title: Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific nonstandard amino acid incorporation.
abstract: Site-specific incorporation of nonstandard amino acids (NSAAs) into proteins enables the creation of biopolymers, proteins, and enzymes with new chemical properties, new structures, and new functions. To achieve this, amber (TAG codon) suppression has been widely applied. However, the suppression efficiency is limited due to the competition with translation termination by release factor 1 (RF1), which leads to truncated products. Recently, we constructed a genomically recoded Escherichia coli strain lacking RF1 where 13 occurrences of the amber stop codon have been reassigned to the synonymous TAA codon (rEc.E13.ΔprfA). Here, we assessed and characterized cell-free protein synthesis (CFPS) in crude S30 cell lysates derived from this strain. We observed the synthesis of 190±20 μg/mL of modified soluble superfolder green fluorescent protein (sfGFP) containing a single p-propargyloxy-L-phenylalanine (pPaF) or p-acetyl-L-phenylalanine. As compared to the parent rEc.E13 strain with RF1, this results in a modified sfGFP synthesis improvement of more than 250%. Beyond introducing a single NSAA, we further demonstrated benefits of CFPS from the RF1-deficient strains for incorporating pPaF at two- and five-sites per sfGFP protein. Finally, we compared our crude S30 extract system to the PURE translation system lacking RF1. We observed that our S30 extract based approach is more cost-effective and high yielding than the PURE translation system lacking RF1, ∼1000 times on a milligram protein produced/$ basis. Looking forward, using RF1-deficient strains for extract-based CFPS will aid in the synthesis of proteins and biopolymers with site-specifically incorporated NSAAs.
authors: Department of Chemical and Biological Engineering, ‡Chemistry of Life Processes Institute, §Department of Chemistry, and ∥Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States of America.
authors: Seok Hoon
authors: SH
authors: Hong
authors: Ioanna
authors: I
authors: Ntai
authors: Adrian D
authors: AD
authors: Haimovich
authors: Neil L
authors: NL
authors: Kelleher
authors: Farren J
authors: FJ
authors: Isaacs
authors: Michael C
authors: MC
authors: Jewett
mesh_terms: D002474:Cell-Free System / Q000737:chemistry*; D018388:Codon, Terminator / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D017353:Gene Deletion; D049452:Green Fluorescent Proteins / Q000138:chemical synthesis; D010454:Peptide Termination Factors / Q000737:chemistry* / Q000235:genetics; D010649:Phenylalanine / Q000031:analogs & derivatives / Q000737:chemistry; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D011487:Protein Conformation
chemical_list: C476995:3-(4-acetylphenyl)-2-aminopropanoic acid; C549407:4-propargyloxyphenylalanine; D018388:Codon, Terminator; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; C489005:prfA protein, E coli; D049452:Green Fluorescent Proteins; D010649:Phenylalanine