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Li J, Gong S, Ma Y, Han P, Wang N, Fu Z, Zhang X, Huang X, Yang T, Tong H, Zhao GR, Wu Y, Yuan YJ. Creation of a eukaryotic multiplexed site-specific inversion system and its application for metabolic engineering. Nat Commun 2025; 16:1918. [PMID: 39994248 PMCID: PMC11850598 DOI: 10.1038/s41467-025-57206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 02/12/2025] [Indexed: 02/26/2025] Open
Abstract
The site-specific recombination system is a versatile tool in genome engineering, enabling controlled DNA inversion or deletion at specific sites to generate genetic diversity. The multiplexed inversion system, which preferentially facilitates inversion at reverse-oriented sites rather than deletion at same-oriented sites, has not been found in eukaryotes. Here, we establish a multiplexed site-specific inversion system, Rci51-5/multi-sfxa101, in yeast. Firstly, we develop a high-throughput screening system based on the on/off transcriptional control of multiple markers by DNA inversion. After two rounds of progressively stringent directed evolution, a mutant Rci51-5 shows an ability of multisite inversion and a ~ 1000-fold increase in total inversion efficiency against the wild-type Rci derived from Salmonella typhimurium. Subsequently, we demonstrate that the Rci51-5/multi-sfxa101 system exhibits significantly lower deletion rate than the Cre/multi-loxP system. Using the synthetic metabolic pathway of β-carotene as an example, we illustrate that the system can effectively facilitate promoter substitution in the metabolic pathway, resulting in a more than 7-fold increase in the yield of β-carotene. In summary, we develop a multiplexed site-specific inversion system in eukaryotes, providing an approach to metabolic engineering and a tool for eukaryotic genome manipulation.
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Affiliation(s)
- Jieyi Li
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Simiao Gong
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Yuan Ma
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Peiyan Han
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Nan Wang
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Zongheng Fu
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Xinyi Zhang
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Xinyang Huang
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Tianyu Yang
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Hanze Tong
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Guang-Rong Zhao
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China.
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China.
| | - Ying-Jin Yuan
- State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
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Li R, Chen S, Li Y, Chen X, Ye BC. Development of a "Turn off-on" whole-cell biosensor for sulforaphane detection based on the ultrasensitive activator HrpRS. Biotechnol Appl Biochem 2022; 70:798-810. [PMID: 36070874 DOI: 10.1002/bab.2400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/13/2022] [Indexed: 11/09/2022]
Abstract
Sulforaphane (SFN), a defense secondary metabolite, can be used to predict the health status of plants and also has pharmacological effects, including anticancer, antioxidant, and anti-inflammatory properties. The detection of SFN is therefore of great significance for the prevention and treatment of diseases. In this study, a "Turn off" whole-cell biosensor that can rapidly and robustly respond to the presence of SFN was constructed based on the orthogonal genetic components (hrpR, hrpS, and PhrpL ) of Pseudomonas syringae (PS). The final optimized biosensor, p114(30R-30S), was able to inhibit 91.7% of the fluorescence intensity in the presence of 100-μM SFN. Subsequently, a HrpRS-regulated OFF-ON genetic switch was designed by reconstituting a reverse σ70 promoter on the σ54 -PhrpL promoter sequence; this was coupled with dual-color reporter genes to construct a "Turn off-on" whole-cell SFN biosensor. The PhrpLB variant increased the expression of green fluorescence a factor of 11.9 and reduced the expression of red fluorescence by 85.8% compared with the system in the absence of SFN. Thus, a robust switching of signal output from "turn off" to "turn on" was realized. In addition, the biosensor showed good linearity in the SFN concentration ranges of 0.1-10 μM (R2 = 0.99429) and 10-100 μM (R2 = 0.99465) and a detection limit of ⁓0.1 μM. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Renjie Li
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China
| | - Shengyan Chen
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China
| | - Yangguang Li
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China
| | - Xuan Chen
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China
| | - Bang-Ce Ye
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, 832003, China.,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.,Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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Becklin KL, Draper GM, Madden RA, Kluesner MG, Koga T, Huang M, Weiss WA, Spector LG, Largaespada DA, Moriarity BS, Webber BR. Developing Bottom-Up Induced Pluripotent Stem Cell Derived Solid Tumor Models Using Precision Genome Editing Technologies. CRISPR J 2022; 5:517-535. [PMID: 35972367 PMCID: PMC9529369 DOI: 10.1089/crispr.2022.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genome and tissue engineering have spurred significant progress and opportunity for innovation in cancer modeling. Human induced pluripotent stem cells (iPSCs) are an established and powerful tool to study cellular processes in the context of disease-specific genetic backgrounds; however, their application to cancer has been limited by the resistance of many transformed cells to undergo successful reprogramming. Here, we review the status of human iPSC modeling of solid tumors in the context of genetic engineering, including how base and prime editing can be incorporated into "bottom-up" cancer modeling, a term we coined for iPSC-based cancer models using genetic engineering to induce transformation. This approach circumvents the need to reprogram cancer cells while allowing for dissection of the genetic mechanisms underlying transformation, progression, and metastasis with a high degree of precision and control. We also discuss the strengths and limitations of respective engineering approaches and outline experimental considerations for establishing future models.
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Affiliation(s)
- Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Garrett M. Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca A. Madden
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, La Jolla, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Miller Huang
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - William A. Weiss
- Departments of Neurology, Pediatrics, Neurosurgery, Brain Tumor Research Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; and Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - David A. Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
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