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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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Microorganisms-An Effective Tool to Intensify the Utilization of Sulforaphane. Foods 2022; 11:foods11233775. [PMID: 36496582 PMCID: PMC9737538 DOI: 10.3390/foods11233775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Sulforaphane (SFN) was generated by the hydrolysis of glucoraphanin under the action of myrosinase. However, due to the instability of SFN, the bioavailability of SFN was limited. Meanwhile, the gut flora obtained the ability to synthesize myrosinase and glucoraphanin, which could be converted into SFN in the intestine. However, the ability of microorganisms to synthesize myrosinase in the gut was limited. Therefore, microorganisms with myrosinase synthesis ability need to be supplemented. With the development of research, microorganisms with high levels of myrosinase synthesis could be obtained by artificial selection and gene modification. Researchers found the SFN production rate of the transformed microorganisms could be significantly improved. However, despite applying transformation technology and regulating nutrients to microorganisms, it still could not provide the best efficiency during generating SFN and could not accomplish colonization in the intestine. Due to the great effect of microencapsulation on improving the colonization ability of microorganisms, microencapsulation is currently an important way to deliver microorganisms into the gut. This article mainly analyzed the possibility of obtaining SFN-producing microorganisms through gene modification and delivering them to the gut via microencapsulation to improve the utilization rate of SFN. It could provide a theoretical basis for expanding the application scope of SFN.
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Lee HM, Ren J, Yu MS, Kim H, Kim WY, Shen J, Yoo SM, Eyun SI, Na D. Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:228. [PMID: 34863247 PMCID: PMC8645107 DOI: 10.1186/s13068-021-02077-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/16/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform because of its relatively fast growth. However, the lack of genetic engineering tools hampers its wide use in the bioindustry. RESULTS Through three different approaches, we constructed a tunable promoter library comprising 33 promoters that can be used for the metabolic engineering of Methylomonas sp. DH-1. The library had an expression level of 0.24-410% when compared with the strength of the lac promoter. For practical application of the promoter library, we fine-tuned the expressions of cadA and cadB genes, required for cadaverine synthesis and export, respectively. The strain with PrpmB-cadA and PDnaA-cadB produced the highest cadaverine titre (18.12 ± 1.06 mg/L) in Methylomonas sp. DH-1, which was up to 2.8-fold higher than that obtained from a non-optimized strain. In addition, cell growth and lysine (a precursor of cadaverine) production assays suggested that gene expression optimization through transcription tuning can afford a balance between the growth and precursor supply. CONCLUSIONS The tunable promoter library provides standard and tunable components for gene expression, thereby facilitating the use of methanotrophs, specifically Methylomonas sp. DH-1, as a sustainable cell factory.
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Affiliation(s)
- Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Hyunjoo Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Woo Young Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea.
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Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
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Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Ren J, Lee HM, Thai TD, Na D. Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:200. [PMID: 33372613 PMCID: PMC7720504 DOI: 10.1186/s13068-020-01846-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism. RESULTS We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5 × 103 CFU/μg (124%). The introduced gene increased the production of carotenoid by 26%. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70% as well. The production of carotenoid was decreased by 40% when the psy gene was translationally repressed by anti-psy sRNA. CONCLUSIONS Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.
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Affiliation(s)
- Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Wang Y, Wang X, Yu L, Tian Y, Li S, Leng F, Ma J, Chen J. Effects of Sr 2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation. PeerJ 2020. [DOI: 10.7717/peerj.9480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology
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Affiliation(s)
- Yonggang Wang
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Xinjian Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Linmiao Yu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Yuan Tian
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Shaowei Li
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jixiang Chen
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
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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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Cho SW, Yim J, Seo SW. Engineering Tools for the Development of Recombinant Lactic Acid Bacteria. Biotechnol J 2020; 15:e1900344. [DOI: 10.1002/biot.201900344] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Sung Won Cho
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Jaewoo Yim
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
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Ren J, Karna S, Lee HM, Yoo SM, Na D. Artificial transformation methodologies for improving the efficiency of plasmid DNA transformation and simplifying its use. Appl Microbiol Biotechnol 2019; 103:9205-9215. [PMID: 31650193 DOI: 10.1007/s00253-019-10173-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/23/2023]
Abstract
The uptake of exogenous DNA materials through the cell membrane by bacteria, known as transformation, is essential for the genetic manipulation of bacteria and, thus, plays key roles in biotechnological and biological research. The efficiency of natural transformation is very low; therefore, various artificial transformation methods have been developed for simple and efficient bacterial transformation. The basic bacterial transformation method is based on chemical, physical, and electrical processes and other means to permeabilize the bacterial cell membrane to allow plasmid DNA uptake. With the introduction of novel chemicals, materials, and devices and the optimization of protocols, new transformation methods have become simpler, cheaper, and more reproducible for use in diverse bacterial species compared with conventional methods. In this review, artificial transformation methods have been classified according to the membrane-permeabilizing mechanisms employed by them. Their influential factors, transformation efficiency, advantages, disadvantages, and practical applications are briefly illustrated. Finally, physicochemical transformation as a new bacterial transformation technique has also been described.
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Affiliation(s)
- Jun Ren
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sandeep Karna
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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