IPiB Thesis Defense November 29, 2023: Expery Omollo

Expery OmolloExpery Omollo, an IPiB graduate student, will be defending his Ph.D. research on November 29, 2023.

RNA polymerase is essential to the process by which DNA is transcribed into mRNA. Omollo’s research in the Landick Lab focused on how interactions among newly produced mRNA, RNA polymerase, and additional proteins result in RNA polymerase pausing or terminating transcription altogether.

Although RNA polymerase transcribes DNA to mRNA at a rate of about 100 nucleotides per second in E. coli, the process does not chug along continuously. Rather, there are periodic pauses in the process. In E. coli, for example, these pauses can each last for up to fifteen seconds, a timespan that would amount to the transcription of 1,500 nucleotides. These pauses are an important regulatory mechanism that, among other things, allows cellular processes to slow down under sub-optimal environmental conditions.

While the duration of average pausing periods varies, the cellular signals that promote transcriptional pausing are highly conserved among bacteria and eukaryotes. Omollo worked with collaborators at Rockefeller University to identify the mechanisms responsible for RNA polymerase pausing using biochemical research methods, CRISPR technology, and cryo-electron microscopy. They demonstrated that transcriptional pauses in E. coli and Mycobacterium tuberculosis (a bacterium that causes tuberculosis) is impacted by NusG, a protein present in all living organisms. The research, published in Molecular Cell, highlights how interactions among RNA polymerase, mRNA, and NusG lead RNA polymerase to change its orientation. This, in turn, pauses or resumes transcription. Knowing more about how these pauses occur could be a key to treating diseases such as tuberculosis, says Omollo.

Mycobacterium tuberculosis can slow down its growth drastically. Its pauses during transcription can be very long — fifteen minutes, maybe half an hour. That means the disease can lay dormant until conditions are optimal for it to grow,” explains Omollo. “You might think a patient has been cured and then a decade later, the infection returns and is even more aggressive. Targeting the pause mechanism may be a way to disrupt important regulatory mechanisms in tuberculosis or other diseases.”

In addition to examining transcriptional pauses, Omollo explored how transcription is terminated in collaboration with scientists at the Chinese Academy of Sciences in Shanghai, China. In this work, they used biochemistry and cryo-electron microscopy to visualize the mechanism of transcription termination in E. coli. They visualized RNA polymerase pausing at terminator sequences (a series of nucleotides indicating the end point for transcription), and how the newly formed RNA folds inside the RNA polymerase and disengages from the RNA polymerase complex. Their findings were published in Nature.

Omollo’s interest in research related to tuberculosis was inspired by his experiences as a child in Nairobi, Kenya. When his uncle, who was from a rural part of the country, fell sick with the disease, he moved in with Omollo’s family to receive treatment in the city. Omollo watched his uncle over the six-month-long treatment, which required the use of multiple strong drugs.

Complex treatment plans involving numerous medications have made tuberculosis an especially pernicious disease, leading to antibiotic-resistant strains, especially if someone doesn’t take a full course of medication due to access to drugs or other considerations. Omollo wants to help solve this problem through basic science research. “The first step to developing more effective treatments is knowing more about the disease,” says Omollo. “Then we can target its weaknesses. Many drugs target the transcription process so that the cells can no longer make proteins they need to survive. Maybe these long transcriptional pauses in tuberculosis can be a target for therapeutic drugs.”

Omollo has long been interested in identifying problems and finding creative solutions. As an undergraduate student at Michigan State University, he started his first company, which collected waste around Kenya selling it to recycling companies. He continued to explore his entrepreneurial interests at UW–Madison as a member of UW’s WiSolve Consulting Group, where he worked collaboratively with graduate students across campus to provide research-based business recommendations for clients. He also participated in the UW-Madison chapter of Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS), which serves as a space for professional development and discussion among minority students in the College of Agricultural and Life Sciences. After graduating, he is interested in pursuing an industry-based career that will allow him to interface with customers and clients.

To learn more about Omollo’s research, attend his Ph.D. defense, “Role of nascent RNA structures and transcription factors in regulating bacterial transcription,” on Wednesday, November 29, 2023, at 9:00 a.m. in 1211 of the Hector F. DeLuca Biochemical Science Building.