Postdoc-position | Functional proteomics of microorganisms and bioprocesses

Description of project:

The identification of novel biocatalysts and development of bioprocesses for industrial applications has been significantly advanced by omics technologies, bioinformatics, and engineering. Redox-stress can be a relevant limiting factor with regards to yield and product quality. However, a global, comprehensive and systematic analysis of redox-stress with molecular resolution of different hosts, promoters, products and process parameters is lacking and one major aim of this project, which will be supported by a PhD student and performed in collaboration with Oliver Spadiut, Robert Kourist, Wolfgang Kroutil, Matthias Steiger and Florian Rudroff (program 3). The second major aim is to identify novel enzymes including oxidoreductases and hydrolases accepting selected substrates, e.g., lignocellulose, without prior information about their sequence or structure through functional proteomics approaches, including secretomics, thermal proteome profiling and activity-based proteomics of selected microorganisms and environments such as rumen or elephant faeces, which will be supported by a PhD student and performed in collaboration with Doris Ribitsch (programs 1 and 3). A third aim will be to perform subcellular proteomics as part of developing compartmentalized multi-omics workflows in collaboration with Gunda Koellensperger, Brigitte Gasser and Matthias Steiger (program 2).

Background:

The working group has experience in functional proteomics, such as redox-proteomics and -metabolite analysis [1-3], activity-based proteomics [4-7], secretomics and enzyme discovery [8,9].

Research Objectives:

- Elucidation of redox-stress mechanisms and pathways in diverse hosts

- Identification of critical bioprocess parameters causing redox-stress

- Identification of new biocatalysts for decomposition of natural and synthetic polymers

Methods:

- Establishment of redox-proteomics and -metabolite analysis of diverse hosts including E. coli, P. pastoris, cyanobacteria and archaea

- Redox-proteomics and -metabolite analyses

- Pathway analysis, gene ontology enrichments

- Product analysis by mass spectrometry

- 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

- 7Screening of strains (anaerobe, aerobe) and microbial communities from underexplored sources for new enzyme activities

Job requirements:

The ideal candidate should hold a PhD degree in biotechnology, biochemistry, chemistry, or equivalent and have international experience, proven publication and presentation activity and experience in proteomics and bioinformatics. Experience in metabolomics, recombinant expression in different hosts 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.

References:

1) Tomin T, Honeder S, Liesinger L, Gremel D, Retzl B, Lindenmann J, Brcic L, Schittmayer M*, Birner-Gruenberger R. (2025) Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in NSCLC patients. Nat Commun, accepted; preprint on Research Square 2024; doi: 10.21203/rs.3.rs-4535848/v1 (*co-corresponding author))

2) Tomin T, Schittmayer M, Sedej S, Bugger H, Gollmer J, Honeder S, Darnhofer B, Liesinger L, Zuckermann A, Rainer PP and Birner-Gruenberger R. (2021) Mass spectrometry-based redox proteome profiling of failing human hearts. Int. J. Mol. Sci. 2021, 22, 1787. doi:10.3390/ijms22041787

3) Tomin T, Schittmayer M, Birner-Gruenberger R. (2020) Addressing glutathione redox-status in clinical samples by two step alkylation with N-ethylmaleimide isotopologues. Metabolites. 2020, 10(2):71. doi: 10.3390/metabo10020071.

4) Krammer L, Darnhofer B#, Kljajic M, Liesinger L, Schittmayer M, Neshchadin D, Gescheidt G, Kollau A, Mayer B, Fischer RC, Wallner S, Macheroux P, Birner-Gruenberger R*, Breinbauer R. (2025) A general approach for activity-based protein profiling of oxidoreductases with redox-differentiated diarylhalonium warheads. Chem Sci; doi: 10.1039/d4sc08454c. Epub ahead of print. PMID: 40103729; PMCID: PMC11912224. (#co-first author, *co-corresponding author)

5) 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

6) 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

7) 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

8) 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

Where to apply:

https://www.circularbioengineering.at/