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Investigation of the Effect of Phase Separation on RNA Metabolism in Bacteria

Collins, Michael (2023) Investigation of the Effect of Phase Separation on RNA Metabolism in Bacteria. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Despite their simplicity, bacteria are capable of carrying out complex biology including chromosome replication, cell division, and motility. These complex tasks require both the spatiotemporal organization of biomolecules and biochemistry and the communication between these molecules. One mechanism that bacteria use to achieve subcellular organization of biomolecules is phase separation into biomolecular condensates, which are formed by weak multivalent interactions between proteins and nucleic acids. Recently, many phase separating proteins have been identified in bacteria. However, the role of phase separation in regulating cellular function and implications of phase separation on client enzyme activity are still being uncovered. Additionally, while many signaling cascades in bacteria have been characterized, others may remain silent in the lab environment. For these systems, few tools exist to probe their function. In this dissertation, I will explore the effect of phase separation on RNA degradation systems and discuss methods to activate silent signaling pathways in bacteria.
Chapter 2 will discuss the effect of phase separation of the Caulobacter crescentus RNA degradosome on the activity of its client riboexonuclease. I provide evidence for the mechanism of rate enhancement in the phase separated environment. Chapter 3 discusses the interaction between the degradosome scaffold and a metabolic enzyme client with putative RNA-binding function.
Chapter 4 discusses various pseudoenzymes that retain important roles in cell signaling despite having lost catalytic function. In Chapter 5, I explore the development of synthetic biology tools to study these pseudoenzymes and other silent signaling pathways by using light to activate signaling networks.
In each chapter, I discuss questions remaining and directions for future study. Overall, this dissertation aims to develop new methods to understand the complex interplay between RNA degradation, metabolism, and cell signaling.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Collins, Michaelmjc178@pitt.edumjc1780000-0002-0272-9968
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairChilders, W. Sethwschild@pitt.eduwschild
Committee MemberHorne, W. Sethhorne@pitt.eduhorne
Committee MemberWeber, Stephenweber@pitt.eduweber
Committee MemberBerman, Andreaajb190@pitt.eduajb190
Date: 25 January 2023
Date Type: Publication
Defense Date: 19 October 2022
Approval Date: 25 January 2023
Submission Date: 25 October 2022
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 235
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Chemistry
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Phase separation; Biomolecular condensates; BR-bodies; PNPase; RNA biochemistry; RNA degradation;
Date Deposited: 25 Jan 2023 14:50
Last Modified: 25 Jan 2023 14:50


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