Roadmap to Building a Cell: An Evolutionary Approach

Laboratory synthesis of an elementary biological cell from isolated components may aid in understanding of the fundamental principles of life and will provide a platform for a range of bioengineering and medical applications. In essence, building a cell consists in the integration of cellular modules into system’s level functionalities satisfying a definition of life. To achieve this goal, we propose in this perspective to undertake a semi-rational, system’s level evolutionary approach. The strategy would require iterative cycles of genetic integration of functional modules, diversification of hereditary information, compartmentalized gene expression, selection/screening, and possibly, assistance from open-ended evolution. We explore the underlying challenges to each of these steps and discuss possible solutions toward the bottom-up construction of an artificial living cell.

[1]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[2]  Fumihito Arai,et al.  Intelligent image-activated cell sorting 2.0. , 2020, Lab on a chip.

[3]  Kepa Ruiz-Mirazo,et al.  Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems , 2017, Open Biology.

[4]  Susan Stepney,et al.  Defining and simulating open-ended novelty: requirements, guidelines, and challenges , 2016, Theory in Biosciences.

[5]  Fumihito Arai,et al.  Intelligent Image-Activated Cell Sorting , 2018, Cell.

[6]  Takuya Ueda,et al.  Cell-free translation reconstituted with purified components , 2001, Nature Biotechnology.

[7]  Ryota Fujii,et al.  Error-prone rolling circle amplification greatly simplifies random mutagenesis. , 2014, Methods in molecular biology.

[8]  Tetsuya Yomo,et al.  Liposome display for in vitro selection and evolution of membrane proteins , 2014, Nature Protocols.

[9]  F. Arnold,et al.  Innovation by Evolution: Bringing New Chemistry to Life (Nobel Lecture). , 2019, Angewandte Chemie.

[10]  P. Stano.  Gene Expression Inside Liposomes: From Early Studies to Current Protocols. , 2019, Chemistry.

[11]  Jamie L. Marshall,et al.  Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor , 2019, Nature Biotechnology.

[12]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[13]  Tetsuya Yomo,et al.  In vitro evolution of proteins. , 2006, Journal of bioscience and bioengineering.

[14]  P. Hogeweg,et al.  Conceptualizing the origin of life in terms of evolution , 2017, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[15]  Gaelen T. Hess,et al.  Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells , 2016, Nature Methods.

[16]  J. Szostak,et al.  In vitro selection of functional nucleic acids. , 1999, Annual review of biochemistry.

[17]  P. Schwille,et al.  Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. , 2017, New biotechnology.

[18]  Vincent Noireaux,et al.  Development of an artificial cell, from self-organization to computation and self-reproduction , 2011 .

[19]  K. Ruiz-Mirazo,et al.  A Universal Definition of Life: Autonomy and Open-Ended Evolution , 2004, Origins of life and evolution of the biosphere.

[20]  Tetsuya Yomo,et al.  Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes , 2012, Journal of nucleic acids.

[21]  Christophe Danelon,et al.  Self-replication of DNA by its encoded proteins in liposome-based synthetic cells , 2018, Nature Communications.

[22]  Tim Taylor,et al.  Evolutionary Innovations and Where to Find Them: Routes to Open-Ended Evolution in Natural and Artificial Systems , 2018, Artificial Life.

[23]  Huimin Zhao,et al.  Applying Advanced DNA Assembly Methods to Generate Pathway Libraries , 2018 .

[24]  Martin Fussenegger,et al.  Synthetic Biology-The Synthesis of Biology. , 2017, Angewandte Chemie.

[25]  G. Verleden,et al.  Foreword , 1992, Steroids.

[26]  Alvaro Moreno,et al.  Autonomy in evolution: from minimal to complex life , 2012, Synthese.

[27]  Xiaoyuan Chen,et al.  Artificial cells: from basic science to applications , 2016, Materials today.

[28]  Swapnil Bhatia,et al.  Functional optimization of gene clusters by combinatorial design and assembly , 2014, Nature Biotechnology.

[29]  Christophe Danelon,et al.  Toward the assembly of a minimal divisome , 2014, Systems and Synthetic Biology.

[30]  M. Mahfouz,et al.  CRISPR base editors: genome editing without double-stranded breaks , 2018, The Biochemical journal.

[31]  A. Pross.  The Evolutionary Origin of Biological Function and Complexity , 2013, Journal of Molecular Evolution.

[32]  Bastiaan C. Buddingh,et al.  Artificial Cells: Synthetic Compartments with Life-like Functionality and Adaptivity , 2017, Accounts of chemical research.

[33]  J. Reisse,et al.  Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry , 2010, Origins of Life and Evolution of Biospheres.

[34]  K. Ruiz-Mirazo,et al.  Definitions of life as epistemic tools that reflect and foster the advance of biological knowledge , 2020, Synthese.

[35]  B. Poolman,et al.  Cell Fuelling and Metabolic Energy Conservation in Synthetic Cells , 2019, Chembiochem : a European journal of chemical biology.

[36]  Ahmed H Badran,et al.  Modern methods for laboratory diversification of biomolecules. , 2017, Current opinion in chemical biology.

[37]  Alex Lu,et al.  Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting , 2018, bioRxiv.

[38]  S. Roffler,et al.  Transient AID expression for in situ mutagenesis with improved cellular fitness , 2018, Scientific Reports.

[39]  Vincent Noireaux,et al.  Integration of biological parts toward the synthesis of a minimal cell. , 2014, Current opinion in chemical biology.

[40]  George M Church,et al.  Towards synthesis of a minimal cell , 2006, Molecular systems biology.

[41]  David R. Liu,et al.  Methods for the directed evolution of proteins , 2015, Nature Reviews Genetics.

[42]  Pasquale Stano,et al.  Approaches to semi-synthetic minimal cells: a review , 2005, Naturwissenschaften.

[43]  Daniel E. Koshland,et al.  The Seven Pillars of Life , 2002, Science.

[44]  Manuel Porcar,et al.  The long journey towards standards for engineering biosystems , 2020, EMBO reports.

[45]  A. Ellington,et al.  Compartmentalized partnered replication for the directed evolution of genetic parts and circuits , 2017, Nature Protocols.

[46]  J. Voldman,et al.  Image-based single-cell sorting via dual-photopolymerized microwell arrays. , 2014, Analytical chemistry.