Looking back on BaSyC PhD research part 2

Charlotte Koster, Ludo Schoenmakers and Melanie König all graduated from university in the past months and became a doctor. They now look back on their doctoral research and on being a part of the BaSyC Consortium and take us along in this article. We asked them:

1. What was your thesis briefly about and what was the main conclusion for BaSyC research?

Charlotte her thesis was performed at the TU Delft with Pascale Daran-Lapujade and consisted of 2 main research topics. Her second research topic was studying and engineering yeast mitochondria. This second topic may seem unrelated to synthetic cell research, but mitochondria occur from an endosymbiotic event, and over time the mitochondrial ancestor ‘lost’ most of its genome to their host cell: this is essentially nature’s way of minimizing a cell! More knowledge on how mitochondria still function regardless of their minimal genome could lead to better insight in what is needed in a minimal synthetic cell. Additionally, we could use them as a ‘starting platform’ for synthetic cell.

Charlotte discovered in her thesis that there are still many surprising gaps in the knowledge of the mitochondria, despite their small size. They especially focused on the streamlined, intricate, genome structure of the mitochondria and mapped its highly spliced transcriptome using Nanopore sequencing. This led to some surprising insights in how seemingly redundant sequences still play a role in the mitochondria, which she is sure can inspire the genome design of a synthetic cell! Despite gaining more knowledge on how mitochondria work, they were not able to engineer them, which may be a task for future synthetic cell enthusiasts!

Additionally, together with Céline Charlotte researched using yeast as a factory for the assembly of a synthetic cell genome through homologous recombination of gene fragments. This appeared more challenging than foreseen, since the yeast had some unpredictable responses to hosting an additional ‘unnecessary’ genome. During her PhD they mostly worked on bypassing this, so hopefully soon the first synthetic genomes can be built in yeast!

Ludo investigated, during his time with BaSyC, how we might realise membrane protein insertion in synthetic cells, how the central dogma may be captured in coacervates, and how this type of research is related to definitions of life. Membrane protein insertion turned out to be a tough nut to crack, but encapsulating the central dogma worked out surprisingly well. His conclusion for BaSyC would be that there is still a lot to do when it comes to synthetic membrane protein insertion, which he guesses is true in general: there is still a lot to do for the bottom-up syncell community.

Melanie focused on the functional role of cellular membranes in vital biological processes such as cell signaling and division in her PhD research. Designing a synthetic cell and its outer barrier, the so-called plasma membrane, from the bottom up requires a fundamental understanding of structure-function relationships at the molecular and cellular level. Using coarse-grained molecular dynamics simulations, she was able to show that cellular functionality and even evolution can arise on all scales of membrane complexity originating from simple physical principles on the molecular level. Taking inspiration from nature, she showed how simple fatty acid-based protocells could have played an active role in the evolution of modern phospholipid-based cells and fostered the emergence of protein transport machineries. Furthermore, her work contributed novel insights into the dynamic relationship between lateral organization and membrane shape and how these two are intricately linked at the nanoscale.

2. What do you think about the BaSyC consortium and did it bring you benefits during your PhD? 

Charlotte thinks it’s is really great to be part of such a large consortium as a PhD student. Labs are generally specialized towards one certain organism or technique, so being able to freely go to other labs to do experiments and learn new techniques rather than setting it up in your own lab really accelerated experiments. She did quite some cell-free experiments in the group of Christophe Danelon that she would otherwise not encounter in her yeast-focused research group. On top of that, it was really fun regularly meeting other PhD’s in the same stage of their research, sharing ideas and experiences. Even now she’s done she keeps running into fellow BaSyC—PhD’s so it is really cool to see we have built quite the network!

Ludo found working within BaSyC to be a great experience all in all. There is an intellectual component to this – with all of the different perspectives on the same problem there is never a dull day – but there is a personal component as well. Doing a PhD can be an isolating experience, even if your day-to-day collaborations with others are close. To be able to share both the woes and successes of that experience with a group of people who often met very similar challenges, has meant a great deal to him personally. He thinks we can be proud of having brought together so many scientists within the Netherlands through BaSyC and he’s sure many fruitful contacts and collaborations will follow.

Melanie lets us know that working in a highly interdisciplinary consortium like BaSyC broadened her perspective on her PhD topic and allowed her to see how her research ties in with the work of others. During many exciting workshops and meetings, she learned how to communicate her work to both experts and the general public, which positively impacted her academic and personal growth during her PhD journey.

3. What did you start doing after BaSyC and tell us a little more about that? 

Charlotte didn’t move too far away from the programme: she joined the lab of BaSyC PI’s John van der Oost and Nico Claassens in Wageningen as a postdoc! Although she is no longer working on synthetic cells, she is continuing the work of BaSyC PhD Thijs Nieuwkoop on unraveling how protein expression is controlled in prokaryotes, and she wants to use this knowledge to improve heterologous protein expression in relevant protein production hosts. Although she really enjoys this topic, it is really nice to still work in a lab involved in BaSyC and watch the project progress from the sidelines.

Ludo thinks it’s fair to say that his work on definitions of life is what got him his next job. He wanted to do a postdoc, but he was unsure about pursuing natural science. This in itself is nothing special – he has vacillated between science and philosophy for most of his academic career – but the postdoc-phase is a crucial one if you want to continue in academia. So he decided to take a gamble and applied for a postdoctoral fellowship at the Konrad Lorenz Institute in Klosterneuburg, right next to Vienna, finally combining science and philosophy by pitching a project aimed at studying the role of evolution at the origins of life. (If the relevance of philosophy isn’t immediately clear, do send him an e-mail!) He has been at the KLI for almost four months now and both the institute and Vienna have been fantastic.

Melanie is currently a PostDoc in Siewert-Jan’s group continuing her PhD research. She also works on building a realistic model of the Syn3A minimal cell, where we are trying to establish a robust pipeline for the setup of functional membrane protein complexes based on experimental data.

4. How do you see your future (short-term or long-term)? 

Charlotte has at least one more year to go in her postdoc for now and she hopes to publish some of the experiments she’s working on; the results look promising! What happens after is still a mystery, but she’s sure it will be something with synthetic biology, she’s definitely not done with research yet!

Ludo thinks it’s a loaded question, but if you learn one thing from studying evolution, is that if you find your niche you must colonise it aggressively. (Although you might equally well say that the niche is just there waiting to be filled by any odd thing.) He’s hoping to do interesting research – well, to him anyway – at the interface of philosophy and the molecular sciences. For now the focus is on the origins of life, with an eye to synthetic biology. Another interesting topic is the somewhat mythical Last Universal Common Ancestor, which he wants to build his next postdoc around, hopefully in the US. As for the time in-between, there is the Molecular Origins of Life conference in Munich in July this year, where he hopes to see many of his former colleagues and friends from BaSyC as well!

Melanie envisions her future as a dedicated scientist, using simulations to address the challenges of the 21st century. She hopes to use her scientific expertise to contribute to innovative solutions, bridging the gap between theoretical and experimental work.