Date of Award

1-1-2021

Language

English

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College/School/Department

Department of Biological Sciences

Content Description

1 online resource (xi, 164 pages) : color illustrations.

Dissertation/Thesis Chair

Marlene Belfort

Committee Members

Daniele Fabris, Gabriele Fuchs, Pan Li

Keywords

Introns, Transposons, Mobile genetic elements, Lactococcus lactis, Eukaryotic cells, RNA splicing

Subject Categories

Biochemistry | Microbiology | Molecular Biology

Abstract

Group II introns are self-splicing mobile elements that are thought to be the evolutionary ancestors of eukaryotic retrotransposons, the spliceosome, and spliceosomal introns. Yet, little is known about how group II introns have coevolved within their native hosts or about the corresponding host biology.Using the Ll.LtrB intron in its native host, Lactococcus lactis, I first sought to identify host factors that influence retrotransposition. Since retrotransposition can be costly to the host organism, group II introns must achieve a delicate balance between self-proliferation and host preservation. By utilizing the native host organism, my goal was to unearth retrotransposition-related mechanisms that have coevolved with the group II intron. This project reaffirmed previous findings in heterologous hosts that group II intron retromobility is linked to the metabolic state of the host cell and amino acid starvation. In addition, I discovered a mechanism by which ribosomes can serve as suppressors of retrotransposition. To examine a wider variety of group II introns in nature, I also took a computational approach examining the genomic neighborhoods of group II introns from sequenced genomes. By examining the regions flanking group II introns, I obtained a window into how group II introns have evolved to colocalize with genes that benefited the mobile intron. Although different group II introns were rarely found in identical genes, I observed a significant neighborhood bias for gene functionality. There was a clear preference for group II introns residing with genes that either provide opportunities for the group II introns to avoid counter-selection or enhance their proliferation. By colocalizing with other mobile elements, group II introns may be able to avoid selective removal by being rarely transcribed or by simply avoiding genes that are critical to host survival. Additionally, group II introns may hijack host gene functionality by residing in or around genes that can assist in retromobility and/or are expressed under conditions favorable for retrotransposition. By analyzing the neighborhood of group II introns, I have unearthed elements of the host genes that may have contributed to group II intron persistence in these genomes. Mobile elements survive in a delicate relationship with their host organism, and group II introns are no exception. In this work, I have experimentally demonstrated host functions that limit group II intron retrotransposition, as well as computationally identified trends of group II intron localization suggestive of introns persisting in genes that promote group II intron survival or proliferation. Taken together, this dissertation combined genetic studies of a model group II intron with a computational survey of sequenced genomes in order to elucidate how group II introns have coevolved with their native hosts. Overall, this work represents major strides in studying group II introns in their native host.

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Waldern_Supplemental_Files.zip (1137 kB)
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