title: Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies.
abstract: Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, morphologies, and architectures in systems composed of multiple agents such as cells and swarm robots. Synthetic biology, on the other hand, aims to develop tools and formalisms that increase reproducibility, tractability, and efficiency in the engineering of biological systems. We seek to apply synthetic biology approaches to the engineering of morphologies in multicellular systems. Here, we describe the engineering of two mechanisms, symmetry-breaking and domain-specific cell regulation, as elementary functions for the prototyping of morphogenetic instructions in bacterial colonies. The former represents an artificial patterning mechanism based on plasmid segregation while the latter plays the role of artificial cell differentiation by spatial colocalization of ubiquitous and segregated components. This separation of patterning from actuation facilitates the design-build-test-improve engineering cycle. We created computational modules for CellModeller representing these basic functions and used it to guide the design process and explore the design space in silico. We applied these tools to encode spatially structured functions such as metabolic complementation, RNAPT7 gene expression, and CRISPRi/Cas9 regulation. Finally, as a proof of concept, we used CRISPRi/Cas technology to regulate cell growth by controlling methionine synthesis. These mechanisms start from single cells enabling the study of morphogenetic principles and the engineering of novel population scale structures from the bottom up.
authors: Escuela de Ingeniería, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.|Fondo de Desarrollo de Areas Prioritarias Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
authors: Isaac N
authors: IN
authors: Nuñez
authors: Escuela de Ingeniería, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.|Fondo de Desarrollo de Areas Prioritarias Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
authors: Tamara F
authors: TF
authors: Matute
authors: Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , 8331150, Santiago, Chile.
authors: Ilenne D
authors: ID
authors: Del Valle
authors: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge, CB2 3EA, United Kingdom.
authors: Anton
authors: A
authors: Kan
authors: Department of Bioengineering, Stanford University , Stanford, California 94305, United States.
authors: Atri
authors: A
authors: Choksi
authors: Department of Bioengineering, Stanford University , Stanford, California 94305, United States.
authors: Drew
authors: D
authors: Endy
authors: Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge, CB2 3EA, United Kingdom.
authors: Jim
authors: J
authors: Haseloff
authors: Escuela de Ingeniería, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
authors: Timothy J
authors: TJ
authors: Rudge
authors: Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , 8331150, Santiago, Chile.|Department of Plant Sciences, University of Cambridge , Downing Street, Cambridge, CB2 3EA, United Kingdom.|Fondo de Desarrollo de Areas Prioritarias Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
authors: Fernan
authors: F
authors: Federici
mesh_terms: D001419:Bacteria / Q000235:genetics*; D064113:CRISPR-Cas Systems / Q000235:genetics; D003198:Computer Simulation; D015870:Gene Expression / Q000235:genetics; D005818:Genetic Engineering / Q000379:methods; D008715:Methionine / Q000235:genetics; D012313:RNA / Q000235:genetics; D015203:Reproducibility of Results; D058615:Synthetic Biology / Q000379:methods
chemical_list: D012313:RNA; D008715:Methionine
keywords: CRISPR; modeling; morphogenesis; morphogenetic engineering; synthetic biology