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Hu M, Ge J, Jiang Y, Sun X, Guo D, Gu Y. Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica. Synth Syst Biotechnol 2024; 9:618-626. [PMID: 38784195 PMCID: PMC11109602 DOI: 10.1016/j.synbio.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.
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Affiliation(s)
- Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Dongshen Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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Park YK, Rossignol T. Broadening the application of Yarrowia lipolytica synthetic biology tools to explore the potential of Yarrowia clade diversity. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001472. [PMID: 38913407 PMCID: PMC11261841 DOI: 10.1099/mic.0.001472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
Yeasts have established themselves as prominent microbial cell factories, and the availability of synthetic biology tools has led to breakthroughs in the rapid development of industrial chassis strains. The selection of a suitable microbial host is critical in metabolic engineering applications, but it has been largely limited to a few well-defined strains. However, there is growing consideration for evaluating strain diversity, as a wide range of specific traits and phenotypes have been reported even within a specific yeast genus or species. Moreover, with the advent of synthetic biology tools, non-type strains can now be easily and swiftly reshaped. The yeast Yarrowia lipolytica has been extensively studied for various applications such as fuels, chemicals, and food. Additionally, other members of the Yarrowia clade are currently being evaluated for their industrial potential. In this study, we demonstrate the versatility of synthetic biology tools originally developed for Y. lipolytica by repurposing them for engineering other yeasts belonging to the Yarrowia clade. Leveraging the Golden Gate Y. lipolytica tool kit, we successfully expressed fluorescent proteins as well as the carotenoid pathway in at least five members of the clade, serving as proof of concept. This research lays the foundation for conducting more comprehensive investigations into the uncharacterized strains within the Yarrowia clade and exploring their potential applications in biotechnology.
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Affiliation(s)
- Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Tristan Rossignol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Amorós Morales LC, Marchesini A, Gómez Bergna SM, García Fallit M, Tongiani SE, Vásquez L, Ferrelli ML, Videla-Richardson GA, Candolfi M, Romanowski V, Pidre ML. PluriBAC: A Versatile Baculovirus-Based Modular System to Express Heterologous Genes in Different Biotechnological Platforms. Viruses 2023; 15:1984. [PMID: 37896762 PMCID: PMC10610652 DOI: 10.3390/v15101984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Baculoviruses are insect-specific pathogens widely used in biotechnology. In particular, the Autographa californica nucleopolyhedrovirus (AcMNPV) has been exploited as a platform for bio-inputs production. This is why the improvement of the technologies used for the production of recombinant baculoviruses takes on particular relevance. To achieve this goal, we developed a highly versatile baculoviral transfer vector generation system called PluriBAC. The PluriBAC system consists of three insert entry levels using Golden Gate assembly technology. The wide availability of vectors and sticky ends allows enough versatility to combine more than four different promoters, genes of interest, and terminator sequences. Here, we report not only the rational design of the PluriBAC system but also its use for the generation of baculoviral reporter vectors applied to different fields of biotechnology. We demonstrated that recombinant AcMNPV baculoviruses generated with the PluriBAC system were capable of infecting Spodoptera frugiperda larvae. On the other hand, we found that the recombinant budded virions (BV) generated using our system were capable of transducing different types of tumor and normal cells both in vitro and in vivo. Our findings suggest that the PluriBAC system could constitute a versatile tool for the generation of insecticide and gene therapy vectors.
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Affiliation(s)
- Leslie C. Amorós Morales
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Abril Marchesini
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Santiago M. Gómez Bergna
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Matías García Fallit
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1121A6B, Argentina; (M.G.F.); (M.C.)
| | - Silvana E. Tongiani
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Larisa Vásquez
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - María Leticia Ferrelli
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Guillermo A. Videla-Richardson
- Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Ciudad Autónoma de Buenos Aires C1121A6B, Argentina;
| | - Marianela Candolfi
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1121A6B, Argentina; (M.G.F.); (M.C.)
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
| | - Matías L. Pidre
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata B1900, Argentina; (L.C.A.M.); (A.M.); (S.M.G.B.); (S.E.T.); (L.V.); (M.L.F.); (V.R.)
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Cao L, Li J, Yang Z, Hu X, Wang P. A review of synthetic biology tools in Yarrowia lipolytica. World J Microbiol Biotechnol 2023; 39:129. [PMID: 36944859 DOI: 10.1007/s11274-023-03557-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
Yarrowia lipolytica is a non-conventional oleaginous yeast with great potential for industrial production. Y. lipolytica has a high propensity for flux through tricarboxylic acid cycle intermediates. Therefore, this host is currently being developed as a workhorse, and is rapidly emerging in biotechnology fields, especially for industrial chemical production, whole-cell bioconversion, and the treatment and recycling of industrial waste. In recent studies, Y. lipolytica has been rewritten and introduced with non-native metabolites of certain compounds of interest owing to the advancement in synthetic biology tools. In this review, we collate recent progress to present a detailed and insightful summary of the major developments in synthetic biology tools and techniques for Y. lipolytica, including promoters, terminators, selection markers, autonomously replicating sequences, DNA assembly techniques, genome editing techniques, and subcellular organelle engineering. This comprehensive overview would be a useful resource for future genetic engineering studies to improve the yield of desired metabolic products in Y. lipolytica.
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Affiliation(s)
- Linshan Cao
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Jiajie Li
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zihan Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Xiao Hu
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Pengchao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.
- Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, 150040, Heilongjiang, People's Republic of China.
- Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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Abioye J, Lawson-Williams M, Lecanda A, Calhoon B, McQue AL, Colloms SD, Stark WM, Olorunniji FJ. High fidelity one-pot DNA assembly using orthogonal serine integrases. Biotechnol J 2023; 18:e2200411. [PMID: 36504358 DOI: 10.1002/biot.202200411] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Large serine integrases (LSIs, derived from temperate phages) have been adapted for use in a multipart DNA assembly process in vitro, called serine integrase recombinational assembly (SIRA). The versatility, efficiency, and fidelity of SIRA is limited by lack of a sufficient number of LSIs whose activities have been characterized in vitro. METHODS AND MAJOR RESULTS In this report, we compared the activities in vitro of 10 orthogonal LSIs to explore their suitability for multiplex SIRA reactions. We found that Bxb1, ϕR4, and TG1 integrases were the most active among the set we studied, but several others were also usable. As proof of principle, we demonstrated high-efficiency one-pot assembly of six DNA fragments (made by PCR) into a 7.5 kb plasmid that expresses the enzymes of the β-carotenoid pathway in Escherichia coli, using six different LSIs. We further showed that a combined approach using a few highly active LSIs, each acting on multiple pairs of att sites with distinct central dinucleotides, can be used to scale up "poly-part" gene assembly and editing. CONCLUSIONS AND IMPLICATIONS We conclude that use of multiple orthogonal integrases may be the most predictable, efficient, and programmable approach for SIRA and other in vitro applications.
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Affiliation(s)
- Jumai Abioye
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Makeba Lawson-Williams
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
| | - Alicia Lecanda
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Brecken Calhoon
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Arlene L McQue
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Sean D Colloms
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - W Marshall Stark
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Femi J Olorunniji
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
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