Author ORCID Identifier
0000-0003-4888-643X
Date of Graduation
5-2018
Document Type
Dissertation (PhD)
Program Affiliation
Microbiology and Molecular Genetics
Degree Name
Doctor of Philosophy (PhD)
Advisor/Committee Chair
Ambro van Hoof, Ph.D.
Committee Member
Richard Behringer, Ph.D.
Committee Member
Michael Lorenz, Ph.D.
Committee Member
Kevin Morano, Ph.D.
Committee Member
Eric Wagner, Ph.D.
Abstract
Gene duplication and alternative splicing are both recognized as important drivers of proteomic diversity and innovation during evolution, but the evolutionary changes over long periods of time or the interrelations of the two processes has not been extensively studied. Here I study these phenomena for the SKI7 and HBS1 gene pair. These Saccharomyces cerevisiae genes were created as part of a whole genome duplication (WGD) event and have since functionally diverged. Although both genes function in mRNA surveillance pathways, the two genes act on different RNAs and have different effects on the target mRNAs. Ski7 brings the Ski complex and exosome together to perform degradation of cytoplasmic mRNAs, but has a specific, poorly understood function in the nonstop decay pathway. In nonstop decay, Ski7 is thought to interact with a ribosome that has stalled while translating through the poly-A tail of a nonstop mRNA. Hbs1 disassembles ribosomes stalled within the coding region and may trigger endonuclease cleavage of some target mRNAs. In order to better understand their functions in mRNA surveillance, this dissertation focuses on dissecting their evolutionary relationship. I show that the pre-WGD SKI7/HBS1 gene produces two distinct proteins via alternative splicing. One of these proteins functions as Ski7, while the other function as Hbs1. Further examination of SKI7/HBS1 genes via transcriptome sequencing demonstrates that alternative splicing in this gene is extremely ancient and widespread among eukaryotes. Duplication of the SKI7 and HBS1 genes has also occurred in six independent instances. Changes in the alternative splicing pattern and in the genes following duplication has led to a variety of Ski7-like proteins that likely have an impact on Ski7 function. Post-duplication changes include loss of an Hbs1 N-terminal motif and changes in the conserved GTPase domain. When these changes are introduced into the Lachancea SKI7/HBS1 gene they disrupt Hbs1 function but not Ski7 function, consistent with the idea that they were important for functional divergence following duplication. Additionally, I have found that the Lachancea SKI7 isoform performs nonstop decay suboptimally compared to Saccharomyces SKI7, indicating that duplication may have allowed SKI7 to specialize in nonstop mRNA decay.
Keywords
Alternative splicing, gene duplication, subfunctionalization, RNA decay, Ski7, Hbs1