Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies

Isaac N. Nuñez, Tamara F. Matute, Ilenne D. Del Valle, Anton Kan, Atri Choksi, Drew Endy, Jim Haseloff, Timothy J. Rudge, Fernan Federici

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

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.

Original languageEnglish
Pages (from-to)256-265
Number of pages10
JournalACS Synthetic Biology
Volume6
Issue number2
DOIs
StatePublished - Feb 17 2017
Externally publishedYes

Funding

T.J.R. A.K., and J.H. were supported by the UK Biotechnological and Biological Sciences Research Council (BBSRC) Synthetic Biology Research Centre Open Plant award (BB/L014130/1), F.F. was supported by CONICYT-PAI/Concurso Nacional de Apoyo al Retorno de Investigadores/as desde el Extranjero Folio 82130027, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), Millennium Nucleus Center for Plant Systems and Synthetic Biology (NC130030) and Fondecyt Iniciacion 11140776. A.K. was also supported by BBSRC CASE studentship in partnership with Microsoft Research. A.C. and D.E. were supported by NSF GRFP fellowship and Stanford University. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-114747 and additional support was provided by Stanford University. The authors would like to thank Rodrigo Gutierrez and his group (PUC, Chile) for support and useful comments, Joseph Torella and Pam Silver for UNSes vectors, Cambridge 2009 iGEM team for violacein operon, Registry of Biological Parts (MIT) for RNAPT7 fluorescent proteins, and pSB4K5 vector. pdCas9 was a gift from Luciano Marraffini (Addgene plasmid # 46569).

Keywords

  • CRISPR
  • modeling
  • morphogenesis
  • morphogenetic engineering
  • synthetic biology

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