Date of Award


Document Type

Open Access Master's Thesis

Degree Name

Master of Science in Biological Sciences (MS)

Administrative Home Department

Department of Biological Sciences

Advisor 1

Paul D. Goetsch

Committee Member 1

Thomas Werner

Committee Member 2

Zhiying Shan


As the publications of annotated genomes from species representing most domains of life continue to grow exponentially, we are gaining more insight into how proteins, cellular pathways, and protein complexes evolved. We are interested in understanding how each protein in the 8-subunit transcriptional repressor complex called DREAM interacts with each other. DREAM is comprised of 3 main components: an E2F-DP transcription factor heterodimer, a pocket protein, and the highly conserved 5-subunit subcomplex called MuvB. We hypothesize that the mechanism of DREAM’s formation on chromatin dictates how DREAM functions to turn off target gene expression. Unfortunately, many interaction surfaces remain unknown, especially those that are involved in the formation of the MuvB subcomplex. While protein conservation has been performed on some DREAM subunits, primarily the E2Fs and pocket proteins, an extensive analysis of the MuvB subcomplex itself had yet to be conducted. Not only is the MuvB subcomplex understudied evolutionarily, but the studies that have evaluated MuvB conservation primarily utilize model organisms. Here, we developed a pipeline to perform protein conservation analysis of 4 of the 5 subunits of the MuvB subcomplex and the pocket protein. Our analysis makes full use of the protein sequences uploaded to Uniprot to expand to hundreds of sequences for analysis. By identifying each protein subunit in most annotated genomes, we developed the broadest model for conservation of MuvB and the pocket protein, including individual domains within each protein. We determined that the conservation of known MuvB interactions is observed outside of the animal kingdom, extending into the plant kingdom. We identified a novel conserved region within the MuvB subunit LIN37. Additionally, our protein conservation model revealed how the unique LxCxE motif in the Nematoda LIN52, known to be the MuvB interaction interface with the pocket protein, diverged from the more broadly conserved LxSxExL motif observed in humans. Interestingly, a similar LxCxE motif was observed in LIN54 homologs in plants but did not identify a corresponding LIN52 homolog, suggesting that the LIN54 DNA-binding subunit may have originally served to link the MuvB subcomplex with the pocket protein. Altogether, our findings serve to expand our understanding of the evolution of the MuvB subcomplex and how the complex may assemble.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.