45 research outputs found
Prediction of Cellular Burden with Host--Circuit Models
Heterologous gene expression draws resources from host cells. These resources
include vital components to sustain growth and replication, and the resulting
cellular burden is a widely recognised bottleneck in the design of robust
circuits. In this tutorial we discuss the use of computational models that
integrate gene circuits and the physiology of host cells. Through various use
cases, we illustrate the power of host-circuit models to predict the impact of
design parameters on both burden and circuit functionality. Our approach relies
on a new generation of computational models for microbial growth that can
flexibly accommodate resource bottlenecks encountered in gene circuit design.
Adoption of this modelling paradigm can facilitate fast and robust design
cycles in synthetic biology
Total synthesis of Escherichia coli with a recoded genome
Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA