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Characterization of Two Small Rnas of Streptococcus Mutans UA159

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Characterization of Two Small Rnas of Streptococcus Mutans UA159 Characterization of Two Small RNAs of Streptococcus mutans UA159 by Andrew Latos A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Dentistry University of Toronto © Copyright by Andrew Latos, 2016 Characterization of Two Small RNAs of Streptococcus mutans UA159 Andrew John Latos Master of Science, Graduate Department of Dentistry University of Toronto 2016 I. Abstract Small RNAs (sRNA) regulate several processes including metalloregulation, acid- tolerance, biofilm formation, and virulence. Streptococcus mutans UA159 is an etiological agent of dental caries. Several sRNAs were found in intergenic regions of S. mutans and two were characterized. The first characterized sRNA, SurC, was located within the loci between dnaK and dnaJ (~190 nucleotides) and was developmentally regulated. The second characterized sRNA, MrrC (~420 nucleotides), a metal responsive RNA was located between pyrG and fbaA. In THYE, there was no change observed in growth rate for either ΔSurC and ΔMrrC. In chemically defined medium, the growth rate of ΔMrrC was significantly reduced at pH 5.0 and in 4.0% ethanol. Both ΔSurC and ΔMrrC contain defects in biofilm formation, acid tolerance response, and transformation frequency. Identification of sRNAs and understanding their function within S. mutans is necessary to provide insight into the molecular control of virulence for this caries forming organism. ii II. Acknowledgments I would like to thank my supervisor, Dr. Dennis Cvitkovitch, for providing me the opportunity to perform microbial research. I appreciate the challenges, support, and guidance given during the duration of my research. I would like to thank my committee members, Dr. Tara Moriarty and Dr. Céline Lévesque for intellectually challenging me and for their mentorship. I especially thank everyone in the Cvitkovitch lab for their support throughout the duration of this project. Milos Legner, Martha Cordova, Dilani Senadheera, Gursonika Binepal, Anca Serbanescu, Kamna Singh, Marie-Christine Kean, Kirsten Krastel, and Iwona Wenderska have all provided support, friendship, and guidance throughout my project. I thank my family and friends for kindly listening to my commuting stories and supporting me. I also thank my loving wife, Dr. Janice L. Strap. Her enthusiasm inspired me to go to graduate school and live my dream of performing research. She always believed in my efforts and pushed me to live up to the family motto, “excelsior scientia”. iii Non progredi est regredi. Unknown Sator Arepo tenet opera rotas. Unknown Whatever may come And whatever may go That river's flowing Peter Brian Gabriel All is quiet on New Year's Day A world in white gets underway I want to be with you, be with you night and day Nothing changes on New Year's Day Paul David Hewson iv III. Table of Contents I. Abstract ....................................................................................................................... ii II. Acknowledgments ...................................................................................................... iii III. Table of Contents ........................................................................................................ v IV. List of Tables ............................................................................................................ viii V. List of Figures .......................................................................................................... viii VI. List of Abbreviations .................................................................................................. x 1 Literature Review ....................................................................................................... 1 1.1 Introduction ................................................................................................................... 1 1.2 Nontranscribed regions ................................................................................................ 2 1.3 Types of Transcriptionally Active Regions ................................................................. 3 1.3.1 Examples of Transcriptionally Active Regions .......................................................... 3 1.3.2 Small Proteins and Peptides ........................................................................................ 4 1.3.3 TARs Located Within Annotated Genes .................................................................... 5 1.3.4 Antisense RNA ........................................................................................................... 7 1.3.5 Riboswitches ............................................................................................................... 9 1.3.6 Small RNAs .............................................................................................................. 10 1.4 Small RNAs Form Regulatory Complexes with Proteins ........................................ 13 1.4.1 Small RNA Regulation by Hfq ................................................................................. 14 1.4.2 Small RNA Regulation Involving Transcription and Sigma Factors ....................... 15 1.5 Regulation by sRNA-mRNA Complexes ................................................................... 17 1.5.1 RyhB Iron Concentration Regulation ....................................................................... 17 1.5.2 OxyS Regulation by Oxidative Stress ...................................................................... 18 1.5.3 SgrS Regulates Glucose-Phosphate Stress ............................................................... 19 1.5.4 RNAIII Regulates Virulence Genes ......................................................................... 20 1.6 Streptococcus mutans as a Model Organism ............................................................. 21 1.6.1 The Oral Environment and S. mutans ....................................................................... 22 1.6.2 Virulence Properties of S. mutans ............................................................................. 25 1.6.3 S. mutans and Environmental Response Pathways ................................................... 28 1.6.4 Expression Studies of sRNA in S. mutans UA159 ................................................... 31 v 2 Objective and Hypothesis ........................................................................................ 35 2.1 Statement of the problem ........................................................................................... 35 2.2 General Hypothesis ..................................................................................................... 35 2.3 Primary Objectives ..................................................................................................... 35 3 Materials and Methods ............................................................................................ 36 3.1 Bacterial Strains, Growth Conditions, and Plasmids .............................................. 36 3.2 Intergenic Knockout Construction ............................................................................ 37 3.3 Isolation of RNA, Northern Blot Detection, and qRT-PCR .................................... 38 3.4 Rapid Amplification of cDNA Ends (RACE) ........................................................... 41 3.5 Transformation Assay ................................................................................................ 42 3.6 Biofilm Quantification ................................................................................................ 42 3.7 Acid Tolerance Response Assay ................................................................................. 43 3.8 Antibiotic Minimum Inhibitory Concentration Assay ............................................ 44 3.9 Growth Rate analysis .................................................................................................. 44 3.10 Statistical analyses ....................................................................................................... 45 3.11 Bioinformatics ............................................................................................................. 45 3.11.1 Inverted Repeat Searches Using EMBOSS .......................................................... 45 3.11.2 Promoter and Terminator Predictions .................................................................. 46 3.11.3 Multiple Em for Motif Elicitation (MEME) ......................................................... 46 4 Results ........................................................................................................................ 47 4.1 Identification of Transcriptionally Active Regions .................................................. 47 4.2 Analysis of SurC (smu82-83) ...................................................................................... 49 4.3 Analysis of the intergenic region between pyrG and tRNALeu19 .............................. 54 4.3.1 The expression of the TARs located within IGRpyrG-tRNALeu19 ............................ 54 4.3.2 5’ and 3’ RACE Results of IGRpyrG–tRNALeu19 ..................................................... 62 4.3.3 IGRpyrG-tRNALeu19 in Other Strains of Streptococcus mutans ............................... 65 4.3.4 Growth Under Various Stressors .............................................................................. 68 4.3.5 Growth Under Copper Stress .................................................................................... 71 4.3.6
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