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Meeampun Y, Panyachanakul T, Samosorn S, Dolsophon K, Jiamjariyatam R, Lorliam W, Arnthong J, Suwannarangsee S, Tantayotai P, Krajangsang S. Characterization of yeast mutant strains for starter culture in Arabica coffee fermentation. Sci Rep 2024; 14:6069. [PMID: 38480775 PMCID: PMC10937909 DOI: 10.1038/s41598-024-56298-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/17/2024] Open
Abstract
Arabica coffee is the most popular and best-selling type of coffee. During coffee fermentation, microorganisms are essential for the production of metabolites and volatile compounds that affect coffee flavor quality. This work aimed to study the mutation, selection, and characterization of the Wickerhamomyces anomalus strain YWP1-3 as a starter culture to enhance the flavor quality of Arabica coffee. The results revealed that six mutants could produce relatively high levels of the pectinase enzyme on pectin agar media and exhibited high activity levels, ranging from 332.35 to 415.88 U/ml in mucilage broth. Strains UV22-2, UV22-3, UV41-1 and UV32-1 displayed higher levels of amylase activity than did the wild type. The UV22-2 and UV22-3 mutants exhibited the highest pectin degradation indices of 49.22% and 45.97%, respectively, and displayed significantly enhanced growth rates in nitrogen yeast base media supplemented with various sugars; thus, these mutants were evaluated for their ability to serve as a starter for fermentation of Arabica coffee. The cupping scores of coffees derived from UV22-2 and UV22-3 were 83.5 ± 1.5 and 82.0 ± 2.14, respectively. The volatile compounds in the roasted coffee fermented by UV22-2 were analyzed by GC‒MS, which revealed higher levels of furfuryl alcohol and furfuryl acetate than did the other samples. These findings suggested that UV22-2 could be an influential starter culture for Arabica coffee fermentation.
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Affiliation(s)
- Yaowapa Meeampun
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Titiporn Panyachanakul
- Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Siritron Samosorn
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Kulvadee Dolsophon
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Rossaporn Jiamjariyatam
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Wanlapa Lorliam
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Jantima Arnthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, 12120, Pathumthani, Thailand
| | - Surisa Suwannarangsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, 12120, Pathumthani, Thailand
| | - Prapakorn Tantayotai
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand
| | - Sukhumaporn Krajangsang
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23, Wattana, 10110, Bangkok, Thailand.
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Modulating DNA Repair Pathways to Diversify Genomic Alterations in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0232621. [PMID: 35352941 PMCID: PMC9045378 DOI: 10.1128/spectrum.02326-21] [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] [Indexed: 11/29/2022] Open
Abstract
Nuclease based genome editing systems have emerged as powerful tools to drive genomic alterations and enhance genome evolution via precise engineering in the various human and microbial cells. However, error-prone DNA repair has not been well studied previously to generate diverse genomic alterations and novel phenotypes. Here, we systematically investigated the potential interplay between DNA double strand break (DSB) repair and genome editing tools, and found that modulating the DSB end resection proteins could significantly improve mutational efficiency and diversity without exogenous DNA template in yeast. Deleting SAE2, EXO1, or FUN30, or overexpressing MRE11-H125N (nuclease-dead allele of MRE11), for DSB end resection markedly increased the efficiency of CRISPR/SpCas9 (more than 22-fold) and CRISPR/AsCpf1 (more than 30-fold)-induced mutagenesis. Deleting SAE2 or overexpressing MRE11-H125N substantially diversified CRISPR/SpCas9 or AsCpf1-induced mutation 2–3-fold at URA3 locus, and 3–5-fold at ADE2 locus. Thus, the error-prone DNA repair protein was employed to develop a novel mutagenic genome editing (mGE) strategy, which can increase the mutation numbers and effectively improve the ethanol/glycerol ratio of Saccharomyces cerevisiae through modulating the expression of FPS1 and GPD1. This study highlighted the feasibility of potentially reshaping the capability of genome editing by regulating the different DSB repair proteins and can thus expand the application of genome editing in diversifying gene expression and enhancing genome evolution. IMPORTANCE Most of the published papers about nuclease-assisted genome editing focused on precision engineering in human cells. However, the topic of inducing mutagenesis via error-prone repair has often been ignored in yeast. In this study, we reported that perturbing DNA repair, especially modifications of the various DSB end resection-related proteins, could greatly improve the mutational efficiency and diversity, and thus functionally reshape the capability of the different genome editing tools without requiring an exogenous DNA template in yeast. Specifically, mutagenic genome editing (mGE) was developed based on CRISPR/AsCpf1 and MRE11-H125N overexpression, and used to generate promoters of different strengths more efficiently. Thus, this work provides a novel method to diversify gene expression and enhance genome evolution.
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Enhancing Ethanol Tolerance via the Mutational Breeding of Pichia terricola H5 to Improve the Flavor Profiles of Wine. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8040149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Although using non-Saccharomyces yeasts during alcoholic fermentation can improve the wine aroma, most of them are not ethanol tolerant; therefore, in 2017, this study screened 85 non-Saccharomyces yeasts isolated and identified from 24 vineyards in seven Chinese wine-producing regions, obtaining Pichia terricola strain H5, which displayed 8% ethanol tolerance. Strain H5 was subjected to ultraviolet (UV) irradiation and diethyl sulfate (DES) mutagenesis treatment to obtain mutant strains with different fermentation characteristics from the parental H5. Compared with strain H5, the UV-irradiated strains, UV5 and UV8, showed significantly higher ethanol tolerance and fermentation capacity. Modified aroma profiles were also evident in the fermentation samples exposed to the mutants. Increased ethyl caprate, ethyl caprylate, and ethyl dodecanoate content were apparent in the UV5 samples, providing the wine with a distinctly floral, fruity, and spicy profile. Fermentation with strain UV8 produced a high ethyl acetate concentration, causing the wine to present a highly unpleasant odor. To a certain extent, UV irradiation improved the ethanol tolerance and fermentation ability of strain H5, changing the wine aroma profile. This study provides a theoretical basis for the industrial application of non-Saccharomyces yeasts that can improve wine flavor.
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Veerana M, Yu N, Ketya W, Park G. Application of Non-Thermal Plasma to Fungal Resources. J Fungi (Basel) 2022; 8:jof8020102. [PMID: 35205857 PMCID: PMC8879654 DOI: 10.3390/jof8020102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/21/2022] Open
Abstract
In addition to being key pathogens in plants, animals, and humans, fungi are also valuable resources in agriculture, food, medicine, industry, and the environment. The elimination of pathogenic fungi and the functional enhancement of beneficial fungi have been the major topics investigated by researchers. Non-thermal plasma (NTP) is a potential tool to inactivate pathogenic and food-spoiling fungi and functionally enhance beneficial fungi. In this review, we summarize and discuss research performed over the last decade on the use of NTP to treat both harmful and beneficial yeast- and filamentous-type fungi. NTP can efficiently inactivate fungal spores and eliminate fungal contaminants from seeds, fresh agricultural produce, food, and human skin. Studies have also demonstrated that NTP can improve the production of valuable enzymes and metabolites in fungi. Further studies are still needed to establish NTP as a method that can be used as an alternative to the conventional methods of fungal inactivation and activation.
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Affiliation(s)
- Mayura Veerana
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea; (M.V.); (N.Y.); (W.K.)
| | - Nannan Yu
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea; (M.V.); (N.Y.); (W.K.)
| | - Wirinthip Ketya
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea; (M.V.); (N.Y.); (W.K.)
| | - Gyungsoon Park
- Plasma Bioscience Research Center, Department of Plasma-Bio Display, Kwangwoon University, Seoul 01897, Korea; (M.V.); (N.Y.); (W.K.)
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea
- Correspondence: ; Tel.: +82-2-940-8324
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Wang Q, Zhang Q, Liu K, An J, Zhang S, Chen Q, Zhang J. Optimization of solid-state fermentation technology and analysis of key aroma components of compound rice wine. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2022. [DOI: 10.3136/fstr.fstr-d-21-00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Qi Wang
- College of Food Science and Technology, Key Lab of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher Education, Yunnan Agricultural University
| | - Qian Zhang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University
| | - Kunyi Liu
- College of Wuliangye Technology and Food Engineering, Yibin Vocational and Technical College
| | - Jiangshan An
- College of Longrun Pu-erh Tea, Yunnan Agricultural University
| | - Shufan Zhang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University
| | - Qiuyue Chen
- College of Longrun Pu-erh Tea, Yunnan Agricultural University
| | - Jinghui Zhang
- College of Wuliangye Technology and Food Engineering, Yibin Vocational and Technical College
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Chen S, Xie ZX, Yuan YJ. Discovering and genotyping genomic structural variations by yeast genome synthesis and inducible evolution. FEMS Yeast Res 2021; 20:5809967. [PMID: 32188997 DOI: 10.1093/femsyr/foaa012] [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] [Received: 01/15/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
Genomic structural variations (SVs) promote the evolution of Saccharomyces cerevisiae, and play an important role in phenotypic diversities. Yeast genomic structures can be remodeled by design and bottom-up synthesis. The synthesis of yeast genome creates novel copy number variations (CNVs) and SVs and develops new strategies to discover gene functions. Further, an inducible evolution system SCRaMbLE, consisted of 3,932 loxPsym sites, was incorporated on synthetic yeast genome. SCRaMbLE enables genomic rearrangements at will and rapidly generates chromosomal number variations, and massive SVs under customized conditions. The impacts of genetic variations on phenotypes can be revealed by genome analysis and chromosome restructuring. Yeast genome synthesis and SCRaMbLE provide a new research paradigm to explore the genotypic mechanisms of phenotype diversities, and can be used to improve biological traits and optimize industrial chassis.
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Affiliation(s)
- Si Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Ze-Xiong Xie
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
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7
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Aburatani S, Ishiya K, Itoh T, Hayashi T, Taniguchi T, Takaku H. Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi. Bioengineering (Basel) 2020; 7:bioengineering7040148. [PMID: 33227954 PMCID: PMC7711605 DOI: 10.3390/bioengineering7040148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/14/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.
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Affiliation(s)
- Sachiyo Aburatani
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 305-8568, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
| | - Koji Ishiya
- BPRI, National Institute of Advance Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | - Toshikazu Itoh
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Toshihiro Hayashi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Takeaki Taniguchi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
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8
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Zeng D, Qiu C, Shen Y, Hou J, Li Z, Zhang J, Liu S, Shang J, Qin W, Xu L, Bao X. An innovative protein expression system using RNA polymerase I for large-scale screening of high-nucleic-acid content Saccharomyces cerevisiae strains. Microb Biotechnol 2020; 13:2008-2019. [PMID: 32854170 PMCID: PMC7533336 DOI: 10.1111/1751-7915.13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/19/2020] [Accepted: 08/01/2020] [Indexed: 01/05/2023] Open
Abstract
Saccharomyces cerevisiae is the preferred source of RNA derivatives, which are widely used as supplements for foods and pharmaceuticals. As the most abundant RNAs, the ribosomal RNAs (rRNAs) transcribed by RNA polymerase I (Pol I) have no 5' caps, thus cannot be translated to proteins. To screen high-nucleic-acid content yeasts more efficiently, a cap-independent protein expression system mediated by Pol I has been designed and established to monitor the regulatory changes of rRNA synthesis by observing the variation in the reporter genes expression. The elements including Pol I-recognized rDNA promoter, the internal ribosome entry site from cricket paralytic virus which can recruit ribosomes internally, reporter genes (URA3 and yEGFP3), oligo-dT and an rDNA terminator were ligated to a yeast episomal plasmid. This system based on the URA3 gene worked well by observing the growth phenotype and did not require the disruption of cap-dependent initiation factors. The fluorescence intensity of strains expressing the yEGFP3 gene increased and drifted after mutagenesis. Combined with flow cytometry, cells with higher GFP level were sorted out. A strain showed 58% improvement in RNA content and exhibited no sequence alteration in the whole expression cassette introduced. This study provides a novel strategy for breeding high-nucleic-acid content yeasts.
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Affiliation(s)
- Duwen Zeng
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green PapermakingQilu University of Technology, Shandong Academy of Sciences3501 Daxue RoadJinan250353China
| | - Chenxi Qiu
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong University72 Binhai RoadQingdao266237China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong University72 Binhai RoadQingdao266237China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong University72 Binhai RoadQingdao266237China
| | - Zailu Li
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green PapermakingQilu University of Technology, Shandong Academy of Sciences3501 Daxue RoadJinan250353China
| | - Jixiang Zhang
- Shandong Sunkeen Biological Company6789 Xingfuhe RoadJining273517China
| | - Shuai Liu
- Shandong Sunkeen Biological Company6789 Xingfuhe RoadJining273517China
| | - Jianli Shang
- Shandong Sunkeen Biological Company6789 Xingfuhe RoadJining273517China
| | - Wensheng Qin
- Department of BiologyLakehead University955 Oliver RoadThunder BayONP7B 5E1Canada
| | - Lili Xu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green PapermakingQilu University of Technology, Shandong Academy of Sciences3501 Daxue RoadJinan250353China
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong University72 Binhai RoadQingdao266237China
- Shandong Sunkeen Biological Company6789 Xingfuhe RoadJining273517China
| | - Xiaoming Bao
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green PapermakingQilu University of Technology, Shandong Academy of Sciences3501 Daxue RoadJinan250353China
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong University72 Binhai RoadQingdao266237China
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9
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Applications and research advance of genome shuffling for industrial microbial strains improvement. World J Microbiol Biotechnol 2020; 36:158. [PMID: 32968940 DOI: 10.1007/s11274-020-02936-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022]
Abstract
Genome shuffling, an efficient and practical strain improvement technology via recursive protoplasts fusion, can break through the limits of species even genus to accelerate the directed evolution of microbial strains, without requiring the comprehensively cognized genetic background and operable genetic system. Hence this technology has been widely used for many important strains to obtain the desirable industrial phenotypes. In this review, we introduce the procedure of genome shuffling, discuss the new aid strategies of genome shuffling, summarize the applications of genome shuffling for increasing metabolite yield, improving strain tolerance, enhancing substrate utilization, and put forward the outlook to the future development of this technology.
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10
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de Witt RN, Kroukamp H, Van Zyl WH, Paulsen IT, Volschenk H. QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance. FEMS Yeast Res 2020; 19:5528620. [PMID: 31276593 DOI: 10.1093/femsyr/foz047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Decoding the genetic basis of lignocellulosic inhibitor tolerance in Saccharomyces cerevisiae is crucial for rational engineering of bioethanol strains with enhanced robustness. The genetic diversity of natural strains present an invaluable resource for the exploration of complex traits of industrial importance from a pan-genomic perspective to complement the limited range of specialised, tolerant industrial strains. Natural S. cerevisiae isolates have lately garnered interest as a promising toolbox for engineering novel, genetically encoded tolerance phenotypes into commercial strains. To this end, we investigated the genetic basis for lignocellulosic inhibitor tolerance of natural S. cerevisiae isolates. A total of 12 quantitative trait loci underpinning tolerance were identified by next-generation sequencing linked bulk-segregant analysis of superior interbred pools. Our findings corroborate the current perspective of lignocellulosic inhibitor tolerance as a multigenic, complex trait. Apart from a core set of genetic variants required for inhibitor tolerance, an additional genetic background-specific response was observed. Functional analyses of the identified genetic loci revealed the uncharacterised ORF, YGL176C and the bud-site selection XRN1/BUD13 as potentially beneficial alleles contributing to tolerance to a complex lignocellulosic inhibitor mixture. We present evidence for the consideration of both regulatory and coding sequence variants for strain improvement.
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Affiliation(s)
- R N de Witt
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - H Kroukamp
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - W H Van Zyl
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
| | - I T Paulsen
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde, NSW 2109, Australia
| | - H Volschenk
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch 7600, Western Cape, South Africa
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11
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Qiu X, Xu P, Zhao X, Du G, Zhang J, Li J. Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica. Metab Eng 2020; 60:66-76. [PMID: 32224262 DOI: 10.1016/j.ymben.2020.03.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 12/19/2022]
Abstract
Erythritol is an important sweetener ingredient and chemical precursor for synthesizing materials with phase transition behavior. Commercial erythritol is primarily produced by industrial fermentation. Further strain engineering necessitates the development of high throughput screening method for rapid detection and screening of mutant strain libraries. In this work, we took advantage of the erythritol-responsive transcription factor EryD, and constructed a sensor-regulator system for rapid screening and characterization of erythritol overproducers. We configured the optimal architecture of the EryD sensor-regulator construct with improved sensitivity, specificity and dynamic response range. Coupled with mutagenesis and strain screening based on biosensors, we rapidly screened and characterized a strain library containing 1152 mutants derived from combined UV and ARTP mutagenesis, in a relatively short period of time (1 week). The optimal strain produced more than 148 g/L erythritol in bench-top reactors. This work provides a reference for other metabolic engineering researchers to develop industrially-relevant strains. The reported framework enables us to rapidly improve strain performance and engineer efficient microbial cell factories for industrial applications.
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Affiliation(s)
- Xueliang Qiu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Xinrui Zhao
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Jianghua Li
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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12
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Zeng W, Guo L, Xu S, Chen J, Zhou J. High-Throughput Screening Technology in Industrial Biotechnology. Trends Biotechnol 2020; 38:888-906. [PMID: 32005372 DOI: 10.1016/j.tibtech.2020.01.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.
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Affiliation(s)
- Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Likun Guo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Novel mutagenesis and screening technologies for food microorganisms: advances and prospects. Appl Microbiol Biotechnol 2020; 104:1517-1531. [DOI: 10.1007/s00253-019-10341-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/28/2019] [Indexed: 12/19/2022]
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Hawary H, Rasmey AHM, Aboseidah AA, El-Morsi ES, Hafez M. Enhancement of glycerol production by UV-mutagenesis of the marine yeast Wickerhamomyces anomalus HH16: kinetics and optimization of the fermentation process. 3 Biotech 2019; 9:446. [PMID: 31763124 DOI: 10.1007/s13205-019-1981-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/29/2019] [Indexed: 01/25/2023] Open
Abstract
The current study aims to enhance glycerol production using UV-mutagenesis of the marine yeast Wickerhamomyces anomalus HH16 isolated from marine sediment collected from South Sinai Governorate, Egypt. Besides optimization of the culture conditions and analyzing the kinetic parameters of growth and glycerol biosynthesis by the mutant strain were studied. The marine yeast isolate HH16 was selected as the front runner glycerol-producer among all tested isolates, with glycerol yield recorded as 66.55 gl-1. The isolate was identified based on the phenotypic and genotypic characteristics of W. anomalus. The genotypic characterization based on the internal transcribed spacer (ITS) sequence was deposited in the GenBank database with the accession number MK182824. UV-mutagenesis of W. anomalus HH16 by its exposure to UV radiation (254 nm, 200 mW cm-2) for 5 min; increased its capability in the glycerol production rate with 16.97% (80.15 g l-1). Based on the kinetic and Monod equations, the maximum specific growth rate (μ max) and maximum specific glycerol production rate (v max) by the mutant strain W. anomalus HH16MU5 were 0.21 h-1 and 0.103 g g-1, respectively. Optimization of the fermentation parameters such as nitrogen source, salinity and pH has been achieved. The maximum glycerol production 86.55 g l-1 has been attained in a fermentation medium composed of 200 g l-1 glucose, 1 g l-1 peptone, 3 g l-1 yeast extract, and 58.44 g l-1 NaCl, this medium was adjusted at pH 8 and incubated for 3 days at 30° C. Moreover, results indicated the ability of this yeast to produce glycerol (73.33 g l-1) using a seawater based medium. These findings suggest the applicability of using the yeast isolate W. anomalus HH16MU5 as a potential producer of glycerol for industrial purposes.
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Lin Y, Cai Y, Guo Y, Li X, Qi X, Qi Q, Wang Q. Development and genomic elucidation of hybrid yeast with improved glucose-xylose co-fermentation at high temperature. FEMS Yeast Res 2019; 19:5333307. [DOI: 10.1093/femsyr/foz015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/17/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Enhanced capability of co-fermenting glucose and xylose at high temperature is highly desirable for yeast application in second-generation bioethanol production. Here, we obtained hybrid strains with improved glucose-xylose co-fermentation properties at high temperature by combining genome shuffling and adaptive evolution. Genome resequencing of these strains suggested predominantly inherited genetic information from one parental strain Spathaspora passalidarum SP rather than the other parental strain Saccharomyces cerevisiae ScY01, possibly due to that the CUG codon system of S. passalidarum might have systematically eliminated most of the functional proteins from S. cerevisiae through misfolding. Compared to SP, one-copy loss of a 146-kb fragment was found in the hybrid strain and regained after being evolved for a while, whereas one-copy loss of an 11-kb fragment was only found after being evolved for a longer time. Besides, the genes affected by nonsynonymous variants were also identified, especially the mutation S540F in the endoplasmic reticulum chaperon Kar2. Structural prediction indicated that S540F might change the substrate binding activity of Kar2, and thus play a role in preventing protein aggregation in yeast at high temperature. Our results illustrated genomic alterations during this process and revealed some genomic factors that might be involved to determine yeast thermotolerance.
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Affiliation(s)
- Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanqing Cai
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xin Li
- Impossible Foods Inc., Redwood City, CA 94063, USA
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qi Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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16
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Shi J, Zhu X, Lu Y, Zhao H, Lu F, Lu Z. Improving Iturin A Production of Bacillus amyloliquefaciens by Genome Shuffling and Its Inhibition Against Saccharomyces cerevisiae in Orange Juice. Front Microbiol 2018; 9:2683. [PMID: 30467499 PMCID: PMC6236126 DOI: 10.3389/fmicb.2018.02683] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/19/2018] [Indexed: 11/13/2022] Open
Abstract
Genome shuffling is an effective method for the rapid improvement of the production of secondary metabolites. This study used the principle of gene shuffling to enhance the yield of iturin A produced by Bacillus amyloliquefaciens LZ-5. Improvements in lipopeptide yield were evident among four strains subjected to recursive protoplast fusion. The four strains were obtained through mutagenesis processes: nitrosoguanidine, ultraviolet irradiation, and atmospheric and room temperature plasma. A high yield strain with 179.22 mg/l of iturin A was obtained after two rounds of genome shuffling, which was a 2.03-fold increase compared with the wild strain. To evaluate the efficacy of iturin A for control of spoilage yeast in food, the anti-yeast efficacy of iturin A was evaluated in orange juice incubated with Saccharomyces cerevisiae. The juice treated with 0.76 mg/ml iturin A showed a significant (p < 0.05) control on yeast population during the storage, similar to that of the 0.30 mg/ml natamycin. In addition, iturin A showed a tiny effect on chemical-physical characteristics of orange juice. Our results provide a basis for the application of antimicrobial lipopeptide in juice products.
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Affiliation(s)
- Juran Shi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingjian Lu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD, United States
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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17
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Kordowska-Wiater M, Lisiecka U, Kostro K. Improvement of Candida parapsilosis by genome shuffling for the efficient production of arabitol from l-arabinose. Food Sci Biotechnol 2018; 27:1395-1403. [PMID: 30319849 PMCID: PMC6170280 DOI: 10.1007/s10068-018-0369-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Arabitol is used in the food industry as a low-calorie sweetener. It is produced by yeasts during the biotransformation process of l-arabinose. Genome shuffling was performed in Candida parapsilosis DSM 70125, an efficient producer of arabitol, to obtain fusants with improved arabitol production ability. Four mutants from the parental library were used for the first round of genome shuffling. The best fusants, GSI-1 and GSI-10A, were subjected to a second round of genome shuffling. Finally, two fusants, GSII-3 and GSII-16, produced concentrations of arabitol that were 50% higher than that of the wild-type strain during selection culture. Under the optimal conditions established for C. parapsilosis, the two fusants produced 11.83 and 11.75 g/L of arabitol and were approximately 15-16% more efficient than the wild-type strain. Flow cytometry analysis showed that the ploidy of the new strains did not change.
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Affiliation(s)
- Monika Kordowska-Wiater
- 1Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
| | - Urszula Lisiecka
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
| | - Krzysztof Kostro
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
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18
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Microbial mutagenesis by atmospheric and room-temperature plasma (ARTP): the latest development. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0200-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hu W, Li W, Chen J. Recent advances of microbial breeding via heavy-ion mutagenesis at IMP. Lett Appl Microbiol 2017; 65:274-280. [PMID: 28741678 DOI: 10.1111/lam.12780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. SIGNIFICANCE AND IMPACT OF THE STUDY There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future.
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Affiliation(s)
- W Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - W Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - J Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
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20
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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21
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ARTP mutation and genome shuffling of ABE fermentation symbiotic system for improvement of butanol production. Appl Microbiol Biotechnol 2017; 101:2189-2199. [DOI: 10.1007/s00253-017-8093-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022]
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22
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Zhao Y, Duan C, Gao L, Yu X, Niu C, Li S. Genome shuffling of Lactobacillus plantarum C88 improves adhesion. Biosci Biotechnol Biochem 2017; 81:184-193. [DOI: 10.1080/09168451.2016.1224637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type Lactobacillus plantarum C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The in vivo and in vitro tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of L. plantarum C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function.
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Affiliation(s)
- Yujuan Zhao
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Cuicui Duan
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Lei Gao
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Xue Yu
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Chunhua Niu
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Shengyu Li
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
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23
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Gérando HMD, Fayolle-Guichard F, Rudant L, Millah SK, Monot F, Lopes Ferreira N, López-Contreras AM. Improving isopropanol tolerance and production of Clostridium beijerinckii DSM 6423 by random mutagenesis and genome shuffling. Appl Microbiol Biotechnol 2016; 100:5427-36. [PMID: 26852409 PMCID: PMC4875934 DOI: 10.1007/s00253-016-7302-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
Random mutagenesis and genome shuffling was applied to improve solvent tolerance and isopropanol/butanol/ethanol (IBE) production in the strictly anaerobic bacteria Clostridium beijerinckii DSM 6423. Following chemical mutagenesis with N-methyl-N-nitro-N-nitrosoguanidine (NTG), screening of putatively improved strains was done by submitting the mutants to toxic levels of inhibitory chemicals or by screening for their tolerance to isopropanol (>35 g/L). Suicide substrates, such as ethyl or methyl bromobutyrate or alcohol dehydrogenase inhibitors like allyl alcohol, were tested and, finally, 36 mutants were isolated. The fermentation profiles of these NTG mutant strains were characterized, and the best performing mutants were used for consecutive rounds of genome shuffling. Screening of strains with further enhancement in isopropanol tolerance at each recursive shuffling step was then used to spot additionally improved strains. Three highly tolerant strains were finally isolated and able to withstand up to 50 g/L isopropanol on plates. Even if increased tolerance to the desired end product was not always accompanied by higher production capabilities, some shuffled strains showed increased solvent titers compared to the parental strains and the original C. beijerinckii DSM 6423. This study confirms the efficiency of genome shuffling to generate improved strains toward a desired phenotype such as alcohol tolerance. This tool also offers the possibility of obtaining improved strains of Clostridium species for which targeted genetic engineering approaches have not been described yet.
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Affiliation(s)
- H Máté de Gérando
- Food and Biobased Research Wageningen UR, Wageningen, the Netherlands
- Biotechnology Department, IFP Energies nouvelles, Rueil-Malmaison, France
| | - F Fayolle-Guichard
- Biotechnology Department, IFP Energies nouvelles, Rueil-Malmaison, France
| | - L Rudant
- Biotechnology Department, IFP Energies nouvelles, Rueil-Malmaison, France
| | - S K Millah
- Food and Biobased Research Wageningen UR, Wageningen, the Netherlands
| | - F Monot
- Biotechnology Department, IFP Energies nouvelles, Rueil-Malmaison, France
| | - N Lopes Ferreira
- Biotechnology Department, IFP Energies nouvelles, Rueil-Malmaison, France.
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Jakočiūnas T, Jensen MK, Keasling JD. CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng 2015; 34:44-59. [PMID: 26707540 DOI: 10.1016/j.ymben.2015.12.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/29/2015] [Accepted: 12/10/2015] [Indexed: 12/19/2022]
Abstract
One of the key drivers for successful metabolic engineering in microbes is the efficacy by which genomes can be edited. As such there are many methods to choose from when aiming to modify genomes, especially those of model organisms like yeast and bacteria. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become the method of choice for precision genome engineering in many organisms due to their orthogonality, versatility and efficacy. Here we review the strategies adopted for implementation of RNA-guided CRISPR/Cas9 genome editing with special emphasis on their application for metabolic engineering of yeast and bacteria. Also, examples of how nuclease-deficient Cas9 has been applied for RNA-guided transcriptional regulation of target genes will be reviewed, as well as tools available for computer-aided design of guide-RNAs will be highlighted. Finally, this review will provide a perspective on the immediate challenges and opportunities foreseen by the use of CRISPR/Cas9 genome engineering and regulation in the context of metabolic engineering.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA
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