A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes

Thomas E. Gorochowski, Irem Avcilar-Kucukgoze, Roel A L Bovenberg, J. Roubos, Zoya Ignatova

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.

Original languageEnglish
Pages (from-to)710-720
Number of pages11
JournalACS Synthetic Biology
Volume5
Issue number7
DOIs
Publication statusPublished - Jul 15 2016

Fingerprint

Synthetic Genes
Ribosomes
Genes
Synthetic Biology
Cell Physiological Phenomena
Resource Allocation
Protein Biosynthesis
Proteins
Maintenance
Gene Expression
Growth
Networks (circuits)
Chassis
Physiology
Gene expression
Resource allocation
Elongation

Keywords

  • protein biosynthesis
  • synthetic biology
  • systems biology
  • translation

ASJC Scopus subject areas

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

Cite this

A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes. / Gorochowski, Thomas E.; Avcilar-Kucukgoze, Irem; Bovenberg, Roel A L; Roubos, J.; Ignatova, Zoya.

In: ACS Synthetic Biology, Vol. 5, No. 7, 15.07.2016, p. 710-720.

Research output: Contribution to journalArticle

Gorochowski, Thomas E. ; Avcilar-Kucukgoze, Irem ; Bovenberg, Roel A L ; Roubos, J. ; Ignatova, Zoya. / A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes. In: ACS Synthetic Biology. 2016 ; Vol. 5, No. 7. pp. 710-720.
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