligently converted to a plethora of products, maximizing the valorization of the feedstocks. Innovation is a prerequisite to move a fossil-based economy toward sustainable alternatives, and the viability of the bio-based economy depends on the integration between plant (green) and industrial (white) biotechnology. Green biotechnology deals with primary production through the improvement of biomass crops, while white biotechnology deals with the conversion of biomass into products and energy. Waste streams are minimized during these processes or partly converted to biogas, which can be used to power the processing pipeline. The sustainability of this economy is guaranteed by a third technology pillar that uses thermochemical conversion to valorize waste streams and fix residual carbon as biochar in the soil, hence creating a carbon-negative cycle. These three different multidisciplinary pillars interact through the value chain of the bio-based economy.
    Frontiers in Plant Science 01/2013; 4:174. · 3.60 Impact Factor
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    Koen Beerens, Wim Soetaert, Tom Desmet
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    ABSTRACT: UDP-hexose 4-epimerases are important enzymes that play key roles in various biological pathways, including lipopolysaccharide biosynthesis, galactose metabolism through the Leloir pathway, and biofilm formation. Unfortunately, the determinants of their substrate specificity are not yet fully understood. They can be classified into three groups, with groups 1 and 3 preferring non-acetylated and acetylated UDP-hexoses, respectively, whereas members of group 2 are equally active on both types of substrates. In this study, the UDP-Glc(NAc) 4-epimerase from Marinithermus hydrothermalis (mGalE) was functionally expressed in Escherichia coli and thoroughly characterized. The enzyme was found to be thermostable, displaying its highest activity at 70 °C and having a half-life of 23 min at 60 °C. Activity could be detected on both acetylated and non-acetylated UDP-hexoses, meaning that this epimerase belongs to group 2. This observation correlates well with the identity of the so-called "gatekeeper" residue (Ser279), which has previously been suggested to influence substrate specificity (Schulz et al., J Biol Chem 279:32796-32803, 2004). Furthermore, substituting this serine to a tyrosine brings about a significant preference for non-acetylated sugars, thereby demonstrating that a single residue can determine substrate specificity among type 1 and type 2 epimerases. In addition, two consecutive glycine residues (Gly118 and Gly119) were identified as a unique feature of GalE enzymes from Thermus species, and their importance for activity as well as affinity was confirmed by mutagenesis. Finally, homology modeling and mutational analysis has revealed that the enzyme's catalytic triad contains a threonine residue (Thr117) instead of the usual serine.
    Applied Microbiology and Biotechnology 12/2012; · 3.69 Impact Factor

Publication Stats

1k Citations
313.54 Total Impact Points

Institutions

  • 1970–2013
    • Ghent University
      • • Faculty of Bioscience Engineering
      • • Department of Biochemical and Microbial Technology
      Merelbeke, VLG, Belgium
  • 2012
    • Institut Marqués, Spain, Barcelona
      Barcino, Catalonia, Spain