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Quantitative proteomics of food pathogenic Bacilli - a quest for biomarkers Stelder, S.K.
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Citation for published version (APA): Stelder, S. K. (2016). Quantitative proteomics of food pathogenic Bacilli - a quest for biomarkers
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Download date: 20 Jan 2017
Quantitative proteomics of food pathogenic Bacilli – a quest for biomarkers
Quantitative proteomics of food pathogenic Bacilli – a quest for biomarkers Sacha K. Stelder
UITNODIGING U bent van harte uitgenodigd voor de openbare verdediging van mijn proefschrift: Quantitative Proteomics of Food Pathogenic Bacilli - A Quest for Biomarkers Op dinsdag 31 mei 2016 om 16:00 uur in de Agnietenkapel Oudezijds Voorburgwal 231 Amsterdam Receptie aansluitend in de Agnietenkapel.
Sacha Stelder 06 45992393
[email protected]
Paranimfen
Sacha K. Stelder
Reuben Smith 06 46402842
[email protected] Pascal van Alphen 06 29071812
[email protected]
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Processed on: 22-4-2016
proteomics of Quantitative food pathogenic Bacilli – a quest for biomarkers
Sacha K. Stelder
Quantitative proteomics of food pathogenic Bacilli - a quest for biomarkers Sacha K. Stelder Design by Remco de Vries Copyright © 2016 Sacha K. Stelder All rights reserved. No part of this publication may be reproduced in any form without the express permission of the author, or where appropriate, the publisher involved.
Quantitative proteomics of food pathogenic Bacilli – a quest for biomarkers
ACADEMISCH PROEFSCHRIFT
ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam RSJH]DJYDQGH5HFWRU0DJQLÀFXV prof. dr. D.C. van den Boom ten overstaan van een door het College voor Promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel op dinsdag 31 mei 2016 te 16:00 uur door Sacha Kai Stelder geboren te Amsterdam
Promotiecommissie
Promotores: Copromotor: Overige leden:
Prof. dr. S. Brul, Universiteit van Amsterdam Prof. dr. C.G. de Koster, Universiteit van Amsterdam Dr. L.J. de Koning, Universiteit van Amsterdam Prof. dr. A. Driks, Loyola University Chicago Prof. dr. M. Wuhrer, Leids Universitair Medisch Centrum Prof. dr. T. Abee, Wageningen University and Research centre Prof. dr. O.P. Kuipers, Rijksuniversiteit Groningen Prof. dr. ir. P.J. Schoenmakers, Universiteit van Amsterdam Prof. dr. A.K. Smilde, Universiteit van Amsterdam Prof. dr. L.W. Hamoen, Universiteit van Amsterdam
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
“I think you’ll find it’s a bit more complicated than that” – Ben Goldacre
Table of contents
Abbreviations
8
Chapter 1
General Introduction
9
Chapter 2
7HPSHUDWXUHGHSHQGHQFHRIWKHSURWHRPHSURÀOHRI23 the psychrotolerant pathogenic food spoiler Bacillus weihenstephanensis type strain WSBC 10204
Chapter 3
Sporulation temperature dependence of the spore coat proteome of Bacillus weihenstephanensis
37
Chapter 4
Stoichiometry and absolute abundance of proteins in the Bacillus cereus spore insoluble fraction determined using a QconCAT approach
47
Chapter 5
Proteome wide localisation analysis: 63 CotE dependent proteins in the Bacillus cereus spore insoluble fraction
Chapter 6
Contributions and Recommendations
75
References
81
Published work
95
Summary
97
Samenvatting
99
Acknowledgements
101
Funding information
This thesis is part of NanoNextNL, a micro and nanotechnology innovation consortium of the Government of the Netherlands and 130 partners from academia and industry. More information on www.nanonextnl.nl.
Abbreviations SASP DPA SDS-PAGE 2D-DIGE MS MS/MS LC LC-FT-ICR MS/MS PSM SWATH DDA HP 3$, SILAC L75$4 TMT $48$ QconCAT &'*6 rDNA PCR tRNA rRNA LR-PCR CFU CDS TIGR TCA Hbl Nhe 0XG3,7 SPR
8
Small Acid Soluble Protein Dipicolinic Acid Sodium Dodecyl Sulphate – Polyacrylamide Gel Electrophoresis Two-dimensional – Differential Gel Electrophoresis Mass Spectrometry Tandem Mass Spectrometry Liquid Chromatography Liquid chromatography – Fourier Transform – Ion Cyclotron tandem Mass Spectrometry Peptide Spectrum Matches Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra Data Dependent Acquisition H[SRQHQWLDOO\PRGLÀHG 3URWHLQ$EXQGDQFH,QGH[ Stable Isotope Labelling by Amino acids in Cell culture LVREDULF7DJVIRU5HODWLYHDQG$EVROXWH4XDQWLÀFDWLRQ Tandem Mass Tags $EVROXWH4XDQWLÀFDWLRQ Quantitative concatemer &KHPLFDOO\'HÀQHG*URZWKDQG6SRUXODWLRQPHGLXP ribosomal Deoxyribonucleic Acid Polymerase Chain Reaction transfer Ribonucleic Acid ribosomal Ribonucleic Acid Long Range Polymerase Chain Reaction Colony Forming Units coding sequence The Institute for Genomic Research Tricarboxylic acid haemolysin BL non-haemolytic enterotoxin 0XOWLGLPHQVLRQDO3URWHLQ,GHQWLÀFDWLRQ7HFKQLTXH Surface Plasmon Resonance