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Zhang Y, Bailey TS, Hittmeyer P, Dubois LJ, Theys J, Lambin P. Multiplex genetic manipulations in Clostridium butyricum and Clostridium sporogenes to secrete recombinant antigen proteins for oral-spore vaccination. Microb Cell Fact 2024; 23:119. [PMID: 38659027 PMCID: PMC11040787 DOI: 10.1186/s12934-024-02389-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Clostridium spp. has demonstrated therapeutic potential in cancer treatment through intravenous or intratumoral administration. This approach has expanded to include non-pathogenic clostridia for the treatment of various diseases, underscoring the innovative concept of oral-spore vaccination using clostridia. Recent advancements in the field of synthetic biology have significantly enhanced the development of Clostridium-based bio-therapeutics. These advancements are particularly notable in the areas of efficient protein overexpression and secretion, which are crucial for the feasibility of oral vaccination strategies. Here, we present two examples of genetically engineered Clostridium candidates: one as an oral cancer vaccine and the other as an antiviral oral vaccine against SARS-CoV-2. RESULTS Using five validated promoters and a signal peptide derived from Clostridium sporogenes, a series of full-length NY-ESO-1/CTAG1, a promising cancer vaccine candidate, expression vectors were constructed and transformed into C. sporogenes and Clostridium butyricum. Western blotting analysis confirmed efficient expression and secretion of NY-ESO-1 in clostridia, with specific promoters leading to enhanced detection signals. Additionally, the fusion of a reported bacterial adjuvant to NY-ESO-1 for improved immune recognition led to the cloning difficulties in E. coli. The use of an AUU start codon successfully mitigated potential toxicity issues in E. coli, enabling the secretion of recombinant proteins in C. sporogenes and C. butyricum. We further demonstrate the successful replacement of PyrE loci with high-expression cassettes carrying NY-ESO-1 and adjuvant-fused NY-ESO-1, achieving plasmid-free clostridia capable of secreting the antigens. Lastly, the study successfully extends its multiplex genetic manipulations to engineer clostridia for the secretion of SARS-CoV-2-related Spike_S1 antigens. CONCLUSIONS This study successfully demonstrated that C. butyricum and C. sporogenes can produce the two recombinant antigen proteins (NY-ESO-1 and SARS-CoV-2-related Spike_S1 antigens) through genetic manipulations, utilizing the AUU start codon. This approach overcomes challenges in cloning difficult proteins in E. coli. These findings underscore the feasibility of harnessing commensal clostridia for antigen protein secretion, emphasizing the applicability of non-canonical translation initiation across diverse species with broad implications for medical or industrial biotechnology.
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Affiliation(s)
- Yanchao Zhang
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands.
| | - Tom S Bailey
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Philip Hittmeyer
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
- LivingMed Biotech BV, Clos Chanmurly 13, Liège, 4000, Belgium
| | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Jan Theys
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands.
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Yang Q, Zaongo SD, Zhu L, Yan J, Yang J, Ouyang J. The Potential of Clostridium butyricum to Preserve Gut Health, and to Mitigate Non-AIDS Comorbidities in People Living with HIV. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10227-1. [PMID: 38336953 DOI: 10.1007/s12602-024-10227-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
A dramatic reduction in mortality among people living with HIV (PLWH) has been achieved during the modern antiretroviral therapy (ART) era. However, ART does not restore gut barrier function even after long-term viral suppression, allowing microbial products to enter the systemic blood circulation and induce chronic immune activation. In PLWH, a chronic state of systemic inflammation exists and persists, which increases the risk of development of inflammation-associated non-AIDS comorbidities such as metabolic disorders, cardiovascular diseases, and cancer. Clostridium butyricum is a human butyrate-producing symbiont present in the gut microbiome. Convergent evidence has demonstrated favorable effects of C. butyricum for gastrointestinal health, including maintenance of the structural and functional integrity of the gut barrier, inhibition of pathogenic bacteria within the intestine, and reduction of microbial translocation. Moreover, C. butyricum supplementation has been observed to have a positive effect on various inflammation-related diseases such as diabetes, ulcerative colitis, and cancer, which are also recognized as non-AIDS comorbidities associated with epithelial gut damage. There is currently scant published research in the literature, focusing on the influence of C. butyricum in the gut of PLWH. In this hypothesis review, we speculate the use of C. butyricum as a probiotic oral supplementation may well emerge as a potential future synergistic adjunctive strategy in PLWH, in tandem with ART, to restore and consolidate intestinal barrier integrity, repair the leaky gut, prevent microbial translocation from the gut, and reduce both gut and systemic inflammation, with the ultimate objective of decreasing the risk for development of non-AIDS comorbidities in PLWH.
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Affiliation(s)
- Qiyu Yang
- Department of Radiation Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Silvere D Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Lijiao Zhu
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiangyu Yan
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiadan Yang
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China.
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Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
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Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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Kukhtar D, Fussenegger M. Synthetic biology in multicellular organisms: Opportunities in nematodes. Biotechnol Bioeng 2023. [PMID: 37448225 DOI: 10.1002/bit.28497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/27/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has mainly focused on introducing new or altered functionality in single cell systems: primarily bacteria, yeast, or mammalian cells. Here, we describe the extension of synthetic biology to nematodes, in particular the well-studied model organism Caenorhabditis elegans, as a convenient platform for developing applications in a multicellular setting. We review transgenesis techniques for nematodes, as well as the application of synthetic biology principles to construct nematode gene switches and genetic devices to control motility. Finally, we discuss potential applications of engineered nematodes.
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Affiliation(s)
- Dmytro Kukhtar
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Faculty of Life Science, University of Basel, Basel, Switzerland
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Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
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Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
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Wang G, Yang Y, Zhang S, Lan H, Zheng X. The biological activity and signaling profile of EGF/EGFR were affected under heat stress conditions in IEC6 cells. Gen Comp Endocrinol 2022; 325:114050. [PMID: 35561788 DOI: 10.1016/j.ygcen.2022.114050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 02/03/2023]
Abstract
Epidermal growth factor (EGF) is an effective cytoprotective peptide. It is the main nutritional factor involved in the development of the intestinal tract. It has many important biological effects on the intestinal mucosa. After binding to epidermal growth factor receptor (EGFR), it initiates a signal transduction cascade to jointly promote the migration, proliferation, and differentiation of various cell types. Heat stress severely affects the intestinal health of livestock and is becoming increasingly prevalent due to the yearly increase in ambient temperature and intestinal diseases. However, the effect of heat stress on the activity and signaling of EGF/EGFR in intestinal cells is still unclear. Therefore, rat intestinal crypt epithelial cell line (IEC6) was used as a model to explore this issue, and the results showed that EGF/EGFR is internalized into IEC6 cells in a time-dependent manner under physiological conditions. However, the activity of EGF/EGFR was altered under heat stress. Furthermore, we explored the effect of heat stress on EGF/EGFR-activated signaling transduction in IEC6 cells, and the results showed that levels of factors involved in EGFR-mediated intracellular signaling (such as EGFR, signal transducers and activators of transcription 3/protein kinase B, and extracellular regulatory kinase 1/2) were downregulated under heat stress. In summary, this study shows that heat stress could damage the biological activity and intracellular signaling of EGF/EGFR. These findings have scientific importance in the field of animal husbandry; and lay the foundation for the further study of the biological activities of EGF/EGFR in the intestine.
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Affiliation(s)
- Guoxia Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yu Yang
- Beijing Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences 100193, China
| | - Shuai Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Hainan Lan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xin Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
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Effect of Clostridium butyricum on Gastrointestinal Infections. Biomedicines 2022; 10:biomedicines10020483. [PMID: 35203691 PMCID: PMC8962260 DOI: 10.3390/biomedicines10020483] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Clostridium butyricum is a human commensal bacterium with beneficial effects including butyrate production, spore formation, increasing levels of beneficial bacteria, and inhibition of pathogenic bacteria. Owing to its preventive and ameliorative effects on gastrointestinal infections, C. butyricum MIYAIRI 588 (CBM 588) has been used as a probiotic in clinical and veterinary medicine for decades. This review summarizes the effects of C. butyricum, including CBM 588, on bacterial gastrointestinal infections. Further, the characteristics of the causative bacteria, examples of clinical and veterinary use, and mechanisms exploited in basic research are presented. C. butyricum is widely effective against Clostoridioides difficile, the causative pathogen of nosocomial infections; Helicobacter pylori, the causative pathogen of gastric cancer; and antibiotic-resistant Escherichia coli. Accordingly, its mechanism is gradually being elucidated. As C. butyricum is effective against gastrointestinal infections caused by antibiotics-induced dysbiosis, it can inhibit the transmission of antibiotic-resistant genes and maintain homeostasis of the gut microbiome. Altogether, C. butyricum is expected to be one of the antimicrobial-resistance (AMR) countermeasures for the One-health approach.
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Native and Engineered Probiotics: Promising Agents against Related Systemic and Intestinal Diseases. Int J Mol Sci 2022; 23:ijms23020594. [PMID: 35054790 PMCID: PMC8775704 DOI: 10.3390/ijms23020594] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Intestinal homeostasis is a dynamic balance involving the interaction between the host intestinal mucosa, immune barrier, intestinal microecology, nutrients, and metabolites. Once homeostasis is out of balance, it will increase the risk of intestinal diseases and is also closely associated with some systemic diseases. Probiotics (Escherichia coli Nissle 1917, Akkermansia muciniphila, Clostridium butyricum, lactic acid bacteria and Bifidobacterium spp.), maintaining the gut homeostasis through direct interaction with the intestine, can also exist as a specific agent to prevent, alleviate, or cure intestinal-related diseases. With genetic engineering technology advancing, probiotics can also show targeted therapeutic properties. The aims of this review are to summarize the roles of potential native and engineered probiotics in oncology, inflammatory bowel disease, and obesity, discussing the therapeutic applications of these probiotics.
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