Sabrina Abdulla

PhD Candidate

[email protected]

Department of Microbiology

University of Illinois at Urbana-Champaign


M.S/PhD Project @ Vanderpool Lab
University of Illinois Urbana-Champaign

Small RNA mediated regulation of the hilD mRNA 3'UTR in Salmonella

My thesis project focuses on understanding how Salmonella uses small RNAs to regulate its intricate network of regulators. This several-fold network of regulation is necessary to make sure that Salmonella don't waste energy by making resources they don't need, but do express genes that are required to allow them to invade and survive within their host. We focus on studying a particular regulator, hilD, which has a particularly long 3' UTR. While bacterial 3'UTRs are usually short and thought to function only as the termination point, this long 3' UTR has been observed to have regulatory function by several groups. We think this makes it a great target for small RNA regulation and I am studying the mechanisms and intricacies of small RNAs we have found to regulate here. 

MCB Graduate Student Association - Bake your Research (Audience:  MCB graduate students)

Salmonella is a gut pathogen, most commonly associated with causing food poisoning. During infection, Salmonella use a needle like apparatus to inject their infection genes and invade host cells.
The genes for this machinery, as well as several toxins are found in a cluster in the genome called Salmonella pathogenicity island 1, or SPI-1. SPI-1 is regulated by a feedforward loop.

HilD is the master regulator of the SPI-1 feed-forward loop that regulates the expression of SPI-1 genes. My research aims to identify if and how the regulation of hilD occurs through the hilD untranslated 3' region (3' UTR), specifically looking at the role of small RNAs (sRNA) at the hilD 3' UTR.

Working model depicted by pumpkin spice cookies:

Orange oval: HilD protein
Yellow pac-man: Degradosome
Red ring: Rho terminating factor
Yellow ring: Hfq (small RNA chaperone)

Figure 1: During non-SPI-1 inducing conditions, when SPI-1 expression is not needed, levels of hilD are kept low (indicated by X over HilD protein, orange oval). RNase E degradosome (yellow Pac-Man) often degrades mRNA by interacting at RNase E processing sites along the mRNA and Rho factor (red) can cause premature termination. Both of these mechanisms act at hilD to keep levels low in non-inducing conditions.

Figure 2: During SPI-1 inducing conditions, small RNAs (blue RNAs) bind at the hilD mRNA 3’UTR to stabilize hilD from RNase E and Rho activity. HilD is expressed (orange ovals), which leads to SPI-1 expression. Future directions/thesis work: figuring out how small RNAs can do this.
Undergraduate Biology Honors Thesis @ Selker Lab
University of Oregon

Understanding the role of the BAH domains of the DIM-2 protein in Neurospora crassa
My first undergraduate project involved designing light inducible strains of Neurospora, which allowed for tight control of certain mutants that were otherwise harmful. Later, my post-doc mentor wanted to look into a conserved domain (BAH domain) that was a part of a methyltransferase (DIM-2) which had not yet been characterized in Neurospora. We identified a methylation defect phenotype as a consequence of mutations in this domain and began to characterize this defect .

I began my research journey in the lab of Dr. Eric Selker as a junior at the University of Oregon under the mentorship of Dr. Vincent Bicoccas. I had originally been interested in forensic science, but after working in a forensic lab, I realized that I was more interested in the "why's" of science instead of just analyzing samples for fingerprints or running through databases. My experience in the Selker lab taught me how to hold my first pipette, and lead me to learn several techniques, the intricacies of a wood fungus that somehow shares genetic similarity to humans enough to study epigenetic markers related to cancer. But most importantly, I learned the foundations of how to share my research through writing and presentation of data, which carried me through graduate school.
Laboratory Techniques: DNA/RNA Prep, PCR, Gel Electrophoresis, RNA/DNA sequencing gels (Primer Extension, Footprinting), β-galactosidase assays, Northern/Western/Southern blotting