Cover Page
The handle https://hdl.handle.net/1887/3151637 holds various files of this Leiden
University dissertation.
Author: Kusumawardhani, H.
Title: Solvent tolerance mechanisms in Pseudomonas putida
Issue Date: 2021-03-11
Solvent tolerance mechanisms
in Pseudomonas putida
ISBN:
Author: Hadiastri Kusumawardhani
Cover & Layout design: Raden Lerika Ratri Noorshanti, Hadiastri Kusumawardhani Printing:
Funding statement: This work is financed by Indonesian Endowment Fund for Education (LPDP), The Ministry of Finance, Indonesia (grant number 20150322022595).
Solvent tolerance mechanisms in
Pseudomonas putida
Proefschrift
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus Prof.dr.ir. H. Bijl,
volgens besluit van het College voor Promoties te verdedigen op Donderdag 11 Maart 2021
klokke 16.15 uur
door
Hadiastri Kusumawardhani
geboren te Bandung, Indonesia in 1991
Promotor: Prof. dr. J. H. De Winde
Co-promotor: Dr. Rohola Hosseini
Promotiecommissie: Prof. dr. Gilles P. van Wezel Prof. dr. Ariane Briegel Prof. dr. Nick Wierckx
Prof. dr. Miriam Agler-Rosenbaum Dr. Hermann J. Heipieper
Table of Contents
CHAPTER 1 Aim and scope of this thesis 7
Pseudomonas putida S12 as a solvent-tolerant bacterial strain 8 Scope and outline of this thesis 9
CHAPTER 2 Introduction 15
Solvent Tolerance in Bacteria: Fulfilling the Promise of the Biotech Era?
Abstract 16
Solvent tolerant bacteria are efficient biocatalysts 17 Current understanding of solvent tolerance mechanisms 18 Applications of solvent-tolerant bacteria in biocatalysis of valuable compounds 24 Synthetic biology and engineering towards advanced biocatalysts 28 Concluding Remarks and Future Perspectives 34
CHAPTER 3 47
Comparative analysis reveals the modular functional build-up of megaplasmid pTTS12 of Pseudomonas putida S12: a paradigm for transferable traits, plasmid stability and inheritance?
Abstract 48
Introduction 49
Results 50
Discussion 62
Materials and methods 65 Supplementary Materials 74
CHAPTER 4 79
A novel toxin-antitoxin module SlvT–SlvA regulates megaplasmid stability and incites solvent tolerance in Pseudomonas putida S12
Abstract 80 Importance 80 Introduction 81 Results 82 Discussion 95 Supplementary Materials 110
CHAPTER 5 121 Adaptive laboratory evolution restores solvent tolerance in plasmid-cured
Pseudomonas putida S12; a molecular analysis
Abstract 122
Introduction 123
Materials and Methods 124
Results 128
Discussion 138
Supplementary Materials 147
CHAPTER 6 157
Characterization of an AraC family transcriptional regulator Afr in Pseudomonas putida S12
Abstract 158
Introduction 159
Results 160
Discussion 166
Materials and Methods 169
CHAPTER 7 Discussion 179
Pseudomonas putida as a robust microbial host for the production of high-value chemicals 180 180 181 186 187 195 197 200 203 204
Immediate and adaptive responses are required to circumvent solvent toxicity Solvent tolerance mechanisms in Pseudomonas putida S12
Regulating solvent tolerance mechanisms Conclusion and future outlook
Summary Samenvatting Ringkasan Curriculum vitae Publications
