Date of Award

Spring 1-1-2015

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Robin D. Dowell

Second Advisor

Corrie Detweiler

Third Advisor

Tin Tin Su

Fourth Advisor

Dylan Taatjes

Fifth Advisor

Norman Pace

Abstract

The sudden and widespread introduction of the pesticide pentachlorophenol (PCP) into the environment from 1930 to 1980 created a new global selection pressure on microbes. The subsequent isolation of a pentachlorophenol degrading bacterium, Sphingobium chlorophenolicum, provided a unique opportunity to study an early evolutionary response to the new selective pressure.

The minimal enzymatic pathway required to degrade PCP was laboriously determined before high throughput sequencing was possible. Many of the proteins discovered were identified by following their activities through increasingly stringent fractionations, sequencing the N terminus of the protein, designing degenerate primers, and ultimately cloning the gene from the genome. This highly targeted approach proved to be effective but left many of the evolutionary questions that motivated the study of this pathway and this organism unanswered. Where did these genes come from? Did they originate from horizontal gene transfer, duplication and divergence, or recruitment? What are the regulatory mechanisms of this pathway? Are other genes induced by PCP? To answer these questions, a global perspective of the genome and transcriptome of the organism is required.

In this thesis, I ascertain and discuss the complete genome sequence of S. chlorophenolicum, I discuss the development of a bioinformatics tool to facilitate massively comparative microbial genomics, I uncover and examine the global transcriptional response of S. chlorophenolicum to PCP, and I take a detailed molecular look at the key transcription factors governing this regulatory response.

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