Title Promoter Affiliations Abstract "Concerto for solids and biocatalysts - Cascade biocatalysis and heterogeneous catalysis for fine chemicals production (ConSolid)" "Dirk De Vos" "Membrane Separations, Adsorption, Catalysis, and Spectroscopy for Sustainable Solutions (cMACS), Budapesti Mûszaki és Gasdasagtudomanyi" "Scientific project objectives: 1. To design new solid catalysts for aliphatic amine racemization, and use them for dynamic kinetic resolution (DKR) of racemic aliphatic amines to enantiopure amides, preferably in a flow chemistry setting; Progress in comparison with state-of-the-art: there are so far no such racemisation catalysts known, resulting in a lack of methods for synthesis of enantiopure amides from racemic aliphatic amines via DKR.  2. To use innovative enzymes, like phenyl aminomutases (PAMs), in the context of a DKR, together with a racemization catalyst, allowing production of enantiopure non-natural amino acids. Progress in comparison with state-of-the-art: The opportunities to use PAM and related enzymes in DKR (together with solid catalysts) have so far not been exploited for synthesis of  antiopure amino acids." "Encapsulation of multiple enzymes in hollow Metal-Organic Framework for heterogeneous cascade biocatalysis." "Pascal Van Der Voort" "Department of Chemistry" "We aim at multifunctional biocatalysts, by immobilizing simultaneously several enzymes into hollow Metal-Organic Frameworks, resulting in recyclable heterogeneous biocatalysts for cascade reactions. We will investigate several immobilization techniques and their impact on the catalytic reactions, for several cascade reactions (in vitro), such as the oxidation of o-phenylenediamine by in-situ generated hydrogen peroxide and the conversion of alcohols to chiral amines." "COupling BIocatalysis and heterogeneous CATalysis for the production of aviation fuel from renewable resources (COBICAT)" "Mark Saeys, Ramon Ganigué" "Department of Materials, Textiles and Chemical Engineering, Department of Biotechnology" "The conversion of renewable resources (e.g. biomass, CO2, etc.) to medium- and high volume molecules via catalytic processes (e.g. homogeneous catalysis, heterogeneous catalysis, biocatalysis, etc.) is one of the pillars of the bio-based transition. Yet, when considered individually, most catalytic technologies have intrinsic limitations and critical bottlenecks that hamper their development. Coupling biology and heterogeneous catalysis in tandem reactions has been postulated as a powerful way forward to circumvent individual process bottlenecks and establish novel, more cost-efficient and sustainable catalytic technologies to help make the transition to a bio-based society. COBICAT is an interdisciplinary project that will explore the coupling of biocatalysis and heterogeneous catalysis to produce aviation fuel from renewable resources, as a proof-of-concept to demonstrate the potential of such catalytic tandem coupling." "Self-assembling Multi Layer Enzyme Network for Flow Biocatalysis" "Simon Kuhn" "Process Engineering for Sustainable Systems (ProcESS), Univerza v Ljubljani, Budapesti Mûszaki és Gasdasagtudomanyi" "Small-scale flow reactors have increasingly gained attention in academia and industry as convenient tools for more efficient syntheses compared to the traditional batch procedures. These small-scale reactors provide uniform residence times, well-defined flow patterns, and precise reaction control. However, most of the applications to date focus on synthetic organic chemistry using traditional (precious metal based) catalysts. In this joined project between the Budapest University of Technology and Economics, the University of Ljubljana, and KU Leuven we will explore a novel microreactor for flow biocatalysis, i.e. enzyme catalysed reactions. In these microreactors the enzyme will be immobilized in the reactor in a layer-by-layer structure cross-linked by nanoparticles, resulting in a three-dimensional network. Within this network we will combine the expertise of each partner to manufacture, analyse and apply these reactors: The surface functionalization and creation of the multilayer enzyme network is performed at Budapest University of Technology and Economics. Fundamental insight into the spatial arrangement of the enzymes and nanoparticles in the layers is provided via a modelling approach by the University of Ljubljana. Finally, KU Leuven will perform the reactor characterization, i.e. determine their porosity (free-flow area ratio in the reactor) and mixing properties. Subsequently, these reactors will be applied to transamination reactions. In conclusion, upon finalization this project will deliver a novel microreactor tool enabling flow biocatalysis." "Incorporation of globin enzymes with redoxfunctions in silicamaterials for biosensor and biocatalysis applications." "Sabine Van Doorslaer" "Proteinchemistry, proteomics and epigenetic signalling(PPES), Biophysics and Biomedical Physics" "2 different globin enzymes will be incorporated in mesporous silicamaterials in this project. These 2 globins are neuroglobin and globin 26 of the nematode C. elegans and have en known redoxfunction. The incorporation of these globins wil be studies with spectroscopical techniques such as electron paramagnetic resonance (EPR) and resonance Raman spectroscopy (RRS). Further we will work out an EPR-based methodology in order to study the effect of incorporation of enzymes in matrices." "Epimerases as new tools for the production of rare sugars: a powerful integration of enzyme engineering and systems biocatalysis" "In this project we aim to develop new pathways for the biocatalytic synthesis of rare sugars and derivatives. To that end, various enzymes will be optimized by protein engineering and then combined in a one-pot reaction vessel. The process starts from sucrose as abundant and renewable resource and allows obtaining the target products with high yields and minimal costs." "Phosphorylases as cost-efficient biocatalysts for carbohydrate synthesis: an exploration of natural and mutant diversity" "Tom Desmet" "Department of Biotechnology" "Glycoside phosphorylases are able to synthesize specialty carbohydrates starting from cheap glycosyl phosphates as donor substrates. Unfortunately, the number of available specificities currently is very limited and their products are rarely relevant for the industry. This portfolio will, therefore, be significantly expanded through a combination of state-of-the-art techniques in database mining and enzyme engineering." "Novel biocatalysts for the production of glycosides" "Wim Soetaert" "Department of Biochemical and microbial technology, University of Groningen, Institute of Microbiology, Bio Base Europe, Friedrich Schiller University Jena" "In this project, biocatalytic processes will be developed for the glycosylation of small organic molecules. To that end, new transglycosidases, glycoside phosphorylases and glycoside hydrolases will be identified by screening of natural and mutant libraries, with the use of special fluorescent probes. The reactions will be scaled-up at pilot plant facilities to allow the commercial exploitation of the glycosylated products." "Cultivation independent analysis of the mobilome of polluted ecosystems: a new approach for mining of novel biocatalysts." "Dirk Springael" "Soil and Water Management, Animal and Human Health Engineering (A2H)" "The intensive and widespread use of pesticides over the last decades, has resulted in the contamination of water and soil ecosystems by compounds that are xenobiotic and often persistent. Despite the relative recent introduction of pesticides into our environment, microorganisms have been shown to create novel catabolic pathways allowing to degrade specific xenobiotics. The ability of microorganisms to adapt swiftly to changing environmental conditions and exploit ecological novel niches arises from their genome plasticity and adaptability. A key mechanism in this bacterial genome plasticity is the intra- and extracellular exchange of genetic material facilitated by vehicles called mobile genetic elements (MGEs). Genomic studies from xenobiotic degraders showed that two particular MGEs, I.e., IncP-1 plasmids and IS element IS1071, are often retrieved as carriers of xenobiotic catabolic genes. Therefor it can be hypothesized that IncP-1 and IS1071 play a crucial role in de mobilisation and recruitment of xenobiotic catabolic gene functions in the environment. However, not much is known about their ecology at a community wide base nor about the adaptative genes they carry in complex environmental communities.The objective of this thesis is to contribute in elucidating the role of IS1071 and IncP‑1 in the dissemination of catabolic gene clusters in the microbiome of pesticide contaminated environments. Specifically, the prevalence of these MGEs in microbiomes of different ecosystems were studied and molecular toolboxes developed to assess their accessory gene loads.The first objective was to examine whether a relationship existed between the prevalence of IncP-1/IS1071 and pesticide pollution. Therefore, the prevalence and abundance of IncP-1 plasmids and IS1071 in lab and field ecosystems with and without pesticide pollution history was examined. The ecosystems included on-farm biopurification systems (BPS) processing pesticide contaminated wastewater and pesticide treated soil. Comparison of IncP-1/IS1071 prevalence between pesticide treated and non-treated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071 specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP‑1 plasmids were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. These data suggest that IS1071 and IncP‑1 containing organisms were enriched in pesticide contaminated environments like BPS where they might contribute to the spreading of catabolic genes and to pathway assembly.To further unravel and acknowledge the ecological role of these two MGEs, novel cultural independent toolboxes, based on long-range PCR, were developed that allow the recover and identify in a cultivation-independent way the accessory genes carried by IS1071 composite transposons and IncP‑1 plasmids. First a long-range PCR approach was developed that allowed to amplifying accessory genes between two IS1071 copies from community DNA followed by amplicon sequencing. We applied this method to pesticide exposed environments, i.e., linuron-treated agricultural soil and on-farm BPS treating complex agricultural wastewater, as to non-treated controls. Amplicons were mainly recovered from the pesticide exposed environments and the BPS matrix showed a higher amplicon size diversity compared to the agricultural soil. Retrieved gene functions mirrored the main selection pressure as (i) a large fraction of the BPS amplicons contained genes/gene clusters related to the degradation of organics including herbicides present in the wastewater and (ii) in the agricultural soil, recovered genes were associated with linuron degradation. Our metagenomic analysis extends observations from cultured isolates and provides evidence that IS1071 is a carrier of catabolic genes in xenobiotic stressed environments and contributes to community level adaptation towards pesticide biodegradation.Similarly, a long-range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA was developed. The method amplifies the DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, and analyses its content by high-throughput sequencing, and was applied to DNA of an on-farm BPS, treating pesticide contaminated wastewater. The cargo recovered from BPS community DNA, encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be co-selected with catabolic genes in other insertion hot spots or confer other crucial functions for proliferation in the BPS environment.Our data supports the hypothesis that IS1071 and IncP-1 are linked to xenobiotic degradation in pesticide impacted environments, and that especially IS1071 is an important MGE for distributing xenobiotic catabolic gene functions. To fully understand the role of IS1071 and IncP-1 in bacterial adaptation and the type of traits it disperses throughout the microbial community it is essential to study different ecosystems with different environmental stressors." "Unlocking Synthetic Biology of Deoxy Sugars via Enzyme Engineering and Biocatalytic Cascades" "Tom Desmet" "Department of Biotechnology" "Deoxysugars are important building blocks of several bioactive carbohydrates and derivatives (e.g. glycopeptide antibiotics). Their further exploration is, however, severely hampered by the complex and expensive procedures that are currently required for their production. In this project, new enzymes will be developed and integrated in artificial biosynthetic pathways that make use of sucrose as cheap and abundant starting material."