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Small RNA Sibling Pairs Ryfa and Ryfb in Shigella Dysenteriae and Their Impact On

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Small RNA Sibling Pairs Ryfa and Ryfb in Shigella Dysenteriae and Their Impact On Small RNA Sibling Pairs RyfA and RyfB in Shigella dysenteriae and their Impact on Pathogenesis A dissertation presented to the faculty of the College of Arts and Sciences of Ohio University In partial fulfillment of the requirements for the degree Doctor of Philosophy Megan E. Fris August 2018 © 2018 Megan E. Fris. All Rights Reserved. 2 This dissertation titled Small RNA Sibling Pairs RyfA and RyfB in Shigella dysenteriae and their Impact on Pathogenesis by MEGAN E. FRIS has been approved for the Department of Biological Sciences and the College of Arts and Sciences by Erin R. Murphy Associate Professor of Bacteriology Joseph Shields Interim Dean, College of Arts and Sciences 3 ABSTRACT FRIS, MEGAN E., Ph.D., August 2018, Biological Sciences Small RNA Sibling Pairs RyfA and RyfB in Shigella dysenteriae and their Impact on Pathogenesis Director of Dissertation: Erin R. Murphy Understanding molecular mechanisms which regulate bacterial virulence is essential for discovering new therapeutics. Alarmingly, some bacterial species are already unresponsive to antibiotic cocktails, and in the case of Shigella dysenteriae, will up- regulate virulence factors under the duress of antibiotic treatment. While molecular mechanisms involving the regulation of S. dysenteriae pathogenesis have been studied, many are still unknown, especially those of which are mediated by RNA. Ribo-regulators that have been characterized in Shigella, and published to date, have all been shown to impact virulence processes. Many other sRNAs have been discovered in Shigella and E. coli, yet, remain uncharacterized. One sRNA of interest, RyfA, was originally discovered in Escherichia and found to have nearly exact sequence identity to that of RyfA in Shigella flexneri. Interestingly, in S. dysenteriae, 95% identical twin copies of RyfA, designated RyfA1 and RyfA2 exist in tandem. Intriguingly, ryfA1-like copies of the gene are only found in pathogenic species of Escherichia and all species of Shigella. Non- pathogenic species of Escherichia contain a ryfA2-like copy. Upstream of both RyfA1 and RyfA2, additional sRNAs exist, termed RyfB1 and RyfB2. While RyfB1 and RyfB2 are only 60% identical to each other they each share large amounts of complementarity to RyfA1 and RyfA2 respectively, suggesting that these molecules may interact with each 4 other and thus one sRNA may regulate the abundance and/or activity of the other. Indeed, overexpression of RyfB1 leads to reduced levels of RyfA1 in the bacterial cell but has no effect on the levels of RyfA2. Unexpectedly, it was it was found that RyfB2 alters the abundance of both RyfA1 and RyfA2 when produced in S. dysenteriae. Furthermore, overproduction of RyfA1 slightly inhibits RyfA2 levels, while RyfA2 overproduction strongly inhibits RyfA1 levels. In summary, sRNAs RyfA2, RyfB2, and RyfB1 all function to include tight control over RyfA1. The overproduction of RyfA1 results in a lack of cell to cell spread in S. dysenteriae, suggesting the number of sRNAs regulating RyfA1 is critical for optimal regulation. Lastly, overproduction of RyfB2 in S. dysenteriae results in increased plaque number. The complex interplay between these sRNAs is likely important for fine-tuned regulation of invasion and virulence in S. dysenteriae. Downstream targets of RyfA1 and RyfA2 may shed some light on genes/proteins impacted resulting in the above described phenotypes. 5 DEDICATION Dedicated to Matt, my sister Sarah, and my parents Anna, and Will for encouraging hard work and not sweating the small stuff. 6 ACKNOWLEDGMENTS Special thanks to Michelle Pate, for the technical help, assistance, and unmatched organizational skills. Thank you to Erin Murphy for her invaluable mentorship. I would also like to thank my committee members Ronan Carroll, Peter Coschigano, and Sarah Wyatt for the useful discussion, feedback, and occasional technical assistance. Additionally, a thank you to the NIH for financial support and Ohio University for laboratory space and equipment. 7 TABLE OF CONTENTS Page Abstract ............................................................................................................................... 3 Dedication ........................................................................................................................... 5 Acknowledgments............................................................................................................... 6 List of Tables ...................................................................................................................... 9 List of Figures ................................................................................................................... 10 Chapter 1: Riboregulators: Fine-Tuning Virulence in Shigella ........................................ 12 1.1 Abstract ................................................................................................................... 12 1.2 Introduction ............................................................................................................. 12 1.2.1 CsrB and CsrC ................................................................................................. 16 1.2.2 RyhB ................................................................................................................ 18 1.2.3 RnaG ................................................................................................................ 20 1.2.4 ShuA ................................................................................................................ 21 1.3 Discussion ............................................................................................................... 23 Chapter 2: Sibling sRNA RyfA1 Influences Shigella dysenteriae Pathogenesis ............. 25 2.1 Introduction ............................................................................................................. 25 2.2 Materials and Methods ............................................................................................ 28 2.3 Results ..................................................................................................................... 37 2.3.1 Twin copies of RyfA are produced by Shigella dysenteriae ............................ 37 2.3.2 The presence of a ryfA1-like gene is associated with pathogenicity ............... 42 2.3.3 RyfA1 impacts virulence in Shigella dysenteriae ............................................ 44 2.3.4 Overproduction of RyfA1 leads to inhibition of cell-to-cell spread by Shigella dysenteriae ................................................................................................................ 47 2.3.5 RyfA1 overproduction results in elimination of ompC, a transcript encoding a major outer membrane protein .................................................................................. 49 2.3.6 Regulation of RyfA1 by RyfB1 ....................................................................... 50 2.3.7 RyfA1 does not encode a small protein under conditions tested ..................... 53 2.3.8 RyfB1 Overproduction does not influence plaque formation or ompC ........... 56 2.4 Discussion ............................................................................................................... 57 Chapter 3: RyfA2 and RyfB2 ........................................................................................... 62 8 3.1 Abstract ................................................................................................................... 62 3.2 Methods .................................................................................................................. 62 3.3 Introduction ............................................................................................................. 63 3.3 Results ..................................................................................................................... 64 3.3.1 RyfA2 overproduction does not affect plaquing of Shigella dysenteriae ........ 64 3.3.2 RyfB2 overproduction increases plaquing ability of Shigella dysenteriae ...... 66 3.3.3 RyfB2 inhibits RyfA2 levels ............................................................................ 68 3.3.4 Swapping the RyfB2 putative interaction site ................................................. 70 3.3.5 RyfB2 influences RyfA1 levels ....................................................................... 73 3.3.6 Other sRNA interactions .................................................................................. 75 3.4 Discussion ............................................................................................................... 77 Chapter 4: Downstream Targets of RyfA1 and RyfA2 .................................................... 81 4.1 Abstract ................................................................................................................... 81 4.2 Material and Methods ............................................................................................. 81 4.3 Introduction ............................................................................................................. 83 4.4 Results ..................................................................................................................... 85 4.4.1 Transcriptome of RyfA1 and RyfA2 ............................................................... 85 4.4.2 Proteome of RyfA1 and RyfA2 ....................................................................... 89 4.5 Conclusions and Discussion ..................................................................................
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