The role of smORF encoded polypeptides in lager beer fermentation

(ref. BAP-2023-9)

Laatst aangepast : 11/01/2023

For the Laboratory of Enzyme, Fermentation and Brewing Technology (EFBT), Department Microbial and Molecular Systems (M2S), within the Centre for Food and Microbial Technology (CLMT) at Campus Gent of KU Leuven we are looking for a highly motivated postdoctoral researcher to investigate the role of small open reading frame (smORF) encoded polypeptides (aka microproteins) in lager beer fermentation. EFBT is a leading brewing technology laboratory in which the group of Prof. Florian Weiland is embedded. The research group of Prof. Weiland was established recently and specializes in studying molecular systems using proteome analysis in context of food and drink. Current projects involve (among others) investigating the role of kinases in yeast flocculation and spatio-temporal proteome analysis of barley during germination. In this project, the role of small open reading frames (smORFs) and their protein products (smORF-encoded polypeptides (SEPs)) will be investigated during lager beer fermentation using state-of-the-art genomic and proteomic approaches. SEPs are classified as polypeptides with less than 100 amino acids and unlike other small proteins/peptides, SEPs are not derived from longer precursors but arise directly by translation of smORFs. Over the last years, SEPs have been increasingly shown to be involved in fundamental biological regulatory functions. However, there are major computational hurdles to identify smORFs (and SEPs) from genome sequences and as such they are detected when expressed in situ. The yeast species used in lager beer production (S. pastorianus) was never subjected to investigations in the context of SEPs and their potential functions during fermentation under industrially relevant conditions. Therefore, the project encompasses ribosome sequencing to detect translation initiation sites of actively translated mRNAs (TIS Ribo-Seq) to identify potential smORFs. This approach is subsequently combined with proteome analysis to address the question if the transcript is actually protein coding. Finally, the SEPs will be phenotypically characterised via knock-out experiments using CRISPR/Cas9 and their further application potential on yeast strain selection will be explored. The here advertised position will be in close collaboration with the KU Leuven Next Generation Sequencing Core (Dr. Annelien Verfaillie) and the TU Berlin in Germany (Prof. Brian Gibson).

Responsibilities

Carry out experiments using TIS-RiboSeq, Proteome Analysis and CRISPR/Cas-9 at a postdoctoral level. Dissemination of results via publications and conferences. Supervision of MSc students.

Profile

•    Hold a PhD in Molecular Biology, Biochemistry or related field

•    Strong background in genomic/transcriptomic methods (RiboSeq, CRISPR/Cas-9)

•    Basic ability to use scripting languages (R or Python) for data analysis

•    Genuine interest in learning techniques for Proteome Analysis

•    Excellent command of written and spoken English

The ideal candidate has a very strong background in genomic/transcriptomic methods (RiboSeq, CRISPR/Cas-9), preferably in yeast. Basic knowledge of proteomics is a plus, but the candidate will have ample opportunity to thoroughly learn these techniques in the group of Prof. Weiland. Command of scripting languages (R or Python) for data analysis is desirable.

Offer

We offer a fully funded full-time postdoctoral position for 4 years. The position is available immediately at KU Leuven Campus Gent.

Interested?

For more information please contact Prof. dr. Florian Weiland, tel.: +32 9 398 63 88, mail: [email protected].

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