Dissertations, Theses, and Capstone Projects

Date of Degree

9-2026

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy

Program

Biology

Advisor

Diana P. Bratu

Committee Members

Frida Kleiman

Shana Elbaum Garfinkle

Heather Cook

Hyung Don Ryoo

Subject Categories

Cell Biology | Developmental Biology | Genetics

Keywords

P-bodies, mRNA, Drosophila Melanogaster, Biomolecular Condensates

Abstract

Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein condensates that regulate mRNA storage, translational repression, and decay. While the biochemical principles governing condensate assembly have been extensively studied in vitro, how P-body organization is established and dynamically regulated in vivo to control specific mRNA populations remains poorly understood. This dissertation investigated the molecular and cellular mechanisms that govern P-body architecture and function in the Drosophila melanogaster female germline. First, I identified the conserved LSm protein Trailer Hitch (Tral) as a central organizer of P-body architecture. Using quantitative confocal and super-resolution microscopy combined with chemical perturbations, I showed that Tral coordinates the spatial organization of core P-body proteins, Me31B and Cup. Loss of Tral disrupted condensate organization, promoted demixing into heterogeneous subdomains, and selectively altered the storage of specific maternal mRNAs. These changes revealed a mechanism by which condensate architecture contributes to selective mRNA regulation and transcriptional homeostasis. Second, I demonstrated that endoplasmic reticulum (ER) exit sites contribute to the spatial organization of P-bodies in vivo. P-bodies associated with ER exit sites form a distinct population characterized by increased size and reduced mobility. Perturbation of ER exit site composition compromised P-body integrity and impaired translational repression and stability of maternal mRNAs, indicating that organelle contact sites influence condensate assembly and function. Finally, I showed that P-bodies undergo rapid remodeling during the early response to ER stress. This remodeling preceded stress granule formation and was driven by ATF4-dependent transcriptional upregulation of the RNA-binding protein Bruno 1, which promoted selective stabilization of specific mRNAs within P-bodies. Together, these findings established that P-body organization is controlled by protein scaffolds, organelle interactions, and stress-responsive transcriptional programs, revealing how cytoplasmic condensates dynamically regulate mRNA fate in vivo.

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