University of Groningen Adding tools to the box: facilitating host strain engineering of Penicillium chrysogenum for the production of heterologous secondary metabolites Pohl, Carsten

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University of Groningen

Adding tools to the box: facilitating host strain engineering of Penicillium chrysogenum for the

production of heterologous secondary metabolites

Pohl, Carsten

DOI:

10.33612/diss.119054818

IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.

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Publication date: 2020

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):

Pohl, C. (2020). Adding tools to the box: facilitating host strain engineering of Penicillium chrysogenum for the production of heterologous secondary metabolites. University of Groningen.

https://doi.org/10.33612/diss.119054818

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7

CHAPTER

Acknowledgements

Curriculum vitae

Publications and

patent applications

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Acknowledgements, curriculum vitae, publications and patent applications

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7 Acknowledgements

The curtain has fallen and now it’s time to applaud the actors and stakeholders that were part of this journey towards my graduation. When you embark on such an adventure, you cannot prepare for every situation you will encounter on the way - but you can be lucky and get a helping hand and make friends along the way from people that you’d never expect to meet when you leap across the threshold into this adventure. And while sometimes doubting that I was walking the right road and the path to take seemed not always to be that one leading straight, I was definitely in a lucky situation because I had people around me that encouraged me to push on and walked the same direction. And when you look back after some time, each of them fulfilled a very special role during the time in Groningen and beyond.

To begin with, I want to thank my freedom-loving Prof. Arnold J.M. Driessen for his patience in guiding me towards my graduation. Having Arnold as a mentor means that one has the opportunity to grow into an independent, critical researcher that is credited with endless freedom during the time in the lab. But with endless freedom comes great responsibility – and the challenge of making the right decisions at the right time was not my expertise when I started the journey. So, I often yearned for some external decision-making. But while immersing more and more into research and becoming more knowledgeable, I learned to make my own, justifiable decisions which became increasingly approvable by Arnold. Dear Arnold, thank you for accepting my quirks and training me the 4 years in Groningen to develop a better instinct for priorities and careful decision making.

Besides Arnold, my quest of fungal biotechnology was guided by the knowledgeable Prof. Roel A.L. Bovenberg. Dear Roel, while I sometimes felt like a capricious teenager who did not invest enough time into small-talk and was stressed out when not rushing around in the lab, it was impressive to see how you found the time in your crowded schedule to make us all feel you had endless time to care about what we did, planned and struggled with. Your politeness and sense of humor made though decisions more enjoyable and taught me that we should not forget respect and culture in the heat of science.

The weekly work discussions in the MolMic group would not have been that memorable without the knights of sound science, Prof. Dirk-Jan Scheffers and Dr. Juke Lolkema who asked those wise and challenging questions that made one think more critical about results one started to like and cherish without the bullet-proof control experiment done yet. A great thank you also for my lab mates, the three jolly heralds of yeast: Jeroen, Stefan and Hun-Jiong. You made long sessions at the bench more enjoyable to me and lighted up the day with kuiken-cams, marathon talk, the occasional whiff of ethanol assays, HPLC-support and weekend-emergency-Pizzas for starving PhD students.

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Being a PhD student at MolMic also meant to occasionally deal with some bureaucracy, but this was surprisingly efficient thanks to the fairies of smooth paperwork Bea, Anmara and Jan. Also, before running an experiment, one also needs to order some materials every now and then. In my case, “now” rather seemed to happen more frequently than “then”. Therefore, I want to thank Janny and Greetje, our magicians of unchained supply at MolMic for their patience and support in placing orders.

A huge слова подяки also to Oleksandr Salo, my memorable first encounter with MolMic PhD students. When I joined MolMic as a naïve trainee, you grounded my ambitions with reality and survival lessons, while at the same time where an enormous support in understanding all sorts of lab equipment, especially Lola and reluctant Douwe Egberts coffee machines. Turning me into a grown-up researcher was also the achievement of MolMics finnish fairy-of-the-Why, Yvonne Nygard. Your strategy of systematic thinking, cloning and many other aspects of life remain inspiring to me and before I now start to deviate into another side project, your “Why would you do this?” comes in handy to clarify some cloudy situations. Yvonne, I wish you a great time with your little family and many skilled PhD students for your own research group.

The journey towards a PhD degree leads across many different roads and walking these together with the battle companions from MolMic and the QuantFung project made it certainly more fun. Thank you, Zsofia, Annarita, Tabea, Marten, Riccardo, Fernando, Danae, Sabrina, Min, Sietske, Fabiola, Jens, Reto, André and Min Jin for being all special and wonderful people. Thank you for travelling many places across Europe together: Paris, Lisbon, Ghent, Delft, Prague, Debrecen, Copenhagen, Berlin and for fun evenings in Groningen. Tabea, thank you for your detailed teaching of how to run a bioreactor in Vera Meyers lab in Berlin and for motivating me to push on with writing up this thesis. A special thanks to my first guards and paranymphs László and Niels, who helped me to defend this book in front of the committee.

Becoming a PhD also means to supervise some students and I hope that I have taught you some useful lab skills, Alex, Maaike, Maartje, Hilde, Luc and Natasja, you were the squires of the swift pipette who did an internship for your bachelor or masters project in the MolMic group. Stay curious and remember that fungi are easy to engineer if you use the right tools! When doing a PhD and you get sucked into the lab, your head is getting filled with creative ideas, but your body starts to suffer when not used properly. So, I am very grateful to Johannes, Tobias, Luise, Anna, Chris, Sonja and Christian who were the sportive mob during holidays and weekends. Thank you for every run and ride we made together in the last years, it was so relieving to feel exhausted.

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Life in Groningen would have been much harder without the great support from my roommates. Although you all noted pretty soon that I was the early bird leaving the house, I made that up by ensuring that our flat was not turned into a dungeon of dirty dishes and eventually called for a gathering on our dinner table to feast together on dark winter nights. I wish you, Fruszina, Caroline, James, Matthieu, Linda, Anke, Mareike and Charles all the best for your next adventures and thank you for your warmth, tolerance and great moments we spent together.

Noteworthy, moving abroad to the Netherlands for a PhD in life sciences does not count as being out of reach if your family is based in the region of Berlin but certainly adds some kilometres to bridge. But your biggest support to this book, Monika and Ralf, was the start of this journey 25 years ago, when you took my brother René and me for countless walks into the forest to explore nature. I am certain that you and Grandmother Irmgard sparked the candle of curiosity to understand what make living things work the way they work and eventually, that resulted in high school biology class and a studying biotechnology. And while living the PhD live, your curiosity about the research I was doing taught me to explain things in a lively, colourful way and gave me the opportunity to explain what your tax money is spent upon. In the last 10 years, I saw people becoming increasingly sceptic about all sorts of science, so I am very thankful to see your unbelievably positive attitude towards science shine when we talk about research, Lutz, Dagmar, Nico, Enrico, Matthias, Christiane and Paula. I cannot promise you that 2020 will be the year of the unicorned squirrel (“Einhörnchen”), but keep your eyes open for them in the coming decades.

And finally, I want to give my gratitude to the grandest of all maids I ever met. Dear Sophia, while I am writing these last lines, your feet are tipping a little to remind me that I should hurry up a bit, because new adventures together are laying ahead of us. I’m embracing every day gone and to come together with you. Home is where we are together. The journey has come to and end. Let’s build our future together. I love you.

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7 Curriculum vitae

Carsten Pohl was born in Potsdam, Germany on the 13th November 1987. He started to study Biotechnology at the Technische Universität Berlin and made first contact with the dutch way of life and research during his 6-month Internship in 2013 at at DSM Food Specialties B.V in Delft where he also wrote his diploma thesis “A targeted approach to optimize production of a heterologous expressed phospholipase in Aspergillus niger”. After graduating with a Diploma in Biotechnology from the Technische Universität Berlin in April 2014, he instantly joined the Initial-Training-Network “QUANTFUNG” and started his research at the University of Groningen under the Supervision of Prof. Arnold J. M. Driessen and Roel A. L. Bovenberg in the Molecular Microbiology group. During his PhD-time, he also conducted a 4-month research secondment in the research group Applied and Molecular Microbiology group lead by Prof. Vera Meyer at the Technische Universität Berlin. After completion of the QUANTFUNG research Project, Casten joined the research group of Vera Meyer in August 2018 as a researcher and is currently working on fungal biotechnology and biosensor development.

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7 Publications and patent applications

1. submitted to Scientific Reports (11/2019): A Penicillium rubens platform strain for secondary metabolite production. Pohl C., Polli F. Schütze T., Viggiano A., Mózsik L., Jung S., de Vries M., Bovenberg R. A. L., Meyer V., Driessen A. J. M

2. Fungal Biol. Biotechnol. volume 6, 17 (2019). doi:10.1186/s40694-019-0080-y. Fungi as source for new bio-based materials: a patent review. Cerimi K., Akkaya K. C., Pohl C., Schmidt B., Neubauer P.

3. ACS Synth. Biol. 2019. doi: 10.1021/acssynbio.9b00106. Bacterial MbtH-like Proteins Stimulate Nonribosomal Peptide Synthetase-Derived Secondary Metabolism in Filamentous Fungi. Zwahlen, R. D., Pohl, C., Bovenberg, R. A. L., Driessen, A. J. M.

4. Fungal Biol. Biotechnol. 5, 18 (2018). doi: 10.1186/s40694-018-0063-4. Identification of the decumbenone biosynthetic gene cluster in Penicillium decumbens and the importance for production of calbistrin. Grijseels S., Pohl C., Nielsen J. C., Wasil Z., Nygård Y., Nielsen J., Frisvad J. C., Nielsen K. F., Workman M., Larsen T. O., Driessen A. J. M., Frandsen R. J. M.

5. Synthetic Biology: Methods and Protocols, Braman,J. C. (Ed.) 2018, Vol 1772, Humana Press, doi: 10.1007/978-1-4939-7795-6. Chapter: Genome editing in Penicillium chrysogenum using Cas9 Ribonucleoprotein particles. C. Pohl, L. Mózsik, A. J. M. Driessen, R. A. L. Bovenberg, Y. Nygård

6. WO2017178624 (A1) - MBTH-LIKE PROTEINS IN EUKARYOTIC NRPS-CATALYZED PROCESSES, Bovenberg, R. A. L.; Müller, U. M., Driessen, A. J. M., Pohl, C., Zwahlen, R. D. - filed Oktober 19, 2017

7. WO2016110453 (A1) - A CRISPR-CAS SYSTEM FOR A FILAMENTOUS FUNGAL HOST CELL Meijrink B.,Verwaal R., Gielesen B. E. M., Roubos J. A., Nygård Y. I., Bovenberg R. A. L., Driessen A. J. M. Pohl C. - filed November 15, 2017

8. ACS Synth Biol. 2016 Jul 15;5(7):754-64. doi: 10.1021/acssynbio.6b00082. Epub 2016 May 3. CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum. Pohl C., Kiel J.A., Driessen A.J., Bovenberg R.A., Nygård Y.

9. Fungal Biol Biotechnol. 2015 Sep 16;2:6. doi: 10.1186/s40694-015-0016-0. eCollection 2015. Unlocking the potential of fungi: the QuantFung project. Büttel Z., Díaz R., Dirnberger B., Flak M., Grijseels S., Kwon M. J., Nielsen J. C. F., Nygård Y., Phule P., Pohl C., Prigent S., Randelovic M., Schütze T., Troppens D., Viggiano A.

10. Biomed Microdevices. 2011 Jun;13(3):533-8. doi: 10.1007/s10544-011-9522-x. Development and characterization of a disposable plastic microarray printhead. Griessner M., Hartig D., Christmann A., Pohl C., Schellhase M., Ehrentreich-Förster E.

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