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Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L. Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing. ACS Synth Biol 2024; 13:2045-2059. [PMID: 38934464 DOI: 10.1021/acssynbio.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive oxygen species (ROS) stresses using an industrially important melatonin production strain as an example. ROS stresses often occur during cultivation and negatively affect strain performance. Cellular response to ROS is also linked to the SOS response and resistance to pH fluctuations, which is important to strain robustness in large-scale biomanufacturing. This work integrated more than 7000 E. coli adaptive laboratory evolution (ALE) mutations across 59 experiments to statistically associate mutated genes to 2 ROS tolerance ALE conditions from 72 unique conditions. Mutant oxyR, fur, iscR, and ygfZ were significantly associated and hypothesized to contribute fitness in ROS stress. Across these genes, 259 total mutations were inspected in conjunction with transcriptomics from 46 iModulon experiments. Ten mutations were chosen for reintroduction based on mutation clustering and coinciding transcriptional changes as evidence of fitness impact. Strains with mutations reintroduced into oxyR, fur, iscR, and ygfZ exhibited increased tolerance to H2O2 and acid stress and reduced SOS response, all of which are related to ROS. Additionally, new evidence was generated toward understanding the function of ygfZ, an uncharacterized gene. This meta-analysis approach utilized aggregated and interoperable multiomics data sets to identify mutations conferring industrially relevant phenotypes with the least drawbacks, describing an approach for data-driven strain engineering to optimize microbial cell factories.
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Affiliation(s)
- P V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - S H Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - K Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla ,California92093-0412 ,United States
| | - C Rode
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - F Beulig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - B O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla ,California92093-0412 ,United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla ,California92093-0021, United States
- Department of Pediatrics, University of California, San Diego, La Jolla ,California 92093-0412, United States
| | - L Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
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Wang QQ, Lin J, Zhou QZ, Peng J, Zhang Q, Wang JH. Hyper-Production of Pullulan by a Novel Fungus of Aureobasidium melanogenum ZH27 through Batch Fermentation. Int J Mol Sci 2023; 25:319. [PMID: 38203490 PMCID: PMC10779298 DOI: 10.3390/ijms25010319] [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: 09/13/2023] [Revised: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Pullulan, which is a microbial exopolysaccharide, has found widespread applications in foods, biomedicines, and cosmetics. Despite its versatility, most wild-type strains tend to yield low levels of pullulan production, and their mutants present genetic instability, achieving a limited increase in pullulan production. Therefore, mining new wild strains with robust pullulan-producing abilities remains an urgent concern. In this study, we found a novel strain, namely, Aureobasidium melanogenum ZH27, that had a remarkable pullulan-producing capacity and optimized its cultivation conditions using the one-factor-at-a-time method. To elucidate the reasons that drove the hyper-production of pullulan, we scrutinized changes in cell morphology and gene expressions. The results reveal that strain ZH27 achieved 115.4 ± 1.82 g/L pullulan with a productivity of 0.87 g/L/h during batch fermentation within 132 h under the optimized condition (OC). This pullulan titer increased by 105% compared with the initial condition (IC). Intriguingly, under the OC, swollen cells featuring 1-2 large vacuoles predominated during a rapid pullulan accumulation, while these swollen cells with one large vacuole and several smaller ones were prevalent under the IC. Moreover, the expressions of genes associated with pullulan accumulation and by-product synthesis were almost all upregulated. These findings suggest that swollen cells and large vacuoles may play pivotal roles in the high level of pullulan production, and the accumulation of by-products also potentially contributes to pullulan synthesis. This study provides a novel and promising candidate for industrial pullulan production.
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Affiliation(s)
- Qin-Qing Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Jia Lin
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
| | - Qian-Zhi Zhou
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
| | - Juan Peng
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
| | - Qi Zhang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
| | - Jiang-Hai Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (J.L.); (Q.-Z.Z.); (J.P.); (Q.Z.)
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Bao Z, Zhu Y, Zhang K, Feng Y, Zhang M, Li R, Yu L. New insights into phenotypic heterogeneity for the distinct lipid accumulation of Schizochytrium sp. H016. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:33. [PMID: 35337369 PMCID: PMC8957170 DOI: 10.1186/s13068-022-02126-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Schizochytrium sp. is a marine heterotrophic protist and an important sustainable resource for high value-added docosahexaenoic acid in the future. The production of different phenotypes during the continuous subculture of Schizochytrium sp. results in a serious reduction in lipid yield and complicates the used of this strain in scientific research and industrial production. Hence, obtaining an improved understanding of the phenotypic differences and molecular mechanisms underlying the cell-to-cell heterogeneity of Schizochytrium sp. is necessary. RESULTS After continuous culture passage, Schizochytrium sp. H016 differentiated into two subpopulations with different morphologies and showed decreased capacity for lipid production. The presence of cell subpopulations with degraded lipid droplets led to a substantial decrease in overall lipid yield. Here, a rapid screening strategy based on fluorescence-activated cell sorting was proposed to classify and isolate subpopulations quickly in accordance with their lipid-producing capability. The final biomass and lipid yield of the subpopulation with high cell lipid content (i.e., H016-H) were 38.83 and 17.22 g/L, respectively, which were 2.07- and 5.38-fold higher than those of the subpopulation with low lipid content (i.e., H016-L), respectively. Subsequently, time‑resolved transcriptome analysis was performed to elucidate the mechanism of phenotypic heterogeneity in different subpopulations. Results showed that the expression of genes related to the cell cycle and lipid degradation was significantly upregulated in H016-L, whereas the metabolic pathways related to fatty acid synthesis and glyceride accumulation were remarkably upregulated in H016-H. CONCLUSION This study innovatively used flow cytometry combined with transcriptome technology to provide new insights into the phenotypic heterogeneity of different cell subpopulations of Schizochytrium sp. Furthermore, these results lay a strong foundation for guiding the breeding of oleaginous microorganisms with high lipid contents.
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Affiliation(s)
- Zhendong Bao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China.,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China.,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China
| | - Yuanmin Zhu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China.,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China.,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China
| | - Kai Zhang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China.,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China.,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China
| | - Yumei Feng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China.,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China.,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China
| | - Meng Zhang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China.,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China.,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China
| | - Ruili Li
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan, 430074, China. .,Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, 430074, China. .,Hubei Engineering Research Center for Both Edible and Medicinal Resources, Wuhan, 430074, China.
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Bouchat R, Vélard F, Audonnet S, Rioult D, Delvigne F, Rémond C, Rakotoarivonina H. Xylanase production by Thermobacillus xylanilyticus is impaired by population diversification but can be mitigated based on the management of cheating behavior. Microb Cell Fact 2022; 21:39. [PMID: 35292016 PMCID: PMC8922903 DOI: 10.1186/s12934-022-01762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background The microbial production of hemicellulasic cocktails is still a challenge for the biorefineries sector and agro-waste valorization. In this work, the production of hemicellulolytic enzymes by Thermobacillus xylanilyticus has been considered. This microorganism is of interest since it is able to produce an original set of thermostable hemicellulolytic enzymes, notably a xylanase GH11, Tx-xyn11. However, cell-to-cell heterogeneity impairs the production capability of the whole microbial population. Results Sequential cultivations of the strain on xylan as a carbon source has been considered in order to highlight and better understand this cell-to-cell heterogeneity. Successive cultivations pointed out a fast decrease of xylanase activity (loss of ~ 75%) and Tx-xyn11 gene expression after 23.5 generations. During serial cultivations on xylan, flow cytometry analyses pointed out that two subpopulations, differing at their light-scattering properties, were present. An increase of the recurrence of the subpopulation exhibiting low forward scatter (FSC) signal was correlated with a progressive loss of xylanase activity over several generations. Cell sorting and direct observation of the sorted subpopulations revealed that the low-FSC subpopulation was not sporulating, whereas the high-FSC subpopulation contained cells at the onset of the sporulation stage. The subpopulation differences (growth and xylanase activity) were assessed during independent growth. The low-FSC subpopulation exhibited a lag phase of 10 h of cultivation (and xylanase activities from 0.15 ± 0.21 to 3.89 ± 0.14 IU/mL along the cultivation) and the high-FSC subpopulation exhibited a lag phase of 5 h (and xylanase activities from 0.52 ± 0.00 to 4.43 ± 0.61 over subcultivations). Serial cultivations on glucose, followed by a switch to xylan led to a ~ 1.5-fold to ~ 15-fold improvement of xylanase activity, suggesting that alternating cultivation conditions could lead to an efficient population management strategy for the production of xylanase. Conclusions Taken altogether, the data from this study point out that a cheating behavior is responsible for the progressive reduction in xylanase activity during serial cultivations of T. xylanilyticus. Alternating cultivation conditions between glucose and xylan could be used as an efficient strategy for promoting population stability and higher enzymatic productivity from this bacterium. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01762-z.
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Affiliation(s)
- Romain Bouchat
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France.,Laboratory of Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté 2B, B140, 5030, Gembloux, Belgium
| | - Frédéric Vélard
- BIOS EA 4691 "Biomatériaux et Inflammation en site osseux", Université de Reims Champagne Ardenne, 51097, Reims, France
| | - Sandra Audonnet
- URCACyt, Flow Cytometry Technical Platform, Université de Reims Champagne-Ardenne, 51096, Reims, France
| | - Damien Rioult
- Plateau Technique Mobile de Cytométrie Environnementale MOBICYTE, Université de Reims Champagne-Ardenne, 51097, Reims, France
| | - Frank Delvigne
- Laboratory of Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté 2B, B140, 5030, Gembloux, Belgium
| | - Caroline Rémond
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France
| | - Harivony Rakotoarivonina
- INRAE, FARE, UMR A 614, Chaire AFERE, Université de Reims Champagne Ardenne, 51097, Reims, France.
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Peng M, Zhao Z, Liang Z. Biodegradation of ochratoxin A and ochratoxin B by Brevundimonas naejangsanensis isolated from soil. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Linder M, Haak M, Botes A, Kalinowski J, Rückert C. Construction of an IS-Free Corynebacterium glutamicum ATCC 13 032 Chassis Strain and Random Mutagenesis Using the Endogenous ISCg1 Transposase. Front Bioeng Biotechnol 2021; 9:751334. [PMID: 34976962 PMCID: PMC8715038 DOI: 10.3389/fbioe.2021.751334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022] Open
Abstract
Mobile genetic elements (MGEs) contribute to instability of the host genome and plasmids. Previously, removal of the prophages in the industrial amino acid producer Corynebacterium glutamicum ATCC 13 032 resulted in strain MB001 which showed better survival under stress conditions and increased transformability. Still, eight families of Insertion Sequence (IS) elements with 27 potentially active members remain in MB001, two of which were demonstrated to be detrimental in biotechnological processes. In this study, systematical deletion of all complete IS elements in MB001 resulted in the MGE-free strain CR101. CR101 shows growth characteristics identical to the wildtype and the increased transformability of MB001. Due to its improved genome stability, we consider this strain to be an optimal host for basic research and biotechnology. As a “zero-background” host, it is also an ideal basis to study C. glutamicum IS elements. Re-sequencing of CR101 revealed that only five spontaneous point mutations had occurred during the construction process, highlighting the low mutation rate of C. glutamicum on the nucleotide level. In a second step, we developed an easily applicable ISCg1-based transposon mutagenesis system to randomly transpose a selectable marker. For optimal plasmid stability during cloning in Escherichia coli, the system utilizes a genetic switch based on the phage integrase Bxb1. Use of this integrase revealed the presence of a functional attB site in the C. glutamicum genome. To avoid cross-talk with our system and increase ease-of-use, we removed the attB site and also inserted the Bxb1 encoding gene into the chromosome of CR101. Successful insertion of single markers was verified by sequencing randomly selected mutants. Sequencing pooled mutant libraries revealed only a weak target site specificity, seemingly random distribution of insertion sites and no general strand bias. The resulting strain, ML103, together with plasmid pML10 provides a easily customizable system for random mutagenesis in an otherwise genomically stable C. glutamicum. Taken together, the MGE-free C. glutamicum strain CR101, the derivative ML103, and the plasmid pML10 provide a useful set of tools to study C. glutamicum in the future.
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Affiliation(s)
- Marten Linder
- CeBiTec Bielefeld, Technology Platform Genomics, Bielefeld University, Bielefeld, Germany
| | - Markus Haak
- CeBiTec Bielefeld, Technology Platform Genomics, Bielefeld University, Bielefeld, Germany
| | - Angela Botes
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jörn Kalinowski
- CeBiTec Bielefeld, Technology Platform Genomics, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- CeBiTec Bielefeld, Technology Platform Genomics, Bielefeld University, Bielefeld, Germany
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Christian Rückert ,
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Fadhilah QG, Santoso I, Maryanto AE, Abdullah S, Yasman Y. Evaluation of the antifungal activity of marine actinomycetes isolates against the phytopathogenic fungi Colletotrichum siamense KA: A preliminary study for new antifungal compound discovery. PHARMACIA 2021. [DOI: 10.3897/pharmacia.68.e72817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Marine actinomycetes are being explored to discover potential actinomycetes that produce antifungal compounds. In a previous study, marine actinomycetes isolates from the mangrove ecosystem were found to inhibit growth of the phytopathogenic fungi Colletotrichum siamense KA. In this study, the three of these isolates with the highest antagonistic activity—SM11, SM14, and SM15—were evaluated for their antifungal activity using antibiosis assay. The fermentation was performed in SCB:PDB medium (1:1) for 6, 9, and 12 days. The results showed that SM14 was the strongest potential isolate; it inhibited the growth of C. siamense KA on average up to 64.90% for 12 days on PDA filtrate medium. Molecular identification showed SM14 was closely related to Streptomyces sanyensis, but had differences in morphological and biochemical characteristics compared to SM11 or SM15. This indicated that the three isolates were different strains and may challenge further research on identifying and analyzing their antifungal compounds.
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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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Zhang Y, Yang J, Yang S, Zhang J, Chen J, Tao R, Jiang Y, Yang J, Yang S. Programming Cells by Multicopy Chromosomal Integration Using CRISPR-Associated Transposases. CRISPR J 2021; 4:350-359. [PMID: 34152213 DOI: 10.1089/crispr.2021.0018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Directed evolution and targeted genome editing have been deployed to create genetic variants with usefully altered phenotypes. However, these methods are limited to high-throughput screening methods or serial manipulation of single genes. In this study, we implemented multicopy chromosomal integration using CRISPR-associated transposases (MUCICAT) to simultaneously target up to 11 sites on the Escherichia coli chromosome for multiplex gene interruption and/or insertion, generating combinatorial genomic diversity. The MUCICAT system was improved by replacing the isopropyl-beta-D-thiogalactoside (IPTG)-dependent promoter to decouple gene editing and product synthesis and truncating the right end to reduce the leakage expression of cargo. We applied MUCICAT to engineer and optimize the N-acetylglucosamine (GlcNAc) biosynthesis pathway in E. coli to overproduce the industrially important GlcNAc in only 8 days. Two rounds of transformation, the first round for disruption of two degradation pathways related gene clusters and the second round for multiplex integration of the GlcNAc gene cassette, would generate a library with 1-11 copies of the GlcNAc cassette. We isolated a best variant with five copies of GlcNAc cassettes, producing 11.59 g/L GlcNAc, which was more than sixfold than that of the strain containing the pET-GNAc plasmid. Our multiplex approach MUCICAT has potential to become a powerful tool of cell programing and can be widely applied in many fields such as synthetic biology.
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Affiliation(s)
- Yiwen Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China; Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Jiawei Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China; Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Siqi Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China; Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA; and Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Rongsheng Tao
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Institutes for Biological Sciences, Huzhou, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
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10
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Li YP, Bu QT, Li JF, Xie H, Su YT, Du YL, Li YQ. Genome-based rational engineering of Actinoplanes deccanensis for improving fidaxomicin production and genetic stability. BIORESOURCE TECHNOLOGY 2021; 330:124982. [PMID: 33743279 DOI: 10.1016/j.biortech.2021.124982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Microbial fermentation is currently still the major way to produce structural complicated clinical drugs. Yet, the low productivity and genetic instability of producing strains remain the bottlenecks in microbial pharmaceutical industry. Fidaxomicin is a microbial drug against the Clostridium difficile infection. Here, a genome-based combinatorial engineering strategy was established to improve both fidaxomicin production and the genetic stability of Actinoplanes deccanensis YP-1. Guided by genomic analysis, several genetic instability-associated elements were cumulatively deleted, generating a more genetically stable mutant. Further rational engineering approaches including elimination of a pigment pathway, duplication of the fidaxomicin gene cluster, overexpression of a positive regulator and optimization of the fermentation medium, led to an overall 27-folds improvement in fidaxomicin production. Taken together, the genome-based rational combinatorial engineering strategy was efficient to enhance the fidaxomicin production and ameliorate the genetic stability of YP-1, it can also be widely used in other industrial actinomycetes for strain improvement.
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Affiliation(s)
- Yue-Ping Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Ji-Feng Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Huang Xie
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ting Su
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ling Du
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China.
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