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Title: The influence of IHF and FIS on the ordered binding of DnaA protein to oriC, the E.coli chromosomal origin
Creator: Margulies, Carla Eva
Date: 1997
Collection: Electronic Theses & Dissertations

Title: The evolution of a key innovation in an experimental population of Escherichia coli : a tale of opportunity, contingency, and co-option
Creator: Blount, Zachary David
Date: 2011
Collection: Electronic Theses & Dissertations
Description: The importance of historical contingency in evolution has been extensively debated over the last few decades, but direct empirical tests have been rare. Twelve initially identical populations of E. coli were founded in 1988 to investigate this issue. They have since evolved for more than 50,000 generations in a glucose-limited medium that also contains a citrate. However, the inability to use citrate as a carbon source under oxic conditions is a species-defining trait of ...
Show moreThe importance of historical contingency in evolution has been extensively debated over the last few decades, but direct empirical tests have been rare. Twelve initially identical populations of E. coli were founded in 1988 to investigate this issue. They have since evolved for more than 50,000 generations in a glucose-limited medium that also contains a citrate. However, the inability to use citrate as a carbon source under oxic conditions is a species-defining trait of E. coli. A weakly Cit+ variant capable of aerobic citrate utilization finally evolved in one population just prior to 31,500 generations. Shortly after 33,000 generations, the population experienced a several-fold expansion as strongly Cit+ variants rose to numerical dominance (but not fixation). The Cit+ trait was therefore a key innovation that increased both population size and diversity by opening a previously unexploited ecological opportunity.The long-delayed and unique evolution of the Cit+ innovation might be explained by two possible hypotheses. First, evolution of the Cit+ function may have required an extremely rare mutation. Alternately, the evolution of Cit+ may have been contingent upon one or more earlier mutations that had accrued over the population's history. I tested these hypotheses in a series of experiments in which I "replayed" evolution from different points in the population's history. I observed no Cit+ mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, I observed a significantly greater tendency to evolve Cit+ among later clones. These results indicate that one or more earlier mutations potentiated the evolution of Cit+ by increasing the rate of mutation to Cit+ to an accessible, though still very low, level. The evolution of the Cit+ function was therefore contingent on the particular history of the population in which it occurred.I investigated the Cit+ innovation's history and genetic basis by sequencing the genomes of 29 clones isolated from the population at various time points. Analysis of these genomes revealed that at least 3 distinct clades coexisted for more than 10,000 generations prior to the innovation's evolution. The Cit+ trait originated in one clade by a tandem duplication that produced a new regulatory module in which a silent citrate transporter was placed under the control of an aerobically-expressed promoter. Subsequent increases in the copy number of this new regulatory module refined the initially weak Cit+ phenotype, leading to the population expansion. The 3 clades varied in their propensity to evolve the novel Cit+ function, though genotypes able to do so existed in all 3, implying that potentiation involved multiple mutations.My findings demonstrate that historical contingency can significantly impact evolution, even under the strictest of conditions. Moreover, they suggest that contingency plays an especially important role in the evolution of novel innovations that, like Cit+, require prior construction of a potentiating genetic background, and are thus not easily evolved by gradual, cumulative selection. Contingency may therefore have profoundly shaped life's evolution given the importance of evolutionary novelties in the history of life. Finally, the genetic basis of the Cit+ function illustrates the importance of promoter capture and altered gene regulation in mediation the exaptation events that often underlie evolutionary innovations.
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Title: The evolution of a balanced polymorphism in a long-term laboratory population of Escherichia coli
Creator: Rozen, Daniel E. (Daniel Eric)
Date: 2000
Collection: Electronic Theses & Dissertations

Title: Survival and experimental evolution of Escherichia coli under freeze-thaw stress
Creator: Sleight, Sean Christian
Date: 2007
Collection: Electronic Theses & Dissertations

Title: Semi-synthesis of aromatic diacids and biosynthesis of kanosamine in Escherichia coli
Creator: Miller, Kelly (Kelly Knight)
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Microbial synthesis of chemicals from biobased feedstocks is an alternative to manufacture of materials derived from petroleum or unconventional gases, such as shale gas and coalbed methane. Aromatic diacids, terephthalic acid, isophthalic acid , and phthalic acid, are valuable compounds for the polymers and plasticizers industry. These diacids are currently manufactured via Amoco Mid-Century oxidation of petroleum-derived para-, meta- and ortho-xylenes, respectively; a process not without...
Show moreMicrobial synthesis of chemicals from biobased feedstocks is an alternative to manufacture of materials derived from petroleum or unconventional gases, such as shale gas and coalbed methane. Aromatic diacids, terephthalic acid, isophthalic acid , and phthalic acid, are valuable compounds for the polymers and plasticizers industry. These diacids are currently manufactured via Amoco Mid-Century oxidation of petroleum-derived para-, meta- and ortho-xylenes, respectively; a process not without environmental and economic challenges. In this work, a semi-synthesis of terephthalic, isophthalic, and phthalic acids is outlined using 2-hydroxymuconic acid as a common synthetic precursor. Recombinant Escherichia coli was utilized combining protocatechuic acid anabolic and catabolic pathways to achieve 1.2 g/L 2-hydroxymuconic acid from D-glucose in fed-batch fermentation. Lewis-acid catalysis was explored in a cycloaddition of 2-hydroxymuconic acid with ethylene to produce terephthalic acid. Cyclization of 2-hydroxymuconic acid afforded 6-carboxy-2-pyrone which was reacted with propiolic acid to afford mixtures of isophthalic and phthalic acids. Propiolic acid from biogas methane and ethylene from bioethanol could maximize the amount of renewable carbon in this semi-synthetic strategy, producing all three petroleum-derived aromatic diacids without the need for Amoco Mid-Century oxidation process. In an additional research trajectory, the production of kanosamine (3-amino-3-deoxy-D-glucose) is evaluated in fed-batch fermentation of recombinant E. coli. Two biosynthesis pathways are reported in the literature: one native to Bacillus subtilis and the other reported in Amycolatopsis mediterranei and Bacillus pumilus. Genes encoding kanosamine biosynthetic enzymes from B. subtilis, A. mediterranei, and B. pumilus are expressed in Escherichia coli to determine whether heterologous expression results in kanosamine accumulation and if the system can be manipulated to maximize kanosamine production. Recombinant E. coli expressing genes from B. subtilis 168 produces 12.7 ± 0.6 g/L kanosamine in a 6% mol/mol yield from D-glucose. Kanosamine yields were increased to 18 ± 1% mol/mol by blocking the Embden-Meyerhoff-Parnas pathway through a mutation in pgi-encoded phosphoglucose isomerase. Enzymes native to A. mediterranei proved to be challenging to efficiently express in E. coli, prompting examination of B. pumilus kanosamine biosynthesis. Expression of B. pumilus SH-B11 genes in E. coli results in 6.3 g/L kanosamine titers in 4.4% mol/mol yield from D-glucose in fed-batch fermentation. In vitro feeding experiments suggest a departure from what is in the literature regarding kanosamine production in Bacillus pumilus.
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Title: Regulation of chromosomal DNA replication in Escherichia coli : Function of an N-terminal domain in DnaA oligomer formation : Biochemical and genetic studies of hyperactive dnaA alleles
Creator: Simmons, Lyle Adair
Date: 2003
Collection: Electronic Theses & Dissertations

Title: Population genetics of bacterial adaptation : experiments with Escherichia coli and a simulation model
Creator: Woods, Robert James
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Molecular characterization of the lit gene of Escherichia coli and its interaction with the gol site of bacteriophage T4
Creator: Koa, Cheng
Date: 1988
Collection: Electronic Theses & Dissertations

Title: Molecular characterization of the gol region in the major capsid protein gene of bacteriophage T4
Creator: Bergsland, Kristin Jeanne
Date: 1987
Collection: Electronic Theses & Dissertations

Title: Life history implications of ribosomal RNA gene copy number in Escherichia coli
Creator: Stevenson, Bradley Scott
Date: 2000
Collection: Electronic Theses & Dissertations

Title: Isolation and characterization of the Escherichia Coli K12 Hema gene
Creator: Verkamp, Debra Elizabeth
Date: 1989
Collection: Electronic Theses & Dissertations

Title: Identification of genes regulated by DNAA protein in Escherichia Coli
Creator: Wang, Qingping
Date: 1989
Collection: Electronic Theses & Dissertations

Title: Genomic diversity and virulence of enterohemorrhagic Escherichia coli
Creator: Abu-Ali, Galeb Saif
Date: 2009
Collection: Electronic Theses & Dissertations

Title: Genomic analysis of pathogen evolution : virulence gene acquisition and genetic erosion in Escherichia coli
Creator: Nelson, Adam Michael
Date: 2008
Collection: Electronic Theses & Dissertations

Title: Evolution of invasiveness in Escherichia coli and Shigella
Creator: Bumbaugh, Alyssa Courtney
Date: 2003
Collection: Electronic Theses & Dissertations

Title: DnaA46 protein in initiation of in vitro oriC plasmid replication
Creator: Hwang, Deog Su
Date: 1988
Collection: Electronic Theses & Dissertations

Title: Comparative molecular evolutionary analysis of virulence loci in pathogenic Escherichia coli
Creator: Lacher, David William
Date: 2007
Collection: Electronic Theses & Dissertations

Title: Coevolutionary implications of envelope-mediated resistance to phage
Creator: Burmeister, Alita
Date: 2017
Collection: Electronic Theses & Dissertations
Description: This dissertation concerns the coevolution of pathogens and their hosts. For my thesis, I have worked with Escherichia coli and phage using experimental evolution, molecular biology, and theory that describes general host-pathogen interactions. This work centers on three themes of broad interest to evolutionary biology and microbiology: coevolutionary origins of novelty and diversity, the role of tradeoffs in constraining evolvability, and the ecological impacts of host resistance.In Chapter...
Show moreThis dissertation concerns the coevolution of pathogens and their hosts. For my thesis, I have worked with Escherichia coli and phage using experimental evolution, molecular biology, and theory that describes general host-pathogen interactions. This work centers on three themes of broad interest to evolutionary biology and microbiology: coevolutionary origins of novelty and diversity, the role of tradeoffs in constraining evolvability, and the ecological impacts of host resistance.In Chapter 1, I worked with a set of experimentally coevolved E. coli/ communities to investigate the bacterial genes that gained mutations and whether fitness tradeoffs had constrained the evolution of those mutations. To do this, I isolated bacteria from the coevolution experiment and sequenced the genomes of the isolates. I found resistance mutations that modified the expression or sequence of proteins used by during infection: LamB and OmpF at the outer membrane, and ManY and ManZ at the inner membrane. To test for fitness tradeoffs, I estimated the isolates’ fitness in the presence and absence of . Phage selection strongly favored resistance mutations, despite those mutations incurring pleiotropic costs related to resource acquisition and homeostasis.For my second chapter, I was particularly interested in the E. coli manY and manZ mutations that allowed phage to adsorb to the outside of the cell but limited the phage’s ability to eject its genome into the cytoplasm. I thought that these mutations might effectively “trap” phage in non-productive infections, thereby accelerating the rate of phage loss from the extracellular environment. However, I found no evidence for such traps; instead, had evolved independence of manY and manZ. These results indicate that for each of the known resistance-conferring mutations evolved by E. coli, the coevolving populations discovered evolutionary routes to circumvent the resistance. For Chapter 3, I shifted briefly from laboratory experiments to mathematical theory to further investigate the trap idea. Although it turned out that the manY and manZ mutations don’t act as traps, I was more generally interested in host defenses on the inside of the cell, such as CRISPR-Cas defense and restriction enzymes, which exist for many bacterial species. Comparable to other studies on parasite traps in animal hosts, I used theory to predict that in the presence of trap alleles, bacteriophage densities would be lower than they otherwise would be, even if more permissive hosts were available to them.In my final chapter, I returned to the coevolution experiment with E. coli and . Although it was known that laboratory populations of phage evolved to use OmpF, and that this function required multiple mutations in the phage J gene, it was unknown how those mutations accumulated. I studied how both phage J gene mutations and bacterial malT (a positive regulator of lamB) mutations influenced the phage’s adaptive landscape. I found that bacterial evolution strongly affected selection patterns on different phage genotypes: in many cases the evolution of host resistance more strongly favored increased phage adsorption rate. Because of that, the evolutionary intermediates between the ancestral and OmpF-infecting phage were positively selected, revealing that host coevolution can increase the rate at which phage evolve to use novel host structures.
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Title: Associations between bacteria and conjugative plasmids : model systems for testing evolutionary theory
Creator: Turner, Paul Eugene
Date: 1995
Collection: Electronic Theses & Dissertations

Title: Adaptation and specialization in biological and digital organisms
Creator: Ostrowski, Elizabeth Anne
Date: 2005
Collection: Electronic Theses & Dissertations

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