Date Approved

9-2-2025

Embargo Period

9-2-2025

Document Type

Thesis

Degree Name

M.S. Bioinformatics

Department

Biological and Biomedical Sciences

College

College of Science & Mathematics

Advisor

Jason Heindl, Ph.D.

Committee Member 1

Melissa Manners, Ph.D.

Committee Member 2

Yong Chen, Ph.D.

Disciplines

Bioinformatics | Life Sciences

Abstract

Agrobacterium tumefaciens is a gram-negative alphaproteobacterium that is one of the causative agents of crown gall tumors on plants. Its ability to transform plants using its T-DNA has been studied to improve plant-mediated transformation. sRNAs are small regulatory RNAs that play a role in gene expression in a variety of organisms and bind to target proteins or mRNAs. A. tumefaciens contains two sibling sRNAs, called AbcR1 and AbcR2, which are conserved among alphaproteobacteria. A. tumefaciens AbcR1 and AbcR2 are closely related, exhibiting 69% sequence identity, similar secondary and tertiary structure, and a conserved motif, M2, believed to direct target interactions. An important difference between these sRNAs in A. tumefaciens compared to other organisms is the presence of a motif called the M1 motif or CUCKOO motif (CUCCCA) in AbcR1 and its absence in AbcR2. It is theorized that the presence or absence of this motif is important for differential regulation of gene expression by AbcR1 and AbcR2. Using RNA sequencing and a suite of phenotypic assays, we examined the role of the M1 motif and of AbcR1 in bacterial fitness and gene expression.

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