title: Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.
abstract: Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to experimentally study the impact of alternative genetic codes on the evolution of biological systems. We explored how Escherichia coli strains that incorporate a 21st nonstandard amino acid (nsAA) at the recoded amber (TAG) stop codon evolve resistance to the antibiotic rifampicin. Resistance to rifampicin arises from chromosomal mutations in the β subunit of RNA polymerase (RpoB). We found that a variety of mutations that lead to substitutions of nsAAs in the essential RpoB protein confer robust rifampicin resistance. We interpret these results in a framework in which an expanded code can increase evolvability in two distinct ways: by adding a new letter with unique chemical properties to the protein alphabet and by altering the mutational connectivity of amber-adjacent codons by converting a lethal nonsense mutation into a missense mutation. Finally, we consider the implications of these results for the evolution of alternative genetic codes. In our experiments, reliance on a mutation to a reassigned codon for a vital trait is not required for the long-term maintenance of an expanded genetic code and may even destabilize incorporation of an nsAA, a result that is consistent with the codon capture model of genetic code evolution.
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin mhammerling@gmail.com jbarrick@cm.utexas.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hammerling
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin.
authors.forename: Jimmy
authors.initials: J
authors.lastname: Gollihar
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin.
authors.forename: Catherine
authors.initials: C
authors.lastname: Mortensen
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin.
authors.forename: Razan N
authors.initials: RN
authors.lastname: Alnahhas
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
authors.affiliation: Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, Department of Molecular BioSciences, The University of Texas at Austin mhammerling@gmail.com jbarrick@cm.utexas.edu.
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D005075:Biological Evolution; D003062:Codon; D018388:Codon, Terminator; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D019143:Evolution, Molecular; D005815:Genetic Code; D009154:Mutation; D015202:Protein Engineering; D012293:Rifampin / Q000494:pharmacology*
chemical_list: D000596:Amino Acids; D003062:Codon; D018388:Codon, Terminator; D029968:Escherichia coli Proteins; D012321:DNA-Directed RNA Polymerases; D012293:Rifampin
keywords: antibiotic resistance; codon capture; evolvability; sequence space