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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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2
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Li F, Zhao H, Sui L, Yin F, Liu X, Guo G, Li J, Jiang Y, Cui W, Shan Z, Zhou H, Wang L, Qiao X, Tang L, Wang X, Li Y. Assessing immunogenicity of CRISPR-NCas9 engineered strain against porcine epidemic diarrhea virus. Appl Microbiol Biotechnol 2024; 108:248. [PMID: 38430229 PMCID: PMC10908614 DOI: 10.1007/s00253-023-12989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 03/03/2024]
Abstract
Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV), is an acute and highly infectious disease, resulting in substantial economic losses in the pig industry. Given that PEDV primarily infects the mucosal surfaces of the intestinal tract, it is crucial to improve the mucosal immunity to prevent viral invasion. Lactic acid bacteria (LAB) oral vaccines offer unique advantages and potential applications in combatting mucosal infectious diseases, making them an ideal approach for controlling PED outbreaks. However, traditional LAB oral vaccines use plasmids for exogenous protein expression and antibiotic genes as selection markers. Antibiotic genes can be diffused through transposition, transfer, or homologous recombination, resulting in the generation of drug-resistant strains. To overcome these issues, genome-editing technology has been developed to achieve gene expression in LAB genomes. In this study, we used the CRISPR-NCas9 system to integrate the PEDV S1 gene into the genome of alanine racemase-deficient Lactobacillus paracasei △Alr HLJ-27 (L. paracasei △Alr HLJ-27) at the thymidylate synthase (thyA) site, generating a strain, S1/△Alr HLJ-27. We conducted immunization assays in mice and piglets to evaluate the level of immune response and evaluated its protective effect against PEDV through challenge tests in piglets. Oral administration of the strain S1/△Alr HLJ-27 in mice and piglets elicited mucosal, humoral, and cellular immune responses. The strain also exhibited a certain level of resistance against PEDV infection in piglets. These results demonstrate the potential of S1/△Alr HLJ-27 as an oral vaccine candidate for PEDV control. KEY POINTS: • A strain S1/△Alr HLJ-27 was constructed as the candidate for an oral vaccine. • Immunogenicity response and challenge test was carried out to analyze the ability of the strain. • The strain S1/△Alr HLJ-27 could provide protection for piglets to a certain extent.
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Affiliation(s)
- Fengsai Li
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Haiyuan Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ling Sui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Fangjie Yin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Xinzi Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Guihai Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaxuan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Zhifu Shan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Xinyuan Qiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China
| | - Xiaona Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China.
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, China.
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3
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Cui Y, Qu X. CRISPR-Cas systems of lactic acid bacteria and applications in food science. Biotechnol Adv 2024; 71:108323. [PMID: 38346597 DOI: 10.1016/j.biotechadv.2024.108323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/29/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) systems are widely distributed in lactic acid bacteria (LAB), contributing to their RNA-mediated adaptive defense immunity. The CRISPR-Cas-based genetic tools have exhibited powerful capability. It has been highly utilized in different organisms, accelerating the development of life science. The review summarized the components, adaptive immunity mechanisms, and classification of CRISPR-Cas systems; analyzed the distribution and characteristics of CRISPR-Cas system in LAB. The review focuses on the development of CRISPR-Cas-based genetic tools in LAB for providing latest development and future trend. The diverse and broad applications of CRISPR-Cas systems in food/probiotic industry are introduced. LAB harbor a plenty of CRISPR-Cas systems, which contribute to generate safer and more robust strains with increased resistance against bacteriophage and prevent the dissemination of plasmids carrying antibiotic-resistance markers. Furthermore, the CRISPR-Cas system from LAB could be used to exploit novel, flexible, programmable genome editing tools of native host and other organisms, resolving the limitation of genetic operation of some LAB species, increasing the important biological functions of probiotics, improving the adaptation of probiotics in complex environments, and inhibiting the growth of foodborne pathogens. The development of the genetic tools based on CRISPR-Cas system in LAB, especially the endogenous CRISPR-Cas system, will open new avenues for precise regulation, rational design, and flexible application of LAB.
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Affiliation(s)
- Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
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Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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5
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Debnath N, Yadav P, Mehta PK, Gupta P, Kumar D, Kumar A, Gautam V, Yadav AK. Designer probiotics: Opening the new horizon in diagnosis and prevention of human diseases. Biotechnol Bioeng 2024; 121:100-117. [PMID: 37881101 DOI: 10.1002/bit.28574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/19/2023] [Accepted: 09/23/2023] [Indexed: 10/27/2023]
Abstract
Probiotic microorganisms have been used for therapeutic purposes for over a century, and recent advances in biotechnology and genetic engineering have opened up new possibilities for developing therapeutic approaches using indigenous probiotic microorganisms. Diseases are often related to metabolic and immunological factors, which play a critical role in their onset. With the help of advanced genetic tools, probiotics can be modified to produce or secrete important therapeutic peptides directly into mucosal sites, increasing their effectiveness. One potential approach to enhancing human health is through the use of designer probiotics, which possess immunogenic characteristics. These genetically engineered probiotics hold promise in providing novel therapeutic options. In addition to their immunogenic properties, designer probiotics can also be equipped with sensors and genetic circuits, enabling them to detect a range of diseases with remarkable precision. Such capabilities may significantly advance disease diagnosis and management. Furthermore, designer probiotics have the potential to be used in diagnostic applications, offering a less invasive and more cost-effective alternative to conventional diagnostic techniques. This review offers an overview of the different functional aspects of the designer probiotics and their effectiveness on different diseases and also, we have emphasized their limitations and future implications. A comprehensive understanding of these functional attributes may pave the way for new avenues of prevention and the development of effective therapies for a range of diseases.
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Affiliation(s)
- Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Pooja Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Praveen K Mehta
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok K Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
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6
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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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7
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Arnold J, Glazier J, Mimee M. Genetic Engineering of Resident Bacteria in the Gut Microbiome. J Bacteriol 2023; 205:e0012723. [PMID: 37382533 PMCID: PMC10367592 DOI: 10.1128/jb.00127-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.
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Affiliation(s)
- Jack Arnold
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Joshua Glazier
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Mark Mimee
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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8
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Zhou Y, Song F, Yang H, Li D, Zhang N, Huang K, He X, Wang M, Tian H, Li C. Construction of a food-grade gene editing system based on CRISPR-Cas9 and its application in Lactococcus lactis NZ9000. Biotechnol Lett 2023:10.1007/s10529-023-03398-4. [PMID: 37266879 DOI: 10.1007/s10529-023-03398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system has been widely used in gene editing of various organisms. However, food-grade gene editing systems in lactic acid bacteria are still preliminary. Red/ET-dependent homologous recombination or CRISPR-based systems have been developed to gene editing in Lactococcus lactis, but these methods are overall inefficient. In the present study, a recombinant system based on CRISPR/Cas9 technology combined with Red/ET was developed using the plasmid pMG36e derived from Lactococcus lactis. Then, the developed recombinant system was applied to Lactococcus lactis. Knockout efficiency was significantly higher using the developed system (91%). In addition, this system showed the potential to be used as a high-throughput method for hierarchical screening. Finally, a gene-edited strain was obtained, and no antibiotics or exogenous genes were introduced using the developed gene editing system. Thus, the efficient system in lactic acid bacteria was constructed and optimized.
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Affiliation(s)
- Yangping Zhou
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Fei Song
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
- College of Biological Science and Engineering, Xingtai University, Xingtai, 054001, Hebei, China
| | - Hongru Yang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
- School of Public Health, Hebei University, Baoding, 071000, Hebei, China
| | - Dongyao Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
- Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, 071000, Hebei, China
| | - Na Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
- Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, 071000, Hebei, China
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, 071000, Hebei, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Xiaoyun He
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Miaoshu Wang
- Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, 071000, Hebei, China
- New Hope Tensun (Hebei) Dairy Co. Ltd., Baoding, 071000, Hebei, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China.
- National Engineering Research Center for Agriculture in Northern Mountainous Areas, Baoding, 071000, Hebei, China.
- Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, 071000, Hebei, China.
| | - Chen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China.
- Hebei Technology Innovation Center of Probiotic Functional Dairy Product, Baoding, 071000, Hebei, China.
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Yeom J, Park JS, Jung SW, Lee S, Kwon H, Yoo SM. High-throughput genetic engineering tools for regulating gene expression in a microbial cell factory. Crit Rev Biotechnol 2023; 43:82-99. [PMID: 34957867 DOI: 10.1080/07388551.2021.2007351] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
With the rapid advances in biotechnological tools and strategies, microbial cell factory-constructing strategies have been established for the production of value-added compounds. However, optimizing the tradeoff between the biomass, yield, and titer remains a challenge in microbial production. Gene regulation is necessary to optimize and control metabolic fluxes in microorganisms for high-production performance. Various high-throughput genetic engineering tools have been developed for achieving rational gene regulation and genetic perturbation, diversifying the cellular phenotype and enhancing bioproduction performance. In this paper, we review the current high-throughput genetic engineering tools for gene regulation. In particular, technological approaches used in a diverse range of genetic tools for constructing microbial cell factories are introduced, and representative applications of these tools are presented. Finally, the prospects for high-throughput genetic engineering tools for gene regulation are discussed.
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Affiliation(s)
- Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Seung-Woon Jung
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Sumin Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Hyukjin Kwon
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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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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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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12
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Asai T, Yoshikawa S, Ikeda Y, Taniguchi K, Sawamura H, Tsuji A, Matsuda S. Encouraging Tactics with Genetically Modified Probiotics to Improve Immunity for the Prevention of Immune-Related Diseases including Cardio-Metabolic Disorders. Biomolecules 2022; 13:biom13010010. [PMID: 36671395 PMCID: PMC9855998 DOI: 10.3390/biom13010010] [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] [Received: 10/31/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The PI3K/AKT/mTOR signaling pathway may play crucial roles in the pathogenesis of obesity and diabetes mellitus, as well as metabolic syndromes, which could also be risk factors for cardio-metabolic disorders. Consistently, it has been shown that beneficial effects may be convoyed by the modulation of the PI3K/AKT/mTOR pathway against the development of these diseases. Importantly, the PI3K/AKT/mTOR signaling pathway can be modulated by probiotics. Probiotics have a variety of beneficial properties, with the potential of treating specific diseases such as immune-related diseases, which are valuable to human health. In addition, an increasing body of work in the literature emphasized the contribution of genetically modified probiotics. There now seems to be a turning point in the research of probiotics. A better understanding of the interactions between microbiota, lifestyle, and host factors such as genetics and/or epigenetics might lead to a novel therapeutic approach with probiotics for these diseases. This study might provide a theoretical reference for the development of genetically modified probiotics in health products and/or in functional foods for the treatment of cardio-metabolic disorders.
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13
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Tian K, Hong X, Guo M, Li Y, Wu H, Caiyin Q, Qiao J. Development of Base Editors for Simultaneously Editing Multiple Loci in Lactococcus lactis. ACS Synth Biol 2022; 11:3644-3656. [PMID: 36065829 DOI: 10.1021/acssynbio.1c00561] [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] [Indexed: 01/27/2023]
Abstract
Lactococcus lactis serves as the most extensively studied model organism and an important dairy species. Though CRISPR-Cas9 systems have been developed for robust genetic manipulations, simultaneously editing multiple endogenous loci in L. lactis is still challenging. Herein, we first report the development of a double-strand break-free, robust, multiloci editing system CRISPR-deaminase-assisted base editor (CRISPR-DBE), which comprises a cytidine (CRISPR-cDBE) and an adenosine deaminase-assisted base editor (CRISPR-aDBE). Specifically targeted by a sgRNA, CRISPR-cDBE can efficiently introduce a cytidine-to-thymidine mutation and CRISPR-aDBE can high-efficiently convert adenosine to guanosine within a 5 nt editing window. CRISPR-cDBE was validated and successfully applied to simultaneously inactivate multiple genes using a single plasmid in L. lactis strain NZ9000. Meanwhile, the temperature-sensitive plasmid of CRISPR-DBE can be cured quickly, and the continuous gene editing of L. lactis has been achieved. Furthermore, CRISPR-cDBE can also efficiently convert the targeted C to T in a nisin-producing, industrial L. lactis strain F44. Finally, we applied genome-wide bioinformatics analysis to determine the scope of gene inactivation for these base editors using different Cas9 variants and evaluated the preference of SpGn and SpRYn variants for the protospacer adjacent motif in L. lactis NZ9000. Taken together, our study provides a powerful tool for simultaneously editing multiple loci in L. lactis, which may have a wide range of industrial applications in the future.
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Affiliation(s)
- Kairen Tian
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P. R. China.,SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
| | - Xia Hong
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Manman Guo
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yanni Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P. R. China.,SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
| | - Hao Wu
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, P. R. China
| | - Qinggele Caiyin
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P. R. China.,SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P. R. China.,SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, P. R. China
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14
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Pechenov PY, Garagulya DA, Stanovov DS, Letarov AV. New Effective Method of Lactococcus Genome Editing Using Guide RNA-Directed Transposition. Int J Mol Sci 2022; 23:13978. [PMID: 36430465 PMCID: PMC9696066 DOI: 10.3390/ijms232213978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Lactococcus lactis is an important industrial microorganism and a widely used model object for research in the field of lactic acid bacteria (LAB) biology. The development of new L. lactis and related LAB strains with improved properties, including phage-resistant strains for dairy fermentation, LAB-based vaccines or strains with altered genotypes for research purposes, are hindered by the lack of genome-editing tools that allow for the easy and straightforward incorporation of a significant amount of the novel genetic material, such as large genes or operons, into the chromosomes of these bacteria. We recently employed a suggested system based on the CRISPR-Cas-associated transposon for the editing of the L. lactis genome. After the in-depth redesign of the system, we were able to achieve the stable incorporation of the fragments that were sized up to 10 kbp into the L. lactis beta-galactosidase gene. The efficiency of editing under the optimized conditions were 2 × 10-4 and 4 × 10-5 for 1 kbp and 10 kbp, respectively, which are sufficient for fast and easy modifications if a positive selection marker can be used.
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Affiliation(s)
- Pavel Yu Pechenov
- Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia
| | | | | | - Andrey V. Letarov
- Federal Research Center “Fundamentals of Biotechnology” of Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia
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15
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Zhang H, Zhao H, Zhao Y, Sui L, Li F, Zhang H, Li J, Jiang Y, Cui W, Ding G, Zhou H, Wang L, Qiao X, Tang L, Wang X, Li Y. Auxotrophic Lactobacillus Expressing Porcine Rotavirus VP4 Constructed Using CRISPR-Cas9D10A System Induces Effective Immunity in Mice. Vaccines (Basel) 2022; 10:vaccines10091510. [PMID: 36146587 PMCID: PMC9504633 DOI: 10.3390/vaccines10091510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine rotavirus (PoRV) mainly causes acute diarrhea in piglets under eight weeks of age and has potentially high morbidity and mortality rates. As vaccine carriers for oral immunization, lactic acid bacteria (LAB) are an ideal strategy for blocking PoRV infections. However, the difficulty in knocking out specific genes, inserting foreign genes, and the residues of antibiotic selection markers are major challenges for the oral vaccination of LAB. In this study, the target gene, alanine racemase (alr), in the genome of Lactobacillus casei strain W56 (L. casei W56) was knocked out to construct an auxotrophic L. casei strain (L. casei Δalr W56) using the CRISPR-Cas9D10A gene editing system. A recombinant strain (pPG-alr-VP4/Δalr W56) was constructed using an electrotransformed complementary plasmid. Expression of the alr-VP4 fusion protein from pPG-alr-VP4/Δalr W56 was detected using Western blotting. Mice orally immunized with pPG-alr-VP4/Δalr W56 exhibited high levels of serum IgG and mucosal secretory immunoglobulin A (SIgA), which exhibited neutralizing effects against PoRV. Cytokines levels in serum detected using ELISA, indicated that the recombinant strain induced an immune response dominated by Th2 cells. Our data suggest that pPG-alr-VP4/Δalr W56, an antibiotic-resistance-free LAB, provides a safer vaccine strategy against PoRV infection.
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Affiliation(s)
- Hailin Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Haiyuan Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Jiangsu Hanswine Food Co., Ltd., Ma’anshan 243000, China
| | - Yuliang Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Ling Sui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Fengsai Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Huijun Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jiaxuan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Guojie Ding
- Harbin Vikeses Biological Technology Co., Ltd., Harbin 150030, China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Xinyuan Qiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Xiaona Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
- Correspondence: (X.W.); (Y.L.); Tel./Fax: +86-451-5519-0363 (Y.L.)
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
- Correspondence: (X.W.); (Y.L.); Tel./Fax: +86-451-5519-0363 (Y.L.)
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16
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The performance of lactic acid bacteria in silage production: a review of modern biotechnology for silage improvement. Microbiol Res 2022; 266:127212. [DOI: 10.1016/j.micres.2022.127212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022]
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17
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Wu L, Bao F, Li L, Yin X, Hua Z. Bacterially mediated drug delivery and therapeutics: Strategies and advancements. Adv Drug Deliv Rev 2022; 187:114363. [PMID: 35649449 DOI: 10.1016/j.addr.2022.114363] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
It was already clinically apparent 150 years ago that bacterial therapy could alleviate diseases. Recently, a burgeoning number of researchers have been using bacterial regimens filled with microbial therapeutic leads to diagnose and treat a wide range of disorders and diseases, including cancers, inflammatory diseases, metabolic disorders and viral infections. Some bacteria that were designed to have low toxicity and high efficiency in drug delivery have been used to treat diseases successfully, especially in tumor therapy in animal models or clinical trials, thanks to the progress of genetic engineering and synthetic bioengineering. Therefore, genetically engineered bacteria can serve as efficient drug delivery vehicles, carrying nucleic acids or genetic circuits that encode and regulate therapeutic payloads. In this review, we summarize the development and applications of this approach. Strategies for genetically modifying strains are described in detail, along with their objectives. We also describe some controlled strategies for drug delivery and release using these modified strains as carriers. Furthermore, we discuss treatment methods for various types of diseases using engineered bacteria. Tumors are discussed as the most representative example, and other diseases are also briefly described. Finally, we discuss the challenges and prospects of drug delivery systems based on these bacteria.
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18
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Han X, Zhou X, Pei Z, Stanton C, Ross RP, Zhao J, Zhang H, Yang B, Chen W. Characterization of CRISPR-Cas systems in Bifidobacterium breve. Microb Genom 2022; 8. [PMID: 35451949 PMCID: PMC9453068 DOI: 10.1099/mgen.0.000812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in Bifidobacterium breve, the occurrence and diversity of CRISPR-Cas systems were analysed in 150 B. breve strains. Specifically, 47 % (71/150) of B. breve genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in B. breve can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in B. breve, and the protospacer adjacent motif sequences were further characterized in B. breve type I-C system as 5'-TTC-3'. All these results might provide a molecular basis for the development of endogenous genome editing tools in B. breve.
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Affiliation(s)
- Xiao Han
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Xingya Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Co., Cork, Ireland
| | - R Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, PR China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China
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19
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Wu J, Tian X, Xu X, Gu X, Kong J, Guo T. Engineered Probiotic Lactococcus lactis for Lycopene Production against ROS Stress in Intestinal Epithelial Cells. ACS Synth Biol 2022; 11:1568-1576. [PMID: 35289165 DOI: 10.1021/acssynbio.1c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactococcus lactis is a food-grade chassis for delivery of bioactive molecules to the intestinal mucosa in situ, while its ability to produce lycopene for detoxification of reactive oxidative species (ROS) is not realized yet. Here, L. lactis NZ9000 was engineered to synthesize lycopene by heterologous expression of a gene cluster crtEBI in plasmids or chromosomes, yielding the recombinant strains NZ4 and NZ5 with 0.59 and 0.54 mg/L lycopene production, respectively. To reroute the pyruvate flux to lycopene, the main lactate dehydrogenase and α-acetolactate synthase pathways were sequentially disrupted. The resultant strains NZΔldh-1 and NZΔldhΔals-1 increased lycopene accumulation to 0.70 and 0.73 mg/L, respectively, while their biomasses were reduced by 12.42% and the intracellular NADH/NAD+ ratios increased by 3.05- and 2.10-fold. To increase the biomasses of these engineered strains, aerobic respiration was activated and tuned by the addition of exogenous heme and oxygen. As a result, the engineered L. lactis strains partly recovered the growth and redox balance, yielding the lycopene levels of 0.91-1.09 mg/L. The engineered L. lactis strain protected the intestinal epithelial cells NCM460 against H2O2 challenge, with a 30.09% increase of cell survival and a 29.2% decrease of the intracellular ROS level compared with strain NZ9000 treatment. In summary, this work established the use of the engineered probiotic L. lactis for lycopene production and prospected its potential in the prevention of intestinal oxidative damage.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xingfang Tian
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiaoning Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xinyi Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
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20
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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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21
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Abstract
The bacterial genus Lactobacillus comprises a vast range of strains with varying metabolic and probiotic traits, with genome editing representing an essential tool to probe genotype-phenotype relationships and enhance their beneficial properties. Currently, one of the most effective means of genome editing in bacteria couples low-efficiency recombineering with high-efficiency counterselection by nucleases from CRISPR-Cas systems. In lactobacilli, several CRISPR-based genome editing methods exist that have shown varying success in different strains. Here, we detail a fast and simple approach using two shuttle vectors encoding a recombineering template as well as the Streptococcus pyogenes Cas9, a trans-activating RNA, and a CRISPR array. We provide a step-by-step procedure for cloning the shuttle vectors, sequentially transforming the vectors into lactobacilli, screening for the desired edit, and finally clearing the shuttle vectors from the mutant strain. As CRISPR-based genome editing in bacteria can fail for various reasons, we also lay out instructions for probing mechanisms of escape. Finally, we include practical notes along the way to facilitate each stage of genome editing, and we illustrate the technique using a representative edit in a strain of Lactobacillus plantarum. Overall, this method should serve as a complete guide to performing genome editing in lactobacilli.
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Affiliation(s)
- Justin M Vento
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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22
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Asin-Garcia E, Martin-Pascual M, Garcia-Morales L, van Kranenburg R, Martins dos Santos VAP. ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida. ACS Synth Biol 2021; 10:2672-2688. [PMID: 34547891 PMCID: PMC8524654 DOI: 10.1021/acssynbio.1c00297] [Citation(s) in RCA: 7] [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: 06/29/2021] [Indexed: 12/11/2022]
Abstract
Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottleneck in genome recoding efforts, however, is the low efficiency of recombineering, which hinders large-scale applications at acceptable speed and cost. To relieve this bottleneck, we developed ReScribe, a highly optimized recombineering tool enhanced by CRISPR-Cas9-mediated counterselection built upon the minimal PAM 5'-NNG-3' of the Streptococcus canis Cas9 (ScCas9). As a proof of concept, we used ReScribe to generate a minimally recoded strain of the industrial chassis Pseudomonas putida by replacing TAG stop codons (functioning as PAMs) of essential metabolic genes with the synonymous TAA. We showed that ReScribe enables nearly 100% engineering efficiency of multiple loci in P. putida, opening promising avenues for genome editing and applications thereof in this bacterium and beyond.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Maria Martin-Pascual
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands
- Laboratory
of Microbiology, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
- LifeGlimmer
GmbH, Berlin 12163, Germany
- Bioprocess
Engineering Group, Wageningen University
& Research, Wageningen 6700 AA, The Netherlands
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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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Lee HJ, Lee SJ. Advances in Accurate Microbial Genome-Editing CRISPR Technologies. J Microbiol Biotechnol 2021; 31:903-911. [PMID: 34261850 PMCID: PMC9723281 DOI: 10.4014/jmb.2106.06056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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25
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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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26
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Okano K, Sato Y, Hizume T, Honda K. Genome editing by miniature CRISPR/Cas12f1 enzyme in Escherichia coli. J Biosci Bioeng 2021; 132:120-124. [PMID: 34023220 DOI: 10.1016/j.jbiosc.2021.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/01/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a valuable genome editing tool for microorganisms. However, the commonly used Cas9 nuclease derived from Streptococcus pyogenes (SpCas9) is not applicable to many industrially relevant bacteria, due to its cytotoxicity and large size (1368 amino acids [aa]). We developed an alternative genome editing system using a miniature Cas12f1 nuclease (529 aa) derived from an uncultured archaeon, Un1Cas12f1. When editing four dispensable genes in Escherichia coli MG1655 and BW25113, the CRISPR/Un1Cas12f1 system showed higher efficiency (63%-100%) than the CRISPR/SpCas9 system (50%-79%). The CRISPR/Un1Cas12f1 genome editing system is expected to be applied to the genome editing of a wide variety of bacteria.
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Affiliation(s)
- Kenji Okano
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Yu Sato
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tatsuya Hizume
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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27
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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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28
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Tian X, Liu X, Zhang Y, Chen Y, Hang H, Chu J, Zhuang Y. Metabolic engineering coupled with adaptive evolution strategies for the efficient production of high-quality L-lactic acid by Lactobacillus paracasei. BIORESOURCE TECHNOLOGY 2021; 323:124549. [PMID: 33406469 DOI: 10.1016/j.biortech.2020.124549] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 05/26/2023]
Abstract
The main indicators for industrial production of high-quality lactic acid at elevated temperatures are high titer, productivity, yield, and optical purity. However, no such strains have been reported to meet all these requirements simultaneously. In this study, a high optical purity L-lactic acid producing strain is developed through the CRISPR-Cas9 gene editing platform. Further, adaptive evolution was used to breed and select a high-performance strain (NCBIO01-M2-ldhL1-HT) that could efficiently produce L-lactic acid at a high temperature of 45℃. This strain produced 221.0 g/L of L-lactic acid in open fermentation with high initial glucose concentration. Also, L-lactic acid productivity and yield was above 7.5 g/L/h and 0.96 g/g respectively, as well as the optical purity of L-lactic acid in the fermentation broth exceeded 99.1%. In short, this breeding strain possess high potential to be considered for the commercial production of polymer-grade L-lactic acid.
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Affiliation(s)
- Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuehua Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Haifeng Hang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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29
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Synefiaridou D, Veening JW. Harnessing CRISPR-Cas9 for Genome Editing in Streptococcus pneumoniae D39V. Appl Environ Microbiol 2021; 87:e02762-20. [PMID: 33397704 PMCID: PMC8105017 DOI: 10.1128/aem.02762-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by the detection and cleavage of invading foreign DNA. Modified versions of this system can be exploited as a biotechnological tool for precise genome editing at a targeted locus. Here, we developed a replicative plasmid that carries the CRISPR-Cas9 system for RNA-programmable genome editing by counterselection in the opportunistic human pathogen Streptococcus pneumoniae Specifically, we demonstrate an approach for making targeted markerless gene knockouts and large genome deletions. After a precise double-stranded break (DSB) is introduced, the cells' DNA repair mechanism of homology-directed repair (HDR) is exploited to select successful transformants. This is achieved through the transformation of a template DNA fragment that will recombine in the genome and eliminate recognition of the target of the Cas9 endonuclease. Next, the newly engineered strain can be easily cured from the plasmid, which is temperature sensitive for replication, by growing it at the nonpermissive temperature. This allows for consecutive rounds of genome editing. Using this system, we engineered a strain with three major virulence factors deleted. The approaches developed here could potentially be adapted for use with other Gram-positive bacteria.IMPORTANCEStreptococcus pneumoniae (the pneumococcus) is an important opportunistic human pathogen killing more than 1 million people each year. Having the availability of a system capable of easy genome editing would significantly facilitate drug discovery and efforts to identify new vaccine candidates. Here, we introduced an easy-to-use system to perform multiple rounds of genome editing in the pneumococcus by putting the CRISPR-Cas9 system on a temperature-sensitive replicative plasmid. The approaches used here will advance genome editing projects in this important human pathogen.
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Affiliation(s)
- Dimitra Synefiaridou
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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30
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Portable CRISPR-Cas9 N System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei. Appl Environ Microbiol 2021; 87:AEM.02669-20. [PMID: 33397707 DOI: 10.1128/aem.02669-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Diverse Lactobacillus strains are widely used as probiotic cultures in the dairy and dietary supplement industries, and specific strains, such as Lactobacillus acidophilus NCFM, have been engineered for the development of biotherapeutics. To expand the Lactobacillus manipulation toolbox with enhanced efficiency and ease, we present here a CRISPR (clustered regularly interspaced palindromic repeats)-SpyCas9D10A nickase (Cas9N)-based system for programmable engineering of L. acidophilus NCFM, a model probiotic bacterium. Successful single-plasmid delivery system was achieved with the engineered pLbCas9N vector harboring cas9 N under the regulation of a Lactobacillus promoter and a cloning region for a customized single guide RNA (sgRNA) and editing template. The functionality of the pLbCas9N system was validated in NCFM with targeted chromosomal deletions ranging between 300 bp and 1.9 kb at various loci (rafE, lacS, and ltaS), yielding 35 to 100% mutant recovery rates. Genome analysis of the mutants confirmed precision and specificity of the pLbCas9N system. To showcase the versatility of this system, we also inserted an mCherry fluorescent-protein gene downstream of the pgm gene to create a polycistronic transcript. The pLbCas9N system was further deployed in other species to generate a concurrent single-base substitution and gene deletion in Lactobacillus gasseri ATCC 33323 and an in-frame gene deletion in Lactobacillus paracasei Lpc-37, highlighting the portability of the system in phylogenetically distant Lactobacillus species, where its targeting activity was not interfered with by endogenous CRISPR-Cas systems. Collectively, these editing outcomes illustrate the robustness and versatility of the pLbCas9N system for genome manipulations in diverse lactobacilli and open new avenues for the engineering of health-promoting lactic acid bacteria.IMPORTANCE This work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three Lactobacillus species belonging to the lactic acid bacteria (LAB), which are commonly known for their long history of use in food fermentations and as indigenous members of healthy microbiotas and for their emerging roles in human and animal commercial health-promoting applications. We exploited the established CRISPR-SpyCas9 nickase for flexible and precise genome editing applications in Lactobacillus acidophilus and further demonstrated the efficacy of this universal system in two distantly related Lactobacillus species. This versatile Cas9-based system facilitates genome engineering compared to conventional gene replacement systems and represents a valuable gene editing modality in species that do not possess native CRISPR-Cas systems. Overall, this portable tool contributes to expanding the genome editing toolbox of LAB for studying their health-promoting mechanisms and engineering of these beneficial microbes as next-generation vaccines and designer probiotics.
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31
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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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32
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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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33
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Kohl HM, Castillo AR, Ochoa-Repáraz J. The Microbiome as a Therapeutic Target for Multiple Sclerosis: Can Genetically Engineered Probiotics Treat the Disease? Diseases 2020; 8:diseases8030033. [PMID: 32872621 PMCID: PMC7563507 DOI: 10.3390/diseases8030033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/15/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
There is an increasing interest in the intestinal microbiota as a critical regulator of the development and function of the immune, nervous, and endocrine systems. Experimental work in animal models has provided the foundation for clinical studies to investigate associations between microbiota composition and function and human disease, including multiple sclerosis (MS). Initial work done using an animal model of brain inflammation, experimental autoimmune encephalomyelitis (EAE), suggests the existence of a microbiota-gut-brain axis connection in the context of MS, and microbiome sequence analyses reveal increases and decreases of microbial taxa in MS intestines. In this review, we discuss the impact of the intestinal microbiota on the immune system and the role of the microbiome-gut-brain axis in the neuroinflammatory disease MS. We also discuss experimental evidence supporting the hypothesis that modulating the intestinal microbiota through genetically modified probiotics may provide immunomodulatory and protective effects as a novel therapeutic approach to treat this devastating disease.
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34
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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35
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Wang C, Cui Y, Qu X. Optimization of electrotransformation (ETF) conditions in lactic acid bacteria (LAB). J Microbiol Methods 2020; 174:105944. [DOI: 10.1016/j.mimet.2020.105944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
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36
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Hashemi A. CRISPR-Cas9/CRISPRi tools for cell factory construction in E. coli. World J Microbiol Biotechnol 2020; 36:96. [PMID: 32583135 DOI: 10.1007/s11274-020-02872-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022]
Abstract
The innovative CRISPR-Cas based genome editing technology provides some functionality and advantages such as the high efficiency and specificity as well as ease of handling. Both aspects of the CRISPR-Cas9 system including genetic engineering and gene regulation are advantageously applicable to the construction of microbial cell factories. As one of the most extensively used cell factories, E. coli has been engineered to produce various high value-added chemical compounds such as pharmaceuticals, biochemicals, and biofuels. Therefore, to improve the production of valuable metabolites, many investigations have been performed by focusing on CRISPR-Cas- based metabolic engineering of this host. In the current review, the biology underlying CRISPR-Cas9 system was briefly explained and then the applications of CRISPR-Cas9/CRISPRi tools were considered for cell factory construction in E. coli.
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Affiliation(s)
- Atieh Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, No. 2660, Vali-e-Asr Ave, Tehran, Iran.
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37
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Wannier TM, Nyerges A, Kuchwara HM, Czikkely M, Balogh D, Filsinger GT, Borders NC, Gregg CJ, Lajoie MJ, Rios X, Pál C, Church GM. Improved bacterial recombineering by parallelized protein discovery. Proc Natl Acad Sci U S A 2020; 117:13689-13698. [PMID: 32467157 PMCID: PMC7306799 DOI: 10.1073/pnas.2001588117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Exploiting bacteriophage-derived homologous recombination processes has enabled precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we introduce a high-throughput method for SSAP discovery that we call "serial enrichment for efficient recombineering" (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli, while PapRecT enables efficient recombineering in Pseudomonas aeruginosa, a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.
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Affiliation(s)
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | | | - Márton Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | - Dávid Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | | | | | | | - Marc J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
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38
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Roberts A, Barrangou R. Applications of CRISPR-Cas systems in lactic acid bacteria. FEMS Microbiol Rev 2020; 44:523-537. [DOI: 10.1093/femsre/fuaa016] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022] Open
Abstract
ABSTRACT
As a phenotypically and phylogenetically diverse group, lactic acid bacteria are found in a variety of natural environments and occupy important roles in medicine, biotechnology, food and agriculture. The widespread use of lactic acid bacteria across these industries fuels the need for new and functionally diverse strains that may be utilized as starter cultures or probiotics. Originally characterized in lactic acid bacteria, CRISPR-Cas systems and derived molecular machines can be used natively or exogenously to engineer new strains with enhanced functional attributes. Research on CRISPR-Cas biology and its applications has exploded over the past decade with studies spanning from the initial characterization of CRISPR-Cas immunity in Streptococcus thermophilus to the use of CRISPR-Cas for clinical gene therapies. Here, we discuss CRISPR-Cas classification, overview CRISPR biology and mechanism of action, and discuss current and future applications in lactic acid bacteria, opening new avenues for their industrial exploitation and manipulation of microbiomes.
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Affiliation(s)
- Avery Roberts
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Campus Box 7624, Raleigh, NC 27695, USA
- Genomic Sciences Graduate Program, North Carolina State University, Campus Box 7566, Raleigh, NC 27695, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Campus Box 7624, Raleigh, NC 27695, USA
- Genomic Sciences Graduate Program, North Carolina State University, Campus Box 7566, Raleigh, NC 27695, USA
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39
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Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat Commun 2020; 11:1738. [PMID: 32269218 PMCID: PMC7142098 DOI: 10.1038/s41467-020-15508-1] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/13/2020] [Indexed: 12/29/2022] Open
Abstract
A complex interplay of metabolic and immunological mechanisms underlies many diseases that represent a substantial unmet medical need. There is an increasing appreciation of the role microbes play in human health and disease, and evidence is accumulating that a new class of live biotherapeutics comprised of engineered microbes could address specific mechanisms of disease. Using the tools of synthetic biology, nonpathogenic bacteria can be designed to sense and respond to environmental signals in order to consume harmful compounds and deliver therapeutic effectors. In this perspective, we describe considerations for the design and development of engineered live biotherapeutics to achieve regulatory and patient acceptance. The role microbes play in human health and the ability of synthetic biology to engineer microbial properties opens up new ways of treating disease. In this perspective, the authors describe the design and development of these living therapeutics.
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40
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Bøe CA, Holo H. Engineering Lactococcus lactis for Increased Vitamin K2 Production. Front Bioeng Biotechnol 2020; 8:191. [PMID: 32258010 PMCID: PMC7093718 DOI: 10.3389/fbioe.2020.00191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/27/2020] [Indexed: 01/07/2023] Open
Abstract
Cheese produced with Lactococcus lactis is the main source of vitamin K2 in the Western diet. Subclinical vitamin K2 deficiency is common, calling for foods with enhanced vitamin K2 content. In this study we describe analyses of vitamin K2 (menaquinone) production in the lactic acid bacterium L. lactis ssp. cremoris strain MG1363. By cloning and expression from strong promoters we have identified genes and bottlenecks in the biosynthetic pathways leading to the long-chained menaquinones, MK-8 and MK-9. Key genes of the biosynthetic menaquinone pathway were overexpressed, singly or combined, to examine how vitamin K2 production can be enhanced. We observed that the production of the long menaquinone polyprenyl side chain, rather than production of the napthoate ring (1,4-dihydroxy-2-naphtoic acid), limits total menaquinone synthesis. Overexpression of genes causing increased ring formation (menF and menA) led to overproduction of short chained MK-3, while overexpression of other key genes (mvk and llmg_0196) resulted in enhanced full-length MK-9 production. Of two putatively annotated prenyl diphosphate synthases we pinpoint llmg_0196 (preA) to be important for menaquinone production in L. lactis. The genes mvk, preA, menF, and menA were found to be important contributors to menaquinone levels as single overexpression of these genes double and more than triple the total menaquinone content in culture. Combined overexpression of mvk, preA, and menA increased menaquinone levels to a higher level than obtained individually. When the overproducing strains were applied for milk fermentations vitamin K2 content was effectively increased 3-fold compared to the wild type. The results provide a foundation for development of strains to ferment foods with increased functional value i.e., higher vitamin K2 content.
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Affiliation(s)
- Cathrine Arnason Bøe
- Laboratory of Microbial Gene Technology, Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Helge Holo
- Laboratory of Microbial Gene Technology, Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Tine SA, Oslo, Norway
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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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Pan M, Barrangou R. Combining omics technologies with CRISPR-based genome editing to study food microbes. Curr Opin Biotechnol 2020; 61:198-208. [DOI: 10.1016/j.copbio.2019.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 12/22/2022]
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Markakiou S, Gaspar P, Johansen E, Zeidan AA, Neves AR. Harnessing the metabolic potential of Streptococcus thermophilus for new biotechnological applications. Curr Opin Biotechnol 2020; 61:142-152. [DOI: 10.1016/j.copbio.2019.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023]
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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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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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Barriers to genome editing with CRISPR in bacteria. J Ind Microbiol Biotechnol 2019; 46:1327-1341. [PMID: 31165970 DOI: 10.1007/s10295-019-02195-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
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