Project 4: Profiling microprotein interactions in bacterial pathogen infections (Jyoti Choudhary)

The position involves profiling microprotein interactions in bacterial pathogen infections. Standard protein catalogs list only a fraction of what cells actually make. Scattered across genomes are many small open reading frames (smORFs), short stretches of sequence that are translated into microproteins, tiny proteins that reference catalogs have long overlooked. During a bacterial infection, both the host and the pathogen switch on new programs of translation, and some of these overlooked microproteins are likely to play a role at the host-pathogen interface. Detecting them in a system where host and bacterial proteins are mixed together is technically difficult and largely unexplored.

This project will map microproteins in host-pathogen interactions using Citrobacter rodentium, a model for enteric (gut) infection, combining a dual prokaryotic-eukaryotic proteomics workflow with ribosome profiling (Ribo-seq) to capture host and pathogen translation across the stages of infection. It sits in ORFeus Work Package 1 on uncovering the dark genome and proteome, where its dual-species workflow produces unique training data for the network's computational models. The work connects closely to partner projects on AI-driven translation modeling, complementary microprotein proteomics, thermal proteome profiling, computational protein design, and antigen presentation.

Main tasks:

• Map the microprotein landscape across three stages of infection, from early to peak to resolution, in mouse epithelial cell lines and in a C57BL/6 mouse model, building a dual prokaryotic-eukaryotic Ribo-seq and proteomics workflow that reads host and pathogen translation together.
• Probe the functions of infection-induced microproteins using proximity labeling (BioID) to map their interaction partners, separating genuinely infection-specific responses from general cellular stress across the stages of infection.
• Turn the approach into a dual prokaryotic-eukaryotic microprotein discovery workflow that other groups can adapt, validating BioID interaction maps with thermal proteome profiling together with other doctoral candidates (DCs) in the network, here DC10, and refining AI-driven peptide-spectrum matching during the industry secondment.
• Collaborate across the ORFeus network, providing dual-species training data for the computational models of DC1 and infection-associated microprotein targets for the antigen presentation work of DC14 and the protein-design work of DC6, contribute datasets to the shared ORFeome platform, and produce the project's scientific report.

Methods and platforms: dual prokaryotic-eukaryotic mass-spectrometry proteomics and ribosome profiling (Ribo-seq), proximity labeling (BioID) for interaction mapping, targeted mass spectrometry (parallel reaction monitoring, PRM) for computationally predicted candidates, thermal proteome profiling (TPP), AI-driven peptide-spectrum matching, and Citrobacter rodentium infection models in mouse epithelial cell lines and in vivo, contributing data to the ORFeome platform.

Secondment: you will spend around three months at Tesorai (San Francisco, USA), refining AI-driven peptide-spectrum matching for microprotein identification in the dual-species data. 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 the United Kingdom 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 The Institute of Cancer Research / University of London. 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 relevant degree in biochemistry, proteomics, molecular or cell biology, microbiology, or a related life-science field or analytical chemistry. Hands-on experience with mass-spectrometry-based proteomics or a related experimental technique, and proficiency analyzing quantitative or omics data. Desirable: experience with ribosome profiling or next-generation sequencing, proximity labeling (BioID), knowledge of host-pathogen or infection biology, work with bacterial systems or mouse models, 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: A full-time employment contract for 36 months as a salaried researcher, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. This is a paid employment contract, not a stipend or scholarship. The salary has a living allowance and a mobility allowance, plus a family allowance if you have family obligations when you are recruited. The indicative gross salary for this position is 5,534.35 Euros per month, which includes a living allowance and a mobility allowance, for a duration of 36 months. This is what you are paid before income tax and National Insurance contributions are deducted. Additionally, candidates with a family may be eligible for a monthly family allowance of 428.57 Euros (also subject to tax and National Insurance deductions), provided they meet the eligibility criteria for the MSCA family allowance. In the fourth year of the PhD, the candidate will receive the standard ICR stipend rate.

Beyond salary, you will receive:

• Supervision by a world-leading, interdisciplinary supervisory team.
• A secondment of around three months with an ORFeus industry partner (Tesorai).
• A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.
• Enrolment in a doctoral program leading to a PhD.
• As a member of staff, you'll have exclusive access to a range of staff benefits.

The ICR is committed to supporting overseas applicants applying for roles.

Duration and funding beyond the MSCA contract: In line with the host institution's doctoral policy, the host will provide funding to support completion of the doctorate in the fourth year at the host's standard doctoral stipend rate; during this final year the candidate transitions to student status. Further details confirmed at offer stage.

Working at the Institute of Cancer Research: The Institute of Cancer Research (ICR), London, UK, is a world-leading cancer research institute with an international reputation for excellence in cancer research and strong expertise in functional proteomics and mass spectrometry. Based within the Division of Cell and Molecular Biology, the Functional Proteomics Team provides a highly collaborative research environment, working closely with research groups across the ICR and with external academic and industry partners. The team applies cutting-edge mass spectrometry-based proteomics approaches to investigate molecular organisation, protein function, and the mechanisms that underpin cellular processes and disease. This interdisciplinary environment provides an excellent setting for PhD students to develop expertise in advanced proteomics while addressing important questions in fundamental biology. You will join the group of Prof. Jyoti Choudhary, which develops functional proteomics and mass-spectrometry methods and applies them to host-pathogen interactions, including recent work on bacterial secretion-system effectors. You will work closely with the group of Prof. Petra Van Damme at Ghent University, who brings complementary proteomics and microprotein expertise, including dual-proteome experience from Salmonella infection. You will enroll as a PhD candidate at the University of London, through The Institute of Cancer Research.