title: Genomic analysis of a key innovation in an experimental Escherichia coli population.
abstract: Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit(+)), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit(+) trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population's history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA. blountza@msu.edu
authors.forename: Zachary D
authors.initials: ZD
authors.lastname: Blount
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.forename: Carla J
authors.initials: CJ
authors.lastname: Davidson
authors.forename: Richard E
authors.initials: RE
authors.lastname: Lenski
mesh_terms: D000332:Aerobiosis / Q000235:genetics; D019343:Citric Acid / Q000378:metabolism* / Q000494:pharmacology; D004252:DNA Mutational Analysis; D004843:Epistasis, Genetic; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D005947:Glucose / Q000172:deficiency / Q000378:metabolism / Q000494:pharmacology; D008957:Models, Genetic; D027361:Organic Anion Transporters / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics
chemical_list: C113956:CitT protein, E coli; D029968:Escherichia coli Proteins; D027361:Organic Anion Transporters; D019343:Citric Acid; D005947:Glucose