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Xu H, Shi L, Boob AG, Park W, Tan SI, Tran VG, Schultz JC, Zhao H. Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides. Metab Eng 2025; 89:22-32. [PMID: 39956426 DOI: 10.1016/j.ymben.2025.02.004] [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: 12/03/2024] [Revised: 01/25/2025] [Accepted: 02/13/2025] [Indexed: 02/18/2025]
Abstract
Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.
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Affiliation(s)
- Hao Xu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Longyuan Shi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Wooyoung Park
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Vinh Gia Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - John Carl Schultz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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Bai F, Cai P, Yao L, Shen Y, Li Y, Zhou YJ. Inducible regulating homologous recombination enables precise genome editing in Pichia pastoris without perturbing cellular fitness. Trends Biotechnol 2025:S0167-7799(25)00042-3. [PMID: 40074635 DOI: 10.1016/j.tibtech.2025.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 01/26/2025] [Accepted: 02/04/2025] [Indexed: 03/14/2025]
Abstract
The methylotrophic yeast Pichia pastoris (also known as Komagataella pastoris) is an ideal host for producing proteins and natural products. Enhancing homologous recombination (HR) is helpful for improving the precision of genome editing, but results in stress to cellular fitness and is harmful for industrial applications. To overcome these challenges, we developed a tetracycline repressor protein (TetR)/tetO2 inducible system to dynamically regulate the HR-related gene RAD52 in P. pastoris. This approach significantly improved the positivity rate of single gene deletion to 81%. Furthermore, inducible overexpression of endogenous MUS81-MMS4 resulted in high-efficiency (81%) genome assembly of multiple genes. This inducible system had no adverse effect on cell growth in different media and resulted in greater fatty alcohol production from methanol compared with a strain constitutively overexpressing HR-related genes. We anticipate that this inducible regulation is applicable for enhancing HR for precise genome editing in P. pastoris and other non-conventional microbes without compromising cellular fitness.
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Affiliation(s)
- Fan Bai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China
| | - Peng Cai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China
| | - Yiwei Shen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, PR China.
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3
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Zhu J, Cai HL, Goto S, Shimada M, Yurimoto H, Sakai Y, Yoko-O T, Chiba Y, Nakagawa T. Physiological role of the FDH1 gene in methylotrophic yeast Komagataella phaffii and carbon recovery as formate during methylotrophic growth of the fdh1-deletion strain. J Biosci Bioeng 2025; 139:206-212. [PMID: 39827071 DOI: 10.1016/j.jbiosc.2024.12.007] [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: 10/07/2024] [Revised: 12/09/2024] [Accepted: 12/16/2024] [Indexed: 01/22/2025]
Abstract
During methylotrophic growth of Komagataella phaffii, a large amount of carbon is lost as CO2. In this study, we aimed to construct a recovery system for carbon atoms, which emit as CO2 along the methanol dissimilation pathway in the form of formate when using strain fdh1Δ, the deletion mutant of formate dehydrogenase gene (FDH1). Strain fdh1Δ showed a severe growth defect when using methanol as the sole carbon source. However, using YPM medium (1 % yeast extract, 2 % peptone and 1 % methanol) with pH adjustment, the strain recovered methylotrophic growth and methanol utilization, accumulating high levels of extracellular formate in the medium. In strain fdh1Δ, the final carbon conversion rate of formate from methanol reached 12.9 % by batch cultivation. Moreover, by fed-batch cultivation in a jar fermentor, the formate productivity of strain fdh1Δ achieved approximately 540 mM. These results indicated that strain fdh1Δ possessed a high potential for recovering carbon atoms as formate, which can be a valuable precursor for various industrial applications.
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Affiliation(s)
- Junzhang Zhu
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hao-Liang Cai
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shunta Goto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masaya Shimada
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Preemptive Food Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehiko Yoko-O
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan
| | - Yasunori Chiba
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan
| | - Tomoyuki Nakagawa
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Preemptive Food Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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Kuzman M, Ata Ö, Mattanovich D. Advancing yeast metabolism for a sustainable single carbon bioeconomy. FEMS Yeast Res 2025; 25:foaf020. [PMID: 40246696 PMCID: PMC12020471 DOI: 10.1093/femsyr/foaf020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/10/2025] [Accepted: 04/16/2025] [Indexed: 04/19/2025] Open
Abstract
Single carbon (C1) molecules are considered as valuable substrates for biotechnology, as they serve as intermediates of carbon dioxide recycling, and enable bio-based production of a plethora of substances of our daily use without relying on agricultural plant production. Yeasts are valuable chassis organisms for biotech production, and they are able to use C1 substrates either natively or as synthetic engineered strains. This minireview highlights native yeast pathways for methanol and formate assimilation, their engineering, and the realization of heterologous C1 pathways including CO2, in different yeast species. Key features determining the choice among C1 substrates are discussed, including their chemical nature and specifics of their assimilation, their availability, purity, and concentration as raw materials, as well as features of the products to be made from them.
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Affiliation(s)
- Miriam Kuzman
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology and Food Science, BOKU University, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria
| | - Özge Ata
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology and Food Science, BOKU University, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria
| | - Diethard Mattanovich
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology and Food Science, BOKU University, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria
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5
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Fina A, Àvila-Cabré S, Vázquez-Pereira E, Albiol J, Ferrer P. A Rewired NADPH-Dependent Redox Shuttle for Testing Peroxisomal Compartmentalization of Synthetic Metabolic Pathways in Komagataella phaffii. Microorganisms 2024; 13:46. [PMID: 39858813 PMCID: PMC11767246 DOI: 10.3390/microorganisms13010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 12/23/2024] [Accepted: 12/24/2024] [Indexed: 01/27/2025] Open
Abstract
The introduction of heterologous pathways into microbial cell compartments offers several potential advantages, including increasing enzyme concentrations and reducing competition with native pathways, making this approach attractive for producing complex metabolites like fatty acids and fatty alcohols. However, measuring subcellular concentrations of these metabolites remains technically challenging. Here, we explored 3-hydroxypropionic acid (3-HP), readily quantifiable and sharing the same precursors-acetyl-CoA, NADPH, and ATP-with the above-mentioned products, as a reporter metabolite for peroxisomal engineering in the yeast Komagataella phaffii. To this end, the malonyl-CoA reductase pathway for 3-HP production was targeted into the peroxisome of K. phaffii using the PTS1-tagging system, and further tested with different carbon sources. Thereafter, we used compartmentalized 3-HP production as a reporter system to showcase the impact of different strategies aimed at enhancing the peroxisomal NADPH pool. Co-overexpression of genes encoding a NADPH-dependent redox shuttle from Saccharomyces cerevisiae (IDP2/IDP3) significantly increased 3-HP yields across all substrates, whereas peroxisomal targeting of the S. cerevisiae NADH kinase Pos5 failed to improve 3-HP production. This study highlights the potential of using peroxisomal 3-HP production as a biosensor for evaluating peroxisomal acetyl-CoA and NAPDH availability by simply quantifying 3-HP, demonstrating its potential for peroxisome-based metabolic engineering in yeast.
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Affiliation(s)
| | | | | | | | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Carrer de les Sitges, s/n, 08193 Bellaterra, Catalonia, Spain; (A.F.); (S.À.-C.); (E.V.-P.); (J.A.)
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6
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Saha TR, Kang NK, Lee EY. Advanced metabolic Engineering strategies for the sustainable production of free fatty acids and their derivatives using yeast. J Biol Eng 2024; 18:73. [PMID: 39731138 DOI: 10.1186/s13036-024-00473-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 12/18/2024] [Indexed: 12/29/2024] Open
Abstract
The biological production of lipids presents a sustainable method for generating fuels and chemicals. Recognized as safe and enhanced by advanced synthetic biology and metabolic engineering tools, yeasts are becoming versatile hosts for industrial applications. However, lipids accumulate predominantly as triacylglycerides in yeasts, which are suboptimal for industrial uses. Thus, there have been efforts to directly produce free fatty acids and their derivatives in yeast, such as fatty alcohols, fatty aldehydes, and fatty acid ethyl esters. This review offers a comprehensive overview of yeast metabolic engineering strategies to produce free fatty acids and their derivatives. This study also explores current challenges and future perspectives for sustainable industrial lipid production, particularly focusing on engineering strategies that enable yeast to utilize alternative carbon sources such as CO2, methanol, and acetate, moving beyond traditional sugars. This review will guide further advancements in employing yeasts for environmentally friendly and economically viable lipid production technologies.
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Affiliation(s)
- Tisa Rani Saha
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Nam Kyu Kang
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, Yongin- si, Gyeonggi-do, 17104, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
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7
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Inoue Y, Yamada R, Matsumoto T, Ogino H. Enhancing D-lactic acid production by optimizing the expression of D-LDH gene in methylotrophic yeast Komagataella phaffii. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:149. [PMID: 39710696 DOI: 10.1186/s13068-024-02596-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 12/15/2024] [Indexed: 12/24/2024]
Abstract
BACKGROUND Currently, efficient technologies producing useful chemicals from alternative carbon resources, such as methanol, to replace petroleum are in demand. The methanol-utilizing yeast, Komagataella phaffii, is a promising microorganism to produce chemicals from methanol using environment-friendly microbial processes. In this study, to achieve efficient D-lactic acid production from methanol, we investigated a combination of D-lactate dehydrogenase (D-LDH) genes and promoters in K. phaffii. The yeast strain was constructed by integrating a gene cassette containing the identified gene and promoter into the rDNA locus of K. phaffii, followed by post-transformational gene amplification. Subsequently, D-lactic acid production from methanol was evaluated. RESULTS Among the five D-LDH genes and eight promoters tested, the combination of LlDLDH derived from Leuconostoc lactis and CAT1 and FLD1 promoters was suitable for expression in K. phaffii. GS115_CFL/Z3/04, the best-engineered strain constructed via integration of LlDLDH linked to CAT1 and FLD1 promoters into the rDNA locus and post-transformational gene amplification, produced 5.18 g/L D-lactic acid from methanol. To the best of our knowledge, the amount of D-lactic acid from methanol produced by this engineered yeast is the highest reported value to date when utilizing methanol as the sole carbon source. CONCLUSIONS This study demonstrated the effectiveness of combining different enzyme genes and promoters using multiple promoters with different induction and repression conditions, integrating the genes into the rDNA locus, and further amplifying the genes after transformation in K. phaffii. Using our established method, other K. phaffii strains can be engineered to produce various useful chemicals in the future.
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Affiliation(s)
- Yoshifumi Inoue
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531, Japan
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531, Japan.
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531, Japan
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8
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Jia M, Shao L, Jiang J, Jiang W, Xin F, Zhang W, Jiang Y, Jiang M. Mitigating toxic formaldehyde to promote efficient utilization of C1 resources. Crit Rev Biotechnol 2024:1-13. [PMID: 39647989 DOI: 10.1080/07388551.2024.2430476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 09/10/2024] [Accepted: 10/27/2024] [Indexed: 12/10/2024]
Abstract
The C1 resource is widely considered because of its abundance and affordability. In the context of extensive utilization of C1 resources by methylotrophic microorganisms, especially for methanol, formaldehyde is an important intermediate metabolite that is at the crossroads of assimilation and dissimilation pathways. However, formaldehyde is an exceedingly reactive compound that can form covalent cross-linked complexes with amine and thiol groups in cells, which causes irreversible damage to the organism. Thus, it is important to balance the intensity of the assimilation and dissimilation pathways of formaldehyde, which can avoid formaldehyde toxicity and improve the full utilization of C1 resources. This review details the source of endogenous formaldehyde and its toxicity mechanism, explaining the harm of excessive accumulation of formaldehyde to metabolism. Importantly, the self-detoxification and various feasible strategies to mitigate formaldehyde toxicity are discussed and proposed. These strategies are meant to help appropriately handle formaldehyde toxicity and accelerate the effective use of C1 resources.
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Affiliation(s)
- Mengshi Jia
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Lei Shao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Jie Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, P.R. China
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9
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Zhao B, Li Y, Zhang Y, Pan M, Zhao G, Guo Y. Low-carbon and overproduction of cordycepin from methanol using engineered Pichia pastoris cell factory. BIORESOURCE TECHNOLOGY 2024; 413:131446. [PMID: 39241814 DOI: 10.1016/j.biortech.2024.131446] [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: 06/18/2024] [Revised: 09/03/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Cordycepin, a nucleoside analog, is widely used in medicine and health products. However, the production of cordycepin from Cordyceps militaris faces the challenges of low productivity and high rate of greenhouse gas emissions. In this study, by optimizing the cordycepin biosynthesis pathway through promoter combination, Kozak sequence, and enzyme fusion, enhancing the methanol assimilation capacity in peroxisomes, adjusting the synthesis of NADPH and ATP, and combining the enhanced supply of adenosine and 3'-AMP, the cordycepin high-yield strain Pp29 was constructed, which produced 1551.44 mg/L cordycepin by shake-flask fermentation. In fed-batch fermentation, Pp29 achieved the highest yield (8.11 g/L, 67.64 mg/g DCW, and 1.35 g/L/d) to date in 10 L fermenter, and the CO2-eq emissions were 1.9-17.3 times lower than C. militaris and other yeast systems. This study provide basis for Pichia pastoris to be used as chassis cell for synthesizing cordycepin and other nucleoside analogs by methanol as carbon source.
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Affiliation(s)
- Bingjie Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yu Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yong Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Meixi Pan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Guishen Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China.
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10
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Guo Q, Yang YX, Li DX, Ji XJ, Wu N, Wang YT, Ye C, Shi TQ. Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory. Biotechnol Adv 2024; 77:108453. [PMID: 39278372 DOI: 10.1016/j.biotechadv.2024.108453] [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: 07/03/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Na Wu
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
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11
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Jia M, Liu M, Li J, Jiang W, Xin F, Zhang W, Jiang Y, Jiang M. Formaldehyde: An Essential Intermediate for C1 Metabolism and Bioconversion. ACS Synth Biol 2024; 13:3507-3522. [PMID: 39395007 DOI: 10.1021/acssynbio.4c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2024]
Abstract
Formaldehyde is an intermediate metabolite of methylotrophic microorganisms that can be obtained from formate and methanol through oxidation-reduction reactions. Formaldehyde is also a one-carbon (C1) compound with high uniquely reactive activity and versatility, which is more amenable to further biocatalysis. Biosynthesis of high-value-added chemicals using formaldehyde as an intermediate is theoretically feasible and promising. This review focuses on the design of the biosynthesis of high-value-added chemicals using formaldehyde as an essential intermediate. The upstream biosynthesis and downstream bioconversion pathways of formaldehyde as an intermediate metabolite are described in detail, aiming to highlight the important role of formaldehyde in the transition from inorganic to organic carbon and carbon chain elongation. In addition, challenges and future directions of formaldehyde as an intermediate for the chemicals are discussed, with the expectation of providing ideas for the utilization of C1.
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Affiliation(s)
- Mengshi Jia
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Mengge Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Jiawen Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu Biochemical Chiral Engineering Technology Reseach Center, Changmao Biochemical Engineering Co., Ltd., Changzhou 213034, P. R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
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12
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Shen Y, Cai P, Gao L, Wu X, Yao L, Zhou YJ. Engineering high production of fatty alcohols from methanol by constructing coordinated dual biosynthetic pathways. BIORESOURCE TECHNOLOGY 2024; 412:131396. [PMID: 39216706 DOI: 10.1016/j.biortech.2024.131396] [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: 06/25/2024] [Revised: 08/20/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Microbial cell factories provide an efficient approach for the green manufacturing of chemicals. However, the excessive use of sugars increases the potential risk of food crisis. Methanol, an abundant feedstock, holds promise in facilitating low-carbon production processes. However, the current methanol bioconversion is hindered by limited regulatory strategies and relatively low conversion efficiency. Here, a yeast biocatalyst was extensively engineered for efficient biosynthesis of fatty alcohols through reinforcement of precursor supply and methanol assimilation in Pichia pastoris. Furthermore, the dual cytoplasmic and peroxisomal biosynthetic pathways were constructed by mating and exhibited robust production of 5.6 g/L fatty alcohols by using methanol as the sole carbon source. This study provides a heterozygous diploid P. pastoris strain with dual cytoplasmic and peroxisomal biosynthetic pathways, which achieved the highest fatty alcohol production from one-carbon feedstocks to date.
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Affiliation(s)
- Yiwei Shen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Cai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Linhui Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Wu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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13
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Xie L, Yu W, Gao J, Wang H, Zhou YJ. Ogataea polymorpha as a next-generation chassis for industrial biotechnology. Trends Biotechnol 2024; 42:1363-1378. [PMID: 38622041 DOI: 10.1016/j.tibtech.2024.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.
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Affiliation(s)
- Linfeng Xie
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Haoyu Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China.
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14
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Shen J, Huang W, You Y, Zhan J. Controlling strategies of methanol generation in fermented fruit wine: Pathways, advances, and applications. Compr Rev Food Sci Food Saf 2024; 23:e70048. [PMID: 39495577 DOI: 10.1111/1541-4337.70048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/24/2024] [Accepted: 10/02/2024] [Indexed: 11/06/2024]
Abstract
Methanol is widely existed in fermented fruit wines (FFWs), and the concentration is excessive at times due to inappropriate fermentation conditions. Methanol is neurotoxic, and its metabolites of formaldehyde and formic acid can cause organic lesions and central respiratory system disorders. FFWs with unspecified methanol limits are often produced with reference to grape wine standards (250/400 mg/L). To clarify the causes of methanol production in FFWs and minimize the methanol content, this study summarizes the current process methods commonly applied for methanol reduction in FFWs and proposes novel potential controlling strategies from the perspective of raw materials (pectin, pectinase, and yeast), which are mainly the low esterification modification and removal of pectin, passivation of the pectinase activity, and the gene editing of yeast to target the secretion of pectinases and modulation of the glycine metabolic pathway. The modified raw materials combined with optimized fermentation processes will hopefully be able to improve the current situation of high methanol content in FFWs. Methanol detection technologies have been outlined and combined with machine learning that will potentially guide the production of low-methanol FFWs and the setting of methanol limits for specific FFW.
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Affiliation(s)
- Ju Shen
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Weidong Huang
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Yilin You
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Jicheng Zhan
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
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15
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Ni X, Zhai X, Yu W, Ye M, Yang F, Zhou YJ, Gao J. Dynamically Regulating Homologous Recombination Enables Precise Genome Editing in Ogataea polymorpha. ACS Synth Biol 2024; 13:2938-2947. [PMID: 39230514 DOI: 10.1021/acssynbio.4c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Methylotrophic yeast Ogataea polymorpha has become a promising cell factory due to its efficient utilization of methanol to produce high value-added chemicals. However, the low homologous recombination (HR) efficiency in O. polymorpha greatly hinders extensive metabolic engineering for industrial applications. Overexpression of HR-related genes successfully improved HR efficiency, which however brought cellular stress and reduced chemical production due to constitutive expression of the HR-related gene. Here, we engineered an HR repair pathway using the dynamically regulated gene ScRAD51 under the control of the l-rhamnose-induced promoter PLRA3 based on the previously constructed CRISPR-Cas9 system in O. polymorpha. Under the optimal inducible conditions, the appropriate expression level of ScRAD51 achieved up to 60% of HR rates without any detectable influence on cell growth in methanol, which was 10-fold higher than that of the wild-type strain. While adopting as the chassis strain for bioproductions, the dynamically regulated recombination system had 50% higher titers of fatty alcohols than that static regulation system. Therefore, this study provided a feasible platform in O. polymorpha for convenient genetic manipulation without perturbing cellular fitness.
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Affiliation(s)
- Xin Ni
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoxin Zhai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Min Ye
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, PR China
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16
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Li J, Gao J, Ye M, Cai P, Yu W, Zhai X, Zhou YJ. Engineering yeast for high-level production of β-farnesene from sole methanol. Metab Eng 2024; 85:194-200. [PMID: 39181436 DOI: 10.1016/j.ymben.2024.08.006] [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: 06/04/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Methanol, a rich one-carbon feedstock, can be massively produced from CO2 by the liquid sunshine route, which is helpful to realize carbon neutrality. β-Farnesene is widely used in the production of polymers, surfactants, lubricants, and also serves as a suitable substitute for jet fuel. Constructing an efficient cell factory is a feasible approach for β-farnesene production through methanol biotransformation. Here, we extensively engineered the methylotrophic yeast Ogataea polymorpha for the efficient bio-production of β-farnesene using methanol as the sole carbon source. Our study demonstrated that sufficient supply of precursor acetyl-CoA and cofactor NADPH in an excellent yeast chassis had a 1.3-fold higher β-farnesene production than that of wild-type background strain. Further optimization of the mevalonate pathway and enhancement of acetyl-CoA supply led to a 7-fold increase in β-farnesene accumulation, achieving the highest reported sesquiterpenoids production (14.7 g/L with a yield of 46 mg/g methanol) from one-carbon feedstock under fed-batch fermentation in bioreactor. This study demonstrates the great potential of engineering O. polymorpha for high-level terpenoid production from methanol.
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Affiliation(s)
- Jingjing Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiaoqi Gao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Min Ye
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Peng Cai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wei Yu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaoxin Zhai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yongjin J Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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17
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Song S, Ye C, Jin Y, Dai H, Hu J, Lian J, Pan R. Peroxisome-based metabolic engineering for biomanufacturing and agriculture. Trends Biotechnol 2024; 42:1161-1176. [PMID: 38423802 DOI: 10.1016/j.tibtech.2024.02.005] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Subcellular compartmentalization of metabolic pathways plays a crucial role in metabolic engineering. The peroxisome has emerged as a highly valuable and promising compartment for organelle engineering, particularly in the fields of biological manufacturing and agriculture. In this review, we summarize the remarkable achievements in peroxisome engineering in yeast, the industrially popular biomanufacturing chassis host, to produce various biocompounds. We also review progress in plant peroxisome engineering, a field that has already exhibited high potential in both biomanufacturing and agriculture. Moreover, we outline various experimentally validated strategies to improve the efficiency of engineered pathways in peroxisomes, as well as prospects of peroxisome engineering.
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Affiliation(s)
- Shuyan Song
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Cuifang Ye
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Yijun Jin
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Huaxin Dai
- Beijing Life Science Academy, Changping 102209, Beijing, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Jiazhang Lian
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
| | - Ronghui Pan
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
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18
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de Lange EM, Mol FN, van der Klei IJ, Vlijm R. STED super-resolution microscopy unveils the dynamics of Atg30 on yeast Pex3-labeled peroxisomes. iScience 2024; 27:110481. [PMID: 39156652 PMCID: PMC11326945 DOI: 10.1016/j.isci.2024.110481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/26/2024] [Accepted: 07/08/2024] [Indexed: 08/20/2024] Open
Abstract
Peroxisomes are dynamic organelles with important metabolic functions. Yeast Pex3 is a multifunctional membrane protein aiding in peroxisomal biogenesis, inheritance, and degradation (pexophagy), by interacting with process-specific factors. Using multicolor (live-cell) stimulated emission depletion (STED) nanoscopy, we studied the localization of Pex3 and its binding partners in Hansenula polymorpha. Unlike confocal microscopy, STED allows resolving the membrane of tiny peroxisomes, enabling accurate measurements of the size of all Pex3-labeled peroxisomes. We localized Pex3 and its binding partners at peroxisome-repressing and -inducing conditions and during pexophagy. In-depth quantitative analysis of Pex3 and pexophagy receptor Atg30 showed dynamic changes in their (co)localization. One remarkable response of Atg30 was the shift in position from being sandwiched between clustered peroxisomes at proliferation conditions, to the cytosolically exposed parts of peroxisome clusters upon pexophagy induction. Summarizing, we show that STED allows characterizing dynamics of the localization of peroxisomal proteins in yeast cells.
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Affiliation(s)
- Eline M.F. de Lange
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Frank N. Mol
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Ida J. van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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19
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Gao L, Hou R, Cai P, Yao L, Wu X, Li Y, Zhang L, Zhou YJ. Engineering Yeast Peroxisomes for α-Bisabolene Production from Sole Methanol with the Aid of Proteomic Analysis. JACS AU 2024; 4:2474-2483. [PMID: 39055156 PMCID: PMC11267555 DOI: 10.1021/jacsau.4c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 07/27/2024]
Abstract
Microbial metabolic engineering provides a feasible approach to sustainably produce advanced biofuels and biochemicals from renewable feedstocks. Methanol is an ideal feedstock since it can be massively produced from CO2 through green energy, such as solar energy. However, engineering microbes to transform methanol and overproduce chemicals is challenging. Notably, the microbial production of isoprenoids from methanol is still rarely reported. Here, we extensively engineered Pichia pastoris (syn. Komagataella phaffii) for the overproduction of sesquiterpene α-bisabolene from sole methanol by optimizing the mevalonate pathway and peroxisomal compartmentalization. Furthermore, through label-free quantification (LFQ) proteomic analysis of the engineered strains, we identified the key bottlenecks in the peroxisomal targeting pathway, and overexpressing the limiting enzyme EfmvaE significantly improved α-bisabolene production to 212 mg/L with the peroxisomal pathway. The engineered strain LH122 with the optimized peroxisomal pathway produced 1.1 g/L α-bisabolene under fed-batch fermentation in shake flasks, achieving a 69% increase over that of the cytosolic pathway. This study provides a viable approach for overproducing isoprenoid from sole methanol in engineered yeast cell factories and shows that proteomic analysis can help optimize the organelle compartmentalized pathways to enhance chemical production.
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Affiliation(s)
- Linhui Gao
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Hou
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Peng Cai
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lun Yao
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Xiaoyan Wu
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunxia Li
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Yongjin J. Zhou
- Division
of Biotechnology, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
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20
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Park YK, Sellés Vidal L, Bell D, Zabret J, Soldat M, Kavšček M, Ledesma-Amaro R. Efficient synthesis of limonene production in Yarrowia lipolytica by combinatorial engineering strategies. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:94. [PMID: 38961416 PMCID: PMC11223395 DOI: 10.1186/s13068-024-02535-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Limonene has a variety of applications in the foods, cosmetics, pharmaceuticals, biomaterials, and biofuels industries. In order to meet the growing demand for sustainable production of limonene at industry scale, it is essential to find an alternative production system to traditional plant extraction. A promising and eco-friendly alternative is the use of microbes as cell factories for the synthesis of limonene. RESULTS In this study, the oleaginous yeast Yarrowia lipolytica has been engineered to produce D- and L-limonene. Four target genes, l- or d-LS (limonene synthase), HMG (HMG-CoA reductase), ERG20 (geranyl diphosphate synthase), and NDPS1 (neryl diphosphate) were expressed individually or fused together to find the optimal combination for higher limonene production. The strain expressing HMGR and the fusion protein ERG20-LS was the best limonene producer and, therefore, selected for further improvement. By increasing the expression of target genes and optimizing initial OD, 29.4 mg/L of L-limonene and 24.8 mg/L of D-limonene were obtained. We also studied whether peroxisomal compartmentalization of the synthesis pathway was beneficial for limonene production. The introduction of D-LS and ERG20 within the peroxisome improved limonene titers over cytosolic expression. Then, the entire MVA pathway was targeted to the peroxisome to improve precursor supply, which increased D-limonene production to 47.8 mg/L. Finally, through the optimization of fermentation conditions, D-limonene production titer reached 69.3 mg/L. CONCLUSIONS In this work, Y. lipolytica was successfully engineered to produce limonene. Our results showed that higher production of limonene was achieved when the synthesis pathway was targeted to the peroxisome, which indicates that this organelle can favor the bioproduction of terpenes in yeasts. This study opens new avenues for the efficient synthesis of valuable monoterpenes in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Lara Sellés Vidal
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - David Bell
- SynbiCITE Innovation and Knowledge Centre, Imperial College London, London, SW7 2AZ, UK
| | - Jure Zabret
- Acies Bio d.o.o., 1000, Tehnološki Park 21Ljubljana, Slovenia
| | - Mladen Soldat
- Acies Bio d.o.o., 1000, Tehnološki Park 21Ljubljana, Slovenia
| | - Martin Kavšček
- Acies Bio d.o.o., 1000, Tehnološki Park 21Ljubljana, Slovenia
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
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21
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Ye C, Li M, Gao J, Zuo Y, Xiao F, Jiang X, Cheng J, Huang L, Xu Z, Lian J. Metabolic engineering of Pichia pastoris for overproduction of cis-trans nepetalactol. Metab Eng 2024; 84:83-94. [PMID: 38897449 DOI: 10.1016/j.ymben.2024.06.007] [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: 02/17/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Monoterpene indole alkaloids (MIAs) are a group of plant-derived natural products with high-value medicinal properties. However, their availability for clinical application is limited due to challenges in plant extraction. Microbial production has emerged as a promising strategy to meet the clinical demands for MIAs. The biosynthetic pathway of cis-trans nepetalactol, which serves as the universal iridoid scaffold for all MIAs, has been successfully identified and reconstituted. However, bottlenecks and challenges remain to construct a high-yielding platform strain for cis-trans nepetalactol production, which is vital for subsequent MIAs biosynthesis. In the present study, we focused on engineering of Pichia pastoris cell factories to enhance the production of geraniol, 8-hydroxygeraniol, and cis-trans nepetalactol. By targeting the biosynthetic pathway from acetyl-CoA to geraniol in both peroxisomes and cytoplasm, we achieved comparable geraniol titers in both compartments. Through protein engineering, we found that either G8H or CPR truncation increased the production of 8-hydroxygeraniol, with a 47.8-fold and 14.0-fold increase in the peroxisomal and cytosolic pathway strain, respectively. Furthermore, through a combination of dynamical control of ERG20, precursor and cofactor supply engineering, diploid engineering, and dual subcellular compartmentalization engineering, we achieved the highest ever reported production of cis-trans nepetalactol, with a titer of 4429.4 mg/L using fed-batch fermentation in a 5-L bioreactor. We anticipate our systematic metabolic engineering strategies to facilitate the development of P. pastoris cell factories for sustainable production of MIAs and other plant natural products.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Feng Xiao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Xiaojing Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jintao Cheng
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China.
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22
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Ye M, Gao J, Li J, Yu W, Bai F, Zhou YJ. Promoter engineering enables precise metabolic regulation towards efficient β-elemene production in Ogataea polymorpha. Synth Syst Biotechnol 2024; 9:234-241. [PMID: 38385152 PMCID: PMC10877135 DOI: 10.1016/j.synbio.2024.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/23/2024] Open
Abstract
Precisely controlling gene expression is beneficial for optimizing biosynthetic pathways for improving the production. However, promoters in nonconventional yeasts such as Ogataea polymorpha are always limited, which results in incompatible gene modulation. Here, we expanded the promoter library in O. polymorpha based on transcriptional data, among which 13 constitutive promoters had the strengths ranging from 0-55% of PGAP, the commonly used strong constitutive promoter, and 2 were growth phase-dependent promoters. Subsequently, 2 hybrid growth phase-dependent promoters were constructed and characterized, which had 2-fold higher activities. Finally, promoter engineering was applied to precisely regulate cellular metabolism for efficient production of β-elemene. The glyceraldehyde-3-phosphate dehydrogenase gene GAP was downregulated to drive more flux into pentose phosphate pathway (PPP) and then to enhance the supply of acetyl-CoA by using phosphoketolase-phosphotransacetylase (PK-PTA) pathway. Coupled with the phase-dependent expression of synthase module (ERG20∼LsLTC2 fusion), the highest titer of 5.24 g/L with a yield of 0.037 g/(g glucose) was achieved in strain YY150U under fed-batch fermentation in shake flasks. This work characterized and engineered a series of promoters, that can be used to fine-tune genes for constructing efficient yeast cell factories.
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Affiliation(s)
- Min Ye
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Jingjing Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Fan Bai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
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Chen Q, Chen Y, Hou Z, Ma Y, Huang J, Zhang Z, Chen Y, Yang X, Zhang Y, Zhao G. Unlocking the formate utilization of wild-type Yarrowia lipolytica through adaptive laboratory evolution. Biotechnol J 2024; 19:e2400290. [PMID: 38900053 DOI: 10.1002/biot.202400290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Synthetic biology is contributing to the advancement of the global net-negative carbon economy, with emphasis on formate as a member of the one-carbon substrate garnering substantial attention. In this study, we employed base editing tools to facilitate adaptive evolution, achieving a formate tolerance of Yarrowia lipolytica to 1 M within 2 months. This effort resulted in two mutant strains, designated as M25-70 and M25-14, both exhibiting significantly enhanced formate utilization capabilities. Transcriptomic analysis revealed the upregulation of nine endogenous genes encoding formate dehydrogenases when cultivated utilizing formate as the sole carbon source. Furthermore, we uncovered the pivotal role of the glyoxylate and threonine-based serine pathway in enhancing glycine supply to promote formate assimilation. The full potential of Y. lipolytica to tolerate and utilize formate establishing the foundation for pyruvate carboxylase-based carbon sequestration pathways. Importantly, this study highlights the existence of a natural formate metabolic pathway in Y. lipolytica.
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Affiliation(s)
- Qian Chen
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Yunhong Chen
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Zeming Hou
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Yuyue Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yefu Chen
- Tianjin University of Science & Technology, Tianjin, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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24
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Hou R, Shan M, Liu X, Yao M, Yang K, Wang Y, Sui Z, Liang Z, Zhang Y, Zhang L. Proteomic analysis reveals that the co-ordination of cytosolic and mitochondrial pathways is beneficial for sabinene biosynthesis in engineered Saccharomyces cerevisiae. Biotechnol J 2024; 19:e2300710. [PMID: 38581096 DOI: 10.1002/biot.202300710] [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: 12/15/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/08/2024]
Abstract
Reconstruction and optimization of biosynthetic pathways can help to overproduce target chemicals in microbial cell factories based on genetic engineering. However, the perturbation of biosynthetic pathways on cellular metabolism is not well investigated and profiling the engineered microbes remains challenging. The rapid development of omics tools has the potential to characterize the engineered microbial cell factory. Here, we performed label-free quantitative proteomic analysis and metabolomic analysis of engineered sabinene overproducing Saccharomyces cerevisiae strains. Combined metabolic analysis andproteomic analysis of targeted mevalonate (MVA) pathway showed that co-ordination of cytosolic and mitochondrial pathways had balanced metabolism, and genome integration of biosynthetic genes had higher sabinene production with less MVA enzymes. Furthermore, comparative proteomic analysis showed that compartmentalized mitochondria pathway had perturbation on central cellular metabolism. This study provided an omics analysis example for characterizing engineered cell factory, which can guide future regulation of the cellular metabolism and maintaining optimal protein expression levels for the synthesis of target products.
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Affiliation(s)
- Rui Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengying Shan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Xinxin Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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25
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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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26
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Zhong W, Li H, Wang Y. Design and Construction of Artificial Biological Systems for One-Carbon Utilization. BIODESIGN RESEARCH 2023; 5:0021. [PMID: 37915992 PMCID: PMC10616972 DOI: 10.34133/bdr.0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.
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Affiliation(s)
- Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
| | - Hailong Li
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
- School of Materials Science and Engineering,
Zhejiang University, Zhejiang Province, Hangzhou 310000, PR China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
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