Project 10: Mining the functional microproteome landscape...

The position

Only a fraction of the genome codes for the proteins in standard reference catalogs. Many small open reading frames (smORFs) scattered across the genome are translated into microproteins that these catalogs miss, and while growing numbers of microproteins are being discovered, their biological functions and the molecular interactions through which they act remain largely unknown. Thermal proteome profiling (TPP), a mass-spectrometry method that measures how the thermal stability of a protein shifts when its binding partners or conditions change, offers a way to assign function to these previously hidden proteins.

This project will systematically characterize the functional landscape of microproteins in the enteropathogen Salmonella enterica serovar Typhimurium, using TPP across smORF deletion strains and multiple conditions to build a comprehensive interaction map for the Salmonella microproteome. It sits at the center of ORFeus Work Package 2, which moves from discovery to function: the structural and biophysical data it generates feed an iterative design-test cycle with a computational protein-design project, while the standardized TPP workflows developed here are adapted for host-pathogen proteomics elsewhere in the network. The work also connects to evolutionary analysis of microprotein function and to the wider consortium through the shared ORFeome platform.

Main tasks

● Develop and standardize thermal proteome profiling protocols to measure changes in protein stability and abundance across a panel of smORF deletion strains and multiple growth conditions in Salmonella .

● Integrate the thermal proteome profiling data with protein structure prediction (for example AlphaFold and RoseTTAFold), working with the computational protein design project of another doctoral candidate (DC) in the network, here DC6, to infer protein-protein interactions involving microproteins.

● Validate high-confidence interactions in vitro using biophysical methods such as biolayer interferometry and SEC-MALS, building a validated interaction map for the Salmonella microproteome.

● Collaborate across the ORFeus network by sharing standardized TPP workflows with related projects, including host-pathogen proteomics in DC4, contribute datasets to the shared ORFeome platform, and producing the project's scientific report.

Methods and platforms : thermal proteome profiling (TPP) and quantitative mass spectrometry-based proteomics, construction and phenotyping of smORF deletion strains in Salmonella , protein structure prediction (AlphaFold, RoseTTAFold) for interaction modeling, and in vitro biophysical validation (biolayer interferometry, SEC-MALS), with datasets shared through the ORFeome platform.

Secondment : you will spend around three months at Bruker (Bremen, Germany), optimizing the thermal proteome profiling workflows on advanced mass-spectrometry platforms. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Your profile

MSCA eligibility

You must meet all of the following on your recruitment date:

● You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.

● Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in Belgium for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.

● You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at Ghent University.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

Project-specific profile

● A master's degree (or equivalent) in biochemistry, molecular biology, microbiology, biotechnology, biomedical sciences, analytical chemistry, or a related life-science field.

● Hands-on laboratory experience, ideally including protein biochemistry, mass spectrometry, or proteomics, and comfort working with quantitative data.

● Desirable: experience with mass-spectrometry-based proteomics, bacterial genetics or Salmonella work, biophysical interaction methods (for example biolayer interferometry or SEC-MALS), and an interest in microproteins and the dark proteome.

● Good written and spoken English.

● Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

What we offer

We offer a full-time position as a doctoral fellow, consisting of an initial period of 12 months, which, after a positive evaluation, will be extended to a total maximum of 48 months.

The fellowship amount is 100% of the net salary of an AAP member in equal family circumstances. The individual fellowship amount is determined by Ghent University HR based on family status and seniority. A grant that meets the conditions and criteria of the regulations for doctoral fellowships is considered free of personal income tax.

The position is funded within the Marie Skłodowska-Curie Actions Doctoral Network ORFeus. Applicable MSCA-DN mobility and family allowances will be handled in accordance with the MSCA-DN and Ghent University regulations.

Beyond the fellowship, you will receive:

● Supervision by a world-leading, interdisciplinary supervisory team.

● A secondment of around three months with an ORFeus industry partner (Bruker).

● A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.

● Enrollment in a doctoral program leading to a PhD.

● All Ghent University staff members enjoy a number of benefits, including a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time position), supplemented by annual fixed bridge days, bicycle allowance and eco-vouchers.

Duration and funding

The doctoral fellowship can run for a total maximum of 48 months, subject to a positive evaluation after the initial 12-month period. The first 36 months are funded through the Marie Skłodowska-Curie Doctoral Network ORFeus. Ghent University provides funding for an additional 12 months to allow the doctoral candidate to finalize the PhD.

Working at Ghent University

Ghent University is a world of its own. Employing more than 15.000 people, it is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis.

With its 11 faculties and more than 85 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University is a logical choice for its staff and students.

You will join the group of Prof. Petra Van Damme at the Laboratory of Microbiology, Department of Biochemistry and Microbiology, where you will work in an interdisciplinary research environment combining molecular microbiology, bacterial infection biology, and advanced proteomics, including thermal proteome profiling, to study microproteins and the dark proteome. You will work closely with the group of Dr. Danny Sahtoe at the Hubrecht Institute, who brings complementary expertise in computational protein design and structural biology. You will enroll as a PhD candidate at Ghent University and participate in the doctoral training program of the Doctoral School of Sciences.