Efficient retroelement-mediated DNA writing in bacteria

Fahim Farzadfard; Nava Gharaei; Robert J Citorik; Timothy K Lu

doi:10.1016/j.cels.2021.07.001

Efficient retroelement-mediated DNA writing in bacteria

Cell Syst. 2021 Sep 22;12(9):860-872.e5. doi: 10.1016/j.cels.2021.07.001. Epub 2021 Aug 5.

Authors

Fahim Farzadfard¹, Nava Gharaei², Robert J Citorik³, Timothy K Lu⁴

Affiliations

¹ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address: ffard@mit.edu.
² MCO Graduate Program, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
³ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
⁴ Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA; MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address: timlu@mit.edu.

PMID: 34358440
DOI: 10.1016/j.cels.2021.07.001

Abstract

The ability to efficiently and dynamically change information stored in genomes would enable powerful strategies for studying cell biology and controlling cellular phenotypes. Current recombineering-mediated DNA writing platforms in bacteria are limited to specific laboratory conditions, often suffer from suboptimal editing efficiencies, and are not suitable for in situ applications. To overcome these limitations, we engineered a retroelement-mediated DNA writing system that enables efficient and precise editing of bacterial genomes without the requirement for target-specific elements or selection. We demonstrate that this DNA writing platform enables a broad range of applications, including efficient, scarless, and cis-element-independent editing of targeted microbial genomes within complex communities, the high-throughput mapping of spatial information and cellular interactions into DNA memory, and the continuous evolution of cellular traits.

Keywords: DNA memory; DNA writing; cellular connectome mapping; editing microbial communities in situ; in vivo evolution.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacteria* / genetics
Genome, Bacterial / genetics
Retroelements* / genetics
Writing

Substances

Retroelements