Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Year: 2020

Type: article

Abstract: Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity. Computer-aided design strategies require quantitative representations of cells, able to capture multiscale processes and link genotypes to phenotypes. Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology. We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems, and we discuss several challenges for the realization of our vision. The possibility to describe and build in silico whole-cells offers an opportunity to develop increasingly automatized, precise and accessible computer-aided design tools and strategies throughout novel interdisciplinary collaborations.

Source: Frontiers in Bioengineering and Biotechnology

DOI: 10.3389/fbioe.2020.00942

Authors: Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook, William Shaw, Christopher Woods

Institutions: University of Bristol, BrisSynBio, University of Surrey, University of Amsterdam, Icahn School of Medicine at Mount Sinai, Universidade de Brasília, Embrapa, University of Manchester, Imperial College London

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,950

Funders: University of Bristol, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, University of Surrey, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Apoio à Pesquisa do Distrito Federal, Ministério da Saúde, National Institutes of Health, Directorate for Biological Sciences, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, BrisSynBio, National Institute of General Medical Sciences

OpenAlex ID: W3033761774