Author ORCID Identifier

0000-0003-3115-4566

Date of Graduation

8-2017

Document Type

Dissertation (PhD)

Program Affiliation

Microbiology and Molecular Genetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Ambro van Hoof

Committee Member

Swathi Arur

Committee Member

Theresa M. Koehler

Committee Member

Michael C. Lorenz

Committee Member

Eric J. Wagner

Abstract

The RNA exosome is an essential 3’-5 ribonuclease that processes or degrades a variety of RNA species in eukaryotes. It is composed of nine structural cores and one catalytic subunit, Rrp44. Structural studies captured two different conformations of Rrp44, Rrp44ch (channel) and Rrp44da (direct-access). The Rrp44ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44da bypassing the central channel. Although in vivo function of the Rrp44ch-exosome is extensively studied, the function or even the presence of the Rrp44da-exosome in cell has not been tested. In this study, I show the first in vivo evidence that the Rrp44da is important for the RNA exosome function. I also found that the Rrp44da and Rrp44ch have distinct substrates, indicating that the RNA exosome alternates its conformation to exert specific functions. Furthermore, RNA sequencing analysis suggests that Rrp44ch-exosome indirectly regulates expression of genes encoding ribosomal proteins.

The substrate specificity of the RNA exosome is partly determined by its cofactors that bind substrates. Rrp6 is a ribonuclease that interacts with the RNA exosome in the nucleus. It functions not only as a nuclease but also as an adaptor protein that bridges the RNA exosome to other cofactors such as an RNA helicase, Mtr4. In this study, I found that Rrp6 and Mtr4 function beyond known biochemical and structural interactions. Mtr4 seems to interact with the RNA exosome independent of the Rrp6 N- terminus. In addition, the C-terminal domain of Rrp6 has functions other than the exosome interaction. Moreover, another exosome cofactor, Mpp6, appears to mediate the interaction of the RNA exosome with other nuclear cofactors, and this function is redundant with Rrp6.

This work demonstrates that there are two different RNA exosome conformations present in vivo, and they have specific functions. Additionally, I show that there are multiple dynamic interactions among the RNA exosome with its cofactors, which ensures proper processing or degradation of transcripts.

Keywords

RNA exosome, Rrp6, RNA decay, Mpp6, RNA processing, Dis3, Rrp44

Available for download on Thursday, August 09, 2018

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