Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering

Nat Commun. 2021 Mar 11;12(1):1579. doi: 10.1038/s41467-021-21876-z.

Abstract

Random mutagenesis is a technique used to generate diversity and engineer biological systems. In vivo random mutagenesis generates diversity directly in a host organism, enabling applications such as lineage tracing, continuous evolution, and protein engineering. Here we describe TRIDENT (TaRgeted In vivo Diversification ENabled by T7 RNAP), a platform for targeted, continual, and inducible diversification at genes of interest at mutation rates one-million fold higher than natural genomic error rates. TRIDENT targets mutagenic enzymes to precise genetic loci by fusion to T7 RNA polymerase, resulting in mutation windows following a mutation targeting T7 promoter. Mutational diversity is tuned by DNA repair factors localized to sites of deaminase-driven mutation, enabling sustained mutation of all four DNA nucleotides at rates greater than 10-4 mutations per bp. We show TRIDENT can be applied to routine in vivo mutagenesis applications by evolving a red-shifted fluorescent protein and drug-resistant mutants of an essential enzyme.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antifungal Agents / pharmacology
  • DNA-Directed RNA Polymerases / metabolism*
  • Directed Molecular Evolution / methods*
  • Drug Resistance, Fungal / genetics*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Mutagenesis / genetics
  • Promoter Regions, Genetic / genetics
  • Protein Engineering / methods*
  • Pyrimethamine / pharmacology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Viral Proteins / metabolism*

Substances

  • Antifungal Agents
  • Saccharomyces cerevisiae Proteins
  • URA3 protein, S cerevisiae
  • Viral Proteins
  • bacteriophage T7 RNA polymerase
  • DNA-Directed RNA Polymerases
  • Pyrimethamine