Date Approved

9-10-2024

Embargo Period

9-10-2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy (Ph.D.)

Department

Molecular Cell Biology and Neuroscience

College

Rowan-Virtua School of Translational Biomedical Engineering & Sciences

Advisor

Katrina Cooper, D. Phil. & Brian Weiser, Ph.D.

Committee Member 1

Natalia Shcherbik, Ph.D.

Committee Member 2

Jessica Loweth, Ph.D.

Committee Member 3

Kiran Madura, Ph.D.

Keywords

autophagy; cellular stress; mRNA; transcription; translation; ubiquitin

Subject(s)

Cytology--Research

Disciplines

Biochemistry, Biophysics, and Structural Biology | Life Sciences | Molecular Biology

Abstract

Adaptation to stress requires cells to reprogram transcription, translation, and proteolytic pathways. Although much is known about the response of each program, it remains unclear how they coordinate following stress. My studies in S. cerevisiae identified the Cdk8 kinase module (CKM) of the Mediator complex as a new player in coordinating these processes. It is well established that the CKM consists of four highly conserved proteins (cyclin C, its cognate kinase Cdk8, and two structural proteins Med12 and Med13) and predominantly represses a subset of stress responsive genes in yeast. We demonstrated for the first time that the CKM also positively regulates the transcription of a subset of translation initiation factor (TIF) and ribosomal protein (RP) genes through an indirect mechanism. Consistent with this, we observed that the CKM is important for survival under conditions which alter or inhibit protein synthesis. Moreover, during nutrient deprivation, cells repress translation by degrading specific TIFs and storing mRNA in processing bodies (P-bodies). We found that nitrogen starvation causes Med13 to relocate to P-bodies, where it aids in the degradation of Edc3, showing a novel cytoplasmic role for Med13. Lastly, I demonstrated the degradation of the TIF eIF4G1 during nitrogen starvation involves K33 and K63-linked ubiquitination by the Cul3 E3 ligase complex and requires Atg8’s ubiquitin (Ub) interacting motif (UIM), indicating a new role of Ub in selective autophagy. Given the conserved nature of all the players, these studies are highly relevant to the control of proteostasis in higher eukaryotes.

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