University of Groningen RNA regulation in Lactococcus lactis van der Meulen, Sjoerd Bouwe

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University of Groningen

RNA regulation in Lactococcus lactis

van der Meulen, Sjoerd Bouwe

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Publication date: 2018

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van der Meulen, S. B. (2018). RNA regulation in Lactococcus lactis. Rijksuniversiteit Groningen.

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Acknowledgements / dankwoord

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Acknowledgements / dankwoord

Would it be inhumane to start the acknowledgements by thanking the billions of bacterial cells that were sacrificed to enable this research? Possibly, especially since we humans tend to consider ourselves as a superior organism with unique features that are unequalled in the rest of the world. On the other hand, we humans do not have a lot more genes in comparison with for example a mouse. Actually, on this point we are beaten by corn! Also, we carry ten times more bacterial cells in our gut and other parts of our body than our own cells. And these bacteria encode in total hundred times more genes than we have ourselves! From that genetics perspective, it makes totally sense to first thank Lactococcus lactis for

its kind cooperation during this research project (at least for most of the time). A special gratitude goes to the model strain L. lactis MG1363, that received its name in the exact

same year as I did, the year 1983.

It was in the beginning of September 2007 that a meeting with professor Kok (Jan) made the fundament that resulted in a Master project and later a PhD and a Postdoc position in the group of Molecular Genetics (MolGen). The Master project on “Genomic Array Footprinting” in L. lactis was supervised by João Pinto. João, I am intensely grateful for your excellent

introduction to science and the guidance during this project. I still remember a lot of little details that were useful to construct a high number of (successful) clones for roughly the past ten years or so. With a 2.5 year employment at Bioclear BV, I returned back to MolGen for a PhD project within the TI Food and Nutrition (TIFN).

The members of the Functional Fermentation team within TIFN, directed by Michiel Kleerebezem, were located in various institutes and companies. I have always enjoyed the expert meetings that were excellently organized by Herwig Bachmann. Herwig, thanks for the helpful discussions and valuable insights! From the WUR I would like to thank Eddy Smid, Svetlana Alexeeva and my fellow PhD Maciek Spus, as well as Mariya Tarazanova, Marke Beerthuyzen and Arno Wegkamp from the NIZO. Bioinformatics support was facilitated by Roland Siezen and Michiel Wels, and Greer Wilson was always on the lookout for patentable IP. Three companies were funding partners in the TIFN project, but also contributed to the meetings. I would like to thank Paul Bruinenberg, Claire Price and Thijs Kouwen from DSM; Arjen Nauta from Friesland Campina; and Hans Brandsma, Wilco Meijer, Mariela Serrano and Ineke van Boeijen from CSK. Within MolGen, Jimmy, Anne, Harma, Akos and Jeroen made the team complete and I will certainly remember all the driving’s to Wageningen and other places.

MolGen has always felt as a very warm and welcome place to work, but also a very social one. Oscar and Jan, you are the driving forces behind this great group and I hope that the MolGen spirit will continue to thrive even in 25 years from now! The group runs along with a few experienced MolGenners. First of all Anne de Jong, thank you for the great collaboration during my time in MolGen, your Bio-IT experience was extremely helpful and I am particular proud on our T-REx tool and paper. Lately, you have become a skilled beer

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brewer and fermentation expert and I very much enjoy our brewing discussions. Our trips to Würzburg and Mexico were fantastic and I am happy that you are my paranymph! I also would like to thank Anne Hesseling for the collaboration during various proteomics courses and the valuable work on ArgX. Siger, thanks for all the technical and IT help during my time in MolGen! Also, the support of Mozes, Anna and Peter from the kitchen was very instrumental, as was the help of Manon and Jannet from the secretary.

Office 6.60, where I spent more than seven years, was by far the best of the building. You only have to take a look at the carpet to fully agree with this statement. It all started with Tom, Ana and me. Shortly after that, the burgers came, then the pizza’s (Taketo), potato pancakes (Ana), the vegetarian wraps (Amanda), various Chinese dishes (Qian and Fangfang) and finally the Aztec cake (Eduardo). Tom left for a great job in Denmark and took lots of humoristic jokes and T-shirts with him. Taketo went back to Japan and got a baby boy named Kengo. Ana went to Ireland, and took Andrius and her Axolotls with her. However Ana, I am very pleased that you come back to support me during my defense as a paranymph! Your knowledge on metabolic processes is truly amazing and our many discussions were very insightful! For all of the 6.60 roommates, thanks for trying all my liquid and solid ferments, acetic berries and other greeneries. I am sure I drop by soon, most probably at lunch time ;-) Within Molgen I started more or less together with you Lieke, both during our internships and our PhD’s. We shared labs together and I always admired your persistence and creativity. I will miss you at my defense, but that’s because the US wants to keep you there (for a reason!). Thanks for the nice time and of course for the great logo that you created for me! Former iGEM’ers were extremely popular to enter MolGen. So besides myself also Martijn, Auke, Ruud and Mirjam, with her great cakes, joined the group. In random order, I would like to name the people who I worked with and share many memories with: Jaap, Gert, Jan-Willem, Evert-Jan, Mariëlle, Andrius, Katrin, Robyn, Maarten, Anne-Stephanie, Sulman, Hein, Julio, Angel, Imke, Maike, Rutger, Yoshi, Elrike, Mikkil, Lance, Rustem, Morten, Tomas, Bogusia, Manolo, Dongdong, Wout, Stefano, Chunxu, Robin, Tariq, Ganesh, Jason, Ruben, Anna Lauxen, Irfan, Renske, Sornchai, Robin, Dimitra, Yi, Xin, Liang, Afzal, Arnoldas, Tonia, Xue, Rieza, Patricia, Fleur, Jingqui, Jingjing, David, Ard Jan, Jhonatan, Chenxi, Zhibo, Meishan, Barbara, Luiza, Claudia, Jelle, Anne-Marie, Jakob, Xinghong, Lu. I also had the honor to guide various hard working master students: Di, Blanca, Lucas, Mariëlle, Aishwarya and Koen. Thank you all for your own contributions to enable a wonderful time @MolGen for me. Tot slot wil ik graag mijn familie graag in het Nederlands bedanken. Heit en mem, bedankt voor alle steun die ik heb gehad en nog steeds ontvang. Ik waardeer enorm jullie vertrouwen in mij en alle keuzevrijheid die jullie mij hebben gegeven. Ytsje, als ik het kon had ik dit in het Fries gedaan maar hoogstwaarschijnlijk had je mij op alle woorden moeten verbeteren. Ik kan mij geen liever zusje voorstellen en ben heel blij met jou! Ik wens jou en Auke een hele mooie tijd toe samen met Germ! Mijn levenspartner Anja, het boekje is af! Je hebt alle keren dat ik het over kolonies en genen had goed doorstaan en mij er doorheen gesleept. Ik hou van jou en onze mooie jongens Chris en Richard!

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List of publications

Daszczuk A., Dessalegne Y., Drenth I., Hendriks E., Jo E., van Lente T., Oldebesten A., Parrish J., Poljakova W., Purwanto A.A., van Raaphorst, R., Boonstra, M., van Heel, A., Herber, M., van der Meulen, S.B., Siebring, J., Sorg, R.A., Heinemann, M., Kuipers, O.P., Veening, J-W. 2014. Bacillus subtilis biosensor engineered to assess meat spoilage. ACS Synthic Biology,

3:999–1002.

de Jong A., van der Meulen S.B., Kuipers O.P., Kok J. 2015. T-REx: Transcriptome analysis webserver for RNA-seq Expression data. BMC Genomics 16:663.

van der Meulen S.B., de Jong A., Kok J. 2016. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biology 13:353-366.

Tarazanova M., Beerthuyzen M., Siezen R., Fernandez-Gutierrez M.M., de Jong A., van der Meulen S.B., Kok J., Bachmann H. 2016. Plasmid Complement of Lactococcus lactis NCDO712 Reveals a Novel Pilus Gene Cluster. PloS one 11:e0167970.

van der Meulen, S.B., de Jong A., Kok J. 2017. Early Transcriptome Response of Lactococcus

lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and

tRNAs. Frontiers in Microbiology 8:1704.

Kok J., van Gijtenbeek L.A., de Jong A, van der Meulen S.B., Solopova A., Kuipers O.P. 2017. The Evolution of gene regulation research in Lactococcus lactis. FEMS Microbiol Rev

41:S220-S243.

van Tilburg A.Y., Cao H., van der Meulen S.B., Solopova A., Kuipers O.P. 2018. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell

factories. Current Opinion in Biotechnology. In revision.

van der Meulen S.B., Hesseling-Meinders A., de Jong A., Kok J. 2018. The protein regulator ArgR and the sRNA derived from the 3’-UTR of its gene, ArgX, both regulate the arginine deiminase pathway in Lactococcus lactis. Submitted.

de Jong A., van der Meulen S.B., Kok J., Kuipers O.P. 2018. GSEA-Pro: web-server for Gene Set Enrichment Analysis of Prokaryotes. In preparation.

van der Meulen S.B., Giesbers K., Ravi A., de Jong A., Kuipers O.P. 2018. Heterologous expression and modification of antimicrobial peptides from eukaryotes in Lactococcus lactis. In preparation.

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Stellingen behorend bij het proefschrift

“RNA regulation in Lactococcus lactis”

door Sjoerd Bouwe van der Meulen

1. Lactococcus lactis MG1363 harbors hundreds of uncharacterized sRNAs that

potentially act as small regulatory RNAs (Chapter 2).

2. 5’-Enrichment of primary transcripts in combination with RNA sequencing is

a powerful technique providing an enormous amount of new research leads (Chapter 2).

3. A 5-minute exposure to various stress conditions changes the transcriptome

dramatically and could be used profitably in future culture handling (Chapter 3).

4. The expression and function of ArgX suggest that the primary use of arginine by

L. lactis might be as a carbon and energy source (Chapter 4).

5. Finding targets for novel sRNAs is a challenging endeavor and can result in

contradicting results (Chapter 5).

6. Analyzing large RNA sequencing data sets does not require a lot of time and

statistical knowledge, if one uses the proper tool (Chapter 6).

7. Since the L. lactis genome does not encode the RNA binding proteins HfQ and

ProQ, an alternative sRNA chaperone is yet to be discovered (this thesis).

8. The moment we stop innovating, we stop living (Joel Salatin/Addendum this

thesis).

9. Changing locus tags in L. lactis MG1363 by NCBI in 2015 is like changing city

names without changing the signs. That is why no new locus tags have been used throughout this thesis.

10. Printing this thesis was an excellent way of storing CO2, in contrast to online

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