University of Groningen
RNA regulation in Lactococcus lactis
van der Meulen, Sjoerd Bouwe
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2018
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van der Meulen, S. B. (2018). RNA regulation in Lactococcus lactis. Rijksuniversiteit Groningen.
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RNA regulation in Lactococcus lactis
Sjoerd Bouwe van der Meulen
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UITNODIGING /
INVITATION
voor het bijwonen van de openbare
verdediging van het proefschrift:
RNA regulation in
Lactococcus lactis
van
Sjoerd Bouwe van der Meulen
op vrijdag 23 november 2018
om 11.00 uur
In de aula van het Academiegebouw
van de Rijksuniversiteit Groningen
Broerstraat 5
Na afloop bent u van harte
welkom op de receptie in het
Academiegebouw
Feest
vanaf 20.30 uur
Huis de Beurs
A-Kerkhof 4, Groningen
Paranimfen
Anne de Jong
anne.de.jong@rug.nl
Ana Solopova
anna.solopova@gmail.com
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RNA regulation in Lactococcus lactis
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The work described in this thesis was performed at the Department of Molecular Genetics, Groningen Institute for Molecular Biology and Biotechnology, Faculty of Science and Engineering, University of Groningen, the Netherlands. The studies presented in this thesis were performed within the framework of TiFN. Friesland Campina, CSK and DSM acted as industrial partners within this research project.
Printing of this thesis was financially supported by the Graduate School of Science and the University of Groningen.
Printed by Ipskamp Printing, Enschede, the Netherlands.
Cover design by Sjoerd van der Meulen and Anja Blom with charcoal on paper, representing the hands of Chris van der Meulen (left) and Richard van der Meulen (right) touching a piece of RNA. ISBN (printed): 978-94-034-1176-7
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RNA regulation in Lactococcus lactis
Proefschrift
ter verkrijging van de graad van doctor aan de Rijksuniversiteit Groningen
op gezag van de
rector magnificus prof. dr. E. Sterken en volgens besluit van het College voor Promoties.
De openbare verdediging zal plaatsvinden op vrijdag 23 november 2018 om 11.00 uur
door
Sjoerd Bouwe van der Meulen
geboren op 26 december 1983 te Sneek
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Promotor
Prof. dr. J. Kok
Beoordelingscommissie
Prof. dr. B. Poolman Prof. dr. J.M. van Dijl Prof. dr. D. van Sinderen
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CONTENTS
Chapter 1 General introduction 7
Chapter 2 Transcriptome landscape of Lactococcus lactis reveals many novel 31 RNAs including a small regulatory RNA involved in carbon uptake and metabolism
Chapter 3 Early transcriptome response of Lactococcus lactis to environmental 61
stresses reveals differentially expressed small regulatory RNAs and
tRNAs
Chapter 4 The protein regulator ArgR and the sRNA derived from the 3’-UTR 89
of its gene, ArgX, both regulate the arginine deiminase pathway in
Lactococcus lactis
Chapter 5 Target identification of the cold stress induced sRNA CisR in 113
Lactococcus lactis
Chapter 6 T-REx: Transcriptome analysis webserver for RNA-seq Expression 137 data
Chapter 7 Summary, discussion and future perspectives 149
Addendum 159
Wetenschappelijke samenvatting 163
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