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Comparison of Cellular, Surface and Secreted Proteins Produced During Starvation and Acid Stress Conditions for Lactobacillus Casei Using Proteomics

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Comparison of Cellular, Surface and Secreted Proteins Produced During Starvation and Acid Stress Conditions for Lactobacillus Casei Using Proteomics Comparison of Cellular, Surface and Secreted Proteins Produced During Starvation and Acid Stress Conditions for Lactobacillus casei Using Proteomics By Syed Shahzad Shah BSc (Hons) Agriculture, MSc (Hons) Food Technology Supervisors Prof. Margaret L. Britz Assoc. Prof John P. Bowman Dr. Anthony L. Baker A thesis Submitted in fulfilment of the requirements for the Doctor of Philosophy University of Tasmania, School of Land and Food, February, 2018 Statements and Declarations Declaration of Originality ‘This thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in the thesis, and to the best of my knowledge and belief no material previously published or written by another person except where due acknowledgement is made in the text of the thesis, nor does the thesis contain any material that infringes copyright.’ Syed Shahzad Shah February, 2018 ii Statement on Authority of Access to the Thesis The authority of access statement should reflect any agreement which exists between the University and an external organisation (such as a sponsor of the research) regarding the Work: “There are no agreements between the University and any external organisation regarding work reported in this thesis so the thesis may be made available for loan and limited copying and communication in accordance with the Copyright Act 1968”. Syed Shahzad Shah February, 2018 iii Statement on Published Work The abstract based on Chapter 4 has been published in scientific tracts and abstract book of “International Conference on Food Microbiology” August 08-10, 2016 Birmingham, UK (J Food Process Technol 2016, 7:9 Suppl.). Copyright is held by the publisher over the contents of the abstract which describes some of the data reported in Chapter 4 of this thesis and access to the published contents of the abstract should be sought from respective publisher. Non-published thesis content may be made available on loan basis in accordance with Copyright Act 1968. Syed Shahzad Shah February, 2018 iv Statement of Co-Authorship This thesis comprises published/non-published contents. The details of proportion of co- authors is given as under. Chapter 1: Syed Shahzad Shah (60%), Anthony Baker (10%), Margaret Britz (25%), John Bowman (5%) Chapter 2: Syed Shahzad Shah (60%), Anthony Baker (20%), Margaret Britz (15%), John Bowman (5%) Chapter 3: Syed Shahzad Shah (60%), Richard Wilson (2%), Noel Davies (2%), David Nichols (2%), Margaret Britz (29%), John Bowman (5%) Chapter 4: Syed Shahzad Shah (60%), Richard Wilson (5%), John Bowman (5%), Margaret Britz (30%), Chapter 5: Syed Shahzad Shah (60%), Margaret Britz (35%), John Bowman (5%) Chapter 6: Syed Shahzad Shah (60%), Margaret Britz (40%) Syed Shahzad Shah (PhD candidate) made a major contribution in performing experiments related to the research, proteomic data analysis, results interpretation and thesis write up under close guidance of supervisors, co-supervisors and researchers of CSL staff. Dr. Anthony Baker, co-supervisor from Food Innovation and Safety Centre of University of Tasmania (Australia), provided laboratory support, advised in conduct of experiments related to Chapter 3 and literature review. Adu Titus (PhD candidate) conducted sample preparation for extracellular fluid sample preparation (Chapter 4) and Akhikun Nahar (PhD candidate) assisted in sample preparation step for fatty acid analysis of whole cells (Chapter 4 & 5) however they did not contribute in authorship. v Dr. Jay Kocharunchitt Food Innovation and Safety Centre of University of Tasmania (Australia) assisted in explaining T profiler and heat map generation of one proteomic data set however he did not contribute in authorship. Dr. Richard Wilson from the Central Science Laboratory of University of Tasmania (Australia) provided support in explaining the software used for data analysis and writing method section (Chapter 2) for database searching criteria for protein identification and analysis by nanoLC-MS/MS. Dr. Noel Davies from the Central Science Laboratory of University of Tasmania (Australia) analysed and provided data on fermentation end-products analysis by GC/MS and glycerol analysis by UPLC (Chapter 2 & 4). Dr. David Nichols from the Central Science Laboratory of University of Tasmania (Australia) analysed and provided the table on whole cell fatty acid analysis by GC- MS/MS (Chapter 2 & 4). Dr. John Bowman, co-supervisor from the Food Innovation and Safety Centre, University of Tasmania (Australia) contributed in data analysis and proteomics data interpretation guidance related to the research. Prof. Margaret Britz (Principal Supervisor) from Food Innovation and Safety Centre, University of Tasmania (Australia) provided major input as a supervisor in experimental design planning, data analysis, interpretation of the results and research planning/implementation and extensive reviews of several drafts of the whole thesis. The undersigned hereby agree with the above-mentioned work and proportion of work undertaken for this thesis: (Prof. Margaret Britz) (Prof. Holger Meinke) Principal supervisor Head of School/Director Tasmanian Institute of Agriculture Tasmanian Institute of Agriculture University of Tasmania, Australia University of Tasmania, Australia February, 2018 vi Acknowledgments I would like to acknowledge the hard work, dedication and continuous support provided by Principal Supervisor Prof. Margaret Britz (Former Dean, SET, University of Tasmania) who provided vision to complete the research project. My special thanks are for Co-Supervisors Assoc. Prof. John P. Bowman (Leader of the Food Safety and Innovation Center) and Dr. Anthony L. Baker (Operations Manager, TIA and School of Land and Food) who provided technical knowledge and excellent research based laboratory facilities throughout studies at (UTAS). This work was only possible due to wisdom, leadership, in-depth subject based discussions and suggestions of the research group and Supervisory Team. In particular, I am thankful to Prof. Britz who played a key central role in all operational and research activities regardless of the time constraints and busy meeting schedules. Services of the Central Science Laboratory of UTAS is highly acknowledged in provision of latest research equipment and technical expertise to conduct proteomics and biochemical sample analysis by a Team of experts: Dr. Richard Wilson, Assoc/Profs Noel Davies, David Nichols. Useful tips given by Richard Wilson and John Bowman in proteomic data analysis helped in organising complex proteomic data set in a meaningful way. Prof. Britz has provided a very deep insight to handle the proteomics data in so many different angles to get meaningful results and underpin novel areas of the research. I am extremely thankful to Michelle Williams, Lauri Parkinson, Dr. Jay Kocharunchitt, Dr. Shane M. Powell, sincere appreciation also goes to Prof. David Ratkowsky, Assoc. Prof. Tom Ross, Prof. Tom McMeekin, Adam Smolenski, and all other members of the Food Safety and Innovation Centre and Tasmanian Institute of Agriculture (TIA) to help me all the times on academic and social matters. I also would like to thank Dr. Richard Wilson and Assoc/Prof Noel Davies from Central Science Laboratory, University of Tasmania for the technical assistance. I appreciate support of my seniors and all colleague, Ali, Kevin, Akhikun, Adu, Bianca, Ibrahim, Mona, Wossen, Pei Pei and Kaniz. The PhD scholarship provided by UTAS enabled me to meet research and living expenses during my studies for which I am extremely grateful. vii I dedicate this thesis to my loving father Engr. (Late) Syed Ahmed Shah and my loving mother (Late) Naseem Kokab who always encouraged me for higher studies. My special thanks and appreciation is for my loving wife, Hina Shahzad and my cute daughters: Amina Shahzad and Mina Shahzad, who never kept me alone and always supported me in my life. I also acknowledge my all brothers, sisters, cousins, uncles and aunts for their love. viii TABLE OF CONTENTS Title Page……………………………………………………………………………………………………………………………i Statements and Declarations……………………………………………………………………………………………..ii Statement on Authority of Access to the Thesis………………………………………………………………..iii Statement on Published Work……………………………………………………………………………………………iv Statement of Co-Authorship……………………………………………………………………………………………….v Acknowledgments ……………………………………………………………………………………………………………vii Table of Contents………………………………………………………………………………………………………………viii List of Abbreviations ………………………………………………………………………………………………………….xv Abstract…………………………………………………………………………………………………………………………….xvii Appendices ………………………………………………………………………………………………………………………..xxi CHAPTER 1: Introduction and literature review ................................................................................ 1 1.1 Introduction to lactic acid bacteria ................................................................................. 1 1.1.1 The genus Lactobacillus and its salient features................................................................. 1 1.2 Identification of Lactobacillus ....................................................................................................... 2 1.2.1 Phenotypic characterisation ............................................................................................... 2 1.2.2 Molecular characterisation ................................................................................................. 3 1.3 Industrial importance
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