PhD candidate; Mechanism and assembly of type VII secretion system machineries

We are looking for an enthusiastic and motivated PhD candidate to join Dr. Catalin Bunduc’s team in the Molecular Microbiology Section of the Amsterdam Institute for Life and Environment (A-LIFE).

Join Our Research on Bacterial Protein Secretion Systems

All bacteria depend on extracellular proteins to be able to communicate and interact with their environment. A particular biological challenge is to get these relatively large molecules from the cytosol and across the surrounding multi-layered bacterial cell envelope without compromising its integrity. To achieve protein transport, bacteria have evolved a suite of specialized protein secretion systems, with up to eleven systems discovered so far, across different species.

Mycobacteria, such as the human bacterial pathogen Mycobacterium tuberculosis, rely on such a system, called type VII secretion system (T7SS), to transport proteins important for their physiology but also virulence. In the mycobacterial inner membrane, T7SSs assemble a large complex, responsible for translocating large, folded protein substrates. We have recently isolated and solved the structure of this fragile inner membrane assembly as a 33 subunit, 2.3 MDa complex with 165 transmembrane domains (Bunduc et al., Nature 593:445-448). Building on this and other novel findings in our group, we aim to understand how this large membrane complex is assembled and uncover the mechanism by which it translocates folded proteins.

The position involves both wet and dry lab experimentation. Using state-of-the-art molecular and biochemical methods, you will isolate these membrane complexes from different genetic backgrounds, characterize their biochemical properties and analyse their molecular structure using cryo-electron microscopy (cryo-EM). The latest AI tools, such as Alphafold and BindCraft, will be integrated to complement the analysis.

The planned starting date for the project is flexible.

Your Profile

We are looking for a PhD candidate who has:

• MSc-degree in biochemistry, molecular biology or a related discipline. Candidates close to graduating are also encouraged to apply.
• Strong motivation to solve scientific problems and a curiosity driven approach.
• Theoretical knowledge of molecular biology, biochemistry, protein science.
• A keen interest in membrane proteins and/or structural biology (cryo-EM). Previous experience in one of these topics is a plus.
• Affinity for both wet and dry lab methodology.
• Proficiency in English.

What We Offer

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So, in return for your efforts, we offer you:

• A salary of € 3.059,00 (PhD) and maximum € 3.881,00 (PhD) gross per month in the fourth year, for a full-time employment.
• An employment contract of initially 1 year. If there is sufficient perspective, this will be extended to a total of 4 years.

We also offer you attractive fringe benefits and arrangements. Some examples:

• A collegial atmosphere in a vibrant research group with excellent opportunities for training.
• A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
• 8% holiday allowance and 8.3% end-of-year bonus
• Contribution to commuting expenses
• Space for personal development
• Discount on (and occasionally exclusive access to) theatre performances and courses at the Griffioen Cultural Center

About Us

About the team

The Molecular Microbiology section concentrates on the microbial cell envelope, protein secretion systems, novel antibiotics and phage biology. Our section is located together and working closely with the Medical Microbiology and Infection Prevention unit of the AUMC focusing on infection models. Combined, the two groups have ~35 members.

In this project you will work closely together with one more PhD student and be part of a larger group working on mycobacterial secretion systems.

Amsterdam Institute for Life and Environment (A-LIFE)

A-LIFE brings together the groups of Molecular Microbiology, Systems Biology, Environment & Health, and Ecological Sciences, with the aim to advance the fundamental understanding of the interplay between life and its environment. A-LIFE seeks to connect properties and emergent behaviours across all scales, from molecules to ecosystems, including human populations. The research of the department covers a broad range of research topics, including ecology and evolution, microbiology, (eco)toxicology and analytical chemistry of pollutants, global change biology, and biotechnology, and the associated state-of-the-art methods and technologies, both computational and experimental.

The department is located in a new research building together with other biological, chemical and medical disciplines offering key research infrastructure and opportunities for collaboration. Part of the research in this building is clustered in the Amsterdam Institute of Molecular and Life Sciences (AIMMS).

Faculty of Science

Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Vrije Universiteit Amsterdam

Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. Maintaining an entrepreneurial perspective and concentrating on significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 5,500 staff work at the VU and over 30,000 students attend academic education.