1
|
Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023; 69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.
Collapse
Affiliation(s)
- Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zijian Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| |
Collapse
|
2
|
Madhavan A, Arun KB, Alex D, Anoopkumar AN, Emmanual S, Chaturvedi P, Varjani S, Tiwari A, Kumar V, Reshmy R, Awasthi MK, Binod P, Aneesh EM, Sindhu R. Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:2092-2104. [PMID: 37273565 PMCID: PMC10232702 DOI: 10.1007/s13197-022-05482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/20/2022] [Accepted: 05/07/2022] [Indexed: 06/06/2023]
Abstract
Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.
Collapse
Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - K. B. Arun
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014 India
| | - Deepthy Alex
- Department of Biotechnology, Mar Ivanios College, Trivandrum, Kerala 695015 India
| | - A. N. Anoopkumar
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Shibitha Emmanual
- Department of Zoology, St. Joseph’s College, Thrissur, Kerala 680121 India
| | - Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow, 226001 India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Paryavaran Bhavan, CHH Road, Sector 10 A, Gandhinagar, Gujarat 382010 India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Noida, 201301 India
| | - Vinod Kumar
- Fermentation Technology Division, CSIR- Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, J & K 180001 India
| | - R. Reshmy
- Department of Science and Humanities, Providence College of Engineering, Chengannur, Kerala 689122 India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695019 India
| | - Embalil Mathachan Aneesh
- Department of Zoology, Centre for Research in Emerging Tropical Diseases (CRET‑D), University of Calicut, Malappuram, Kerala India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, Kerala 691505 India
| |
Collapse
|
3
|
Xu S, Gao S, An Y. Research progress of engineering microbial cell factories for pigment production. Biotechnol Adv 2023; 65:108150. [PMID: 37044266 DOI: 10.1016/j.biotechadv.2023.108150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
Pigments are widely used in people's daily life, such as food additives, cosmetics, pharmaceuticals, textiles, etc. In recent years, the natural pigments produced by microorganisms have attracted increased attention because these processes cannot be affected by seasons like the plant extraction methods, and can also avoid the environmental pollution problems caused by chemical synthesis. Synthetic biology and metabolic engineering have been used to construct and optimize metabolic pathways for production of natural pigments in cellular factories. Building microbial cell factories for synthesis of natural pigments has many advantages, including well-defined genetic background of the strains, high-density and rapid culture of cells, etc. Until now, the technical means about engineering microbial cell factories for pigment production and metabolic regulation processes have not been systematically analyzed and summarized. Therefore, the studies about construction, modification and regulation of synthetic pathways for microbial synthesis of pigments in recent years have been reviewed, aiming to provide an up-to-date summary of engineering strategies for microbial synthesis of natural pigments including carotenoids, melanins, riboflavins, azomycetes and quinones. This review should provide new ideas for further improving microbial production of natural pigments in the future.
Collapse
Affiliation(s)
- Shumin Xu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China; Shenyang Key Laboratory of Microbial Resources Mining and Molecular Breeding, Shenyang, China; Liaoning Provincial Key Laboratory of Agricultural Biotechnology, Shenyang, China.
| |
Collapse
|
4
|
Žun G, Doberšek K, Petrovič U. Construction and evaluation of gRNA arrays for multiplex CRISPR-Cas9. Yeast 2023; 40:32-41. [PMID: 36536407 PMCID: PMC10107897 DOI: 10.1002/yea.3833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Endonuclease system CRISPR-Cas9 represents a powerful toolbox for the budding yeast's Saccharomyces cerevisiae genome perturbation. The resulting double-strand breaks are preferentially repaired via highly efficient homologous recombination, which subsequently leads to marker-free genome editing. The goal of this study was to evaluate precise targeting of multiple loci simultaneously. To construct an array of independently expressing guide RNAs (gRNAs), the genes encoding them were assembled through a BioBrick construction procedure. We designed a multiplex CRISPR-Cas9 system for targeting 6 marker genes, whereby the gRNA array was expressed from a single plasmid. To evaluate the performance of the gRNA array, the activity of the designed system was assessed by the success rate of the introduction of perturbations within the target loci: successful gRNA expression, followed by target DNA double-strand breaks formation and their repair by homologous recombination led to premature termination of the coding sequence of the marker genes, resulting in the prevention of growth of the transformants on the corresponding selection media. In conclusion, we successfully introduced up to five simultaneous perturbations within single cells of yeast S. cerevisiae using the multiplex CRISPR-Cas9 system. While this has been done before, we here present an alternative sequential BioBrick assembly with the capability to accommodate many highly similar gRNA-expression cassettes, and an exhaustive evaluation of their performance.
Collapse
Affiliation(s)
- Gašper Žun
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| |
Collapse
|
5
|
Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.
Collapse
|
6
|
Malcı K, Jonguitud-Borrego N, van der Straten Waillet H, Puodžiu̅naitė U, Johnston EJ, Rosser SJ, Rios-Solis L. ACtivE: Assembly and CRISPR-Targeted in Vivo Editing for Yeast Genome Engineering Using Minimum Reagents and Time. ACS Synth Biol 2022; 11:3629-3643. [PMID: 36252276 PMCID: PMC9680028 DOI: 10.1021/acssynbio.2c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Thanks to its sophistication, the CRISPR/Cas system has been a widely used yeast genome editing method. However, CRISPR methods generally rely on preassembled DNAs and extra cloning steps to deliver gRNA, Cas protein, and donor DNA. These laborious steps might hinder its usefulness. Here, we propose an alternative method, Assembly and CRISPR-targeted in vivo Editing (ACtivE), that only relies on in vivo assembly of linear DNA fragments for plasmid and donor DNA construction. Thus, depending on the user's need, these parts can be easily selected and combined from a repository, serving as a toolkit for rapid genome editing without any expensive reagent. The toolkit contains verified linear DNA fragments, which are easy to store, share, and transport at room temperature, drastically reducing expensive shipping costs and assembly time. After optimizing this technique, eight loci proximal to autonomously replicating sequences (ARS) in the yeast genome were also characterized in terms of integration and gene expression efficiencies and the impacts of the disruptions of these regions on cell fitness. The flexibility and multiplexing capacity of the ACtivE were shown by constructing a β-carotene pathway. In only a few days, >80% integration efficiency for single gene integration and >50% integration efficiency for triplex integration were achieved on Saccharomyces cerevisiae BY4741 from scratch without using in vitro DNA assembly methods, restriction enzymes, or extra cloning steps. This study presents a standardizable method to be readily employed to accelerate yeast genome engineering and provides well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
Collapse
Affiliation(s)
- Koray Malcı
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | - Nestor Jonguitud-Borrego
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | | | - Urtė Puodžiu̅naitė
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Emily J. Johnston
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Susan J. Rosser
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Leonardo Rios-Solis
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Natural and Environmental Sciences, Newcastle
University, Newcastle upon TyneNE1 7RU, U.K.,
| |
Collapse
|
7
|
Singh R, Chandel S, Ghosh A, Gautam A, Huson DH, Ravichandiran V, Ghosh D. Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system. Bioengineered 2022; 13:14857-14871. [PMID: 36602175 PMCID: PMC10109214 DOI: 10.1080/21655979.2022.2162667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
During the last two decades, yeast has been used as a biological tool to produce various small molecules, biofuels, etc., using an inexpensive bioprocess. The application of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein (Cas) techniques in yeast genetic and metabolic engineering has made a paradigm shift, particularly with a significant improvement in targeted chromosomal integration using synthetic donor constructs, which was previously a challenge. This study reports the CRISPR-Cas9-based highly efficient strategy for targeted chromosomal integration and in-frame expression of a foreign gene in the genome of Saccharomyces cerevisiae (S. cerevisiae) by homology-dependent recombination (HDR); our optimized methods show that CRISPR-Cas9-based chromosomal targeted integration of small constructs at multiple target sites of the yeast genome can be achieved with an efficiency of 74%. Our study also suggests that 15 bp microhomology flanked arms are sufficient for 50% targeted knock-in at minimal knock-in construct concentration. Whole-genome sequencing confirmed that there is no off-target effect. This study provides a comprehensive and streamlined protocol that will support the targeted integration of essential genes into the yeast genome for synthetic biology and other industrial purposes.Highlights• CRISPR-Cas9 based in-frame expression of foreign protein in Saccharomyces cerevisiae using Homology arm without a promoter.• As low as 15 base pairs of microhomology (HDR) are sufficient for targeted integration in Saccharomyces cerevisiae.• The methodology is highly efficient and very specific as no off-targeted effects were shown by the whole-genome sequence.
Collapse
Affiliation(s)
- Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Arijit Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India.,Department of Molecular Biology and Gynaecological Oncology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Daniel H Huson
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - V Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| |
Collapse
|
8
|
Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
Collapse
Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
| |
Collapse
|
9
|
Smirnov D, Schlieben LD, Peymani F, Berutti R, Prokisch H. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes. Hum Mutat 2022; 43:1056-1070. [DOI: 10.1002/humu.24416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lea D. Schlieben
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Fatemeh Peymani
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
| | - Riccardo Berutti
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- School of Medicine, Institute of Human GeneticsTechnical University of MunichMunichGermany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum MünchenNeuherbergGermany
| |
Collapse
|
10
|
Utomo JC, Hodgins CL, Ro DK. Multiplex Genome Editing in Yeast by CRISPR/Cas9 - A Potent and Agile Tool to Reconstruct Complex Metabolic Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:719148. [PMID: 34421973 PMCID: PMC8374951 DOI: 10.3389/fpls.2021.719148] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 05/22/2023]
Abstract
Numerous important pharmaceuticals and nutraceuticals originate from plant specialized metabolites, most of which are synthesized via complex biosynthetic pathways. The elucidation of these pathways is critical for the applicable uses of these compounds. Although the rapid progress of the omics technology has revolutionized the identification of candidate genes involved in these pathways, the functional characterization of these genes remains a major bottleneck. Baker's yeast (Saccharomyces cerevisiae) has been used as a microbial platform for characterizing newly discovered metabolic genes in plant specialized metabolism. Using yeast for the investigation of numerous plant enzymes is a streamlined process because of yeast's efficient transformation, limited endogenous specialized metabolism, partially sharing its primary metabolism with plants, and its capability of post-translational modification. Despite these advantages, reconstructing complex plant biosynthetic pathways in yeast can be time intensive. Since its discovery, CRISPR/Cas9 has greatly stimulated metabolic engineering in yeast. Yeast is a popular system for genome editing due to its efficient homology-directed repair mechanism, which allows precise integration of heterologous genes into its genome. One practical use of CRISPR/Cas9 in yeast is multiplex genome editing aimed at reconstructing complex metabolic pathways. This system has the capability of integrating multiple genes of interest in a single transformation, simplifying the reconstruction of complex pathways. As plant specialized metabolites usually have complex multigene biosynthetic pathways, the multiplex CRISPR/Cas9 system in yeast is suited well for functional genomics research in plant specialized metabolism. Here, we review the most advanced methods to achieve efficient multiplex CRISPR/Cas9 editing in yeast. We will also discuss how this powerful tool has been applied to benefit the study of plant specialized metabolism.
Collapse
|