Defense Date

6-15-2023

Graduation Date

Summer 8-5-2023

Availability

One-year Embargo

Submission Type

dissertation

Degree Name

PhD

Department

Biological Sciences

Committee Chair

Wook Kim

Committee Member

Michael Jensen-Seaman

Committee Member

Dannie Durand

Committee Member

Jana Patton-Vogt

Keywords

bacteria, pseudomonas, mRNA, biofilm, evolution, protein, microscopy, transcriptomics, bioinformatics, structural biology

Abstract

Microorganisms are often found in microbial communities we call biofilms. Organisms living in these crowded environments have significant evolutionary pressure to retain access to the resources necessary to sustain life. My research uses the bacterium Pseudomonas fluorescens Pf0-1 to study how organisms evolve strategies to solve this crowding problem as aging colonies repeatedly generate mutant patches. These mutants expand the reach of the colony resulting in decreased local density as they push themselves up to the resource rich surface. These spatial structures result from social interactions between the mutant and the parental cells mediated through extracellular secretions, resulting in the mutant progeny displaying increased fitness compared to the parent. Loss of function mutations in rsmE are exclusively responsible for every mutant patch observed. RsmE and its two paralogs (RsmA and RsmI) are post-transcriptional gene regulators, described to redundantly repress multiple secretions by sequestering associated mRNA, which contradicts our large mutational data set. With the use of genetic engineering, fluorescent microscopy, competitional, transcriptomic, and proteomic analyses in this dissertation, I characterize the spatiogenetic impact of RsmE regulation. In the following chapters I examine the major RsmE regulated extracellular secretions contributing to the increased fitness of the mutant patches, I explore the impact each Rsm paralog has on the transcriptome, and I use a systematic approach combining proteomics and transcriptomics to identify additional intercellular interactions. Overall, this work provides insight into strategies evolved to survive in dense microbial communities and provides a platform to further explore questions of structure and function at both the protein and cellular levels.

Language

English

Additional Citations

A. F. Evans et al., Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1. Journal of Bacteriology 204, e00285-00222 (2022).

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