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A tale of two condensates: From studying the mechanisms of natural bacterial condensate assembly to developing a novel synthetic condensate

Tomares, Dylan T (2023) A tale of two condensates: From studying the mechanisms of natural bacterial condensate assembly to developing a novel synthetic condensate. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Abstract

In the early 1920s, Aleksander Oparin discovered the ability of biopolymers to phase separate into biomolecular condensates, and postulated that condensates played a role in generating life. Since 2009, biomolecular condensation has been shown to be an important mechanism to organizing protein localization in the eukaryotic cytoplasm. However, whether lower organisms also localized proteins through phase separation remained unexplored. In 2018, I helped characterize the first bacterial condensate protein, RNase E, that organizes RNA decay in bacteria. I then further explored the enrichment profile of RNase E condensates. Lastly, I explored the assembly mechanism of RNase E, uncovering a Cu-mediated redox stress response associated with assembly, as well as the nucleic acid binding specificity of RNase E. I also took a synthetic biology approach to design a novel synthetic condensate, inspired by hydrogel materials, and showed that it can be orthogonal to other condensates that form in the bacterial cytoplasm. Many other examples of bacterial condensates have shown that phase separation is an important mechanism to organize the bacterial cytoplasm. The existence of bacterial condensates supports the idea that condensation is generalizable mechanism of cellular organization. Furthermore, condensates may provide the missing link between the prebiotic primordial soup and life.

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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Tomares, Dylan Tdtt14@pitt.edudtt140000-0002-4686-3915
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairChilders, William Sethwschild@pitt.edu0000-0003-1160-7767
Committee MemberDeiters, AlexanderDEITERS@pitt.edu0000-0003-0234-9209
Committee MemberMeyer, Taratara.meyer@pitt.edu0000-0002-9810-454X
Committee MemberZhang, Huaiyinghuaiyinz@andrew.cmu.edu0000-0002-1784-2664
Date: 6 September 2023
Date Type: Publication
Defense Date: 19 May 2023
Approval Date: 6 September 2023
Submission Date: 23 May 2023
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 306
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: RNase E, biomolecular condensation, phase separation, bacterial ribonucleoprotein bodies, synthetic biology, peptide nanomaterials, hydrogel materials, coiled-coil
Date Deposited: 07 Sep 2023 01:25
Last Modified: 07 Sep 2023 01:25
URI: http://d-scholarship.pitt.edu/id/eprint/44900

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