Date of Award
Spring 5-8-2026
Document Type
Thesis
Degree Name
Bachelor of Science (BS)
Department
Chemistry
College
College of Science
First Advisor
Brian M. Lee
Abstract/Description
The emrB gene is a member of the MFS transporter family (Major Facilitator Superfamily), which aids bacteria in expelling toxic compounds such as antibiotics, bile acids, and other substances. Previous bioinformatic studies identified the emrB motif as a potential regulatory RNA. In Lactobacillus, this motif is generally found in the intergenic region upstream of the emrB transporter gene. Using mFold, secondary structure predictions were created to visualize potential structures of this motif. The motif itself comprises two hairpins, though inclusion of neighboring regions is predicted to cause structural changes. The ARNold program was used to identify a possible terminator present adjacent to the emrBmotif. Our working hypothesis is that the emrB motif acts as an anti-terminator to suppress transcriptional termination and activate emrB gene expression when bacteria are exposed to antibiotics. The operon containing the emrB gene includes: an antibiotic resistance gene, vanZ, and a gene for glucose-6-phosphate-isomerase. The emrB motif may bind to antibiotics that stabilize the antiterminator structure or interact with a small regulatory RNA (sRNA) to promote transcription of the emrB gene. CopraRNA and IntaRNA were used to identify possible sRNAs that may interact with the emrB motif. Initial characterization of the emrB motif used templates obtained from Lactobacillus acidophilus genomic DNA to synthesize various RNA constructs. The results obtained from thermal melt assays of the RNA transcripts indicated that the motif forms a stable secondary structure, which is consistent with 3D structure predictions showing a 3-helix junction that may form a binding site for antibiotics associated with the regulatory function of the emrB motif. Future studies will include characterization of the emrB motif RNA by RNase T1 digestion, NMR spectroscopy, transcriptional assays, and sRNA binding assays. Overall, analyzing the function and structure of the emrB motif will be important to understanding possible mechanisms of antibiotic resistance in the gastrointestinal microbiota of humans.
Recommended Citation
Mezzenga, Isabella J., "Structure and Mechanism of the emrB Motif in Lactobacillus acidophilus as a Small Regulatory RNA" (2026). Honors Theses. 529.
https://digitalcommons.coastal.edu/honors-theses/529