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A Comparative Analysis of Listeria Monocytogenes Plasmids: Presence, Contribution to Stress and Conservation

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A Comparative Analysis of Listeria Monocytogenes Plasmids: Presence, Contribution to Stress and Conservation Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2020 A comparative analysis of Listeria monocytogenes plasmids: Presence, contribution to stress and conservation Annabel Naditz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Naditz, Annabel, "A comparative analysis of Listeria monocytogenes plasmids: Presence, contribution to stress and conservation" (2020). Graduate Theses and Dissertations. 17859. https://lib.dr.iastate.edu/etd/17859 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A comparative analysis of Listeria monocytogenes plasmids: Presence, contribution to stress and conservation by Annabel Naditz A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Microbiology Program of Study Committee: Stephan Schmitz-Esser, Major Professor Gwyn Beattie James Dickson Larry Halverson Melha Mellata The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2020 Copyright © Annabel Naditz, 2020. All rights reserved. ii DEDICATION I would like to dedicate this dissertation to my son, Aidan, whose patience and kindness during my graduate career has been unfathomable. Thank you for making life a little easier and rolling with it when it was a little harder. I would also like to dedicate this to my parents and my sister, whose never-ending support kept me going, especially during the roughest times. Thanks for the food, the Kleenex, the chocolates, and grandson- sitting. iii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ...............................................................................................................v ABSTRACT .................................................................................................................................. vi CHAPTER 1. GENERAL INTRODUCTION ..............................................................................1 Background .............................................................................................................................. 1 Conservation of Plasmids in L. monocytogenes Strains .................................................. 6 Plasmids and Survival of L. monocytogenes in Food and FPEs ..................................... 9 Genetic Content of L. monocytogenes Plasmids in Relation to Stress Survival ........ 11 References ............................................................................................................................. 14 CHAPTER 2. A LARGE-SCALE SEQUENCING-BASED SURVEY OF PLASMIDS IN LISTERIA MONOCYTOGENES ...............................................................................................23 Abstract ................................................................................................................................... 23 Introduction ............................................................................................................................ 24 Materials and Methods ......................................................................................................... 27 Strain Selection ................................................................................................................ 27 Dataset Generation, BLAST Analyses and Plasmid Identification .......................... 35 Gene Content Analysis and Gene Conservation ........................................................ 37 Results and Discussion ........................................................................................................ 38 Overview of the Full Dataset .......................................................................................... 38 Summary of the Generated Dataset ............................................................................. 42 Presence of Plasmids ..................................................................................................... 43 Size Range of Plasmids ................................................................................................. 47 Overall Conservation of Plasmids ................................................................................. 49 Presence and Conservation of Stress-Response Plasmid Genes Across STs ..... 51 Conclusion ............................................................................................................................. 59 References ............................................................................................................................. 61 CHAPTER 3. PLASMIDS CONTRIBUTE TO FOOD PROCESSING ENVIRONMENT- ASSOCIATED STRESS SURVIVAL IN LISTERIA MONOCYTOGENES ST121, ST8, AND ST5 STRAINS ....................................................................................................................70 Abstract ................................................................................................................................... 70 Introduction ............................................................................................................................ 71 Materials and Methods ......................................................................................................... 74 Bacterial Strains, Growth Conditions, Plasmid Curing and Plasmid Screening .... 74 Stress Survival Assays ................................................................................................... 75 Sequence Analysis .......................................................................................................... 77 Statistical Analysis ........................................................................................................... 78 Results .................................................................................................................................... 78 Gene Content of the Analyzed Plasmids ..................................................................... 78 Survival of Wildtype Strains Compared to Plasmid-Cured Strains Without Stress Conditions ............................................................................................................. 87 iv Survival of Wildtype Strains Compared to Plasmid-Cured Strains Exposed to Stress Conditions ............................................................................................................. 88 Discussion .............................................................................................................................. 92 Conclusion ............................................................................................................................. 97 Acknowledgements ............................................................................................................... 97 References ............................................................................................................................. 97 CHAPTER 4. TRANSCRIPTOME SEQUENCING OF LISTERIA MONOCYTOGENES EXPOSED TO OXIDATIVE AND ACID STRESS REVEALS HIGH EXPRESSION OF CHROMOSOMAL AND PLASMID NON-CODING RNAS ..................................................105 Abstract ................................................................................................................................. 105 Introduction .......................................................................................................................... 106 Materials and Methods ....................................................................................................... 109 Bacterial Strains Used in this Study ........................................................................... 109 Experimental Stress Conditions .................................................................................. 109 RNA Extraction, Library Preparation, and Sequencing ........................................... 110 Sequence Analysis ........................................................................................................ 112 BLAST Methods ............................................................................................................. 112 Results and Discussion ...................................................................................................... 113 Chromosomal Gene Expression ................................................................................. 113 Chromosomal Gene Expression Changes in Response to Hydrogen Peroxide . 122 Chromosomal Gene Expression Changes in Response to Lactic Acid Treatment ........................................................................................................................ 124 σB Genes ......................................................................................................................... 129 Plasmid Gene Expression ............................................................................................ 135 Plasmid Gene Expression Changes in Response to Hydrogen
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