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Michael Barber Centre for Mass Spectrometry Partition and turnover of glutathione reductase in Saccharomyces cerevisiae: a proteomic approach. A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2011 Narciso Alves Silva Couto Michael Barber Centre for Mass Spectrometry School of Chemistry ___________________________________________________________________________ Table of Contents Table of Contents 2 List of Abreviations 5 Abstract 7 Declaration 8 Copyright statement 9 Acknowledgements 10 Chapter I – Introduction 11 1 – Introduction to cell biology of Saccharomyces cerevisiae 11 1.1 – Yeast as a model organism 11 1.2 – Post-genomic era: gene and protein function 11 1.3 – Yeast mitochondrion: morphology and functional role in the cell 14 1.4 – How mitochondria import proteins 15 1.5 – Protein isoforms in yeast 17 1.6 – The mitochondrial proteome of Saccharomyces cerevisiae 18 1.7 – Oxidative processes and antioxidant pathways in eukaryotic cells 19 1.7.1 – Reactive oxygen species (ROS) and reactive nitrogen species (RNS) 19 1.7.2 – Sources of reactive oxygen species: endogenous and exogenous 20 1.7.3 – Anti-oxidant protection: enzymes and small molecules 21 1.7.4 – Cellular damage occurring due to ROS 22 1.7.5 – Changes in mitochondrial antioxidant defences: apoptosis and ageing 23 1.8 – Protein turnover in yeast 24 1.9 – Glutathione reductase in yeast cells 24 1.10 – Aims and objectives 27 1.11- References 27 Chapter II – Introduction 34 2 – Experimental technologies in proteomics 34 2.1 – From genomics to proteomics 34 2.2 – Separation tools for comprehensive studies of proteins 35 2.2.1 – Electrophoretic techniques 36 2.2.1.1 – Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) 36 2.2.1.2 – Detection of proteins after gel electrophoresis 37 2.2.2 – Chromatographic techniques 38 2.2.2.1 – Reverse phase (RP) chromatography 38 2.2.2.2 – Ion exchange chromatography 39 2.2.2.3 – Affinity chromatography 40 2.2.3 – Western blotting 43 2 ___________________________________________________________________________ 2.3 – Mass spectrometry in proteomics 44 2.3.1 – Ionisation source 44 2.3.1.1 – Matrix-assisted laser desorption/ionisation (MALDI) 45 2.3.1.2 – Electrospray ionisation (ESI) 46 2.3.2 – Mass analyser 49 2.3.2.1 – Time of flight (ToF) 50 2.3.2.2 – Quadrupole mass filter 52 2.3.2.3 – Quadrupole ion trap 54 2.3.3 – Detector 57 2.3.4 – Tandem mass spectrometry (MS/MS) 58 2.3.4.1 – Activation methods in tandem mass spectrometry 58 2.3.4.1.1 – Collision induced dissociation (CID) 59 2.3.4.1.2 – Electron transfer dissociation (ETD) 60 2.3.4.2 – Types of tandem mass spectrometry experiments 61 2.3.4.3 – Tandem mass spectrometry in a MALDI-ToF/ToF instrument 62 2.3.5 – Ion mobility mass spectrometry 63 2.3.6 – Peptide fragmentation in mass spectrometry 64 2.3.7 – Response factors in MALDI and ESI 72 2.3.7.1 – Access to gas-phase properties 72 2.3.7.2 – The kinetic method 73 2.4 – Proteome analysis: ―top-down‖ and ―bottom-up‖ strategies 74 2.5 – Quantitative proteomics by mass spectrometry 75 2.6 – Bioinformatics tools 78 2.7 – References 79 Chapter III – MALDI mass spectrometric response factors of peptides generated 95 using different proteolytic enzymes 3.1 – Introduction 95 3.2 – Experimental 98 3.3 – Results and discussion 103 3.4 – Conclusions 124 3.5 – References 124 Chapter IV – Mass spectrometric analysis of the cytosolic and the mitochondrial 128 glutathione reductase isoforms from baker’s yeast. 4.1 – Introduction 128 4.2 – Experimental 130 4.3 – Results and discussion 141 4.4 – Conclusions 166 4.5 – References 167 Chapter V – Proteomics strategies to determine glutathione reductase turnover 171 in both cytosolic and mitochondrial compartments of the yeast cells 3 ___________________________________________________________________________ 5.1 – Introduction 171 5.2 – Experimental 172 5.3 – Results and discussion 175 5.4 – Conclusions 185 5.5 – References 185 Chapter VI – The membrane vesicles and matrix sub-proteomes of 187 Pseudomonas aeruginosa PAO1 biofilms. 6.1 – Introduction 187 6.2 – Experimental 190 6.3 – Results and discussion 192 6.4 – Conclusions 229 6.5 – References 230 Chapter VII – Summary and conclusions 237 7.1 – Summary and conclusions 237 7.5 – References 241 Curriculum vitae 242 4 ___________________________________________________________________________ List of Abreviations 1D One-dimensional 2D Two-dimensional AC Alternating current ATP Adenosine-5'-triphosphate BSA Bovine serum albumin CI Chemical ionisation CID Collision induced dissociation Da Dalton DC Direct current DNA Deoxyribonucleic acid DTT Dithiothreitol EDTA Ethylenediaminetetraacetic acid ESI Electrospray ionisation ETD Electron-transfer dissociation FA Formic acid FAB Fast atom bombardment FADH2 Flavin adenine dinucleotide, reduced form FT-ICR Fourier transform ion cyclotron resonance HCT High capacity trap HPLC High-performance liquid chromatography ICAT Isotope-coded affinity tagging IEF Isoelectric focusing IgG Immunoglobulin G IMAC Immobilised metal ion affinity chromatography iTRAQ Isobaric tag for relative and absolute quantitation LC Liquid chromatography LC-MS Liquid chromatography on-line with mass spectrometry m/z Mass to charge ratio MALDI Matrix-assisted laser desorption/ionisation MORF Moveable open reading frame MRM Multiple reaction monitoring mRNA Messenger RNA MS Mass spectrometry MS/MS Tandem mass spectrometry mtRNA Mitochondrial messenger RNA Mw Molecular weight NADH Nicotinamide adenine dinucleotide NADPH Nicotinamide adenine dinucleotide phosphate pI Isoelectric point PMF Peptide mass fingerprinting ppm Parts per million PSD Post-source decay 5 ___________________________________________________________________________ PTM Post-translational modification QconCAT Quantification conCATamers Q-ToF Quadrupole time-of-flight RF Radio frequency RNA Ribonucleic acid RNS Reactive nitrogen species ROS Reactive oxygen species RP Reverse phase rpm Revolutions per minute SCX Strong cation exchange SDS-PAGE Sodium dodecyl sulfate polyacrylamide gel electrophoresis, SILAC Stable isotope labelling by amino acids in cell culture TAP Tandem affinity purification TCA Tricarboxylic acid TFA Trifluoroacetic acid ToF Time-of-flight tRNA Transfer RNA UV Ultraviolet YPD Yeast proteome database Saccharomyces cerevisiae genes are referred to be a three letters mnemonic followed by a number and are capitalised. Protein gene product is named according to the gene with the first letter capitalised. 6 ___________________________________________________________________________ Abstract The main work presented in this thesis describes proteomics strategies applied to study the trafficking and turnover of glutathione reductase (Glr1) isoforms in the cytosol and mitochondria of Saccharomyces cerevisiae. Additional work was performed in order to understand mass spectrometric response factors and how they can affect peptides representation in the mass spectra. The opportunity to study two sub proteomes involved in biofilm formation of Pseudomonas aeruginosa PAO1 arose during my PhD and their analysis is also presented. Glr1 is a low abundant protein involved in the defence mechanisms against reactive oxygen species, which are sources of many diseases. Because of its biological relevance, considerable effort has been made in order to understand its functional role in the cell. This protein has been studied using biochemical strategies. In yeast, the cytosolic and mitochondrial forms of glutathione reductase are expressed by the same gene, GLR1, using alternative start codons. Translation from the first AUG codon generates the mitochondrial form incorporating a transit peptide necessary for import into the mitochondria. If the translation starts at the second AUG codon, the cytosolic counterpart is generated. Biochemical approaches show that the first AUG codon is not in favourable context and it has been suggested that leaky scanning accounts for the abundance of the cytosolic protein. The analysis of Glr1 forms by mass spectrometry was demanded because only the N-terminal region is informative about similarities and differences between cytosolic and mitochondrial forms. The protein is also of low abundance in both cytosol and mitochondrial compartments. A genetically modified strain, over-expressing this protein was, therefore, used throughout this work in order to analyse glutathione reductase in the mitochondria. This was not possible with the wild-type strain. Because the first AUG codon is now in context, the over-producing strain (MORF) yields both cytosolic and full length mitochondrial isoforms in the cytosol. Analysis of the mitochondrial protein shows that the cleavage of the pre-sequence is not specific. Three different forms of the mitochondrial N-terminal peptide were detected. Some attention was also devoted to glutathione reductase turnover in both cytosol and mitochondrial compartments using the genetically modified strain. Both N-terminal peptides generated from translation starting in the first and second AUG codon as well as mid-chain peptides from the cytosol fraction and one mid-chain peptide from the mitochondrial fraction, were used to calculate relative turnover measurements. My results illustrate that the mitochondrial protein is in faster turnover than the cytosolic counterpart. Moreover, the long and short forms observed in the cytosol also show slightly different turnover rates, the long form presenting faster turnover than the short form. Rapid turnover
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