title: Programmed evolution for optimization of orthogonal metabolic output in bacteria.
abstract: Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation.
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Todd T
authors.initials: TT
authors.lastname: Eckdahl
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: A Malcolm
authors.initials: AM
authors.lastname: Campbell
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Laurie J
authors.initials: LJ
authors.lastname: Heyer
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Poet
authors.affiliation: Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: David N
authors.initials: DN
authors.lastname: Blauch
authors.affiliation: Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Nicole L
authors.initials: NL
authors.lastname: Snyder
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Dustin T
authors.initials: DT
authors.lastname: Atchley
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Erich J
authors.initials: EJ
authors.lastname: Baker
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Micah
authors.initials: M
authors.lastname: Brown
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Elizabeth C
authors.initials: EC
authors.lastname: Brunner
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Sean A
authors.initials: SA
authors.lastname: Callen
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Jesse S
authors.initials: JS
authors.lastname: Campbell
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Carr
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: David R
authors.initials: DR
authors.lastname: Carr
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Spencer A
authors.initials: SA
authors.lastname: Chadinha
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Grace I
authors.initials: GI
authors.lastname: Chester
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Josh
authors.initials: J
authors.lastname: Chester
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Ben R
authors.initials: BR
authors.lastname: Clarkson
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Kelly E
authors.initials: KE
authors.lastname: Cochran
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Shannon E
authors.initials: SE
authors.lastname: Doherty
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Catherine
authors.initials: C
authors.lastname: Doyle
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Sarah
authors.initials: S
authors.lastname: Dwyer
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Linnea M
authors.initials: LM
authors.lastname: Edlin
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Evans
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Taylor
authors.initials: T
authors.lastname: Fluharty
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Janna
authors.initials: J
authors.lastname: Frederick
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Jonah
authors.initials: J
authors.lastname: Galeota-Sprung
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Betsy L
authors.initials: BL
authors.lastname: Gammon
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Brandon
authors.initials: B
authors.lastname: Grieshaber
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Jessica
authors.initials: J
authors.lastname: Gronniger
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Katelyn
authors.initials: K
authors.lastname: Gutteridge
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Joel
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authors.lastname: Henningsen
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Bradley
authors.initials: B
authors.lastname: Isom
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Hannah L
authors.initials: HL
authors.lastname: Itell
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Erica C
authors.initials: EC
authors.lastname: Keffeler
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Lantz
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Jonathan N
authors.initials: JN
authors.lastname: Lim
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Erin P
authors.initials: EP
authors.lastname: McGuire
authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Alexander K
authors.initials: AK
authors.lastname: Moore
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Jerrad
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authors.lastname: Morton
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Meredith
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authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Sara A
authors.initials: SA
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authors.affiliation: Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Virginia
authors.initials: V
authors.lastname: Perkins
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Phoebe
authors.initials: P
authors.lastname: Parrish
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Claire E
authors.initials: CE
authors.lastname: Pierson
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Sachith
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authors.lastname: Polpityaarachchige
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Quaney
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Abagael
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authors.lastname: Slattery
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Smith
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Jackson
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authors.lastname: Spell
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Morgan
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authors.lastname: Spencer
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Telavive
authors.initials: T
authors.lastname: Taye
authors.affiliation: Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America.
authors.forename: Kamay
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authors.lastname: Trueblood
authors.affiliation: Department of Biology, Davidson College, Davidson, North Carolina, United States of America.
authors.forename: Caroline J
authors.initials: CJ
authors.lastname: Vrana
authors.affiliation: Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America.
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mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D005075:Biological Evolution; D015374:Biosensing Techniques; D018628:Gene Dosage; D005818:Genetic Engineering; D056084:Genetic Fitness; D014644:Genetic Variation; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010957:Plasmids / Q000235:genetics