Job openings in Program 1

The aim of the project is to identify and verify suitable strategies to strongly bond structural colors formed out of CNCs to the wood substrate and to overcome the disadvantage of the current absence of water resistance. Design principles and approaches found in nature may act as a starting point. As possible approaches we see enzymatic modification of the wood surface to enhance interaction, physical methods to induce energy (heat, rays), green chemical approaches to improve the cohesion of the cellulose assembly or incorporation of fully biobased matrix polymers or waxes.

Background:

Formation of vivid colours is already nicely possible with Cellulose Nanocrystals. For the mechanism of colour adjustment several strategies are established, while the understanding of interaction of wood and its role in colour formation is in the early stage. As main barrier moisture stability is close to zero, as a single drop of water is able to destroy or remove the structure, as the interaction of CNC is based on weak secondary bonds only.

Based on biomimetic approaches, green chemistry or biotechnological methods CNC shall be connected to the wood structure and interconnected with each other.

Research Objectives:

• As an outcome an ideally purely lignocellulose based structural colour should be able to coat the lignocellulosic material wood and thus enable realizing a single material concept.

• Identifying and analyzing possible modification approaches addressing the interaction within the CNC structure, as well as between wood and the structure

• Verify and develop selected strategies

Methods:

Color formation by CNC self-assembly. Biotechnological, chemical or physical methods to be identified depending on approaches selected. Analyses of structural color assemblies by various microscopic techniques on suitable length scales (light microscopy, atomic force microscopy, scanning electron microscopy) including ultramicrotomy as sample preparation. Color determination, surface resistance in dry state and towards water, nanoindentation, …

Main supervisor: Univ.-Prof. Johannes Konnerth

Location: BOKU University (UFT Tulln)

Submission Deadline: 31.03.2025

Background

Lignin acidolysis is one of the most classical methods for lignin depolymerization, however it is typically associated with significant recondensation phenomena that lead to formation of recalcitrant side products instead of valuable aromatics. We have introduced the stabilization of reactive intermediates during acidolysis in conjunction with stabilization of reactive fragments. (JACS, 2015, JACS 2016) One of the most successful stabilization methods was achieved with applying ethylene glycol to deliver C2-Acetals. The system was thoroughly studied with respect to lignin type, reaction conditions, acids, diol and solvent type, as well as in alternative reaction media (DES) (Green Chem 2017, NatureComm2021). Moreover, the method was successfully extended to lignocellulose (ChemSusChem2020), now dubbed as diol assisted fractionation (DAF), which has been established as a distinct ‘lignin-first’ method (EES 2021).  

While this method offers the possibility to deliver well-defined C2-Acetals in high selectivity, mechanistic questions remain largely unanswered. Firstly, the exact mechanism of acidolysis/stabilization has not yet been uncovered, but needed to understand the extent of condensation processes. Secondly, next to aromatic monomers and some dimers identified, a large portion of the mass balance is still structurally ambiguous, clarification of the nature of especially lignin fragments containing C-C linkages is needed in order to understand possibilities for further use of such fractions. Thirdly, when lignocellulose is applied, the extent of hemicellulose retention and depolymerization, as well as the nature of hemicellulose-derived products largely depends on reaction conditions, and systematic understanding is needed. Lastly, the morphology and nature of cellulose after treatment also strongly depends on the reaction conditions, influencing the further usability of such cellulose streams for enzymatic depolymerization or material fabrication purposes. Further research should shine light on optimal reaction conditions, maximizing the value of derived product streams.

Research Objectives

• Mechanistic studies of acidolysis/EG stabilization with dedicated model compounds as well as organosolv lignins, following the methods of common mechanistic work, possibly including labelling studies

• Structural elucidation of depolymerization mixtures starting from organosolv lignin (and possibly native lignin from lignocellulose) with special focus on elucidating elusive dimer/oligomer regions containing C-C linkages. Multi technique analysis required. (both spectroscopy and chromatograph)

• Development of fractionation strategies to treat depolymerization mixtures and isolate different Mw fractions

• Analysis of hemicellulose-retention and derived products; analysis of cellulose depending on reaction conditions.

• Co-development of reassembled materials with other groups

Methods:

• Lignocellulose work (composition analysis, fractionation, organosolv processing)

• Lignin chemistry

• Synthetic and mechanistic organic chemistry

• 2D NMR analysis and other spectroscopic methods

• Chromatographic methods

Qualifications & Profile requirements

• Master’s degree in chemistry or chemical engineering, focus on sustainable catalysis organic chemistry, green chemistry

• Hands-on experience with lignocellulosic biomass, or at least with complex biomass starting materials and related analysis of substrates and product mixtures  

• Ample interest in in-depth mechanistic studies combined with spectroscopy

• Eligible as a graduate student at the University of Graz (Austria) (Klick here for further information)

• Proficiency in English (written and oral)

Main supervisor: Univ.-Prof. Katalin Barta

Co-supervisors: Univ.-Prof. Antje Potthast

Location: University of Graz

Duration: 4 years

Submission Deadline: 31.03.2025

Background

Diol assisted fractionation has emerged as an efficient ‘lignin-first’ method, capable of delivering aromatic C2-Acetals in high selectivity from lignin, beside high-quality cellulose. However, useful aromatic monomer yield is limited by the amount of cleavable b-O-4 linkages in the lignin, that is present in the respective lignocellulose source used. Since other linkages types, characterized by at least one C-C linkage are not cleaved by this method, they result in a varying degree of dimer and oligomer products in the depolymerization streams. In order to increase biomass utilization efficiency, these product streams should be also converted to useful products. We have previously developed fractionation methods to isolate such product streams, however the valorization of dimer/ oligomer fractions and of hemicellulose derived products, has not yet been attempted.

In other, parallel activities, we have developed integrated biorefinery strategies centered around reductive catalytic fractionation. Hereby we relied on catalytic funneling strategies to channel product composition into well-defined products amenable to further conversion to bio-based polymers (Nature Comm 2022). In other activities, we have prepared bio-based polymers (polycarbonates, polyesters, polybenzoxazines and recyclable epoxy-amine thermosets (Science 2024)) from MBC diol obtained from Kraft-lignin depolymerization mixtures. Some of this knowledge can be utilized here.

Furthermore, we have developed chemo-catalytic strategies for the further conversion of the C2-Acetal monomers towards biologically active compounds, however biocatalysts were not yet attempted.

By finding isolation/separation and novel catalytic strategies for the further valorization of product streams of diol-assisted fractionation, will significantly increase the biomass utilization efficiency of this method, in accordance with circular economy principles.

Research Objectives

• Lignocellulose fractionation, diol-assisted fractionation, lignin acidolysis/stabilization.

• The development of separation/purification methods to get access to specific monomer, dimer and oligomer streams from lignin, and hemicellulose-derived products

• The direct conversion of oligomers to recyclable polymers (epoxy-thermosets, polyurethanes, polycarbonates)

• The separation and further catalytic funneling of oligomers to well-defined compounds usable for polymer synthesis.

• The conversion of C2-Acetal monomers to recyclable polymers by in house developed methods

• The conversion of monomers, dimers and oligomers by bio-catalytic strategies (amination, cyclization, C-O and/or C-C bond scission) in cooperation

Methods:

1. Lignocellulose work (composition analysis, fractionation, organosolv processing)

2. Lignin chemistry

3. Separations and fractionation

4. Catalytic conversion focusing on C-C and C-O bond cleavage, catalytic funneling combined with appropriate analytics

5. Development of thermosets and thermoplastics from monomers, dimers, oligomers

6. Bio-catalytic conversions in cooperation

Qualifications & Profile requirements

• Master’s degree in chemistry or chemical engineering, focus on sustainable catalysis organic chemistry, green chemistry

• Hands-on experience with lignocellulosic biomass, or at least with complex biomass starting materials and related analysis of substrates and product mixtures  

• Ample interest in in-depth mechanistic studies combined with spectroscopy

• Eligible as a graduate student at the University of Graz (Austria) (Klick here for further information)

• Proficiency in English (written and oral)

Main supervisor: Univ.-Prof. Katalin Barta

Co-supervisors: Univ.-Prof. Wolfgang Kroutil

Location: University of Graz

Duration: 4 years

Submission Deadline: 31.03.2025

Description of project

Development of enzymatic cascades in fast growing cyanobacteria based on degradation products of lignin. Predominately ferulic acid and other aromatic phenylpropanoid metabolites should be applied for the production of high value chemicals. The enzyme cascades should contain enzymes from different classes, like phenolic acid decacboxylases, aromatic dioxygenases/isomerases and subsequently either amindehydrogenases or alcohldehydrogenases. The expression of these enzymes will be achieved by the close collaboration with PostDoc#1 from my group who will establish a new expression platform in fast growing cyanobacteria. Additionally it more enzymes for functional group interconversion will be expressed. With the cascade at hand quantitative preparative scale experiments will be performed to prove the feasibility and applicability of the cascade.

Background

The working group has experience in redox biocatalysis and cascade reactions. Additionally, the group is well experienced in the genetic modification and cultivation of phototrophic bacteria.

Research Objectives

• Efficient utilization of renewable resources and waste streams for the production of fine and bulk chemicals

• Identification of bottlenecks in the production of chemicals starting from renewable resources.

Methods

• Selection of potential enzyme candidates for suitable cascades.

• Cloning of heterologous genes into different fast growing phototrophic bacteria by Gibson cloning.

• Testing of single-step and multi-step biocatalysis in different hosts by GC and HPLC analysis

• Investigation of different waste and renewable carbon streams on growth and productivity.

Main supervisor: Associate Prof. Florian Rudroff

Co-supervisors: Univ.-Prof. Katharina Schröder, Univ.-Prof. Oliver Spadiut

Location: TU Wien (Vienna)

Submission Deadline: 31.03.2025

Description of project

Background:

Polylobate (puzzle) sclerenchyma cells from walnut and/or pistachio shells are suggested as building blocks in new materials. The multilayered entities are optimized on compression strength and we aim to entangle/connect them via tensile strength resistant fibrils (cellulose or chitin). Depending on final processing (lyophilsation  or cold and hot-pressing or 3D printing) different final products in form of foams or films or molded materials will be achieved. Focus is on creating strong interfaces between puzzle cells and fibrils, which involves different isolation/ modification processes of the nutshell cells as well as growth culture conditions of fungi. By in-situ characterization, we will probe composition and mechanics on the micro-and nano-scale and relate to macroscopic properties to derive structure-function relationships. With this understanding, we finally aim to tune the materials to specific properties and applications from packaging to medicine and include cradle to cradle options.

Research Objectives:

• Dissolving puzzle cells from walnut and pistachio shells through different extraction procedures

• Achieve strong interfaces between microscale puzzle cells and nanofibrils (cellulose and/or chitin) (e.g. functionalization of surfaces,…)

• Reveal properties of cells and nanofibrils and their interfaces as well as macroscale properties

• Unravel structure-function relationships and tune material properties accordingly

• Develop and test possibilities to dissolve and re-use in a second cycle

Methods:

• Extraction and modification of puzzle cells out of walnut and pistaccio shells

• Preparation/growth of bacterial cellulose and/or fungi

• Nanocomposite preparation (spin coating, sheets, moulds, different drying methods,..)

• Mechanical, chemical and surface/interface characterization (e.g. Raman imaging, Atomic force microscopy,..) at different hierarchical levels (macro to nano)

Candidates should have a background in chemistry, material science or biology and experience and/or interest in microscopic (SEM, Raman microscopy) and scanning probe techniques (AFM).

Main supervisor: Associate Prof. Notburga Gierlinger

Co-supervisors: Univ.-Prof. Alexander Bismarck, Univ.-Prof. Katalin Barta, Univ.-Prof. Katharina Schröder

Location: BOKU University (Muthgasse)

Submission Deadline: 31.03.2025

Description of project

Biological materials such as wood or plant cell walls are well known for their optimized structure and properties. In this project, bio-insipired, all-biobased functional composite materials with smart arrangement of fibers and micro- or nanofillers shall be created. To achieve this goal, physical micro- and nanostructuring methods will be developed and applied.

Background:

All bio-based polymers and polymer composites are an important means to replace fossil based materials and obtain environmentally friendly products. A promising strategy to reinforce biopolymers is the addition of natural micro- and nanofillers. Currently, the state of the art consists of mixing fillers randomly into a biopolymer matrix. Material performance can further be enhanced by bio-inspired concepts, such as controlled filler arrangement and orientation as it is typically found in biological materials. The present project aims at implementing such concepts by physics based methods to achieve achieve new materials with tunable functionalities.

Aims:

• To develop hierarchically structured bio-composite materials

• Tailoring of material properties

Methods:

• Screening suitable biopolymer–filler combinations

• Wet chemical functionalization of fillers

• Controlled orientation of fillers by physics based methods (shear, external fields)

• Composite fabrication

• Mechanical testing

• Characterization by SEM, SAXS, AFM, Light microscopy, Raman, FTIR, TGA, DSC, Rheology

Qualifications & Profile requirements:

• Master’s degree in (bio-)physics, materials science, (materials-)chemistry, or a related discipline

• Hands-on experience in a physics or chemistry laboratory

• Experience with biological materials (specifically biopolymers and cellulose) or nanocomposite materials will be an asset.

• Experience with materials characterization will also be of advantage.

• Eligible as a graduate student at BOKU University (Austria)

• Proficiency in English (written and oral)

Main supervisor: Univ.Prof. Helga Lichtenegger

Location: BOKU University (Peter-Jordan-Str. 82, 1190 Wien)

Submission Deadline: 31.03.2025

Description of project:

The fungal biorefinery is a versatile biofabrication process able to utilise many different substrates or biobased wastes unsuitable for recycling or upcycling applications. The aim is to produce a wide range of assessable products (co-)created using the fungal biorefinery, which include ligno/cellulose nanomaterials, sheet-based and larger 3D geometry mycelium composites, food, and fungal nanomaterials, for applications such as coatings, membranes, leather alternatives or yarns.

Background:

Fungi-derived materials have a history of several thousand years, dating back to amadou, a soft, felt-like material used as absorbent styptics, dressings, bandages, and clothing garments. However, amadou does not resemble textiles mechanically, exhibits low tear resistance and tensile strength and is susceptible to abrasion. A process that provides consistent mechanical and surface properties of homogenous engineered fungal mats is needed. Produced mats constitute engineered fibrous sheets which are homogenous, theoretically contain no defects and can be produced at a consistent thickness that can take any value provided filtration and drying are still possible. One challenge remains the full ultilisation of the substrate used to grow fungal fruiting bodies. Discarded cellulose-rich substrates may enable the production of next generation mycelium composites.

Research Objectives:

• Achieve consistently high digestion across various substrates.

• Determine the mechanism and efficiency of cellulose/lignocellulose degradation by fungal enzymatic digestion

• Develop procedures for fungal cultivation in larger 3D geometries.

• Determine property envelopes and applications of new mycelium-substrate composites

• Produce fungal nanomaterials using chitin-β-glucan complexes from fruited substrates.

• Determine environmental sustainability of a fungal biorefinery system for upcycling textile waste into composites and chitin-β-glucan complexes

Methods:

Fungal biorefinery (composition analysis: substrate, spent mushroom substrate, fungal fibomass, fractionation), materials production, material property envelop: mycelium composites and fungal sheet materials, TEA/LCA calculations

Main supervisor: Prof. Alexander Bismarck

Co-supervisors: Prof. Antje Potthast & Prof. Thomas Rosenau

Location: University of Vienna (Faculty of Chemistry)

Submission deadline: 31.03.2025

Description of project

Water contamination by heavy metals, microplastics, and persistent pollutants presents a major environmental and health challenge. Hybrid membranes that combine ultrafiltration with selective adsorption offer a sustainable solution. This project will develop nanocellulose-porous organic polymer hybrid membranes that selectively remove toxic metals, valuable elements (e.g., gold, platinum, REEs), and emerging pollutants (e.g., PFAS). We will also explore the recovery and reuse of porous organic polymer sorbents via the hydrolysis of the nanocellulose matrix at the membranes end-of-life.

Background:

In our previous work, sulfonated hypercrosslinked polymers (SHCPs) embedded in cellulose nanofibril (CNF) matrices demonstrated high metal ion adsorption capacity (Cu2+, St2+, Ba2+ etc.).  By further tailoring their composition and structure, this project aims to enhance selectivity, permeability, and stability for practical water purification applications. Substrate targets will include valuable metals, REEs, and emerging pollutants.

Research objectives:

• Synthesize functionalised HCPs for selective metal and pollutant adsorption.

• Integrate HCPs into CNF matrices to fabricate hybrid membranes.

• Characterize membrane performance in metal ion removal and ultrafiltration.

• Investigate membrane regeneration and long-term stability.

Methods:

Polymer synthesis, membrane fabrication, gas sorption analysis, FTIR, TGA, SEM, ICP-MS, filtration and adsorption experiments.

Main supervisor: Assoc.-Prof. Robert T. Woodward

Co-supervisors: Prof. Gunda Köllensperger, Prof. Alexander Bismarck

Location: University of Vienna (Faculty of Chemistry)

Submission deadline: 31.03.2025

Description of project
Although we already have a large set of characterization techniques available, we still fail in many instances to describe the behavior of lignins not only in simple chemical reactions (derivatization, degradation), but also under natural degradation conditions (e.g., in sea water or soil or upon aging in composite materials).   

This project will focus on so far hidden structural features in (technical) lignins in order to understand their role and their influence on lignin reactivity and application in different fields. 

Background:

Lignin structures are among the most complex organic molecules on earth. The structural variability in plants, with regard to starting monomers and different linkage types, allows nature synthesizing lignin molecules tailored to specific needs. This “natural” complexity is further increased by the isolation procedure used for lignin extraction. High temperature combined with drastic conditions and hard chemistry result in a lignin structure which is strongly different from the native original. Although we understand the basic reactions during classical extraction procedures (pulping), many side reactions lead to unknown structural elements. Their presence is currently only visible from certain properties of lignin, such as a high fluorescence for kraft lignins, higher acidity than relatable to known structural features, or an increase in carbon-carbon connections which lead to an undesired decrease in reactivity in most application trails. This project will focus on technical lignins, as they must be utilized in a non-energetic manner for future zero-emission technologies.

Research objectives:

• Investigate “hidden” and NMR-silent chemical features of technical lignins

• Understand the structure of non-lignin side components in lignin

• Develop analytical methods for better lignin characterization

Methods:

• Lignin degradation and enrichment, chemometry in combination with spectroscopic methods

• Chromatographic hyphenation methods

• NMR spectroscopy

Main supervisor: Univ.-Prof. Antje Potthast

Co-supervisors: Univ.-Prof. Thomas Rosenau, Univ.-Prof. Katalin Barta

Location: BOKU University (UFT Tulln)

Submission deadline: 31.03.2025

Description of project

Biomass and products from biomass are rich in complex molecules. Often, the unambiguous structural elucidation is necessary to identify unwanted byproducts (e. g. chromophores), to increase the understanding of a process (e. g. degradation products, unintended byproducts), and to describe newly discovered bioactive compounds. The availability of the compounds of interest is often limited either because the effort to isolate sizeable amounts is prohibitive, or because the compounds occur only in minute amounts. Current methodology – the combination of mass spectroscopy after chromatography, nuclear magnetic resonance spectroscopy, infrared spectroscopy – quickly reaches its limit when the available amount of substance is small (microgram). Crystallography allows to determine the structure of organic compounds directly and without ambiguity. The main requirement and obstacle – the availability of single crystals – can be mitigated by two recent developments: crystalline sponges and electron diffraction. These make even volatile and oily substances accessible for structural analysis by crystallography.

Crystalline sponges evade the need to grow single crystals and are compatible with widely available instrumentation for X-ray diffraction. They are porous crystalline metal-organic frameworks (MOFs) that act as a crystalline template for the compounds of interest. The target compounds are dissolved and allowed to diffuse into the MOF that soaks them up like a sponge. In the MOF, the target compounds are adsorbed in an orderly, practically crystalline fashion, which allows a structure elucidation by crystallography.

The field of Crystalline Sponges offers the option to elucidate compounds that so far have evaded a comprehensive analysis or were not available as crystals (examples see “Research objectives”). The combination with chromatographic techniques has been demonstrated and is especially powerful if an adsorption chromatographic method such as supercritical fluid chromatography or normal-phase chromatography is used. Normal-phase thin-layer chromatography with direct bioautographic detection of bioactive molecules that are then embedded in a crystalline sponge for crystallography could become an extremely rapid approach for bioactivity studies.

Research Objectives:

• Synthesis of established crystalline sponges (apolar, polar, carbohydrate-based) for first tests with model compounds.

• Application of the crystalline sponges to the identification of the target compounds which so far have evaded a comprehensive analysis as they were not available as crystals: a) di- and oligosaccharides of celluloses and hemicelluloses, b) chromophores and byproducts formed during pulp processing, fiber manufacturing and cellulose aging, c) extractives and bioactive compounds form plants (secondary metabolites).

• Establishing the combination with preceding chromatographic techniques: supercritical fluid chromatography and high-performance thin-layer chromatography with direct bioautographic detection of bioactive molecules.

Methods:

• Synthesis of established crystalline sponges (apolar, polar, carbohydrate based) for first tests with model compounds.

• Tests of suitability of different MOFs for different model compounds. Type of MOF and the properties of the solvent for infusion will be screened. Inclusion rate is determined from the supernatant before crystallography. Robustness of the developed methodology is evaluated. If necessary: definition of requirements of MOFs that need to be developed.

• Combination of established chromatographic methods – gas chromatography, thin-layer chromatography, liquid chromatography, supercritical fluid chromatography – for selected use cases, e. g. identification of bioactive compounds after bioautography, identification of unknown peaks in gas chromatography

Main supervisor: Univ.-Prof. Thomas Rosenau

Co-supervisors:, Univ.-Prof. Antje Potthast

Location: BOKU University (UFT Tulln)

Submission deadline: 31.03.2025

Description of project

The identification of novel enzymes for industrial applications has been significantly advanced by new approaches that leverage modern technologies in biology, bioinformatics, and engineering. The identification of new enzyme scaffolds is the first essential step in the development of new biocatalysts and is the aim of this project to identify new oxidoreductases and hydrolases and will be achieved through different approaches.

In a first step, functional screening of anaerobic fungi and archaea as well as strain collections isolated from selected environments such as wastewater treatment plants will be performed to discover new enzyme activities. One new approach is to generate metagenomic or metatranscriptomic libraries, such as from elefant faeces. Such libraries offer the advantage to screen also otherwise non-culturable microorganisms, in particular new bacterial taxa or unknown bacteria, since it has a high probability of yielding genes encoding novel enzymes.

In a second step, the responsible enzymes will be identified and isolated. Rapid high-throughput sequencing of whole genomes and metagenomes will be applied to explore sequences by computational tools for identification of novel enzymes, also known as in-silico bioprospecting, which has come up as an efficient, cost and time effective method that also allows identification of enzymes even from non-cultivable strains.

In addition, the (meta)genomic data can be used as database for functional proteomics screens performed in collaboration with Ruth Birner-Gruenberger. Finally, the identified sequences by functional screening, in-silico bioprospecting and functional proteomics approaches will be produced in expression hosts like E.coli and P.pastoris, purified and characterized in term of biochemical and kinetic parameters, substrate specificities and reaction mechanisms.

Background:

The working group has already carried out extensive screenings of strain collections from soil, water and anaerobic sludge as well as of metagenomic libraries for identification of new polymer hydrolases and oxidoreductases such as polymer hydrolases and laccases [1-3]. The enzymes identified in this project will be used to decompose natural and synthetic polymer substrates into defined, low-molecular-weight products that will be used to develop novel and sustainable materials.

Research Objectives:

• Identification of new oxidoreductases and hydrolases for decomposition of natural (cellulose, lignin, suberin, cutin, fatty acids) and synthetic (PE, PP) polymers

• Enzymatic decomposition of natural and synthetic polymers into uniform products

• Clarification of enzymatic reaction mechanisms and synergisms

Methods:

• Establishment of screening assays with target substrates

• Screening of strains (anaerobe, aerobe) and metagenomic libraries from underexplored sources for new enzyme activities

• Identification of novel enzymes by whole-genome sequencing

• Recombinant production of enzymes in E.coli and P.pastoris

• Investigation of substrate specificities and reaction mechanisms by GPC, HPLC, SEM differential scanning calorimetry (DSG), thermogravimetric analysis (TGA) as well as scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM).

Job requirements:

The ideal candidate should hold an MSc degree in biotechnology, biochemistry, chemistry, or equivalent. Experience in working with enzymes (hydrolases), recombinant expression and characterization of enzymes together with knowledge of analytical methods (e.g. HPLC, GPC) will be an added advantage. He or she is ready to dive quickly into this project, has strong communication skills in English and is motivated to work in an inter- and transdisciplinary team at the BOKU-Campus in Tulln.

References:

Diefenbach, T; Sumetzberger-Hasinger, M; Braunschmid, V; Konegger, H; Heipieper, HJ; Guebitz, GM; Lackner, M; Ribitsch, D; Loibner, AP. Laccase-mediated degradation of petroleum hydrocarbons in historically contaminated soil. Chemosphere. 2024; 348:140733.

Weinberger, S; Beyer, R; Schuller, C; Strauss, J; Pellis, A; Ribitsch, D*; Guebitz, GM. High Throughput Screening for New Fungal Polyester Hydrolyzing Enzymes. Front Microbiol. 2020; 11, 554

Quartinello F, Kremser K, Schoen H, Tesei D, Ploszczanski L, Nagler M, Podmirseg SM, Insam H, Piñar G, Sterflingler K, Ribitsch D* and Guebitz GM 2021. Together Is Better: The Rumen Microbial Community as Biological Toolbox for Degradation of Synthetic Polyesters 2021. Front. Bioeng. Biotechnol., https://doi.org/10.3389/fbioe.2021.684459

Main supervisor: Priv.-Doz. Dr. Doris Ribitsch

Co-supervisors: Univ.-Prof. Birner-Gruenberger

Location: BOKU University (UFT Tulln)

Submission deadline: 31.03.2025

Description of project

The identification of novel enzymes for industrial applications has been significantly advanced by omics technologies, bioinformatics, and engineering. The identification of new enzyme scaffolds is the first essential step in the development of new biocatalysts. The aim of this project is to identify novel enzymes including oxidoreductases and hydrolases through functional proteomics approaches. To this end, functional proteomic screening of anaerobic fungi and archaea as well as strain collections isolated from selected environments such as wastewater treatment plants, or microbial communities such as rumen or elephant gut microbiome, will be performed in collaboration with Doris Ribitsch to discover new enzyme activities without prior information about their sequence or structure. Three different proteomics approaches will be pursued: Secretomics will reveal proteins expressed and secreted in response to the substrate of interest (e.g. native and artificial polymers, such as lignocellulose). Thermal proteome profiling will reveal proteins binding to native substrates. Activity-based screens using probes for hydrolases and oxidoreductases will allow to identify new enzyme scaffolds. The latter two approaches offer the advantage to screen also otherwise non-culturable microorganisms, in particular new bacterial taxa or unknown bacteria, since it has a high probability of yielding genes encoding novel enzymes. The identified sequences will be produced in expression hosts like E.coli or P.pastoris, purified, validated and characterized in collaboration with Doris Ribitsch.

Background:

The working group has experience in functional proteomics [1-4].

Research Objective:

Identification of new biocatalysts for decomposition of natural and synthetic polymers

Methods

• Establishment of functional proteomics screening assays with target substrates (secretomics, thermal proteome profiling)

• Establishment of activity-based proteomics of hydrolases and oxidoreductases

• Establishment of habitat specific metaproteomics workflows

• Screening of strains (anaerobe, aerobe) and microbial communities from underexplored sources for new enzyme activities

• Recombinant production of enzymes and validation of enzymatic activities

Job requirements:

The ideal candidate should hold an MSc degree in biotechnology, biochemistry, chemistry, or equivalent. Experience in proteomics, LC-M/MS, bioinformatics, working with enzymes, recombinant expression and characterization of enzymes will be an added advantage. The candidate is ready to dive quickly into this project, has strong communication skills in English and is motivated to work in an active and interdisciplinary team at TU Wien.

1. Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner-Gruenberger R. (2023) Research advances through activity-based lipid hydrolase profiling. Israel Journal of Chemistry; doi: 10.1002/ijch.202200078

2. Schittmayer, M., Vujic, N., Darnhofer, B., Korbelius, M., Honeder, S., Kratky, D., Birner-Gruenberger, R. (2020) Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases. Molecular & Cellular Proteomics, 19:2104-2115. DOI:10.1074/mcp.RA120.002171

3. Wallace, P. W., Haernvall, K., Ribitsch, D., Zitzenbacher, S., Schittmayer, M., Steinkellner, G., Gruber, K., Guebitz, G. M., Birner-Gruenberger, R. (2017) PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes. Applied Microbiology and Biotechnology, 101:2291–2303. DOI:10.1007/s00253-016-7992-8

4. Sturmberger, L., Wallace, P. W., Glieder, A., Birner-Gruenberger, R. (2016) Synergism of proteomics and mRNA sequencing for enzyme discovery. Journal of Biotechnology, 235:132-138. DOI:10.1016/j.jbiotec.2015.12.015

Main supervisor: Univ.-Prof. Ruth Birner-Gruenberger

Co-supervisors: Priv.-Doz. Dr. Doris Ribitsch

Duration: 4 years (30 h/week)

Location: TU Wien, Research Group Bioanalytics: https://www.tuwien.at/en/tch/bioanalytics

Submission deadline: 31.03.2025