Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes

• Published in: Nature communications 2018-02, Vol.9 (1), p.695-12, Article 695
• Main Authors: Darlington, Alexander P. S., Kim, Juhyun, Jiménez, José I., Bates, Declan G.
• Format: Article
• Language: English
• Subjects: 38/22; 38/35; 38/39; 38/77; 42/44; 631/337/574/1789; 631/553/552; 631/61/338/318; Algorithms; Bacteriophage T7 - genetics; Bacteriophage T7 - physiology; Binding sites; Biosynthesis; Circuit design; Circuits; Competition; Design; Division of labor; Escherichia coli - genetics; Escherichia coli - virology; Gene Expression; Gene Regulatory Networks - genetics; Genes; Host-Pathogen Interactions - genetics; Humanities and Social Sciences; Mathematical models; Metabolic flux; Metabolism; Metabolites; Models, Genetic; multidisciplinary; Physiology; Proteins; Resource allocation; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; rRNA 16S; Science; Science (multidisciplinary); Synthetic biology
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-02898-6

Introduction of synthetic circuits into microbes creates competition between circuit and host genes for shared cellular resources, such as ribosomes. This can lead to the emergence of unwanted coupling between the expression of different circuit genes, complicating the design process and potentially leading to circuit failure. By expressing a synthetic 16S rRNA with altered specificity, we can partition the ribosome pool into host-specific and circuit-specific activities. We show mathematically and experimentally that the effects of resource competition can be alleviated by targeting genes to different ribosomal pools. This division of labour can be used to increase flux through a metabolic pathway. We develop a model of cell physiology which is able to capture these observations and use it to design a dynamic resource allocation controller. When implemented, this controller acts to decouple genes by increasing orthogonal ribosome production as the demand for translational resources by a synthetic circuit increases. Competition between synthetic genetic circuits and host genes for shared resources can complicate circuit design and lead to failure. Here the authors demonstrate, mathematically and experimentally, the use of orthogonal ribosomes to decouple competing genes.