First Advisor

Justin Courcelle

Term of Graduation

Summer 2021

Date of Publication


Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Biology






Non-coding RNA, Oxidative stress, Streptococcus mutans, Gene expression



Physical Description

1 online resource (vi, 193 pages)


Non-coding small RNAs (sRNAs) are ubiquitous post-transcriptional regulators found in both gram-negative and gram-positive bacteria. Despite their integral role in many regulatory pathways, including those that facilitate stress-tolerance, little is known about the evolutionary forces that drive the emergence of novel sRNAs, how prevalent sRNAs are within bacterial species, or the functions of a majority of these transcripts. In this work, I first describe the evolution of OxyS, a well-characterized sRNA in gram-negative Enterobacteriaceae that is involved in coordinating the bacterial response to oxidative stress. Next, I identify novel sRNAs differentially produced by the gram-positive oral pathogen Streptococcus mutans in response to multiple stress conditions. Finally, I investigate the function of one novel sRNA, SmsR4, in fine-tuning sugar-alcohol metabolism in S. mutans. These findings reveal protein coding genes to be a new reservoir for sRNA emergence and define a novel evolutionary path through which new sRNAs become incorporated into regulatory networks. Additionally, I show evidence for abundant regulation by sRNAs in S. mutans during a variety of stress responses and outline how SmsR4 participates in the regulation of sugar metabolism. Taken together, this work presents a new paradigm for sRNA emergence from protein coding genes and demonstrates the prevalence and utility of the understudied phenomenon of post-transcriptional regulation in oral bacteria.


©2021 Madeline Claire Krieger

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Persistent Identifier

TableS1.csv (6 kB)
Table S1. Predicted age of sRNAs

TableS2.csv (2 kB)
Table S2. Predicted age of regulatory proteins

TableS3.csv (8 kB)
Table S3. sRNAs that overlap ORFs

TableS4.csv (170 kB)
Table S4. Accessions for Enterobacterales genomes used to determine sRNA age and prevalence