Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements
Abstract Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-03-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-45893-w |
| _version_ | 1797266679349116928 |
|---|---|
| author | Naoki Hayashi Yong Lai Jay Fuerte-Stone Mark Mimee Timothy K. Lu |
| author_facet | Naoki Hayashi Yong Lai Jay Fuerte-Stone Mark Mimee Timothy K. Lu |
| author_sort | Naoki Hayashi |
| collection | DOAJ |
| description | Abstract Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine. |
| first_indexed | 2024-04-25T01:04:31Z |
| format | Article |
| id | doaj.art-16a155c2953f4ff78cb197b9d63816ff |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-25T01:04:31Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-16a155c2953f4ff78cb197b9d63816ff2024-03-10T12:17:37ZengNature PortfolioNature Communications2041-17232024-03-0115111710.1038/s41467-024-45893-wCas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elementsNaoki Hayashi0Yong Lai1Jay Fuerte-Stone2Mark Mimee3Timothy K. Lu4Department of Biological Engineering, Massachusetts Institute of TechnologySynthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT)Department of Microbiology, The University of ChicagoDepartment of Microbiology, The University of ChicagoDepartment of Biological Engineering, Massachusetts Institute of TechnologyAbstract Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.https://doi.org/10.1038/s41467-024-45893-w |
| spellingShingle | Naoki Hayashi Yong Lai Jay Fuerte-Stone Mark Mimee Timothy K. Lu Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements Nature Communications |
| title | Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| title_full | Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| title_fullStr | Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| title_full_unstemmed | Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| title_short | Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| title_sort | cas9 assisted biological containment of a genetically engineered human commensal bacterium and genetic elements |
| url | https://doi.org/10.1038/s41467-024-45893-w |
| work_keys_str_mv | AT naokihayashi cas9assistedbiologicalcontainmentofageneticallyengineeredhumancommensalbacteriumandgeneticelements AT yonglai cas9assistedbiologicalcontainmentofageneticallyengineeredhumancommensalbacteriumandgeneticelements AT jayfuertestone cas9assistedbiologicalcontainmentofageneticallyengineeredhumancommensalbacteriumandgeneticelements AT markmimee cas9assistedbiologicalcontainmentofageneticallyengineeredhumancommensalbacteriumandgeneticelements AT timothyklu cas9assistedbiologicalcontainmentofageneticallyengineeredhumancommensalbacteriumandgeneticelements |