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Haryani Y, Halid NA, Guat GS, Nor-Khaizura MAR, Hatta MAM, Sabri S, Radu S, Hasan H. Efficient Metabolic Pathway Modification in Various Strains of Lactic Acid Bacteria using CRISPR/Cas9 System for elevated synthesis of Antimicrobial Compounds. J Biotechnol 2024:S0168-1656(24)00239-6. [PMID: 39245212 DOI: 10.1016/j.jbiotec.2024.09.002] [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: 04/05/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
Lactic acid bacteria (LAB) are known to exhibit various beneficial roles in fermentation, serving as probiotics, and producing a plethora of valuable compounds including compounds with antimicrobial activity including bacteriocin-like inhibitory substance (BLIS) that can be used as biopreservative to improve food safety and quality. However, the yield of BLIS is often limited, which poses a challenge to be commercially competitive with the current preservation practice. Therefore, the present work aimed to establish an optimised two-plasmid CRISPR/Cas9 system to redirect the carbon flux away from lactate towards compounds with antimicrobial activity by disrupting lactate dehydrogenase gene (ldh) on various strains of LAB. The lactic acid-deficient (ldhΔ) strains caused a metabolic shift resulting in increased inhibitory activity against selected foodborne pathogens up to 78% than the wild-type (WT) strain. The most significant effect was depicted by Enterococcus faecalis-ldh∆ which displayed prominent bactericidal effects against all foodborne pathogens as compared to the WT that showed no antimicrobial activity. The present work provided a framework model for economically important LAB and other beneficial bacteria to synthesise and increase the yield of valuable food and industrial compounds. The present work reported for the first time that the metabolism of selected LAB can be manipulated by modifying ldh to attain metabolites with higher antimicrobial activity.
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Affiliation(s)
- Yuli Haryani
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Riau University, 28293 Pekanbaru, Riau, Indonesia
| | - Nadrah Abdul Halid
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Goh Sur Guat
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mahmud Ab Rashid Nor-Khaizura
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Hanan Hasan
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Laboratory of Halal Science Research, Halal Research Product Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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2
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Xie Z, McAuliffe O, Jin YS, Miller MJ. Genomic Modifications of Lactic Acid Bacteria and Their Applications in Dairy Fermentation. J Dairy Sci 2024:S0022-0302(24)00981-0. [PMID: 38969005 DOI: 10.3168/jds.2024-24989] [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: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024]
Abstract
Lactic Acid Bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. LAB are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications. Here, this review describes (1) the potential opportunities for application of genetically modified LAB strains in dairy fermentation and (2) the various genomic modification tools for LAB strains, such as random mutagenesis, adaptive laboratory evolution, conjugation, homologous recombination, recombineering, and CRISPR (clustered regularly interspaced short palindromic repeat)- Cas (CRISPR-associated protein) based genome engineering. Lastly, this review also discusses the potential future developments of these genomic modification technologies and their applications in dairy fermentations.
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Affiliation(s)
- Zifan Xie
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Yong-Su Jin
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael J Miller
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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3
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Murali SK, Mansell TJ. Next generation probiotics: Engineering live biotherapeutics. Biotechnol Adv 2024; 72:108336. [PMID: 38432422 DOI: 10.1016/j.biotechadv.2024.108336] [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: 09/16/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
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Affiliation(s)
- Sanjeeva Kumar Murali
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA.
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Campos GM, Américo MF, Dos Santos Freitas A, Barroso FAL, da Cruz Ferraz Dutra J, Quaresma LS, Cordeiro BF, Laguna JG, de Jesus LCL, Fontes AM, Birbrair A, Santos TM, Azevedo V. Lactococcus lactis as an Interleukin Delivery System for Prophylaxis and Treatment of Inflammatory and Autoimmune Diseases. Probiotics Antimicrob Proteins 2024; 16:352-366. [PMID: 36746838 PMCID: PMC9902259 DOI: 10.1007/s12602-023-10041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Target delivery of therapeutic agents with anti-inflammatory properties using probiotics as delivery and recombinant protein expression vehicles is a promising approach for the prevention and treatment of many diseases, such as cancer and intestinal immune disorders. Lactococcus lactis, a Lactic Acid Bacteria (LAB) widely used in the dairy industry, is one of the most important microorganisms with GRAS status for human consumption, for which biotechnological tools have already been developed to express and deliver recombinant biomolecules with anti-inflammatory properties. Cytokines, for example, are immune system communication molecules present at virtually all levels of the immune response. They are essential in cellular and humoral processes, such as hampering inflammation or adjuvating in the adaptive immune response, making them good candidates for therapeutic approaches. This review discusses the advances in the development of new therapies and prophylactic approaches using LAB to deliver/express cytokines for the treatment of inflammatory and autoimmune diseases in the future.
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Affiliation(s)
- Gabriela Munis Campos
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Monique Ferrary Américo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andria Dos Santos Freitas
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Joyce da Cruz Ferraz Dutra
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ludmila Silva Quaresma
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bárbara Fernandes Cordeiro
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Juliana Guimarães Laguna
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Aparecida Maria Fontes
- Genetics Department, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tulio Marcos Santos
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Uniclon Biotecnologia, Belo Horizonte, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Parvin T, Sadras SR. Advanced probiotics: bioengineering and their therapeutic application. Mol Biol Rep 2024; 51:361. [PMID: 38403783 DOI: 10.1007/s11033-024-09309-8] [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: 12/27/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
The role of gut bacteria in human health has long been acknowledged and dysbiosis of the gut microbiota has been correlated with a variety of disorders. Synthetic biology has rapidly grown over the past few years offering a variety of biological applications such as harnessing the relationship between bacteria and human health. Lactic acid bacteria (LAB) are thought to be appropriate chassis organisms for genetic modification with potential biomedical applications. A thorough understanding of the molecular mechanisms behind their beneficial qualities is essential to assist the multifunctional medicinal sectors. Effective genome editing will aid in the creation of next-generation designer probiotics with enhanced resilience and specialized capabilities, furthering our knowledge of the molecular mechanisms behind the physiological impacts of probiotics and their interactions with the host and microbiota. The goal of this review is to provide a brief overview of the methods used to create modified probiotics with the scientific rationale behind gene editing technology, the mechanism of action of engineered probiotics along with their application to treat conditions like inflammatory bowel disease, cancer, bacterial infections, and various metabolic diseases. In addition, application concerns and future directions are also presented.
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Affiliation(s)
- Tamanna Parvin
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India.
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India
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Lv X, Li Y, Xiu X, Liao C, Xu Y, Liu Y, Li J, Du G, Liu L. CRISPR genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnol Adv 2023; 69:108261. [PMID: 37741424 DOI: 10.1016/j.biotechadv.2023.108261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Production of food-related products using microorganisms in an environmentally friendly manner is a crucial solution to global food safety and environmental pollution issues. Traditional microbial modification methods rely on artificial selection or natural mutations, which require time for repeated screening and reproduction, leading to unstable results. Therefore, it is imperative to develop rapid, efficient, and precise microbial modification technologies. This review summarizes recent advances in the construction of gene editing and metabolic regulation toolkits based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems and their applications in reconstructing food microorganism metabolic networks. The development and application of gene editing toolkits from single-site gene editing to multi-site and genome-scale gene editing was also introduced. Moreover, it presented a detailed introduction to CRISPR interference, CRISPR activation, and logic circuit toolkits for metabolic network regulation. Moreover, the current challenges and future prospects for developing CRISPR genetic toolkits were also discussed.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xiang Xiu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chao Liao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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7
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Chen Z, Jin W, Hoover A, Chao Y, Ma Y. Decoding the microbiome: advances in genetic manipulation for gut bacteria. Trends Microbiol 2023; 31:1143-1161. [PMID: 37394299 DOI: 10.1016/j.tim.2023.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 07/04/2023]
Abstract
Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene-host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to 'taming' the gut microbiome, GM tools allow molecular understanding of host-microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.
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Affiliation(s)
- Ziying Chen
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200031, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200031, China; The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenbing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alex Hoover
- Ben May Department for Cancer Research, the University of Chicago, Chicago, IL, USA
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200031, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200031, China.
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Liu L, Helal SE, Peng N. CRISPR-Cas-Based Engineering of Probiotics. BIODESIGN RESEARCH 2023; 5:0017. [PMID: 37849462 PMCID: PMC10541000 DOI: 10.34133/bdr.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Probiotics are the treasure of the microbiology fields. They have been widely used in the food industry, clinical treatment, and other fields. The equivocal health-promoting effects and the unknown action mechanism were the largest obstacles for further probiotic's developed applications. In recent years, various genome editing techniques have been developed and applied to explore the mechanisms and functional modifications of probiotics. As important genome editing tools, CRISPR-Cas systems that have opened new improvements in genome editing dedicated to probiotics. The high efficiency, flexibility, and specificity are the advantages of using CRISPR-Cas systems. Here, we summarize the classification and distribution of CRISPR-Cas systems in probiotics, as well as the editing tools developed on the basis of them. Then, we discuss the genome editing of probiotics based on CRISPR-Cas systems and the applications of the engineered probiotics through CRISPR-Cas systems. Finally, we proposed a design route for CRISPR systems that related to the genetically engineered probiotics.
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Affiliation(s)
- Ling Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, China
| | - Shimaa Elsayed Helal
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Zheng L, Zhang L, Tan F, Wang C, Lv X, Bai R, Huo N, Zheng M. Prevention and control of chicken coccidiosis construction of recombinant Lactococcus lactis expressing chicken IL-4 and IL-2 fusion protein and its immune synergistic effect on chicken coccidia live vaccine. Poult Sci 2023; 102:102530. [PMID: 36805402 PMCID: PMC9969317 DOI: 10.1016/j.psj.2023.102530] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/21/2022] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Intestinal mucosa injury and loss of weight gain are unavoidable while using live vaccine strain to prevent chicken coccidiosis. In this study, recombinant Lactococcus lactis NZ3900/pNZ8149-IL-4-IL-2, expressing the fusion protein of chicken IL-4 and IL-2, was constructed using food-grade NICE expression system, trying to develop a possible oral immune adjuvant to enhance the immune effect of the live vaccine against chicken coccidiosis and minimize its adverse effects. Chickens were given different doses of recombinant L. lactis together with the live vaccine, then experimently attacked with coccidia virulent strains. Results showed that weight gains of co-immunization groups, given both 1 × 109 or 1 × 1010 CFU recombinant L. lactis and the live vaccine, were significantly higher than the vaccine-only group (P<0.05), while intestinal lesion scores of duodenum, jejunum, and cecum were significantly lower than the vaccine-only group (P<0.05), so was the oocyst shedding. The anticoccidial indexes (ACI) of the co-immunized groups given 1 × 109 and 1 × 1010 CFU recombinant L. lactis were 187.85 and 193.33, respectively, higher than 174.61 of the vaccine-only group. In addition, chickens in co-immunization groups gained more body weight than the vaccine-only group before being challenged with the virulent strains (P<0.05). All the results indicated that the constructed recombinant L. lactis NZ3900/ pNZ8149-IL-4-IL-2 exhibited an immune synergistic function to coccidiosis live vaccine, and could alleviate its adverse effect affecting weight gain. The application of the recombinant L. lactis showed the potency to lift the anticoccidial efficiency of the live vaccine from a medium level to a high level.
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Affiliation(s)
| | | | | | | | | | | | - Nairui Huo
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong, 030801, China.
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10
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Recent advances in genetic tools for engineering probiotic lactic acid bacteria. Biosci Rep 2023; 43:232386. [PMID: 36597861 PMCID: PMC9842951 DOI: 10.1042/bsr20211299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.
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11
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Kong LH, Liu TY, Yao QS, Zhang XH, Xu WN, Qin JY. Enhancing the biosynthesis of nicotinamide mononucleotide in Lactococcus lactis by heterologous expression of FtnadE. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:450-456. [PMID: 36205212 DOI: 10.1002/jsfa.12253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Nicotinamide mononucleotide (NMN), a key intermediate of nicotinamide adenine dinucleotide, plays an important in anti-aging and disease. Lactococcus lactis, an important probiotic lactic acid bacteria (LAB), has shown great potential for the biosynthesis of NMN, which will significantly affect the probiotic effects of the dairy products. RESULTS We used the CRISPR/nCas9 technique to knockout nadR gene of L. lactis NZ9000 to enhance the accumulation of NMN by 61%. The nadE* gene from Francisella tularensis with codon optimization was heterologous in L. lactis NZ9000ΔnadR and has a positive effect on NMN production. Combined with optimization of the concentration of substrate nicotinamide, a final intracellular NMN titer was 2289 μmol L-1 mg-1 with 10 g L-1 nicotinamide supplement, which was 5.7-fold higher than that of the control. The transcription levels of key genes (pncA, nadD and prs1) involved in NMN biosynthesis were up-regulated by more than two-fold, indicating that the increase of NMN titer was attributed to FtnadE* heterologous expression. CONCLUSION Our study provides a better understanding of the NMN biosynthesis pathway in L. lactis, and can facilitate NMN production in LAB via synthetic biology approaches. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Ling-Hui Kong
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Tai-Yu Liu
- Shanghai BEIONMED Technology Co., Ltd., Shanghai, China
| | - Qing-Shou Yao
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Xiao-Hua Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Wei-Na Xu
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
| | - Jia-Yang Qin
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong Province, China
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12
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Dong H, Wang H, Fu S, Zhang D. CRISPR/Cas tools for enhancing the biopreservation ability of lactic acid bacteria in aquatic products. Front Bioeng Biotechnol 2022; 10:1114588. [PMID: 36619383 PMCID: PMC9816425 DOI: 10.3389/fbioe.2022.1114588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Lactic acid bacteria (LAB) plays a crucial role in aquatic products biopreservation as it can inhibit many bacteria, in particular the specific spoilage organisms (SSOs) of aquatic products, by competing for nutrients or producing one or more metabolites which have antimicrobial activity, such as bacteriocins. Lactobacillus spp. and Lactococcus spp. are the most commonly used Lactic acid bacterias in aquatic products preservation. The improvement of gene editing tools is particularly important for developing new lactic acid bacteria strains with superior properties for aquatic products biopreservation. This review summarized the research progress of the most widely used CRISPR/Cas-based genome editing tools in Lactobacillus spp. and Lactococcus spp. The genome editing tools based on homologous recombination and base editor were described. Then, the research status of CRISPRi in transcriptional regulation was reviewed briefly. This review may provide a reference for the application of CRISPR/Cas-based genome editing tools to other lactic acid bacteria species.
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Affiliation(s)
- Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,*Correspondence: Huina Dong, ; Dawei Zhang,
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shaoping Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Huina Dong, ; Dawei Zhang,
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13
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Kong L, Xiong Z, Song X, Xia Y, Ai L. CRISPR/dCas9-based metabolic pathway engineering for the systematic optimization of exopolysaccharide biosynthesis in Streptococcus thermophilus. J Dairy Sci 2022; 105:6499-6512. [PMID: 35691751 DOI: 10.3168/jds.2021-21409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Streptococcus thermophilus is used extensively in the dairy industry and has shown great promise as a chassis cell for the biosynthesis of high-value metabolites. However, metabolic engineering in S. thermophilus lacks effective genetic modification tools to modulate gene expression to relieve metabolic burden and maximize the production of desired compounds. Here, we developed a clustered regularly interspaced short palindromic repeats interference (CRISPRi) system for efficient gene transcriptional modulation in S. thermophilus. Our CRISPRi system typically achieved 66 to 98% knockdown of single or multiple gene expression. We used CRISPRi for the biosynthesis of a new exopolysaccharide (EPS) as a paradigm model. Repression of galK at module of uridine diphosphate glucose sugar metabolism and overexpression of epsA and epsE at EPS synthesis module resulted in an approximately 2-fold increase in EPS titer (277 mg/L) when compared with a control strain. This study demonstrated the effectiveness of CRISPRi as a powerful metabolic engineering tool and synthetic biology strategy for S. thermophilus.
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Affiliation(s)
- Linghui Kong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; School of Pharmacy (School of Enology), Binzhou Medical University, Yantai, 264003, Shandong Province, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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14
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
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15
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Kazi TA, Acharya A, Mukhopadhyay BC, Mandal S, Arukha AP, Nayak S, Biswas SR. Plasmid-Based Gene Expression Systems for Lactic Acid Bacteria: A Review. Microorganisms 2022; 10:1132. [PMID: 35744650 PMCID: PMC9229153 DOI: 10.3390/microorganisms10061132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023] Open
Abstract
Lactic acid bacteria (LAB) play a very vital role in food production, preservation, and as probiotic agents. Some of these species can colonize and survive longer in the gastrointestinal tract (GIT), where their presence is crucially helpful to promote human health. LAB has also been used as a safe and efficient incubator to produce proteins of interest. With the advent of genetic engineering, recombinant LAB have been effectively employed as vectors for delivering therapeutic molecules to mucosal tissues of the oral, nasal, and vaginal tracks and for shuttling therapeutics for diabetes, cancer, viral infections, and several gastrointestinal infections. The most important tool needed to develop genetically engineered LABs to produce proteins of interest is a plasmid-based gene expression system. To date, a handful of constitutive and inducible vectors for LAB have been developed, but their limited availability, host specificity, instability, and low carrying capacity have narrowed their spectrum of applications. The current review discusses the plasmid-based vectors that have been developed so far for LAB; their functionality, potency, and constraints; and further highlights the need for a new, more stable, and effective gene expression platform for LAB.
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Affiliation(s)
- Tawsif Ahmed Kazi
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Aparupa Acharya
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Bidhan Chandra Mukhopadhyay
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India;
| | - Ananta Prasad Arukha
- Researcher 5 Department of Neurosurgery, Medical School, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Subhendu Nayak
- Sr. Scientist, Clorox, Better Health VMS, Durham, NC 27701, USA;
| | - Swadesh Ranjan Biswas
- Department of Botany, Visva-Bharati University, Santiniketan 731235, West Bengal, India; (T.A.K.); (A.A.); (B.C.M.)
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16
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Pesce M, Seguella L, Del Re A, Lu J, Palenca I, Corpetti C, Rurgo S, Sanseverino W, Sarnelli G, Esposito G. Next-Generation Probiotics for Inflammatory Bowel Disease. Int J Mol Sci 2022; 23:ijms23105466. [PMID: 35628274 PMCID: PMC9141965 DOI: 10.3390/ijms23105466] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022] Open
Abstract
Engineered probiotics represent a cutting-edge therapy in intestinal inflammatory disease (IBD). Genetically modified bacteria have provided a new strategy to release therapeutically operative molecules in the intestine and have grown into promising new therapies for IBD. Current IBD treatments, such as corticosteroids and immunosuppressants, are associated with relevant side effects and a significant proportion of patients are dependent on these therapies, thus exposing them to the risk of relevant long-term side effects. Discovering new and effective therapeutic strategies is a worldwide goal in this research field and engineered probiotics could potentially provide a viable solution. This review aims at describing the proceeding of bacterial engineering and how genetically modified probiotics may represent a promising new biotechnological approach in IBD treatment.
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Affiliation(s)
- Marcella Pesce
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (M.P.); (S.R.); (G.S.)
| | - Luisa Seguella
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.R.); (I.P.); (C.C.); (G.E.)
- Correspondence: ; Tel.: +39-06-4991-2948
| | - Alessandro Del Re
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.R.); (I.P.); (C.C.); (G.E.)
| | - Jie Lu
- Department of Anatomy and Cell Biology, China Medical University, Shenyang 110122, China;
| | - Irene Palenca
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.R.); (I.P.); (C.C.); (G.E.)
| | - Chiara Corpetti
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.R.); (I.P.); (C.C.); (G.E.)
| | - Sara Rurgo
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (M.P.); (S.R.); (G.S.)
| | | | - Giovanni Sarnelli
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (M.P.); (S.R.); (G.S.)
- Nextbiomics S.r.l., 80100 Naples, Italy;
| | - Giuseppe Esposito
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.D.R.); (I.P.); (C.C.); (G.E.)
- Nextbiomics S.r.l., 80100 Naples, Italy;
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17
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Peter SB, Qiao Z, Godspower HN, Ajeje SB, Xu M, Zhang X, Yang T, Rao Z. Biotechnological Innovations and Therapeutic Application of Pediococcus and Lactic Acid Bacteria: The Next-Generation Microorganism. Front Bioeng Biotechnol 2022; 9:802031. [PMID: 35237589 PMCID: PMC8883390 DOI: 10.3389/fbioe.2021.802031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/08/2021] [Indexed: 01/27/2023] Open
Abstract
Lactic acid bacteria represent a worthwhile organism within the microbial consortium for the food sector, health, and biotechnological applications. They tend to offer high stability to environmental conditions, with an indicated increase in product yield, alongside their moderate antimicrobial activity. Lack of endotoxins and inclusion bodies, extracellular secretion, and surface display with other unique properties, are all winning attributes of these Gram-positive lactic acid bacteria, of which, Pediococcus is progressively becoming an attractive and promising host, as the next-generation probiotic comparable with other well-known model systems. Here, we presented the biotechnological developments in Pediococcal bacteriocin expression system, contemporary variegated models of Pediococcus and lactic acid bacteria strains as microbial cell factory, most recent applications as possible live delivery vector for use as therapeutics, as well as upsurging challenges and future perspective. With the radical introduction of artificial intelligence and neural network in Synthetic Biology, the microbial usage of lactic acid bacteria as an alternative eco-friendly strain, with safe use properties compared with the already known conventional strains is expected to see an increase in various food and biotechnological applications in years to come as it offers better hope of safety, accuracy, and higher efficiency.
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Affiliation(s)
- Sunday Bulus Peter
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhina Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hero Nmeri Godspower
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Samaila Boyi Ajeje
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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18
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19
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Zahirović A, Plavec TV, Berlec A. Dual Functionalized Lactococcus lactis Shows Tumor Antigen Targeting and Cytokine Binding in Vitro. Front Bioeng Biotechnol 2022; 10:822823. [PMID: 35155394 PMCID: PMC8826564 DOI: 10.3389/fbioe.2022.822823] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/10/2022] [Indexed: 01/19/2023] Open
Abstract
Pro-inflammatory cytokines play an important role in the development and progression of colorectal cancer (CRC). Tumor-targeting bacteria that can capture pro-inflammatory cytokines in the tumor microenvironment and thus block their tumor-promoting effects might provide clinical benefits in inflammation-associated CRC. The aim of this study was to develop bacteria with dual functionality for selective delivery of cytokine-binding proteins to the tumor by targeting specific receptors on cancer cells. We engineered a model lactic acid bacterium, Lactococcus lactis, to co-display on its surface a protein ligand for tumor antigens (EpCAM-binding affitin; HER2-binding affibody) and a ligand for pro-inflammatory cytokines (IL-8-binding evasin; IL-6-binding affibody). Genes that encoded protein binders were cloned into a lactococcal dual promoter plasmid, and protein co-expression was confirmed by Western blotting. To assess the removal of IL-8 and IL-6 by the engineered bacteria, we established inflammatory cell models by stimulating cytokine secretion in human colon adenocarcinoma cells (Caco-2; HT-29) and monocyte-like cells (THP-1; U-937). The engineered L. lactis removed considerable amounts of IL-8 from the supernatant of Caco-2 and HT-29 cells, and depleted IL-6 from the supernatant of THP-1 and U-937 cells as determined by ELISA. The tumor targeting properties of the engineered bacteria were evaluated in human embryonic kidney epithelial cells HEK293 transfected to overexpress EpCAM or HER2 receptors. Fluorescence microscopy revealed that the engineered L. lactis specifically adhered to transfected HEK293 cells, where the EpCAM-targeting bacteria exhibited greater adhesion efficiency than the HER2-targeting bacteria. These results confirm the concept that L. lactis can be efficiently modified to display two proteins simultaneously on their surface: a tumor antigen binder and a cytokine binder. Both proteins remain biologically active and provide the bacteria with tumor antigen targeting and cytokine binding ability.
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Affiliation(s)
- Abida Zahirović
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Aleš Berlec,
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20
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Frelet-Barrand A. Lactococcus lactis, an Attractive Cell Factory for the Expression of Functional Membrane Proteins. Biomolecules 2022; 12:180. [PMID: 35204681 PMCID: PMC8961550 DOI: 10.3390/biom12020180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
Membrane proteins play key roles in most crucial cellular processes, ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded membrane proteins in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult to predict whether a protein can be overproduced in a functional state in some expression system(s), though studies of high-throughput screens have been published in recent years. Prokaryotic expression systems present several advantages over eukaryotic ones. Among them, Lactococcus lactis (L. lactis) has emerged in the last two decades as a good alternative expression system to E. coli. The purpose of this chapter is to describe L. lactis and its tightly inducible system, NICE, for the effective expression of membrane proteins from both prokaryotic and eukaryotic origins.
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Affiliation(s)
- Annie Frelet-Barrand
- FEMTO-ST Institute, UMR 6174, CNRS, Université Bourgogne Franche-Comté, 15B Avenue des Montboucons, CEDEX, 25030 Besançon, France
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21
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Henke NA, Göttl VL, Schmitt I, Peters-Wendisch P, Wendisch VF. A synthetic biology approach to study carotenoid production in Corynebacterium glutamicum: Read-out by a genetically encoded biosensor combined with perturbing native gene expression by CRISPRi. Methods Enzymol 2022; 671:383-419. [DOI: 10.1016/bs.mie.2021.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Plavec TV, Ključevšek T, Berlec A. Introduction of Modified BglBrick System in Lactococcus lactis for Straightforward Assembly of Multiple Gene Cassettes. Front Bioeng Biotechnol 2021; 9:797521. [PMID: 34957084 PMCID: PMC8703077 DOI: 10.3389/fbioe.2021.797521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/29/2021] [Indexed: 02/01/2023] Open
Abstract
Genetic modification of lactic acid bacteria is an evolving and highly relevant field of research that allows the engineered bacteria to be equipped with the desired functions through the controlled expression of the recombinant protein. Novel genetic engineering techniques offer the advantage of being faster, easier and more efficient in incorporating modifications to the original bacterial strain. Here, we have developed a modified BglBrick system, originally introduced in Escherichia coli and optimized it for the lactic acid bacterium Lactococcus lactis. Six different expression cassettes, encoding model proteins, were assembled in different order as parts of a modified BglBrick system in a novel plasmid pNBBX. All cassettes included nisin promoter, protein encoding gene and transcription terminator. We demonstrated successful intracellular expression of the two fluorescent proteins and display of the four protein binders on the bacterial surface. These were expressed either alone or concomitantly, in combinations of three model proteins. Thus, a modified BglBrick system developed herein enables simple and modular construction of multigene plasmids and controlled simultaneous expression of three proteins in L. lactis.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tim Ključevšek
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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23
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Song X, Liu L, Liu XX, Xiong ZQ, Xie CL, Wang SJ, Ai LZ. Single-plasmid systems based on CRISPR-Cas9 for gene editing in Lactococcus lactis. J Dairy Sci 2021; 104:10576-10585. [PMID: 34275631 DOI: 10.3168/jds.2020-19901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/15/2021] [Indexed: 01/20/2023]
Abstract
Lactococcus lactis is a food-grade lactic acid bacterial species that is widely used in food and medical industries. Due to its relatively small genome and simple metabolism, L. lactis is commonly engineered to produce large quantities of recombinant proteins. The most common single-gene knockout strategy in L. lactis involves RecA-dependent homologous double-crossover recombination, which is relatively time-consuming and laborious. In this study, a precise and efficient genome-editing plasmid for L. lactis NZ9000 genome engineering, pLL, was established based on clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology. By studying the effects of different single guide RNA (sgRNA) promoters, the efficiency of gene deletion was optimized. For LLNZ_02045 (ldh), gene deletion efficiency of up to 50% was achieved. Effective sequential gene deletion of LLNZ_11240 (upp) and LLNZ_04580 (upp1) was also demonstrated using this tool. Additionally, the gene that encodes for uracil phosphoribosyltransferase was identified using this system. Similar robust gene deletion efficiencies of sgRNA that targeted different regions of a single gene suggested that gene deletion was not affected by the location of sgRNA binding. Thus, our study established a new gene-editing tool that may allow further investigation and understanding of the L. lactis NZ9000 genome.
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Affiliation(s)
- Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lu Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin-Xin Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Chun-Liang Xie
- Institute of Bast Fiber Crop, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Shij-Jie Wang
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, Hebei, China; Shijiazhuang Junlebao Dairy Co. Ltd., Shijiazhuang 050211, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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24
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Plavec TV, Mitrović A, Perišić Nanut M, Štrukelj B, Kos J, Berlec A. Targeting of fluorescent Lactococcus lactis to colorectal cancer cells through surface display of tumour-antigen binding proteins. Microb Biotechnol 2021; 14:2227-2240. [PMID: 34347360 PMCID: PMC8449671 DOI: 10.1111/1751-7915.13907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Development of targeted treatment for colorectal cancer is crucial to avoid side effects. To harness the possibilities offered by microbiome engineering, we prepared safe multifunctional cancer cell-targeting bacteria Lactococcus lactis. They displayed, on their surface, binding proteins for cancer-associated transmembrane receptors epithelial cell adhesion molecule (EpCAM) and human epidermal growth factor receptor 2 (HER2) and co-expressed an infrared fluorescent protein for imaging. Binding of engineered L. lactis to tumour antigens EpCAM and HER2 was confirmed and characterised in vitro using soluble receptors. The proof-of-principle of targeting was demonstrated on human cell lines HEK293, HT-29 and Caco-2 with fluorescent microscopy and flow cytometry. The highest L. lactis adhesion was seen for the HEK293 cells with the overexpressed tumour antigens, where colocalisation with their tumour antigens was seen for 39% and 67% of EpCAM-targeting and HER2-targeting bacteria, respectively. On the other hand, no binding was observed to HEK293 cells without tumour antigens, confirming the selectivity of the engineered L. lactis. Apart from cell targeting in static conditions, targeting ability of engineered L. lactis was also shown in conditions of constant flow of bacterial suspension over the HEK293 cells. Successful targeting by engineered L. lactis support the future use of these bacteria in biopharmaceutical delivery for the treatment of colorectal cancer.
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Affiliation(s)
- Tina Vida Plavec
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Ana Mitrović
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
| | | | - Borut Štrukelj
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Janko Kos
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Aleš Berlec
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
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25
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Dorau R, Liu J, Solem C, Jensen PR. Metabolic Engineering of Lactic Acid Bacteria. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Watthanasakphuban N, Virginia LJ, Haltrich D, Peterbauer C. Analysis and Reconstitution of the Menaquinone Biosynthesis Pathway in Lactiplantibacillus plantarum and Lentilactibacillus buchneri. Microorganisms 2021; 9:1476. [PMID: 34361912 PMCID: PMC8303990 DOI: 10.3390/microorganisms9071476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022] Open
Abstract
In Lactococcus lactis and some other lactic acid bacteria, respiratory metabolism has been reported upon supplementation with only heme, leading to enhanced biomass formation, reduced acidification, resistance to oxygen, and improved long-term storage. Genes encoding a complete respiratory chain with all components were found in genomes of L. lactis and Leuconostoc mesenteroides, but menaquinone biosynthesis was found to be incomplete in Lactobacillaceae (except L. mesenteroides). Lactiplantibacillus plantarum has only two genes (menA, menG) encoding enzymes in the biosynthetic pathway (out of eight), and Lentilactobacillus buchneri has only four (menA, menB, menE, and menG). We constructed knock-out strains of L. lactis defective in menA, menB, menE, and menG (encoding the last steps in the pathway) and complemented these by expression of the extant genes from Lactipl. plantarum and Lent. buchneri to verify their functionality. Three of the Lactipl. plantarum biosynthesis genes, lpmenA1, lpmenG1, and lpmenG2, as well as lbmenB and lbmenG from Lent. buchneri, reconstituted menaquinone production and respiratory growth in the deficient L. lactis strains when supplemented with heme. We then reconstituted the incomplete menaquinone biosynthesis pathway in Lactipl. plantarum by expressing six genes from L. lactis homologous to the missing genes in a synthetic operon with two inducible promoters. Higher biomass formation was observed in Lactipl. plantarum carrying this operon, with an OD600 increase from 3.0 to 5.0 upon induction.
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Affiliation(s)
- Nisit Watthanasakphuban
- Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (N.W.); (L.J.V.); (D.H.)
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ludovika Jessica Virginia
- Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (N.W.); (L.J.V.); (D.H.)
| | - Dietmar Haltrich
- Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (N.W.); (L.J.V.); (D.H.)
| | - Clemens Peterbauer
- Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (N.W.); (L.J.V.); (D.H.)
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Wu J, Xin Y, Kong J, Guo T. Genetic tools for the development of recombinant lactic acid bacteria. Microb Cell Fact 2021; 20:118. [PMID: 34147119 PMCID: PMC8214781 DOI: 10.1186/s12934-021-01607-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Lactic acid bacteria (LAB) are a phylogenetically diverse group with the ability to convert soluble carbohydrates into lactic acid. Many LAB have a long history of safe use in fermented foods and are recognized as food-grade microorganisms. LAB are also natural inhabitants of the human intestinal tract and have beneficial effects on health. Considering these properties, LAB have potential applications as biotherapeutic vehicles to delivery cytokines, antigens and other medicinal molecules. In this review, we summarize the development of, and advances in, genome manipulation techniques for engineering LAB and the expected future development of such genetic tools. These methods are crucial for us to maximize the value of LAB. We also discuss applications of the genome-editing tools in enhancing probiotic characteristics and therapeutic functionalities of LAB.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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Genome Editing in Bacteria: CRISPR-Cas and Beyond. Microorganisms 2021; 9:microorganisms9040844. [PMID: 33920749 PMCID: PMC8071187 DOI: 10.3390/microorganisms9040844] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022] Open
Abstract
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids. The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing. In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs. Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria. CRISPR-Cas still holds promise as a generalized genome-editing tool in bacteria and is developing further optimization for an expanded application in these organisms. This review provides a rarely offered comprehensive view of genome editing. It also aims to familiarize the microbiology community with an ever-growing genome-editing toolbox for bacteria.
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Nehru G, Tadi SRR, Sivaprakasam S. Application of Dual Promoter Expression System for the Enhanced Heparosan Production in Bacillus megaterium. Appl Biochem Biotechnol 2021; 193:2389-2402. [PMID: 33686628 DOI: 10.1007/s12010-021-03541-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Heparosan, a capsular polysaccharide synthesized by certain pathogenic bacteria, is a promising precursor for heparin production. Heparosan production is catalyzed by the formation of KfiC-KfiA complex and the subsequent action of KfiC and KfiA proteins. Polycistronic expression of kfiC and kfiA in Bacillus megaterium yielded an unbalanced expression of KfiC and KfiA proteins resulted in decreased heparosan production. In this study, dual promoter plasmid system was constructed to increase the expression levels of KfiC and KfiA proteins. Dual promoter plasmid system along with UDP-glucuronic acid pathway overexpression (CADuet-DB) increased the heparosan production to 203 mg/L in shake flask experiments. Batch fermentation of strain CADuet-DB under controlled conditions yielded a maximum heparosan concentration of 627 mg/L, which is 59% higher than strain CA-DB. A modified logistic model is applied to describe the kinetics of heparosan production and biomass growth. Fed batch fermentation resulted in 3-fold enhancement in heparosan concentration (1.96 g/L), compared to batch fermentation. Nuclear magnetic resonance analysis revealed that heparosan from strain CADuet-DB was similar to Escherichia coli K5 heparosan. These results suggested that dual promoter expression system is a promising alternative to polycistronic expression system to produce heparosan in B. megaterium.
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Affiliation(s)
- Ganesh Nehru
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Subbi Rami Reddy Tadi
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Senthilkumar Sivaprakasam
- Bioprocess Analytical Technology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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31
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Plavec TV, Zahirović A, Zadravec P, Sabotič J, Berlec A. Lectin-Mediated Binding of Engineered Lactococcus lactis to Cancer Cells. Microorganisms 2021; 9:microorganisms9020223. [PMID: 33499141 PMCID: PMC7911926 DOI: 10.3390/microorganisms9020223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/28/2022] Open
Abstract
Lectins have been increasingly utilized as carriers for targeted drug delivery based on their specific binding to glycans located on mammalian cells. This study employed two lectins, B subunit of bacterial Shiga holotoxin (Stx1B) and fungal Clitocybe nebularis lectin (CNL), for surface display on the lactic acid bacterium Lactococcus lactis. The specific adhesion of these engineered, lectin-displaying L. lactis to cancer cells was evaluated. The expression and surface display of both lectins on L. lactis were demonstrated by western blotting and flow cytometry, respectively. MTS assays revealed that recombinant Stx1B had no effect on Caco-2 cell viability at concentrations of ≤25 µg/mL, whereas CNL was non-toxic even at relatively high concentrations of ≤250 µg/mL. Stx1B bound to Caco-2, HT-29 and HeLa cells after 1 h of incubation. CNL bound to Caco-2 cells and recognized several glycoproteins in HT-29 and Caco-2 cell homogenates of which a 70 kDa protein predominated. Confocal microscopy revealed adhesion of Stx1B-displaying L. lactis to HeLa, Caco-2, and, to a lesser extent, HT-29 cells; CNL-displaying L. lactis showed a relatively similar level of adherence to HT-29 and Caco-2 cells. Thus, lectin-displaying L. lactis might serve as a carrier in targeted drug delivery when coupled to a therapeutic moiety.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (T.V.P.); (A.Z.); (P.Z.); (J.S.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Abida Zahirović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (T.V.P.); (A.Z.); (P.Z.); (J.S.)
| | - Petra Zadravec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (T.V.P.); (A.Z.); (P.Z.); (J.S.)
- Lek d.d., Kolodvorska 27, 1234 Mengeš, Slovenia
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (T.V.P.); (A.Z.); (P.Z.); (J.S.)
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; (T.V.P.); (A.Z.); (P.Z.); (J.S.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
- Correspondence:
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32
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Todor H, Silvis MR, Osadnik H, Gross CA. Bacterial CRISPR screens for gene function. Curr Opin Microbiol 2020; 59:102-109. [PMID: 33285498 DOI: 10.1016/j.mib.2020.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022]
Abstract
In this review we describe the application of CRISPR tools for functional genomics screens in bacteria, with a focus on the use of interference (CRISPRi) approaches. We review recent developments in CRISPRi titration, which has enabled essential gene functional screens, and genome-scale pooled CRISPRi screens. We summarize progress toward enabling CRISPRi screens in non-model and pathogenic bacteria, including the development of new dCas9 variants. Taking into account the current state of the field, we provide a forward-looking analysis of CRISPRi strategies for determining gene function in bacteria.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Melanie R Silvis
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco 94158 CA, USA.
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33
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Tavares LM, de Jesus LCL, da Silva TF, Barroso FAL, Batista VL, Coelho-Rocha ND, Azevedo V, Drumond MM, Mancha-Agresti P. Novel Strategies for Efficient Production and Delivery of Live Biotherapeutics and Biotechnological Uses of Lactococcus lactis: The Lactic Acid Bacterium Model. Front Bioeng Biotechnol 2020; 8:517166. [PMID: 33251190 PMCID: PMC7672206 DOI: 10.3389/fbioe.2020.517166] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Lactic acid bacteria (LAB) are traditionally used in fermentation and food preservation processes and are recognized as safe for consumption. Recently, they have attracted attention due to their health-promoting properties; many species are already widely used as probiotics for treatment or prevention of various medical conditions, including inflammatory bowel diseases, infections, and autoimmune disorders. Some LAB, especially Lactococcus lactis, have been engineered as live vehicles for delivery of DNA vaccines and for production of therapeutic biomolecules. Here, we summarize work on engineering of LAB, with emphasis on the model LAB, L. lactis. We review the various expression systems for the production of heterologous proteins in Lactococcus spp. and its use as a live delivery system of DNA vaccines and for expression of biotherapeutics using the eukaryotic cell machinery. We have included examples of molecules produced by these expression platforms and their application in clinical disorders. We also present the CRISPR-Cas approach as a novel methodology for the development and optimization of food-grade expression of useful substances, and detail methods to improve DNA delivery by LAB to the gastrointestinal tract. Finally, we discuss perspectives for the development of medical applications of recombinant LABs involving animal model studies and human clinical trials, and we touch on the main safety issues that need to be taken into account so that bioengineered versions of these generally recognized as safe organisms will be considered acceptable for medical use.
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Affiliation(s)
- Laísa M Tavares
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luís C L de Jesus
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Tales F da Silva
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda A L Barroso
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Viviane L Batista
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nina D Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Mariana M Drumond
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Departamento de Ciências Biológicas, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Pamela Mancha-Agresti
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil.,FAMINAS - BH, Belo Horizonte, Brazil
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Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
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35
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Kerry RG, Das G, Golla U, Del Pilar Rodriguez-Torres M, Shin H, Patra JK. Engineered probiotic and prebiotic nutraceutical supplementations in combating non-communicable disorders: A review. Curr Pharm Biotechnol 2020; 23:72-97. [PMID: 33050862 DOI: 10.2174/1389201021666201013153142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Nutritional supplementations are a form of nutrition sources that may help in improving health complexities throughout the life span of a person. Under the umbrella of food supplementations, nutraceuticals are products extracted from edible sources that provide medical benefits along with primary nutritional value, these can be considered as functional foods. These nutraceutical supplementations are also evidenced in altering the commensal gut microbiota and help to prevent or fight against chronic non-communicable degenerative diseases in adults including neurological disorders (Autism Spectrum Disorder [ASD], Parkinson's disease [PD] and Multiple sclerosis [MS]) and metabolic disorder (Type-II Diabetes, Obesity and non-alcoholic fatty liver disease). Even the complexities of preterm babies like extra-uterine growth restriction, necrotizing enterocolitis, infant eczema and allergy (during pregnancy) and bronchopulmonary dysplasia, etc. could also be lessened up by providing proper nutrition. Molecular perceptive of inflammatory and apoptotic modulators regulating the pathogenesis of these health risks, their control and management by probiotics and prebiotics could further emphasize the scientific overview of their utility. The pivotal role of nutraceutical supplementations in regulating or modulating molecular pathways coupled with the above mentioned non-communicable diseases are briefly described. Lastly, an overall introduction to the sophisticated genome-editing techniques and advanced delivery systems in therapeutic activities applicable under these health risks are also emphasized in this paper.
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Affiliation(s)
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Upendarrao Golla
- Division of Hematology and Oncology, Penn State College of Medicine, Hershey, PA 17033. United States
| | - Maria Del Pilar Rodriguez-Torres
- Laboratorio de Ondas de Choque (LOCH), Centro de Física Aplicada y Tecnología Avanzada (CFATA), Universidad Nacional Autónoma de México, Campus UNAM Juriquilla Boulevard Juriquilla no. 3001, Santiago de Querétaro, Qro., C.P. 76230. Mexico
| | - HanSeung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
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CRISPR-Cas-mediated gene editing in lactic acid bacteria. Mol Biol Rep 2020; 47:8133-8144. [PMID: 32926267 DOI: 10.1007/s11033-020-05820-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/05/2020] [Indexed: 12/12/2022]
Abstract
The high efficiency, convenience and diversity of clustered regular interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are driving a technological revolution in the gene editing of lactic acid bacteria (LAB). Cas-RNA cassettes have been adopted as tools to perform gene deletion, insertion and point mutation in several species of LAB. In this article, we describe the basic mechanisms of the CRISPR-Cas system, and the current gene editing methods available, focusing on the CRISPR-Cas models developed for LAB. We also compare the different types of CRISPR-Cas-based genomic manipulations classified according to the different Cas proteins and the type of recombineering, and discuss the rapidly evolving landscape of CRISPR-Cas application in LAB.
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38
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Son J, Jang SH, Cha JW, Jeong KJ. Development of CRISPR Interference (CRISPRi) Platform for Metabolic Engineering of Leuconostoc citreum and Its Application for Engineering Riboflavin Biosynthesis. Int J Mol Sci 2020; 21:E5614. [PMID: 32764465 PMCID: PMC7460652 DOI: 10.3390/ijms21165614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Leuconostoc citreum, a hetero-fermentative type of lactic acid bacteria, is a crucial probiotic candidate because of its ability to promote human health. However, inefficient gene manipulation tools limit its utilization in bioindustries. We report, for the first time, the development of a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference (CRISPRi) system for engineering L. citreum. For reliable expression, the expression system of synthetic single guide RNA (sgRNA) and the deactivated Cas9 of Streptococcus pyogenes (SpdCas9) were constructed in a bicistronic design (BCD) platform using a high-copy-number plasmid. The expression of SpdCas9 and sgRNA was optimized by examining the combination of two synthetic promoters and Shine-Dalgarno sequences; the strong expression of sgRNA and the weak expression of SpdCas9 exhibited the most significant downregulation (20-fold decrease) of the target gene (sfGFP), without cell growth retardation caused by SpdCas9 overexpression. The feasibility of the optimized CRISPRi system was demonstrated by modulating the biosynthesis of riboflavin. Using the CRISPRi system, the expression of ribF and folE genes was downregulated (3.3-fold and 5.6-fold decreases, respectively), thereby improving riboflavin production. In addition, the co-expression of the rib operon was introduced and the production of riboflavin was further increased up to 1.7 mg/L, which was 1.53 times higher than that of the wild-type strain.
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Affiliation(s)
- Jaewoo Son
- Department of Chemical and Biomolecular Engineering, BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.S.); (S.H.J.); (J.W.C.)
| | - Seung Hoon Jang
- Department of Chemical and Biomolecular Engineering, BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.S.); (S.H.J.); (J.W.C.)
| | - Ji Won Cha
- Department of Chemical and Biomolecular Engineering, BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.S.); (S.H.J.); (J.W.C.)
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.S.); (S.H.J.); (J.W.C.)
- Institute for The BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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Adiego-Pérez B, Randazzo P, Daran JM, Verwaal R, Roubos JA, Daran-Lapujade P, van der Oost J. Multiplex genome editing of microorganisms using CRISPR-Cas. FEMS Microbiol Lett 2020; 366:5489186. [PMID: 31087001 PMCID: PMC6522427 DOI: 10.1093/femsle/fnz086] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/10/2019] [Indexed: 12/13/2022] Open
Abstract
Microbial production of chemical compounds often requires highly engineered microbial cell factories. During the last years, CRISPR-Cas nucleases have been repurposed as powerful tools for genome editing. Here, we briefly review the most frequently used CRISPR-Cas tools and describe some of their applications. We describe the progress made with respect to CRISPR-based multiplex genome editing of industrial bacteria and eukaryotic microorganisms. We also review the state of the art in terms of gene expression regulation using CRISPRi and CRISPRa. Finally, we summarize the pillars for efficient multiplexed genome editing and present our view on future developments and applications of CRISPR-Cas tools for multiplex genome editing.
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Affiliation(s)
- Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Paola Randazzo
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - René Verwaal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Johannes A Roubos
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Abstract
CRISPR-Cas systems have been engineered as powerful tools to control gene expression in bacteria. The most common strategy relies on the use of Cas effectors modified to bind target DNA without introducing DNA breaks. These effectors can either block the RNA polymerase or recruit it through activation domains. Here, we discuss the mechanistic details of how Cas effectors can modulate gene expression by blocking transcription initiation or acting as transcription roadblocks. CRISPR-Cas tools can be further engineered to obtain fine-tuned control of gene expression or target multiple genes simultaneously. Several caveats in using these tools have also been revealed, including off-target effects and toxicity, making it important to understand the design rules of engineered CRISPR-Cas effectors in bacteria. Alternatively, some types of CRISPR-Cas systems target RNA and could be used to block gene expression at the posttranscriptional level. Finally, we review applications of these tools in high-throughput screens and the progress and challenges in introducing CRISPR knockdown to other species, including nonmodel bacteria with industrial or clinical relevance. A deep understanding of how CRISPR-Cas systems can be harnessed to control gene expression in bacteria and build powerful tools will certainly open novel research directions.
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Affiliation(s)
- Antoine Vigouroux
- Synthetic Biology, Institut Pasteur, Paris, France
- Microbial Morphogenesis and Growth, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology, Institut Pasteur, Paris, France
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41
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Plavec TV, Berlec A. Safety Aspects of Genetically Modified Lactic Acid Bacteria. Microorganisms 2020; 8:E297. [PMID: 32098042 PMCID: PMC7074969 DOI: 10.3390/microorganisms8020297] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023] Open
Abstract
Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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42
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Towards high-throughput genome engineering in lactic acid bacteria. Curr Opin Biotechnol 2020; 61:181-188. [DOI: 10.1016/j.copbio.2019.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/07/2019] [Accepted: 12/17/2019] [Indexed: 11/22/2022]
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43
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Schultenkämper K, Brito LF, Wendisch VF. Impact of CRISPR interference on strain development in biotechnology. Biotechnol Appl Biochem 2020; 67:7-21. [DOI: 10.1002/bab.1901] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/13/2020] [Indexed: 12/17/2022]
Affiliation(s)
| | - Luciana F. Brito
- Department of Biotechnology and Food ScienceNTNUNorwegian University of Science and Technology Trondheim Norway
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44
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Xiong ZQ, Wei YY, Kong LH, Song X, Yi HX, Ai LZ. Short communication: An inducible CRISPR/dCas9 gene repression system in Lactococcus lactis. J Dairy Sci 2020; 103:161-165. [PMID: 31733872 DOI: 10.3168/jds.2019-17346] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2024]
Abstract
Lactococcus lactis, one of the most important probiotic lactic acid bacteria (LAB), is widely used in the dairy industry as a cell factory for recombinant protein production. Currently, a nisin-controlled inducible expression system is used for this purpose and represents the only commercial expression system in LAB. However, the available genetic modification methods are rather limited for modulating gene expression in L. lactis. Here, we developed a 2-plasmid system for gene transcription repression in L. lactis NZ9000 that uses inducible clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9. An inducible promoter Pnisin was used to drive the expression of dCas9 from Streptococcus pyogenes, whereas a strong constitutive promoter P44 drove single guide RNA expression for single or multiple target genes. dCas9 enabled CRISPR interference-mediated silencing of single or multiple target genes with significant reduction of gene expression, up to 99%. In addition, LLNZ_07335, a putative penicillin acylase, was identified as bile salt hydrolase for bile salt resistance in NZ9000 using this system. To our knowledge, this report is the first for a functional gene for bile salt tolerance in L. lactis. Overall, our work introduces a new gene repression tool for various applications in L. lactis or other LAB.
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Affiliation(s)
- Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yun-Ying Wei
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ling-Hui Kong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hua-Xi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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45
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Sharma SG, Sharma NR, Sharma M. Impact of Human Microbiome on Health. MICROBIAL DIVERSITY, INTERVENTIONS AND SCOPE 2020. [PMCID: PMC7315774 DOI: 10.1007/978-981-15-4099-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human genome in the recent years, by the advent of technological advancements, has emerged as a major prolocutor for reciprocity between the human body and the food consumed. As known, microbiome comprises all the genetic materials within a microbiota and can thereby be also referred to as metagenome of the microbiota. Contemporary researches have revealed the influence of microbiome not only on human mind and health status, but also in wide range of disease switching, ranging from cardio-metabolic diseases, allergies and obesities to life-threatening diseases such as cancer. Though the complete mechanism of many diseases is yet unclear, research works have revealed that the metabolites, nutrients and microbes can be regarded as the key players for such physiological state. The major approach of this chapter is to enlighten the interrelationship of the microbiome on the human health either in a synergistic or in an antagonistic manner.
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Affiliation(s)
- Shiwani Guleria Sharma
- School of Bioengineering and Biosciences, Lovely Professional Univeristy, Phagwara, Punjab India
| | - Neeta Raj Sharma
- School of Bioengineering and Biosciences, Lovely Professional Univeristy, Phagwara, Punjab India
| | - Mohit Sharma
- Molecular Genetics Laboratory, Dayanand Medical College and Hospital, Ludhiana, Punjab India
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46
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Restructured Lactococcus lactis strains with emergent properties constructed by a novel highly efficient screening system. Microb Cell Fact 2019; 18:198. [PMID: 31727072 PMCID: PMC6854693 DOI: 10.1186/s12934-019-1249-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Background After 2.83% genome reduction in Lactococcus lactis NZ9000, a good candidate host for proteins production was obtained in our previous work. However, the gene deletion process was time consuming and laborious. Here, we proposed a convenient gene deletion method suitable for large-scale genome reduction in L. lactis NZ9000. Results Plasmid pNZ5417 containing a visually selectable marker PnisZ-lacZ was constructed, which allowed more efficient and convenient screening of gene deletion mutants. Using this plasmid, two large nonessential DNA regions, L-4A and L-5A, accounting for 1.25% of the chromosome were deleted stepwise in L. lactis 9k-3. When compared with the parent strain, the mutant L. lactis 9k-5A showed better growth characteristics, transformability, carbon metabolic capacity, and amino acids biosynthesis. Conclusions Thus, this study provides a convenient and efficient system for large-scale genome deletion in L. lactis through application of visually selectable marker, which could be helpful for rapid genome streamlining and generation of restructured L. lactis strains that can be used as cell factories.
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47
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van Tilburg AY, Cao H, van der Meulen SB, Solopova A, Kuipers OP. Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Curr Opin Biotechnol 2019; 59:1-7. [DOI: 10.1016/j.copbio.2019.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/05/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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48
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Toymentseva AA, Altenbuchner J. New CRISPR-Cas9 vectors for genetic modifications of Bacillus species. FEMS Microbiol Lett 2019; 366:5232309. [PMID: 30520985 DOI: 10.1093/femsle/fny284] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Genetic manipulation is a fundamental procedure for the study of gene and operon functions and new characteristics acquisition. Modern CRISPR-Cas technology allows genome editing more precisely and increases the efficiency of transferring mutations in a variety of hard to manipulate organisms. Here, we describe new CRISPR-Cas vectors for genetic modifications in bacillary species. Our plasmids are single CRISPR-Cas plasmids comprising all components for genome editing and should be functional in a broad host range. They are highly efficient (up to 97%) and precise. The employment and delivery of these plasmids to bacillary strains can be easily achieved by conjugation from Escherichia coli. During our research we also demonstrated the absence of compatibility between CRISPR-Cas system and non-homologous end joining in Bacillus subtilis.
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Affiliation(s)
- Anna A Toymentseva
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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49
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Börner RA, Kandasamy V, Axelsen AM, Nielsen AT, Bosma EF. Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech. FEMS Microbiol Lett 2019; 366:5251984. [PMID: 30561594 PMCID: PMC6322438 DOI: 10.1093/femsle/fny291] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022] Open
Abstract
This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.
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Affiliation(s)
- Rosa A Börner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Amalie M Axelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Elleke F Bosma
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
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50
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Sharshar MM, Samak NA, Hao X, Mu T, Zhong W, Yang M, Peh S, Ambreen S, Xing J. Enhanced growth-driven stepwise inducible expression system development in haloalkaliphilic desulfurizing Thioalkalivibrio versutus. BIORESOURCE TECHNOLOGY 2019; 288:121486. [PMID: 31128536 DOI: 10.1016/j.biortech.2019.121486] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 05/13/2023]
Abstract
Highly toxic and flammable H2S gas has become an environmental threat. Because of its ability to efficiently remove H2S by oxidation, Thioalkalivibrio versutus is gaining more attention. Haloalkaliphilic autotrophs, like the bio-desulfurizing T. versutus, grow weakly. Weak growth makes any trial for developing potent genetic tools required for genetic engineering far from achieved. In this study, the fed-batch strategy improved T. versutus growth by 1.6 fold in maximal growth rate, 9-fold in O.D600 values and about 3-fold in biomass and protein productions. The strategy also increased the favorable desulfurization product, sulfur, by 2.7 fold in percent yield and 1.5-fold in diameter. A tight iron-inducible expression system for T. versutus was successfully developed. The system was derived from fed-batch cultivation coupled with new design, build, test and validate (DPTV) approach. The inducible system was validated by toxin expression. Fed-batch cultivation coupled with DPTV approach could be applied to other autotrophs.
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Affiliation(s)
- Moustafa Mohamed Sharshar
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Abdrabo Samak
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt
| | - Xuemi Hao
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingzhen Mu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Wei Zhong
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maohua Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Sumit Peh
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sadaf Ambreen
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Genomics and Precision Medicine, Institute of Genomics, CAS, Beijing 100101, China
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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