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Lammens EM, Volke DC, Schroven K, Voet M, Kerremans A, Lavigne R, Hendrix H. A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing. Microbiol Spectr 2023; 11:e0270723. [PMID: 37975669 PMCID: PMC10715078 DOI: 10.1128/spectrum.02707-23] [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] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations in Pseudomonas putida and Pseudomonas aeruginosa in a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established Standard European Vector Architecture (SEVA) vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets the origin-of-transfer, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally occurring plasmids from bacteria.
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Affiliation(s)
| | - Daniel Christophe Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kaat Schroven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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2
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Nonaka K, Osamura T, Takahashi F. A 4-hydroxybenzoate 3-hydroxylase mutant enables 4-amino-3-hydroxybenzoic acid production from glucose in Corynebacterium glutamicum. Microb Cell Fact 2023; 22:168. [PMID: 37644492 PMCID: PMC10466732 DOI: 10.1186/s12934-023-02179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Microbial production of aromatic chemicals is an attractive method for obtaining high-performance materials from biomass resources. A non-proteinogenic amino acid, 4-amino-3-hydroxybenzoic acid (4,3-AHBA), is expected to be a precursor of highly functional polybenzoxazole polymers; however, methods for its microbial production have not been reported. In this study, we attempted to produce 4,3-AHBA from glucose by introducing 3-hydroxylation of 4-aminobenzoic acid (4-ABA) into the metabolic pathway of an industrially relevant bacterium, Corynebacterium glutamicum. RESULTS Six different 4-hydroxybenzoate 3-hydroxylases (PHBHs) were heterologously expressed in C. glutamicum strains, which were then screened for the production of 4,3-AHBA by culturing with glucose as a carbon source. The highest concentration of 4,3-AHBA was detected in the strain expressing PHBH from Caulobacter vibrioides (CvPHBH). A combination of site-directed mutagenesis in the active site and random mutagenesis via laccase-mediated colorimetric assay allowed us to obtain CvPHBH mutants that enhanced 4,3-AHBA productivity under deep-well plate culture conditions. The recombinant C. glutamicum strain expressing CvPHBHM106A/T294S and having an enhanced 4-ABA biosynthetic pathway produced 13.5 g/L (88 mM) 4,3-AHBA and 0.059 g/L (0.43 mM) precursor 4-ABA in fed-batch culture using a nutrient-rich medium. The culture of this strain in the chemically defined CGXII medium yielded 9.8 C-mol% of 4,3-AHBA from glucose, corresponding to 12.8% of the theoretical maximum yield (76.8 C-mol%) calculated using a genome-scale metabolic model of C. glutamicum. CONCLUSIONS Identification of PHBH mutants that could efficiently catalyze the 3-hydroxylation of 4-ABA in C. glutamicum allowed us to construct an artificial biosynthetic pathway capable of producing 4,3-AHBA on a gram-scale using glucose as the carbon source. These findings will contribute to a better understanding of enzyme-catalyzed regioselective hydroxylation of aromatic chemicals and to the diversification of biomass-derived precursors for high-performance materials.
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Affiliation(s)
- Kyoshiro Nonaka
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan.
| | - Tatsuya Osamura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
| | - Fumikazu Takahashi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
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3
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Neff A, Lück R, Hövels M, Deppenmeier U. Expanding the repertoire of counterselection markers for markerless gene deletion in the human gut bacterium Phocaeicola vulgatus. Anaerobe 2023:102742. [PMID: 37244477 DOI: 10.1016/j.anaerobe.2023.102742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/24/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
OBJECTIVE Phocaeicola (P.) vulgatus (formerly Bacteroides vulgatus) is a highly abundant and ubiquitous member of the human gut microbiota, associated with human health and disease, and therefore represents an important target for further investigations. In this study a novel gene deletion method was developed for P. vulgatus, expanding the tools available for genetic manipulation of members of the microbial order Bacteroidales. MATERIAL AND METHODS The study used a combination of bioinformatics and growth experiments in interaction with molecular cloning to validate the applicability of SacB as a counterselection marker in P. vulgatus. RESULTS In this study, the levansucrase gene sacB from Bacillus subtilis was verified as a functional counterselection marker for P. vulgatus, conferring a lethal sensitivity towards sucrose. Markerless gene deletion based on SacB was applied to delete a gene encoding a putative endofructanase (BVU1663). The P. vulgatus Δbvu1663 deletion mutant displayed no biomass formation when grown on levan, inulin or their corresponding fructooligosaccharides. This system was also applied for the deletion of the two genes bvu0984 and bvu3649, which are involved in the pyrimidine metabolism. The resulting P. vulgatus Δ0984 Δ3649 deletion mutant no longer showed sensitivity for the toxic pyrimidine analogon 5-fluorouracil, allowing a counterselection with this compound in the double knockout strain. CONCLUSION The genetic toolbox for P. vulgatus was expanded by a markerless gene deletion system based on SacB as an efficient counterselection marker. The system was employed to successfully delete three genes in P. vulgatus which all resulted in expected phenotypes as confirmed by subsequent growth experiments.
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Affiliation(s)
- André Neff
- Institute for Microbiology and Biotechnology, University of Bonn, 53115, Bonn, Germany
| | - Rebecca Lück
- Institute for Microbiology and Biotechnology, University of Bonn, 53115, Bonn, Germany
| | - Marcel Hövels
- Institute for Microbiology and Biotechnology, University of Bonn, 53115, Bonn, Germany
| | - Uwe Deppenmeier
- Institute for Microbiology and Biotechnology, University of Bonn, 53115, Bonn, Germany.
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4
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Kim GY, Kim J, Park G, Kim HJ, Yang J, Seo SW. Synthetic biology tools for engineering Corynebacterium glutamicum. Comput Struct Biotechnol J 2023; 21:1955-1965. [PMID: 36942105 PMCID: PMC10024154 DOI: 10.1016/j.csbj.2023.03.004] [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] [Received: 11/05/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Corynebacterium glutamicum is a promising organism for the industrial production of amino acids, fuels, and various value-added chemicals. From the whole genome sequence release, C. glutamicum has been valuable in the field of industrial microbiology and biotechnology. Continuous discovery of genetic manipulations and regulation mechanisms has developed C. glutamicum as a synthetic biology platform chassis. This review summarized diverse genomic manipulation technologies and gene expression tools for static, dynamic, and multiplex control at transcription and translation levels. Moreover, we discussed the current challenges and applicable tools to C. glutamicum for future advancements.
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Affiliation(s)
- Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jinyoung Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Geunyung Park
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyeon Jin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jina Yang
- Department of Chemical Engineering, Jeju National University, 102, Jejudaehak-ro, Jeju-si, Jeju-do 63243, South Korea
- Corresponding author.
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Bio-MAX Institute, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Engineering Research Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Corresponding author at: School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
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Zhang Y, Bailey TS, Kubiak AM, Lambin P, Theys J. Heterologous Gene Regulation in Clostridia: Rationally Designed Gene Regulation for Industrial and Medical Applications. ACS Synth Biol 2022; 11:3817-3828. [PMID: 36265075 PMCID: PMC9680021 DOI: 10.1021/acssynbio.2c00401] [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] [Indexed: 01/27/2023]
Abstract
Several species from the Clostridium genus show promise as industrial solvent producers and cancer therapeutic delivery vehicles. Previous development of shuttle plasmids and genome editing tools has aided the study of these species and enabled their exploitation in industrial and medical applications. Nevertheless, the precise control of gene expression is still hindered by the limited range of characterized promoters. To address this, libraries of promoters (native and synthetic), 5' UTRs, and alternative start codons were constructed. These constructs were tested in Escherichia coli K-12, Clostridium sporogenes NCIMB 10696, and Clostridium butyricum DSM 10702, using β-glucuronidase (gusA) as a gene reporter. Promoter activity was corroborated using a second gene reporter, nitroreductase (nmeNTR) from Neisseria meningitides. A strong correlation was observed between the two reporters. In C. sporogenes and C. butyricum, respectively, changes in GusA activity between the weakest and strongest expressing levels were 129-fold and 78-fold. Similar results were obtained with the nmeNTR. Using the GusA reporter, translation initiation from six alternative (non-AUG) start codons was measured in E. coli, C. sporogenes, and C. butyricum. Clearly, species-specific differences between clostridia and E. coli in translation initiation were observed, and the performance of the start codons was influenced by the upstream 5' UTR sequence. These results highlight a new opportunity for gene control in recombinant clostridia. To demonstrate the value of these results, expression of the sacB gene from Bacillus subtilis was optimized for use as a novel negative selection marker in C. butyricum. In summary, these results indicate improvements in the understanding of heterologous gene regulation in Clostridium species and E. coli cloning strains. This new knowledge can be utilized for rationally designed gene regulation in Clostridium-mediated industrial and medical applications, as well as fundamental research into the biology of Clostridium species.
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Affiliation(s)
- Yanchao Zhang
- The
M-Lab, Department of Precision Medicine, GROW - School of Oncology
and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands,
| | - Tom S. Bailey
- The
M-Lab, Department of Precision Medicine, GROW - School of Oncology
and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aleksandra M. Kubiak
- The
M-Lab, Department of Precision Medicine, GROW - School of Oncology
and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands,Exomnis
Biotech BV, Oxfordlaan
55, 6229 EV Maastricht, The Netherlands
| | - Philippe Lambin
- The
M-Lab, Department of Precision Medicine, GROW - School of Oncology
and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Jan Theys
- The
M-Lab, Department of Precision Medicine, GROW - School of Oncology
and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
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Genome engineering of the Corynebacterium glutamicum chromosome by the Extended Dual-In/Out strategy. METHODS IN MICROBIOLOGY 2022; 200:106555. [DOI: 10.1016/j.mimet.2022.106555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022]
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7
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Li J, Wang B, Yang Q, Si H, Zhao Y, Zheng Y, Peng W. Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu. Front Microbiol 2022; 13:848964. [PMID: 35308340 PMCID: PMC8928166 DOI: 10.3389/fmicb.2022.848964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudonocardia species are emerging as important microorganisms of global concern with unique and increasingly significant ecological roles and represent a prominent source of bioactive natural products, but genetic engineering of these organisms for biotechnological applications is greatly hindered due to the limitation of efficient genetic manipulation tools. In this regard, we report here the establishment of an efficient genetic manipulation system for a newly isolated strain, Pseudonocardia alni Shahu, based on plasmid conjugal transfer from Escherichia coli to Pseudonocardia. Conjugants were yielded upon determining the optimal ratio between the donor and recipient cells, and designed genome modifications were efficiently accomplished, including exogenous gene integration based on an integrative plasmid and chromosomal stretch removal by homologous recombination using a suicidal non-replicating vector. Collectively, this work has made the P. alni Shahu accessible for genetic engineering, and provided an important reference for developing genetic manipulation methods in other rare actinomycetes.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Baiyang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Han Si
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yuting Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yanli Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- *Correspondence: Yanli Zheng,
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- Wenfang Peng,
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8
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Chai M, Deng C, Chen Q, Lu W, Liu Y, Li J, Du G, Lv X, Liu L. Synthetic Biology Toolkits and Metabolic Engineering Applied in Corynebacterium glutamicum for Biomanufacturing. ACS Synth Biol 2021; 10:3237-3250. [PMID: 34855356 DOI: 10.1021/acssynbio.1c00355] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum is an important workhorse in industrial white biotechnology. It has been widely applied in the producing processes of amino acids, fuels, and diverse value-added chemicals. With the continuous disclosure of genetic regulation mechanisms, various strategies and technologies of synthetic biology were used to design and construct C. glutamicum cells for biomanufacturing and bioremediation. This study mainly aimed to summarize the design and construction strategies of C. glutamicum-engineered strains, which were based on genomic modification, synthetic biological device-assisted metabolic flux optimization, and directed evolution-based engineering. Then, taking two important bioproducts (N-acetylglucosamine and hyaluronic acid) as examples, the applications of C. glutamicum cell factories were introduced. Finally, we discussed the current challenges and future development trends of C. glutamicum-engineered strain construction.
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Affiliation(s)
- Meng Chai
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Qi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Wei Lu
- Shandong Runde Biotechnology Co., Ltd., Tai’an 271000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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9
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Jatuponwiphat T, Namrak T, Nitisinprasert S, Nakphaichit M, Vongsangnak W. Integrative growth physiology and transcriptome profiling of probiotic Limosilactobacillus reuteri KUB-AC5. PeerJ 2021; 9:e12226. [PMID: 34707932 PMCID: PMC8500091 DOI: 10.7717/peerj.12226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Limosilactobacillus reuteri KUB-AC5 has been widely used as probiotic in chicken for Salmonella reduction. However, a preferable carbon source and growth phase is poorly characterized underlying metabolic responses on growth and inhibition effects of L. reuteri KUB-AC5. This study therefore aimed to investigate transcriptome profiling of L. reuteri KUB-AC5 revealing global metabolic responses when alteration of carbon sources and growth phases. Interestingly, L. reuteri KUB-AC5 grown under sucrose culture showed to be the best for fast growth and inhibition effects against Salmonella Enteritidis S003 growth. Towards the transcriptome profiling and reporter proteins/metabolites analysis, the results showed that amino acid transport via ABC systems as well as sucrose metabolism and transport are key metabolic responses at Logarithmic (L)-phase of L. reuteri KUB-AC5 growth. Considering the Stationary (S)-phase, we found the potential reporter proteins/metabolites involved in carbohydrate metabolism e.g., levansucrase and levan. Promisingly, levansucrase and levan were revealed to be candidates in relation to inhibition effects of L. reuteri KUB-AC5. Throughout this study, L. reuteri KUB-AC5 had a metabolic control in acclimatization to sucrose and energy pools through transcriptional co-regulation, which supported the cell growth and inhibition potentials. This study offers a perspective in optimizing fermentation condition through either genetic or physiological approaches for enhancing probiotic L. reuteri KUB-AC5 properties.
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Affiliation(s)
- Theeraphol Jatuponwiphat
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thanawat Namrak
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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10
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Plasmid Curing and Exchange Using a Novel Counter-Selectable Marker Based on Unnatural Amino Acid Incorporation at a Sense Codon. Int J Mol Sci 2021; 22:ijms222111482. [PMID: 34768910 PMCID: PMC8583848 DOI: 10.3390/ijms222111482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/25/2022] Open
Abstract
A protocol was designed for plasmid curing using a novel counter-selectable marker, named pylSZK-pylT, in Escherichia coli. The pylSZK-pylT marker consists of the archaeal pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA (tRNApyl) with modification, and incorporates an unnatural amino acid (Uaa), Nε-benzyloxycarbonyl-l-lysine (ZK), at a sense codon in ribosomally synthesized proteins, resulting in bacterial growth inhibition or killing. Plasmid curing is performed by exerting toxicity on pylSZK-pylT located on the target plasmid, and selecting only proliferative bacteria. All tested bacteria obtained using this protocol had lost the target plasmid (64/64), suggesting that plasmid curing was successful. Next, we attempted to exchange plasmids with the identical replication origin and an antibiotic resistance gene without plasmid curing using a modified protocol, assuming substitution of plasmids complementing genomic essential genes. All randomly selected bacteria after screening had only the substitute plasmid and no target plasmid (25/25), suggesting that plasmid exchange was also accomplished. Counter-selectable markers based on PylRS-tRNApyl, such as pylSZK-pylT, may be scalable in application due to their independence from the host genotype, applicability to a wide range of species, and high tunability due to the freedom of choice of target codons and Uaa’s to be incorporated.
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11
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Yang FY, Wei N, Zhang ZH, Wang M, Liu YC, Zhang LF, Gu F. Genome editing of Corynebacterium glutamicum mediated with Cpf1 plus Ku/LigD. Biotechnol Lett 2021; 43:2273-2281. [PMID: 34669078 DOI: 10.1007/s10529-021-03195-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Corynebacterium glutamicum (C. glutamicum) has been harnessed for multi-million-ton scale production of glutamate and lysine. To further increase its amino acid production for fermentation industry, there is an acute need to develop next-generation genome manipulation tool for its metabolic engineering. All reported methods for genome editing triggered with CRISPR-Cas are based on the homologous recombination. While, it requires the generation of DNA repair template, which is a bottle-neck for its extensive application. RESULTS In this study, we developed a method for gene knockout in C. glutamicum via CRISPR-Cpf1-coupled non-homologous end-joining (CC-NHEJ). Specifically, CRISPR-Cpf1 introduced double-strand breaks in the genome of C. glutamicum, which was further repaired by ectopically expressed two NHEJ key proteins (Mycobacterium tuberculosis Ku and ligase D). We provide the proof of concept, for CC-NHEJ, by the successful knockout of the crtYf/e gene in C. glutamicum with the efficiency of 22.00 ± 5.56%, or something like that. CONCLUSION The present study reported a novel genome manipulation method for C. glutamicum.
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Affiliation(s)
- Fa-Yu Yang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Nan Wei
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Zhi-Hao Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Ying-Chun Liu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Li-Fang Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Feng Gu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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12
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Jones CM, Parrish S, Nielsen DR. Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria. ACS Synth Biol 2021; 10:2371-2382. [PMID: 34530614 DOI: 10.1021/acssynbio.1c00269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being delivered via replicating plasmids, genes encoding for DNA modifying enzymes are instead integrated into essential genes on the chromosome by allelic exchange, as facilitated by antibiotic selection, a process that occurs readily and with only minor fitness defects. By virtue of the essentiality of these integration sites, full segregation is never achieved, with the strain instead remaining as a merodiploid so long as antibiotic selection is maintained. As a result, once the desired genome modification is complete, removal of antibiotic selection results in the gene encoding for the DNA modifying enzyme to then be promptly eliminated from the population. Proof of concept of this new and generalizable strategy is provided using two different site-specific recombination systems, CRE-lox and DRE-rox, in the fast-growing cyanobacterium Synechococcus sp. PCC 7002, as well as CRE-lox in the model cyanobacterium Synechocystis sp. PCC 6803. Reusability of the method, meanwhile, is demonstrated by constructing a high-CO2 requiring and markerless Δndh3 Δndh4 ΔbicA ΔsbtA mutant of Synechococcus sp. PCC 7002. Overall, this method enables the simple and efficient construction of stable and unmarked mutants in cyanobacteria without the need to develop additional shuttle vectors nor counterselection systems.
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Affiliation(s)
- Christopher M. Jones
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Sydney Parrish
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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13
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Rodriguez A, Meadows JA, Sun N, Simmons BA, Gladden JM. Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol. Microb Cell Fact 2021; 20:181. [PMID: 34526022 PMCID: PMC8442356 DOI: 10.1186/s12934-021-01670-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Hydroxycinnamic acids such as p-coumaric acid (CA) are chemically linked to lignin in grassy biomass with fairly labile ester bonds and therefore represent a straightforward opportunity to extract and valorize lignin components. In this work, we investigated the enzymatic conversion of CA extracted from lignocellulose to 4-vinylphenol (4VP) by expressing a microbial phenolic acid decarboxylase in Corynebacterium glutamicum, Escherichia coli, and Bacillus subtilis. The performance of the recombinant strains was evaluated in response to the substrate concentration in rich medium or a lignin liquor and the addition of an organic overlay to perform a continuous product extraction in batch cultures. We found that using undecanol as an overlay enhanced the 4VP titers under high substrate concentrations, while extracting > 97% of the product from the aqueous phase. C. glutamicum showed the highest tolerance to CA and resulted in the accumulation of up to 187 g/L of 4VP from pure CA in the overlay with a 90% yield when using rich media, or 17 g/L of 4VP with a 73% yield from CA extracted from lignin. These results indicate that C. glutamicum is a suitable host for the high-level production of 4VP and that further bioprocess engineering strategies should be explored to optimize the production, extraction, and purification of 4VP from lignin with this organism.
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Affiliation(s)
- Alberto Rodriguez
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA.,Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94551, USA
| | - Jamie A Meadows
- Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94551, USA
| | - Ning Sun
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA. .,Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94551, USA.
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14
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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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15
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Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Hoffmann SL, Kohlstedt M, Jungmann L, Hutter M, Poblete-Castro I, Becker J, Wittmann C. Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering. Metab Eng 2021; 67:293-307. [PMID: 34314893 DOI: 10.1016/j.ymben.2021.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds emerge as promising third-generation renewable for sustainable bioproduction. In the present work, we valorized brown seaweed to produce l-lysine, the world's leading feed amino acid, using Corynebacterium glutamicum, which was streamlined by systems metabolic engineering. The mutant C. glutamicum SEA-1 served as a starting point for development because it produced small amounts of l-lysine from mannitol, a major seaweed sugar, because of the deletion of its arabitol repressor AtlR and its engineered l-lysine pathway. Starting from SEA-1, we systematically optimized the microbe to redirect excess NADH, formed on the sugar alcohol, towards NADPH, required for l-lysine synthesis. The mannitol dehydrogenase variant MtlD D75A, inspired by 3D protein homology modelling, partly generated NADPH during the oxidation of mannitol to fructose, leading to a 70% increased l-lysine yield in strain SEA-2C. Several rounds of strain engineering further increased NADPH supply and l-lysine production. The best strain, SEA-7, overexpressed the membrane-bound transhydrogenase pntAB together with codon-optimized gapN, encoding NADPH-dependent glyceraldehyde 3-phosphate dehydrogenase, and mak, encoding fructokinase. In a fed-batch process, SEA-7 produced 76 g L-1l-lysine from mannitol at a yield of 0.26 mol mol-1 and a maximum productivity of 2.1 g L-1 h-1. Finally, SEA-7 was integrated into seaweed valorization cascades. Aqua-cultured Laminaria digitata, a major seaweed for commercial alginate, was extracted and hydrolyzed enzymatically, followed by recovery and clean-up of pure alginate gum. The residual sugar-based mixture was converted to l-lysine at a yield of 0.27 C-mol C-mol-1 using SEA-7. Second, stems of the wild-harvested seaweed Durvillaea antarctica, obtained as waste during commercial processing of the blades for human consumption, were extracted using acid treatment. Fermentation of the hydrolysate using SEA-7 provided l-lysine at a yield of 0.40 C-mol C-mol-1. Our findings enable improvement of the efficiency of seaweed biorefineries using tailor-made C. glutamicum strains.
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Affiliation(s)
- Sarah Lisa Hoffmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lukas Jungmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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17
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Yao C, Hu X, Wang X. Construction and application of a CRISPR/Cas9-assisted genomic editing system for Corynebacterium glutamicum. AMB Express 2021; 11:70. [PMID: 34009533 PMCID: PMC8134620 DOI: 10.1186/s13568-021-01231-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
Corynebacterium glutamicum is widely used as microbial cell factory for various bioproducts, but its genomic editing efficiency needs to be improved. In this study, a highly efficient CRISPR/Cas9-assisted genomic editing system for C. glutamicum was constructed. This system mainly involves a plasmid and can be used for both gene insertion and deletion in the chromosome of C. glutamicum. The recombinant plasmid for the target gene containing all the editing elements, and first constructed it in E. coli, then purified and transformed it into C. glutamicum. This temperature-sensitive plasmid was cured at high temperature after the genomic editing was completed in C. glutamicum. Using this genetic editing system, the genetic editing efficiency in C. glutamicum ATCC 13032 could reach 95%. The whole work of editing could be done in 8-9 days and showed most time-saving compared to the reported. Using this system, the native promoter of gdhA1 in ATCC 13032 has been replaced with the strong promoter PtacM, and more than 10 genes in ATCC 13032 have been deleted. The results demonstrate that this CRISPR/Cas9-assisted system is highly efficient and very suitable for genome editing in C. glutamicum.
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18
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Li C, Swofford CA, Rückert C, Sinskey AJ. Optimizing recombineering in Corynebacterium glutamicum. Biotechnol Bioeng 2021; 118:2255-2264. [PMID: 33650120 DOI: 10.1002/bit.27737] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/03/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
Owing to the increasing demand for amino acids and valuable commodities that can be produced by Corynebacterium glutamicum, there is a pressing need for new rapid genome engineering tools that improve the speed and efficiency of genomic insertions, deletions, and mutations. Recombineering using the λ Red system in Escherichia coli has proven very successful at genetically modifying this organism in a quick and efficient manner, suggesting that optimizing a recombineering system for C. glutamicum will also improve the speed for genomic modifications. Here, we maximized the recombineering efficiency in C. glutamicum by testing the efficacy of seven different recombinase/exonuclease pairs for integrating single-stranded DNA and double-stranded DNA (dsDNA) into the genome. By optimizing the homologous arm length and the amount of dsDNA transformed, as well as eliminating codon bias, a dsDNA recombineering efficiency of 13,250 transformed colonies/109 viable cells was achieved, the highest efficiency currently reported in the literature. Using this optimized system, over 40,000 bp could be deleted in one transformation step. This recombineering strategy will greatly improve the speed of genetic modifications in C. glutamicum and assist other systems, such as clustered regularly interspaced short palindromic repeats and multiplexed automated genome engineering, in improving targeted genome editing.
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Affiliation(s)
- Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Charles A Swofford
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Christian Rückert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
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19
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Luo G, Zhao N, Jiang S, Zheng S. Application of RecET-Cre/loxP system in Corynebacterium glutamicum ATCC14067 for L-leucine production. Biotechnol Lett 2020; 43:297-306. [PMID: 32936374 DOI: 10.1007/s10529-020-03000-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/03/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To explore the RecET-Cre/loxP system for chromosomal replacement of promoter and its application on enhancement L-leucine production in Corynebacterium glutamicum (C. glutamicum) ATCC14067. RESULTS The RecET-Cre/loxP system was used to achieve the chromosomal replacement of promoter in C. glutamicum ATCC14067 to adjust the metabolic flux involving the L-leucine synthetic pathway. First, leuAr_13032 from C. glutamicum ATCC13032 which carried two mutations was overexpressed to release enzyme feedback inhibition. Then, comparing different mutations in ilvBNC gene clusters, the results indicated that ilvBNC_CP was most effective to enhance the metabolic flux of pyruvate towards L-leucine synthesis. The promoters of pck, odx and pyk2 were overexpressed under the strong promoter Peftu or Psod to improve the supply of pyruvate. Besides, the promoter PilvBNC was employed to dynamically control the transcription level of icd due to its attenuation mechanism by responding to the concentration of L-leucine. The final engineered strain produced 14.05 g L-leucine/L in flask cultivation. CONCLUSION The RecET-Cre/loxP system is effective for gene manipulation in C. glutamicum ATCC14067. Besides, the results demonstrate the potential of C. glutamicum ATCC14067 for L-leucine production and provide new targets and strategies for strain development.
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Affiliation(s)
- Guangjuan Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shibo Jiang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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20
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CRISPR-Cas9-Mediated Carbapenemase Gene and Plasmid Curing in Carbapenem-Resistant Enterobacteriaceae. Antimicrob Agents Chemother 2020; 64:AAC.00843-20. [PMID: 32631827 DOI: 10.1128/aac.00843-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Combating plasmid-mediated carbapenem resistance is essential to control and prevent the dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Here, we conducted a proof-of-concept study to demonstrate that CRISPR-Cas9-mediated resistance gene and plasmid curing can effectively resensitize CRE to carbapenems. A novel CRISPR-Cas9-mediated plasmid-curing system (pCasCure) was developed and electrotransferred into various clinical CRE isolates. The results showed that pCasCure can effectively cure bla KPC, bla NDM, and bla OXA-48 in various Enterobacteriaceae species of Klebsiella pneumoniae, Escherichia coli, Enterobacter hormaechei, Enterobacter xiangfangensis, and Serratia marcescens clinical isolates, with a >94% curing efficiency. In addition, we also demonstrated that pCasCure can efficiently eliminate several epidemic carbapenem-resistant plasmids, including the bla KPC-harboring IncFIIK-pKpQIL and IncN pKp58_N plasmids, the bla OXA-48-harboring pOXA-48-like plasmid, and the bla NDM-harboring IncX3 plasmid, by targeting their replication and partitioning (parA in pKpQIL) genes. However, curing the bla OXA-48 gene failed to eliminate its corresponding pOXA-48-like plasmid in clinical K. pneumoniae isolate 49210, while further next-generation sequencing revealed that it was due to IS1R-mediated recombination outside the CRISPR-Cas9 cleavage site resulting in bla OXA-48 truncation and, therefore, escaped plasmid curing. Nevertheless, the curing of carbapenemase genes or plasmids, including the truncation of bla OXA-48 in 49210, successfully restore their susceptibility to carbapenems, with a >8-fold reduction of MIC values in all tested isolates. Taken together, our study confirmed the concept of using CRISPR-Cas9-mediated carbapenemase gene and plasmid curing to resensitize CRE to carbapenems. Further work is needed to integrate pCasCure in an optimal delivery system to make it applicable for clinical intervention.
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21
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Krumbach K, Sonntag CK, Eggeling L, Marienhagen J. CRISPR/Cas12a Mediated Genome Editing To Introduce Amino Acid Substitutions into the Mechanosensitive Channel MscCG of Corynebacterium glutamicum. ACS Synth Biol 2019; 8:2726-2734. [PMID: 31790583 PMCID: PMC6994057 DOI: 10.1021/acssynbio.9b00361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Against the background of a growing demand for the implementation
of environmentally friendly production processes, microorganisms are
engineered for the large-scale biosynthesis of chemicals, fuels, or
food and feed additives from sustainable resources. Since strain development
is expensive and time-consuming, continuous improvement of molecular
tools for the genetic modification of the microbial production hosts
is absolutely vital. Recently, the CRISPR/Cas12a technology for the
engineering of Corynebacterium glutamicum as an important
platform organism for industrial amino acid production has been introduced.
Here, this system was advanced by designing an easy-to-construct crRNA
delivery vector using simple oligonucleotides. In combination with
a C. glutamicum strain engineered for the chromosomal
expression of the β-galactosidase-encoding lacZ gene, this new plasmid was used to investigate CRISPR/Cas12a targeting
and editing at various positions relative to the PAM site. Finally,
we used this system to perform codon saturation mutagenesis at critical
positions in the mechanosensitive channel MscCG to identify new gain-of-function
mutations for increased l-glutamate export. The mutations
obtained can be explained by particular demands of the channel on
its immediate lipid environment to allow l-glutamate efflux.
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Affiliation(s)
- Karin Krumbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | | | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
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22
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Wang T, Li Y, Li J, Zhang D, Cai N, Zhao G, Ma H, Shang C, Ma Q, Xu Q, Chen N. An update of the suicide plasmid-mediated genome editing system in Corynebacterium glutamicum. Microb Biotechnol 2019; 12:907-919. [PMID: 31180185 PMCID: PMC6680612 DOI: 10.1111/1751-7915.13444] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/12/2019] [Accepted: 05/16/2019] [Indexed: 12/21/2022] Open
Abstract
Corynebacterium glutamicum is an important industrial microorganism, but the availability of tools for its genetic modification has lagged compared to other model microorganisms such as Escherichia coli. Despite great progress in CRISPR-based technologies, the most feasible genome editing method in C. glutamicum is suicide plasmid-mediated, the editing efficiency of which is low due to high false-positive rates of sacB counter selection, and the requirement for tedious two-round selection and verification of rare double-cross-over events. In this study, an rpsL mutant conferring streptomycin resistance was harnessed for counter selection, significantly increasing the positive selection rate. More importantly, with the aid of high selection efficiencies through the use of antibiotics, namely kanamycin and streptomycin, the two-step verification strategy can be simplified to just one-step verification of the final edited strain. As proof of concept, a 2.5-kb DNA fragment comprising aroGfbr pheAfbr expressing cassettes was integrated into the genome of C. glutamicum, with an efficiency of 20% out of the theoretical 50%. The resulting strain produced 110 mg l-1 l-tyrosine in shake-flask fermentation. This updated suicide plasmid-mediated genome editing system will greatly facilitate genetic manipulations including single nucleotide mutation, gene deletion and gene insertion in C. glutamicum and can be easily applied to other microbes.
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Affiliation(s)
- Ting Wang
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Yanjun Li
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme EngineeringGuangzhou510006China
- Key Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China
| | - Juan Li
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Dezhi Zhang
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Ningyun Cai
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Guihong Zhao
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Hongkun Ma
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Can Shang
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Qian Ma
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
- Key Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China
| | - Qingyang Xu
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
- Key Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China
| | - Ning Chen
- College of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
- Key Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China
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23
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The K296-D320 region of recombinant levansucrase BA-SacB can affect the sensitivity of Escherichia coli host to sucrose. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01496-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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24
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Gießelmann G, Dietrich D, Jungmann L, Kohlstedt M, Jeon EJ, Yim SS, Sommer F, Zimmer D, Mühlhaus T, Schroda M, Jeong KJ, Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum
for High‐Level Ectoine Production: Design, Combinatorial Assembly, and Implementation of a Transcriptionally Balanced Heterologous Ectoine Pathway. Biotechnol J 2019; 14:e1800417. [DOI: 10.1002/biot.201800417] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Gideon Gießelmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Demian Dietrich
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Lukas Jungmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Eun J. Jeon
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Sung S. Yim
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Frederik Sommer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - David Zimmer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Timo Mühlhaus
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Michael Schroda
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Ki J. Jeong
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Judith Becker
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
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25
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Wendisch VF. Metabolic engineering advances and prospects for amino acid production. Metab Eng 2019; 58:17-34. [PMID: 30940506 DOI: 10.1016/j.ymben.2019.03.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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A Counterselectable Sucrose Sensitivity Marker Permits Efficient and Flexible Mutagenesis in Streptococcus agalactiae. Appl Environ Microbiol 2019; 85:AEM.03009-18. [PMID: 30658970 DOI: 10.1128/aem.03009-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/13/2019] [Indexed: 12/25/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) is a cause of severe infections, particularly during the newborn period. While methods exist for generating chromosomal mutations in GBS, they are cumbersome and inefficient and present significant challenges if the goal is to study subtle mutations, such as single-base-pair polymorphisms. To address this problem, we have developed an efficient and flexible GBS mutagenesis protocol based on sucrose counterselection against levansucrase (SacB) expressed from a temperature-selective shuttle vector. GBS containing the SacB expression cassette demonstrates lethal sensitivity to supplemental sucrose whether the plasmid DNA is replicating outside of the chromosome or has been integrated during a crossover event. Transmission electron microscopy shows that SacB-mediated lethal sucrose sensitivity results from the accumulation of inclusion bodies that eventually lead to complete degradation of normal cellular architecture and subsequent lysis. We used this new mutagenesis technique to generate an in-frame, allelic exchange knockout of the GBS sortase gene srtA, demonstrating that >99% of colonies that emerge from our protocol had the expected knockout phenotype and that among a subset tested by sequencing, 100% had the correct genotype. We also generated barcoded nonsense mutations in the cylE gene in two GBS strains, showing that the approach can be used to make small, precise chromosomal mutations.IMPORTANCE The ability to generate chromosomal mutations is fundamental to microbiology. Historically, however, GBS pathogenesis research has been made challenging by the relative genetic intractability of the organism. Generating a single knockout in GBS using traditional techniques can take many months, with highly variable success rates. Furthermore, traditional methods do not offer a straightforward way to generate single-base-pair polymorphisms or other subtle changes, especially to noncoding regions of the chromosome. We have developed a new sucrose counterselection-based method that permits rapid, efficient, and flexible GBS mutagenesis. Our technique requires no additional equipment beyond what is needed for traditional approaches. We believe that it will catalyze rapid advances in GBS genetics research by significantly easing the path to generating mutants.
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Zhu Y, Dong W, Ma J, Zhang Y, Pan Z, Yao H. Utilization of the ComRS system for the rapid markerless deletion of chromosomal genes in Streptococcus suis. Future Microbiol 2019; 14:207-222. [DOI: 10.2217/fmb-2018-0279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To develop a markerless gene deletion strategy in Streptococcus suis to solve the problem that several serotypes against electrotransformation of foreign DNA. Materials & methods: Bioinformatics retrieval was performed to identified ComRS systems functioning for natural transformation. A sacB-spc cassette with the upper and lower homologous fragments was amplification by fusion-PCR for spectinomycin-positive and sucrose-negative selection during gene deletion. Results & conclusion: Three phylogenetic clusters of ComR were identified to function for natural transformation by specific recognition to competence pheromone in S. suis. Thus, they were employed to establish gene deletion method. Its efficiency for genetic replacement was dependent on the length of homologs fragment and the concentration of donor DNA. This rapid gene-editing technique may greatly facilitate molecular studies on S. suis.
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Affiliation(s)
- Yinchu Zhu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wenyang Dong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yue Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- Office International Des Epizooties (OIE) Reference Lab for Swine Streptococcosis, Nanjing Agricultural University, Nanjing 210095, PR China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, PR China
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Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metab Eng 2018; 50:122-141. [DOI: 10.1016/j.ymben.2018.07.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023]
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29
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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Gorshkova NV, Lobanova JS, Tokmakova IL, Smirnov SV, Akhverdyan VZ, Krylov AA, Mashko SV. Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome. Appl Microbiol Biotechnol 2018; 102:2867-2884. [PMID: 29392386 PMCID: PMC5847225 DOI: 10.1007/s00253-018-8767-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 02/05/2023]
Abstract
A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10−4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition–amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.
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Affiliation(s)
- Natalya V Gorshkova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Juliya S Lobanova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Irina L Tokmakova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Smirnov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Valerii Z Akhverdyan
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545.
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31
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Huang Y, Li L, Xie S, Zhao N, Han S, Lin Y, Zheng S. Recombineering using RecET in Corynebacterium glutamicum ATCC14067 via a self-excisable cassette. Sci Rep 2017; 7:7916. [PMID: 28801604 PMCID: PMC5554157 DOI: 10.1038/s41598-017-08352-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
Gene manipulation is essential for metabolic engineering and synthetic biology, but the current general gene manipulation methods are not applicable to the non-model strain Corynebacterium glutamicum (C. glutamicum) ATCC14067, which is used for amino acid production. Here, we report an effective and sequential deletion method for C. glutamicum ATCC14067 using the exonuclease-recombinase pair RecE + RecT (RecET) for recombineering via a designed self-excisable linear double-strand DNA (dsDNA) cassette, which contains the Cre/loxP system, to accomplish markerless deletion. To the best of our knowledge, this is the first effective and simple strategy for recombination with markerless deletion in C. glutamicum ATCC14067. This strategy provides a simple markerless deletion strategy for C. glutamicum and builds a solid basis for producer construction.
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Affiliation(s)
- Yuanyuan Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Shan Xie
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China. .,Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China.
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32
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Signal peptide-dependent protein translocation pathway is crucial for the sucrose sensitivity of SacB-expressing Escherichia coli. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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A novel genetic tool for metabolic optimization of Corynebacterium glutamicum: efficient and repetitive chromosomal integration of synthetic promoter-driven expression libraries. Appl Microbiol Biotechnol 2017; 101:4737-4746. [DOI: 10.1007/s00253-017-8222-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 10/19/2022]
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34
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Becker J, Wittmann C. Industrial Microorganisms: Corynebacterium glutamicum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Judith Becker
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
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35
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Becker J, Gießelmann G, Hoffmann SL, Wittmann C. Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:217-263. [DOI: 10.1007/10_2016_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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36
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Zhang D, Guan D, Liang J, Guo C, Xie X, Zhang C, Xu Q, Chen N. Reducing lactate secretion by ldhA Deletion in L-glutamate- producing strain Corynebacterium glutamicum GDK-9. Braz J Microbiol 2015; 45:1477-83. [PMID: 25763057 PMCID: PMC4323326 DOI: 10.1590/s1517-83822014000400044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 03/14/2014] [Indexed: 11/22/2022] Open
Abstract
L-lactate is one of main byproducts excreted in to the fermentation medium. To improve L-glutamate production and reduce L-lactate accumulation, L-lactate dehydrogenase-encoding gene ldhA was knocked out from L-glutamate producing strain Corynebacterium glutamicum GDK-9, designated GDK-9ΔldhA. GDK-9ΔldhA produced approximately 10.1% more L-glutamate than the GDK-9, and yielded lower levels of such by-products as α-ketoglutarate, L-lactate and L-alanine. Since dissolved oxygen (DO) is one of main factors affecting L-lactate formation during L-glutamate fermentation, we investigated the effect of ldhA deletion from GDK-9 under different DO conditions. Under both oxygen-deficient and high oxygen conditions, L-glutamate production by GDK-9ΔldhA was not higher than that of the GDK-9. However, under micro-aerobic conditions, GDK-9ΔldhA exhibited 11.61% higher L-glutamate and 58.50% lower L-alanine production than GDK-9. Taken together, it is demonstrated that deletion of ldhA can enhance L-glutamate production and lower the unwanted by-products concentration, especially under micro-aerobic conditions.
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Affiliation(s)
- Dalong Zhang
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Dan Guan
- China Biothech Fermentation Industry Association Beijing P.R. China China Biothech Fermentation Industry Association, Beijing, P.R. China
| | - Jingbo Liang
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Chunqian Guo
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Xixian Xie
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Chenglin Zhang
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Qingyang Xu
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
| | - Ning Chen
- College of Biotechnology Tianjin University of Science and Technology Tianjin P.R. China College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China. ; Key Laboratory of Industrial Microbiology Education Ministry Tianjin P.R. China Key Laboratory of Industrial Microbiology, Education Ministry, Tianjin, P.R. China
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37
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Persicke M, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T). Stand Genomic Sci 2015; 10:5. [PMID: 26203323 PMCID: PMC4510995 DOI: 10.1186/1944-3277-10-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/21/2014] [Indexed: 11/23/2022] Open
Abstract
Corynebacterium callunae DSM 20147(T) is a member of the genus Corynebacterium which contains Gram-positive and non-spore forming bacteria with a high G + C content. C. callunae was isolated during a screening for l-glutamic acid producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria. As this is a type strain in a subgroup of industrial relevant bacteria for many of which there are also complete genome sequence available, knowledge of the complete genome sequence might enable genome comparisons to identify production relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647 protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Marcus Persicke
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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38
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Wang Z, Moslehi-Jenabian S, Solem C, Jensen PR. Increased expression of pyruvate carboxylase and biotin protein ligase increases lysine production in a biotin prototrophicCorynebacterium glutamicumstrain. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Zhihao Wang
- The National Food Institute; Technical University of Denmark; Kongens Lyngby Denmark
| | | | - Christian Solem
- The National Food Institute; Technical University of Denmark; Kongens Lyngby Denmark
| | - Peter Ruhdal Jensen
- The National Food Institute; Technical University of Denmark; Kongens Lyngby Denmark
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Development of a markerless gene replacement system in Corynebacterium glutamicum using upp as a counter-selection marker. Biotechnol Lett 2014; 37:609-17. [DOI: 10.1007/s10529-014-1718-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
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40
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Kind S, Neubauer S, Becker J, Yamamoto M, Völkert M, Abendroth GV, Zelder O, Wittmann C. From zero to hero – Production of bio-based nylon from renewable resources using engineered Corynebacterium glutamicum. Metab Eng 2014; 25:113-23. [DOI: 10.1016/j.ymben.2014.05.007] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/03/2014] [Accepted: 05/05/2014] [Indexed: 01/06/2023]
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41
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Li Y, Thompson CM, Lipsitch M. A modified Janus cassette (Sweet Janus) to improve allelic replacement efficiency by high-stringency negative selection in Streptococcus pneumoniae. PLoS One 2014; 9:e100510. [PMID: 24959661 PMCID: PMC4068995 DOI: 10.1371/journal.pone.0100510] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/28/2014] [Indexed: 11/19/2022] Open
Abstract
The Janus cassette permits marker-free allelic replacement or knockout in streptomycin-resistant Streptococcus pneumoniae (pneumococcus) through sequential positive and negative selection. Spontaneous revertants of Janus can lead to high level of false-positives during negative selection, which necessitate a time-consuming post-selection screening process. We hypothesized that an additional counter-selectable marker in Janus would decrease the revertant frequency and reduce false-positives, since simultaneous reversion of both counter-selectable makers is much less likely. Here we report a modified cassette, Sweet Janus (SJ), in which the sacB gene from Bacillus subtilis conferring sucrose sensitivity is added to Janus. By using streptomycin and sucrose simultaneously as selective agents, the frequency of SJ double revertants was about 105-fold lower than the frequency of Janus revertants. Accordingly, the frequency of false-positives in the SJ-mediated negative selection was about 100-fold lower than what was seen for Janus. Thus, SJ enhances negative selection stringency and can accelerate allelic replacement in pneumococcus, especially when transformation frequency is low due to strain background or suboptimal transformation conditions. Results also suggested the sacB gene alone can function as a counter-selectable marker in the Gram-positive pneumococcus, which will have the advantage of not requiring a streptomycin-resistant strain for allelic replacement.
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Affiliation(s)
- Yuan Li
- Department of Epidemiology and Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Claudette M. Thompson
- Department of Epidemiology and Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Department of Epidemiology and Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Mimitsuka T, Sawai H, Hatsu M, Yamada K. Metabolic Engineering ofCorynebacterium glutamicumfor Cadaverine Fermentation. Biosci Biotechnol Biochem 2014; 71:2130-5. [PMID: 17895539 DOI: 10.1271/bbb.60699] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cadaverine, the expected raw material of polyamides, is produced by decarboxylation of L-lysine. If we could produce cadaverine from the cheapest sugar, and as a renewable resource, it would be an effective solution against global warming, but there has been no attempt to produce cadaverine from glucose by fermentation. We focused on Corynebacterium glutamicum, whose L-lysine fermentation ability is superior, and constructed a metabolically engineered C. glutamicum in which the L-homoserine dehydrogenase gene (hom) was replaced by the L-lysine decarboxylase gene (cadA) of Escherichia coli. In this recombinant strain, cadaverine was produced at a concentration of 2.6 g/l, equivalent to up to 9.1% (molecular yield) of the glucose transformed into cadaverine in neutralizing cultivation. This is the first report of cadaverine fermentation by C. glutamicum.
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Affiliation(s)
- Takashi Mimitsuka
- New Frontiers Research Laboratories, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura 248-8555, Japan.
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Hu J, Tan Y, Li Y, Hu X, Xu D, Wang X. Construction and application of an efficient multiple-gene-deletion system in Corynebacterium glutamicum. Plasmid 2013; 70:303-13. [DOI: 10.1016/j.plasmid.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
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Van Laer K, Dziewulska AM, Fislage M, Wahni K, Hbeddou A, Collet JF, Versées W, Mateos LM, Tamu Dufe V, Messens J. NrdH-redoxin of Mycobacterium tuberculosis and Corynebacterium glutamicum dimerizes at high protein concentration and exclusively receives electrons from thioredoxin reductase. J Biol Chem 2013; 288:7942-7955. [PMID: 23362277 PMCID: PMC3597831 DOI: 10.1074/jbc.m112.392688] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022] Open
Abstract
NrdH-redoxins are small reductases with a high amino acid sequence similarity with glutaredoxins and mycoredoxins but with a thioredoxin-like activity. They function as the electron donor for class Ib ribonucleotide reductases, which convert ribonucleotides into deoxyribonucleotides. We solved the x-ray structure of oxidized NrdH-redoxin from Corynebacterium glutamicum (Cg) at 1.5 Å resolution. Based on this monomeric structure, we built a homology model of NrdH-redoxin from Mycobacterium tuberculosis (Mt). Both NrdH-redoxins have a typical thioredoxin fold with the active site CXXC motif located at the N terminus of the first α-helix. With size exclusion chromatography and small angle x-ray scattering, we show that Mt_NrdH-redoxin is a monomer in solution that has the tendency to form a non-swapped dimer at high protein concentration. Further, Cg_NrdH-redoxin and Mt_NrdH-redoxin catalytically reduce a disulfide with a specificity constant 1.9 × 10(6) and 5.6 × 10(6) M(-1) min(-1), respectively. They use a thiol-disulfide exchange mechanism with an N-terminal cysteine pKa lower than 6.5 for nucleophilic attack, whereas the pKa of the C-terminal cysteine is ~10. They exclusively receive electrons from thioredoxin reductase (TrxR) and not from mycothiol, the low molecular weight thiol of actinomycetes. This specificity is shown in the structural model of the complex between NrdH-redoxin and TrxR, where the two surface-exposed phenylalanines of TrxR perfectly fit into the conserved hydrophobic pocket of the NrdH-redoxin. Moreover, nrdh gene deletion and disruption experiments seem to indicate that NrdH-redoxin is essential in C. glutamicum.
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Affiliation(s)
- Koen Van Laer
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Aleksandra M Dziewulska
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Marcus Fislage
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Khadija Wahni
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Abderahim Hbeddou
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium
| | - Jean-Francois Collet
- Brussels Center for Redox Biology, 1050 Brussels, Belgium; de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; Welbio, 1200 Brussels, Belgium
| | - Wim Versées
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Luis M Mateos
- Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | - Veronica Tamu Dufe
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Welbio, 1200 Brussels, Belgium
| | - Joris Messens
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium.
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Neuner A, Wagner I, Sieker T, Ulber R, Schneider K, Peifer S, Heinzle E. Production of l-lysine on different silage juices using genetically engineered Corynebacterium glutamicum. J Biotechnol 2013; 163:217-24. [DOI: 10.1016/j.jbiotec.2012.07.190] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 01/18/2023]
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Pátek M, Nešvera J. Promoters and Plasmid Vectors of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Suzuki N, Inui M. Genome Engineering of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Peifer S, Barduhn T, Zimmet S, Volmer DA, Heinzle E, Schneider K. Metabolic engineering of the purine biosynthetic pathway in Corynebacterium glutamicum results in increased intracellular pool sizes of IMP and hypoxanthine. Microb Cell Fact 2012; 11:138. [PMID: 23092390 PMCID: PMC3538647 DOI: 10.1186/1475-2859-11-138] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background Purine nucleotides exhibit various functions in cellular metabolism. Besides serving as building blocks for nucleic acid synthesis, they participate in signaling pathways and energy metabolism. Further, IMP and GMP represent industrially relevant biotechnological products used as flavor enhancing additives in food industry. Therefore, this work aimed towards the accumulation of IMP applying targeted genetic engineering of Corynebacterium glutamicum. Results Blocking of the degrading reactions towards AMP and GMP lead to a 45-fold increased intracellular IMP pool of 22 μmol gCDW-1. Deletion of the pgi gene encoding glucose 6-phosphate isomerase in combination with the deactivated AMP and GMP generating reactions, however, resulted in significantly decreased IMP pools (13 μmol gCDW-1). Targeted metabolite profiling of the purine biosynthetic pathway further revealed a metabolite shift towards the formation of the corresponding nucleobase hypoxanthine (102 μmol gCDW-1) derived from IMP degradation. Conclusions The purine biosynthetic pathway is strongly interconnected with various parts of the central metabolism and therefore tightly controlled. However, deleting degrading reactions from IMP to AMP and GMP significantly increased intracellular IMP levels. Due to the complexity of this pathway further degradation from IMP to the corresponding nucleobase drastically increased suggesting additional targets for future strain optimization.
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Affiliation(s)
- Susanne Peifer
- Biochemical Engineering Institute, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
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Holátko J, Šilar R, Rabatinová A, Šanderová H, Halada P, Nešvera J, Krásný L, Pátek M. Construction of in vitro transcription system for Corynebacterium glutamicum and its use in the recognition of promoters of different classes. Appl Microbiol Biotechnol 2012; 96:521-9. [DOI: 10.1007/s00253-012-4336-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/19/2012] [Accepted: 07/21/2012] [Indexed: 11/24/2022]
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Kind S, Becker J, Wittmann C. Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway--metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum. Metab Eng 2012; 15:184-95. [PMID: 22871505 DOI: 10.1016/j.ymben.2012.07.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/05/2012] [Accepted: 07/23/2012] [Indexed: 01/16/2023]
Abstract
In this study, we demonstrate increased lysine production by flux coupling using the industrial work horse bacterium Corynebacterium glutamicum, which was mediated by the targeted interruption of the tricarboxylic acid (TCA) cycle at the level of succinyl-CoA synthetase. The succinylase branch of the lysine production pathway functions as the bridging reaction to convert succinyl-CoA to succinate in this aerobic bacterium. The mutant C. glutamicum ΔsucCD showed a 60% increase in the yield of lysine when compared to the advanced lysine producer which was used as parent strain. This mutant was highly vital and exhibited only a slightly reduced specific growth rate. Metabolic flux analysis with (13)C isotope studies confirmed that the increase in lysine production was mediated by pathway coupling. The novel strain exhibited an exceptional flux profile, which was closer to the optimum performance predicted by in silico pathway analysis than to the large set of lysine-producing strains analyzed thus far. Fluxomics and transcriptomics were applied as further targets for next-level strain engineering to identify the back-up mechanisms that were activated upon deletion of the enzyme in the mutant strain. It seemed likely that the cells partly recruited the glyoxylate shunt as a by-pass route. Additionally, the α-ketoglutarate decarboxylase pathway emerged as the potential compensation mechanism. This novel strategy appears equally promising for Escherichia coli, which is used in the industrial production of lysine, wherein this bacterium synthesizes lysine exclusively by succinyl-CoA activation of pathway intermediates. The channeling of a high flux pathway into a production pathway by pathway coupling is an interesting metabolic engineering strategy that can be explored to optimize bio-production in the future.
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Affiliation(s)
- Stefanie Kind
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Gaußstr. 17, D-38106 Braunschweig, Germany
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