University of Groningen
Quantifying the transcriptome of a human pathogen
Aprianto, Rieza
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2018
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Aprianto, R. (2018). Quantifying the transcriptome of a human pathogen: Exploring transcriptional
adaptation of Streptococcus pneumoniae under infection-relevant conditions. Rijksuniversiteit Groningen.
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QUANTIFYING
THE TRANSCRIPTOME
OF A HUMAN
PATHOGEN
Quantifying the transcriptome of a human pathogen
Exploring transcriptional adaptation of Streptococcus pneumoniae under infection-relevant conditions
The scientific studies presented in the thesis were performed in the Molecu-lar Genetics group of the Groningen BiomolecuMolecu-lar Sciences and Biotechnol-ogy Institute, Faculty of Science and Engineering, University of Groningen, The Netherlands. The studies were financially supported by the European Research Council (ERC) Starting Grant awarded to Jan-Willem Veening. Printing was supported by the Graduate School of Science and Engineer-ing and the University Library of the University of GronEngineer-ingen.
ISBN: 978-94-034-0759-3
978-94-034-0760-9 (ebook) Printing: Eikon +
Cover & layout: Lovebird design.
www.lovebird-design.com
© R. Aprianto, Groningen, the Netherlands, 2018
All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, without written permission of the author.
Quantifying the transcriptome of
a human pathogen
Exploring transcriptional adaptation of Streptococcus pneumoniae under infection-relevant conditions
PhD thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. E. Sterken
and in accordance with the decision by the College of Deans. This thesis will be defended in public on
Friday, 13 July 2018 at 14.30 hours
by
Rieza Aprianto
born on 12 April 1986 in Bandung, Indonesia
Supervisors
Prof. J.-W. Veening Prof. O.P. Kuipers
Assessment Committee
Prof. M. Heinemann Prof. J.M. van Dijl Prof. N. van Sorge
Quantifying the transcriptome of
a human pathogen
Exploring transcriptional adaptation of Streptococcus pneumoniae under infection-relevant conditions
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 13 juli 2018 om 14.30 uur
door
Rieza Aprianto
geboren op 12 april 1986 te Bandung, Indonesië
Promotores
Prof. J.-W. Veening Prof. O.P. Kuipers
Beoordelingscommissie
Prof. M. Heinemann Prof. J.M. van Dijl Prof. N. van Sorge
O Sapientia, quae ex ore Altissimi prodiisti, attingens a fine usque ad finem,
fortiter suaviterque disponens omnia: veni ad docendum nos viam prudentiae.
Table of Contents
CHAPTER 1
Introduction 13
CHAPTER 2
Deep genome annotation of the opportunistic human pathogen
Streptococcus pneumoniae D39 27
CHAPTER 3
High-resolution analysis of the pneumococcal transcriptome
under a wide range of infection-relevant conditions 67
CHAPTER 4
Bright fluorescent Streptococcus pneumoniae for live-cell imaging of host-pathogen interactions 97
CHAPTER 5
Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during
early infection 127
CHAPTER 6
Discussion and future perspective 163
