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Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci Adv 2023; 9:eade1285. [PMID: 36897939 PMCID: PMC10005180 DOI: 10.1126/sciadv.ade1285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/01/2023] [Indexed: 05/31/2023]
Abstract
Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration of exogenous DNA with well-characterized functions remains limited to model bacteria. Here, we describe serine recombinase-assisted genome engineering, or SAGE, an easy-to-use, highly efficient, and extensible technology that enables selection marker-free, site-specific genome integration of up to 10 DNA constructs, often with efficiency on par with or superior to replicating plasmids. SAGE uses no replicating plasmids and thus lacks the host range limitations of other genome engineering technologies. We demonstrate the value of SAGE by characterizing genome integration efficiency in five bacteria that span multiple taxonomy groups and biotechnology applications and by identifying more than 95 heterologous promoters in each host with consistent transcription across environmental and genetic contexts. We anticipate that SAGE will rapidly expand the number of industrial and environmental bacteria compatible with high-throughput genetics and synthetic biology.
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Affiliation(s)
- Joshua R. Elmore
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gara N. Dexter
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Henri Baldino
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jay D. Huenemann
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996,USA
| | - Ryan Francis
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - George L. Peabody
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Jessica Martinez-Baird
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Lauren A. Riley
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996,USA
| | - Tuesday Simmons
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94701, USA
| | - Devin Coleman-Derr
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94701, USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Robert G. Egbert
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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