Characterizing and alleviating substrate limitations for improved in vitro ribosome construction

Yi Liu, Brian R. Fritz, Mark J. Anderson, Jennifer A. Schoborg, Michael C. Jewett*

*Corresponding author for this work

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

Complete cell-free synthesis of ribosomes could make possible minimal cell projects and the construction of variant ribosomes with new functions. Recently, we reported the development of an integrated synthesis, assembly, and translation (iSAT) method for in vitro construction of Escherichia coli ribosomes. iSAT allows simultaneous rRNA synthesis, ribosome assembly, and reporter protein expression as a measure of ribosome activity. Here, we explore causes of iSAT reaction termination to improve efficiency and yields. We discovered that phosphoenolpyruvate (PEP), the secondary energy substrate, and nucleoside triphosphates (NTPs) were rapidly degraded during iSAT reactions. In turn, we observed a significant drop in the adenylate energy charge and termination of protein synthesis. Furthermore, we identified that the accumulation of inorganic phosphate is inhibitory to iSAT. Fed-batch replenishment of PEP and magnesium glutamate (to offset the inhibitory effects of accumulating phosphate by repeated additions of PEP) prior to energy depletion prolonged the reaction duration 2-fold and increased superfolder green fluorescent protein (sfGFP) yield by ∼75%. By adopting a semi-continuous method, where passive diffusion enables substrate replenishment and byproduct removal, we prolonged iSAT reaction duration 5-fold and increased sfGFP yield 7-fold to 7.5 ± 0.7 μmol L-1. This protein yield is the highest ever reported for iSAT reactions. Our results underscore the critical role energy substrates play in iSAT and highlight the importance of understanding metabolic processes that influence substrate depletion for cell-free synthetic biology.

Original languageEnglish (US)
Pages (from-to)454-462
Number of pages9
JournalACS synthetic biology
Volume4
Issue number4
DOIs
StatePublished - Apr 17 2015

Keywords

  • Escherichia coli
  • cell-free synthetic biology
  • iSAT
  • in vitro transcription and translation
  • ribosome

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Fingerprint Dive into the research topics of 'Characterizing and alleviating substrate limitations for improved in vitro ribosome construction'. Together they form a unique fingerprint.

  • Cite this