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Ordóñez DAR, Strunck FJBTL, Dutra LS, Brandão ALT. Upcycling glycerol into succinic acid: sustainable integration with biodiesel mills. BIORESOURCE TECHNOLOGY 2025:132716. [PMID: 40418999 DOI: 10.1016/j.biortech.2025.132716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2025] [Revised: 05/18/2025] [Accepted: 05/21/2025] [Indexed: 05/28/2025]
Abstract
This study explores the industrial potential of producing bio-based succinic acid (SA) from crude glycerol, a low-value byproduct of Brazil's biodiesel industry. By integrating green chemistry and biotechnology, the research aims to upcycle crude glycerol into high-value SA. Using Yarrowia lipolytica as a natural SA producer, the study assesses standalone facilities and systems integrated into biodiesel mills. Results show that producing SA from crude glycerol (S1) reduces climate change impact by 47% compared to using pure glycerol (S2), despite lower productivity. Integrating SA production with biodiesel operations (S3) improves economic performance but raises CO2 emissions by 54% relative to standalone biodiesel production (S1). All scenarios are economically feasible, with payback periods under seven years. Energy use and solvent recovery optimization remain essential to boost competitiveness. This work underscores the potential to upcycle crude glycerol, supporting circular economy strategies and informing sustainable biorefinery development and policy.
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Affiliation(s)
- Diego A R Ordóñez
- Departamento de Engenharia Química e de Materiais Pontifícia, Universidade Católica do Rio de Janeiro CP 38097, Rio de Janeiro, RJ 22451-900, Brazil
| | - Francisco J B T L Strunck
- Departamento de Engenharia Química e de Materiais Pontifícia, Universidade Católica do Rio de Janeiro CP 38097, Rio de Janeiro, RJ 22451-900, Brazil
| | - Luciana S Dutra
- Programa de Engenharia Química/COPPE Universidade Federal do Rio de Janeiro, Cidade, Universitária CP 68502, Rio de Janeiro, RJ 21941-972, Brazil
| | - Amanda L T Brandão
- Departamento de Engenharia Química e de Materiais Pontifícia, Universidade Católica do Rio de Janeiro CP 38097, Rio de Janeiro, RJ 22451-900, Brazil.
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2
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Ryu Y, Bouharras FE, Cha M, Mudondo J, Kim Y, Ramakrishnan SR, Shin S, Yu Y, Lee W, Park J, Song Y, Yum SJ, Cha HG, Ahn D, Kim SJ, Kim HT. Recent advancements in the evolution, production, and degradation of biodegradable mulch films: A review. ENVIRONMENTAL RESEARCH 2025; 277:121629. [PMID: 40250592 DOI: 10.1016/j.envres.2025.121629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2025] [Revised: 04/14/2025] [Accepted: 04/15/2025] [Indexed: 04/20/2025]
Abstract
Biomass-based plastic production systems play a crucial role in fostering a sustainable society. Biodegradable mulch films (BDMs) have emerged as a practical solution to environmental pollution in agriculture. Various types of BDMs, including polybutylene adipate-co-terephthalate, polybutylene succinate, and polybutylene succinate-co-adipate, have been developed, though many are still derived from fossil-fuel-based plastics. Furthermore, the adoption of biodegradable materials in agricultural practices remains limited. This review critically assesses the evolution and significance of mulch films, highlighting the transition from traditional polyethylene (PE) to BDMs in response to environmental challenges. We provide an overview of the biorefinery approach to producing biomass-derived BDMs, discussing biomass pretreatment, saccharification, production of plastic monomers using microbial cell factories, purification, and polymerization. The review also explores techniques to enhance the biodegradation capabilities of mulch films during polymerization. Additionally, we emphasize the necessity for advancements in controlling the degradation rates of BDMs. By addressing the environmental concerns associated with the disposal of these materials, this review underscores the importance of developing effective strategies for a more sustainable and environmentally friendly agricultural landscape.
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Affiliation(s)
- Yeonkyeong Ryu
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44429, Republic of Korea
| | - Fatima Ezzahra Bouharras
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan, 44412, Republic of Korea
| | - Minseok Cha
- Research Center for Biological Cybernetics and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Joyce Mudondo
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Younghoon Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44429, Republic of Korea
| | - Sudha Rani Ramakrishnan
- Research Center for Biological Cybernetics and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea; Department of Biotechnology, Anna University, Chennai, 600025, India
| | - Sangbin Shin
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan, 44412, Republic of Korea; Department of Polymer Science and Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Youngchang Yu
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan, 44412, Republic of Korea
| | - Wonjoo Lee
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology, Ulsan, 44412, Republic of Korea
| | - Jiyoung Park
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yunjeong Song
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Su-Jin Yum
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Gil Cha
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44429, Republic of Korea.
| | - Dowon Ahn
- Department of Polymer Science and Engineering, Pusan National University, Busan, 46241, Republic of Korea.
| | - Soo-Jung Kim
- Research Center for Biological Cybernetics and Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Hee Taek Kim
- Department of Food Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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3
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Celińska E, Zhou YJ. Global transcription machinery engineering in Yarrowia lipolytica. FEMS Yeast Res 2025; 25:foaf023. [PMID: 40338609 PMCID: PMC12091107 DOI: 10.1093/femsyr/foaf023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 03/23/2025] [Accepted: 05/07/2025] [Indexed: 05/09/2025] Open
Abstract
Global transcription machinery engineering (gTME) is a strategy for optimizing complex phenotypes in microbes by manipulating transcription factors (TFs) and their downstream transcriptional regulatory networks (TRN). In principle, gTME leads to a focused but comprehensive optimization of a microbe, also enabling the engineering of nonpathway functionalities, like stress resistance, protein expression, or growth rate. A link between a TF and a desired phenotype is to be established for a rationally designed gTME. For use in a high-throughput format with extensive libraries of TRN-engineered clones tested under multiple conditions, well-developed culturing and analytical protocols are needed, to reveal the pleiotropic effects of the TFs. This mini-review summarizes the gTME strategies and TFs described under different contexts in Yarrowia lipolytica. The outcomes of the gTME strategy application are also addressed, demonstrating its effectiveness in engineering complex, industrially relevant traits in Y. lipolytica.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-637 Poznań, Poland
| | - 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
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, China
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Sun T, Sun ML, Lin L, Gao J, Wang K, Ji XJ. Advancing Succinic Acid Biomanufacturing Using the Nonconventional Yeast Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:100-109. [PMID: 39707966 DOI: 10.1021/acs.jafc.4c09990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2024]
Abstract
Succinic acid is an essential bulk chemical with wide-ranging applications in materials, food, and pharmaceuticals. With the advancement of biotechnology, there has been a surge in focus on low-carbon sustainable microbial synthesis methods for producing biobased succinic acid. Due to its high intrinsic acid tolerance, Yarrowia lipolytica has gained recognition as a competitive chassis for the industrial manufacture of succinic acid. This review summarizes the research progress on succinic acid biomanufacturing using Y. lipolytica. First, it introduces the major metabolic routes for succinic acid biosynthesis and the pertinent engineering approaches for building efficient cell factories. Subsequently, we offer a review of methods employed for succinic acid synthesis by Y. lipolytica utilizing alternative substrates as well as the relevant optimization strategies for the fermentation process. Finally, future research directions for improving succinic acid biomanufacturing in Y. lipolytica are delineated in light of the recent progress, obstacles, and trends in this area.
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Affiliation(s)
- Tao Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jian Gao
- School of Marine and Bioengineering, Yancheng Institute of Technology, No. 211 Jianjun Road, Yancheng 224051, People's Republic of China
| | - Kaifeng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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Jenjitwanich A, Marx H, Sauer M. Characterization of the metabolism of the yeast Yarrowia lipolytica growing as a biofilm. FEMS MICROBES 2024; 5:xtae026. [PMID: 39529679 PMCID: PMC11552517 DOI: 10.1093/femsmc/xtae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/04/2024] [Accepted: 09/20/2024] [Indexed: 11/16/2024] Open
Abstract
Yarrowia lipolytica is a well-characterized yeast with remarkable metabolic adaptability. It is capable of producing various products from different carbon sources and easily switching between planktonic and biofilm states. A biofilm represents a natural means of cell immobilization that could support continuous cultivation and production processes, such as perfusion cultivation. However, the metabolic activities of Y. lipolytica in biofilms have not yet been studied in detail. Therefore, this study aimed to compare the metabolic activities of Y. lipolytica in biofilm and planktonic states. Conventionally, a stirred tank bioreactor was used to cultivate Y. lipolytica in a planktonic state. On the other hand, a trickle bed bioreactor system was used for biofilm cultivation. The low pH at 3 was maintained to favor polyol production. The accumulation of citric acid was observed over time only in the biofilm state, which significantly differed from the planktonic state. Although the biofilm cultivation process has lower productivity, it has been observed that the production rate remains constant and the total product yield is comparable to the planktonic state when supplied with 42% oxygen-enriched air. This finding indicates that the biofilm state has the potential for continuous bioprocessing applications and is possibly a feasible option.
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Affiliation(s)
- Akarawit Jenjitwanich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University, Muthgasse 18, 1190 Vienna, Austria
| | - Hans Marx
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University, Muthgasse 18, 1190 Vienna, Austria
- Research Area: Biochemical Engineering, Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University, Muthgasse 18, 1190 Vienna, Austria
- OMV AG, Trabrennstraße 6–8, 1020 Vienna, Austria
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Kayalvizhi R, Sanjana J, Jacob S, Kumar V. An Eclectic Review on Dicarboxylic Acid Production Through Yeast Cell Factories and Its Industrial Prominence. Curr Microbiol 2024; 81:147. [PMID: 38642080 DOI: 10.1007/s00284-024-03654-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 02/29/2024] [Indexed: 04/22/2024]
Abstract
Dicarboxylic acid (DCA) is a multifaceted chemical intermediate, recoursed to produce many industrially important products such as adhesives, plasticizers, lubricants, polymers, etc. To bypass the shortcomings of the chemical methods of synthesis of DCA and to reduce fossil fuel footprints, bio-based synthesis is gaining attention. In pursuit of an eco-friendly sustainable alternative method of DCA production, microbial cell factories, and renewable organic resources are gaining popularity. Among the plethora of microbial communities, yeast is being favored industrially compared to bacterial fermentation due to its hyperosmotic and low pH tolerance and flexibility for gene manipulations. By application of rapidly evolving genetic manipulation techniques, the bio-based DCA production could be made more precise and economical. To bridge the gap between supply and demand of DCA, many strategies are employed to improve the fermentation. This review briefly outlines the advancements in DCA production using yeast cell factories with the exemplification of strain improvement strategies.
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Affiliation(s)
- Ramalingam Kayalvizhi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India
| | - Jayacumar Sanjana
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India.
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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Dietrich D, Jovanovic-Gasovic S, Cao P, Kohlstedt M, Wittmann C. Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability. Microb Cell Fact 2023; 22:199. [PMID: 37773137 PMCID: PMC10540379 DOI: 10.1186/s12934-023-02209-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Long-chain polyunsaturated fatty acids (LC-PUFAs), such as docosahexaenoic acid (DHA), are essential for human health and have been widely used in the food and pharmaceutical industries. However, the limited availability of natural sources, such as oily fish, has led to the pursuit of microbial production as a promising alternative. Yarrowia lipolytica can produce various PUFAs via genetic modification. A recent study upgraded Y. lipolytica for DHA production by expressing a four-gene cluster encoding a myxobacterial PKS-like PUFA synthase, reducing the demand for redox power. However, the genetic architecture of gene expression in Y. lipolytica is complex and involves various control elements, offering space for additional improvement of DHA production. This study was designed to optimize the expression of the PUFA cluster using a modular cloning approach. RESULTS Expression of the monocistronic cluster with each gene under the control of the constitutive TEF promoter led to low-level DHA production. By using the minLEU2 promoter instead and incorporating additional upstream activating UAS1B4 sequences, 5' promoter introns, and intergenic spacers, DHA production was increased by 16-fold. The producers remained stable over 185 h of cultivation. Beneficially, the different genetic control elements acted synergistically: UAS1B elements generally increased expression, while the intron caused gene-specific effects. Mutants with UAS1B16 sequences within 2-8 kb distance, however, were found to be genetically unstable, which limited production performance over time, suggesting the avoidance of long repetitive sequence blocks in synthetic multigene clusters and careful monitoring of genetic stability in producing strains. CONCLUSIONS Overall, the results demonstrate the effectiveness of synthetic heterologous gene clusters to drive DHA production in Y. lipolytica. The combinatorial exploration of different genetic control elements allowed the optimization of DHA production. These findings have important implications for developing Y. lipolytica strains for the industrial-scale production of valuable polyunsaturated fatty acids.
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Affiliation(s)
- Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Georgiadis I, Tsiligkaki C, Patavou V, Orfanidou M, Tsoureki A, Andreadelli A, Theodosiou E, Makris AM. Identification and Construction of Strong Promoters in Yarrowia lipolytica Suitable for Glycerol-Based Bioprocesses. Microorganisms 2023; 11:1152. [PMID: 37317126 DOI: 10.3390/microorganisms11051152] [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: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Yarrowia lipolytica is a non-pathogenic aerobic yeast with numerous industrial biotechnology applications. The organism grows in a wide variety of media, industrial byproducts, and wastes. A need exists for molecular tools to improve heterologous protein expression and pathway reconstitution. In an effort to identify strong native promoters in glycerol-based media, six highly expressed genes were mined from public data, analyzed, and validated. The promoters from the three most highly expressed (H3, ACBP, and TMAL) were cloned upstream of the reporter mCherry in episomal and integrative vectors. Fluorescence was quantified by flow cytometry and promoter strength was benchmarked with known strong promoters (pFBA1in, pEXP1, and pTEF1in) in cells growing in glucose, glycerol, and synthetic glycerol media. The results show that pH3 > pTMAL > pACBP are very strong promoters, with pH3 exceeding all other tested promoters. Hybrid promoters were also constructed, linking the Upstream Activating Sequence 1B (UAS1B8) with H3(260) or TMAL(250) minimal promoters, and compared to the UAS1B8-TEF1(136) promoter. The new hybrid promoters exhibited far superior strength. The novel promoters were utilized to overexpress the lipase LIP2, achieving very high secretion levels. In conclusion, our research identified and characterized several strong Y. lipolytica promoters that expand the capacity to engineer Yarrowia strains and valorize industrial byproducts.
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Affiliation(s)
- Ioannis Georgiadis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Christina Tsiligkaki
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Victoria Patavou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Maria Orfanidou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
- Department of Chemical Engineering, School of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), 57001 Thessaloniki, Greece
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Theodosiou E. Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica. Catalysts 2023. [DOI: 10.3390/catal13040657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.
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Synthesis of Secretory Proteins in Yarrowia lipolytica: Effect of Combined Stress Factors and Metabolic Load. Int J Mol Sci 2022; 23:ijms23073602. [PMID: 35408958 PMCID: PMC8998316 DOI: 10.3390/ijms23073602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
While overproduction of recombinant secretory proteins (rs-Prots) triggers multiple changes in the physiology of the producer cell, exposure to suboptimal growth conditions may further increase that biological response. The environmental conditions may modulate the efficiency of both the rs-Prot gene transcription and translation but also the polypeptide folding. Insights into responses elicited by different environmental stresses on the rs-Prots synthesis and host yeast physiology might contribute to a better understanding of fundamental biology processes, thus providing some clues to further optimise bioprocesses. Herein, a series of batch cultivations of Yarrowia lipolytica strains differentially metabolically burdened by the rs-Prots overproduction have been conducted. Combinations of different stress factors, namely pH (3/7) and oxygen availability (kLa 28/110 h-1), have been considered for their impact on cell growth and morphology, substrate consumption, metabolic activity, genes expression, and secretion of the rs-Prots. Amongst others, our data demonstrate that a highly metabolically burdened cell has a higher demand for the carbon source, although presenting a compromised cell growth. Moreover, the observed decrease in rs-Prot production under adverse environmental conditions rather results from the emergence of a less-producing cell subpopulation than from the decrease of the synthetic capacity of the whole cell population.
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11
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Kubiak M, Białas W, Celińska E. Thermal treatment improves a process of crude glycerol valorization for the production of a heterologous enzyme by Yarrowia lipolytica. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 31:e00648. [PMID: 34221911 PMCID: PMC8243353 DOI: 10.1016/j.btre.2021.e00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022]
Abstract
A crude glycerol valorization process to enzymatic preparation was developed. Impact of thermal treatment on the protein production by Y. lipolytica is studied. Pilot-scale processes with laboratory and technical substrates were simulated. Techno-economic analysis of a pilot-scale waste-free process was conducted. Comprehensive stream analysis and identification of bottlenecks is provided.
Valorization of crude glycerol requires a potent bifunctional biocatalyst, such as Yarrowia lipolytica, capable of high-density growth on this substrate, and having i.a. high propensity for heterologous protein synthesis. Increasing evidence suggests that controlled administration of stress, i.a. thermal treatment, has a positive impact on bioprocess performance. In this study, we systematically adjusted thermal treatment conditions (20 to 42 °C) in order to maximize heterologous protein production by Y. lipolytica growing in crude glycerol-based medium. Our results showed nearly 30% enhancement in the enzyme production triggered by temporary exposure to decreased temperature. Here developed mathematical model indicated optimal treatment conditions (20 °C, 153′) that were later applied to a process with biodiesel-derived glycerol and technical substrates. Techno-economic analysis of a pilot-scale-waste-free process was conducted. Quantitative description of the associated costs and economic gain due to exploitation of industrial substrates, as well as indication of current bottlenecks of the process, are also provided.
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Affiliation(s)
- Monika Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
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12
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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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Billerach G, Preziosi-Belloy L, Lin CSK, Fulcrand H, Dubreucq E, Grousseau E. Impact of nitrogen deficiency on succinic acid production by engineered strains of Yarrowia lipolytica. J Biotechnol 2021; 336:30-40. [PMID: 34090952 DOI: 10.1016/j.jbiotec.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Yarrowia lipolytica strains PGC01003 and PGC202 engineered for succinic acid production were studied and compared to the wild type strain W29. For the first time, these two strains were characterized in a chemically defined medium. Strain growth and organic acid production were investigated in fed-batch mode with glycerol as carbon and energy source. This study evaluated the impact of nitrogen deficiency strategy to redirect carbon flux toward succinic acid synthesis. Strain PGC01003 produced 19 g L-1 succinic acid with an overall yield of 0.23 g g-1 and an overall productivity of 0.23 g L-1 h-1, while strain PGC202 produced 33 g L-1 succinic acid with an overall yield of 0.12 g g-1 and a productivity of 0.57 g L-1 h-1. Nitrogen limitation effectively stopped biomass growth and increased succinic acid yield of PGC01003 and PGC202 by 18 % and 62 %, respectively. However, the specific succinic acid production rate was reduced by 77 % and 66 %, respectively.
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Affiliation(s)
- Guillaume Billerach
- UMR IATE (INRAE, L'Institut Agro-Montpellier SupAgro, University of Montpellier), Montpellier, France.
| | - Laurence Preziosi-Belloy
- UMR IATE (INRAE, L'Institut Agro-Montpellier SupAgro, University of Montpellier), Montpellier, France.
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong.
| | - Hélène Fulcrand
- UMR IATE (INRAE, L'Institut Agro-Montpellier SupAgro, University of Montpellier), Montpellier, France.
| | - Eric Dubreucq
- UMR IATE (INRAE, L'Institut Agro-Montpellier SupAgro, University of Montpellier), Montpellier, France.
| | - Estelle Grousseau
- UMR IATE (INRAE, L'Institut Agro-Montpellier SupAgro, University of Montpellier), Montpellier, France.
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Li C, Ong KL, Cui Z, Sang Z, Li X, Patria RD, Qi Q, Fickers P, Yan J, Lin CSK. Promising advancement in fermentative succinic acid production by yeast hosts. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123414. [PMID: 32763704 DOI: 10.1016/j.jhazmat.2020.123414] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/27/2020] [Accepted: 07/05/2020] [Indexed: 05/22/2023]
Abstract
As a platform chemical with various applications, succinic acid (SA) is currently produced by petrochemical processing from oil-derived substrates such as maleic acid. In order to replace the environmental unsustainable hydrocarbon economy with a renewable environmentally sound carbohydrate economy, bio-based SA production process has been developed during the past two decades. In this review, recent advances in the valorization of solid organic wastes including mixed food waste, agricultural waste and textile waste for efficient, green and sustainable SA production have been reviewed. Firstly, the application, market and key global players of bio-SA are summarized. Then achievements in SA production by several promising yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica are detailed, followed by calculation and comparison of SA production costs between oil-based substrates and raw materials. Lastly, challenges in engineered microorganisms and fermentation processes are presented together with perspectives on the development of robust yeast SA producers via genome-scale metabolic optimization and application of low-cost raw materials as fermentation substrates. This review provides valuable insights for identifying useful directions for future bio-SA production improvement.
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Affiliation(s)
- Chong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Khai Lun Ong
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhenyu Sang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaotong Li
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Raffel Dharma Patria
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech., Av. de la Faculté, 2B, 5030, Gembloux, Belgium
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China.
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15
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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16
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Fickers P, Cheng H, Sze Ki Lin C. Sugar Alcohols and Organic Acids Synthesis in Yarrowia lipolytica: Where Are We? Microorganisms 2020; 8:E574. [PMID: 32326622 PMCID: PMC7232202 DOI: 10.3390/microorganisms8040574] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023] Open
Abstract
Sugar alcohols and organic acids that derive from the metabolism of certain microorganisms have a panoply of applications in agro-food, chemical and pharmaceutical industries. The main challenge in their production is to reach a productivity threshold that allow the process to be profitable. This relies on the construction of efficient cell factories by metabolic engineering and on the development of low-cost production processes by using industrial wastes or cheap and widely available raw materials as feedstock. The non-conventional yeast Yarrowia lipolytica has emerged recently as a potential producer of such metabolites owing its low nutritive requirements, its ability to grow at high cell densities in a bioreactor and ease of genome edition. This review will focus on current knowledge on the synthesis of the most important sugar alcohols and organic acids in Y. lipolytica.
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Affiliation(s)
- Patrick Fickers
- Microbial Process and Interactions, TERRA Teaching and Research Centre, University of Liege—Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;
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Briki A, Kaboré K, Olmos E, Bosselaar S, Blanchard F, Fick M, Guedon E, Fournier F, Delaunay S. Corynebacterium glutamicum, a natural overproducer of succinic acid? Eng Life Sci 2020; 20:205-215. [PMID: 32874184 PMCID: PMC7447883 DOI: 10.1002/elsc.201900141] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 01/09/2023] Open
Abstract
Corynebacterium glutamicum is well known as an important industrial amino acid producer. For a few years, its ability to produce organic acids, under micro-aerobic or anaerobic conditions was demonstrated. This study is focused on the identification of the culture parameters influencing the organic acids production and, in particular, the succinate production, by this bacterium. Corynebacterium glutamicum 2262, used throughout this study, was a wild-type strain, which was not genetically designed for the production of succinate. The oxygenation level and the residual glucose concentration appeared as two critical parameters for the organic acids production. The maximal succinate concentration (4.9 g L-1) corresponded to the lower kLa value of 5 h-1. Above 5 h-1, a transient accumulation of the succinate was observed. Interestingly, the stop in the succinate production was concomitant with a lower threshold glucose concentration of 9 g L-1. Taking into account this threshold, a fed-batch culture was performed to optimize the succinate production with C. glutamicum 2262. The results showed that this wild-type strain was able to produce 93.6 g L-1 of succinate, which is one of the highest concentration reported in the literature.
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Affiliation(s)
- Amani Briki
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Karim Kaboré
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Eric Olmos
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Sabine Bosselaar
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Fabrice Blanchard
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Michel Fick
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Emmanuel Guedon
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Frantz Fournier
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
| | - Stéphane Delaunay
- Laboratoire Réactions et Génie des ProcédésCNRSVandoeuvre CedexFrance
- Laboratoire Réactions et Génie des ProcédésUniversité de LorraineVandoeuvre CedexFrance
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Zhang X, Zhao Y, Liu Y, Wang J, Deng Y. Recent progress on bio-based production of dicarboxylic acids in yeast. Appl Microbiol Biotechnol 2020; 104:4259-4272. [PMID: 32215709 DOI: 10.1007/s00253-020-10537-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
Abstract
Dicarboxylic acids are widely used in fine chemical and food industries as well as the monomer for polymerisation of high molecular material. Given the problems of environmental contamination and sustainable development faced by traditional production of dicarboxylic acids based on petrol, new approaches such as bio-based production of dicarboxylic acids drew more attentions. The yeast, Saccharomyces cerevisiae, was regarded as an ideal organism for bio-based production of dicarboxylic acids with high tolerance to acidic and hyperosmotic environments, robust growth using a broad range of substrates, great convenience for genetic manipulation, stable inheritance via sub-cultivation, and food compatibility. In this review, the production of major dicarboxylates via S. cerevisiae was concluded and the challenges and opportunities facing were discussed.Key Points• Summary of current production of major dicarboxylic acids by Saccharomyces cerevisiae.• Discussion of influence factors on four-carbon dicarboxylic acids production by Saccharomyces cerevisiae.• Outlook of potential production of five- and six-carbon dicarboxylic acids by Saccharomyces cerevisiae.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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19
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Ong KL, Fickers P, Lin CSK. Enhancing succinic acid productivity in the yeast Yarrowia lipolytica with improved glycerol uptake rate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:134911. [PMID: 31733546 DOI: 10.1016/j.scitotenv.2019.134911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 05/22/2023]
Abstract
Development of cost effective and highly efficient process for bio-based succinic acid (SA) production is a main concern for industry. The metabolically engineered Y. lipolytica strain PGC01003 was successfully used for SA production with high titre. However, this strain possesses as main drawback with a low growth rate when glycerol is used as a feedstock. Herein, gene GUT1, encoding glycerol kinase, was overexpressed in strain PGC01003 with the aim to improve glycerol uptake capacity. In the resulting strain RIY420, glycerol uptake was 13.5% higher than for the parental strain. GUT1 gene overexpression also positively influences SA production. In batch bioreactor, SA titre, yield and productivity were 32%, 39% and 143% higher, respectively, than for the parental strain PGC01003. Using a glycerol feeding strategy, SA titre, yield and productivity were further improved by 11%, 5% and 10%, respectively. Moreover, the process duration to yield the highest concentration of SA in the culture supernatant was reduced by 9%. This demonstrated the contribution of metabolically engineered strain RIY420 to lower SA process cost and increase the efficiency of bio-based SA production.
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Affiliation(s)
- Khai Lun Ong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Av. De la Faculté, 2B, 5030 Gembloux, Belgium
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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20
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Babaei M, Rueksomtawin Kildegaard K, Niaei A, Hosseini M, Ebrahimi S, Sudarsan S, Angelidaki I, Borodina I. Engineering Oleaginous Yeast as the Host for Fermentative Succinic Acid Production From Glucose. Front Bioeng Biotechnol 2019; 7:361. [PMID: 31828067 PMCID: PMC6892388 DOI: 10.3389/fbioe.2019.00361] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Oleaginous yeast Yarrowia lipolytica is a prospective host for production of succinic acid. The interruption of tricarboxylic acid cycle through succinate dehydrogenase gene (SDH) deletion was reported to result in strains incapable of glucose utilization and this ability had to be restored by chemical mutation or long adaptive laboratory evolution. In this study, a succinate producing strain of Y. lipolytica was engineered by truncating the promoter of SDH1 gene, which resulted in 77% reduction in SDH activity but did not impair the ability of the strain to grow on glucose. The flux toward succinic acid was further improved by overexpressing the genes in the glyoxylate pathway and the oxidative TCA branch, and expressing phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes. A short adaptation on glucose reduced the lag phase of the strain and increased its tolerance to high glucose concentrations. The resulting strain produced 7.8 ± 0.0 g/L succinic acid with a yield of 0.105 g/g glucose in shake flasks without pH control, while mannitol (11.8 ± 0.8 g/L) was the main by-product. Further investigations showed that mannitol accumulation was caused by low pH stress and buffering the fermentation medium eliminated mannitol formation. In a fed-batch bioreactor in mineral medium at pH 5, at which point according to Ka values of succinic acid, the major fraction of product was in acidic form rather than dissociated form, the strain produced 35.3 ± 1.5 g/L succinic acid with 0.26 ± 0.00 g/g glucose yield.
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Affiliation(s)
- Mahsa Babaei
- Department of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | | | - Aligholi Niaei
- Department of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | - Maryam Hosseini
- Department of Chemical Engineering, Faculty of Engineering, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Sirous Ebrahimi
- Biotechnology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, Tabriz, Iran
| | - Suresh Sudarsan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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21
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Mirończuk AM, Kosiorowska KE, Biegalska A, Rakicka-Pustułka M, Szczepańczyk M, Dobrowolski A. Heterologous overexpression of bacterial hemoglobin VHb improves erythritol biosynthesis by yeast Yarrowia lipolytica. Microb Cell Fact 2019; 18:176. [PMID: 31615519 PMCID: PMC6794898 DOI: 10.1186/s12934-019-1231-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/11/2019] [Indexed: 01/16/2023] Open
Abstract
Background Yarrowia lipolytica is an unconventional yeast with a huge industrial potential. Despite many advantages for biotechnological applications, it possesses enormous demand for oxygen, which is a bottleneck in large scale production. In this study a codon optimized bacterial hemoglobin from Vitreoscilla stercoraria (VHb) was overexpressed in Y. lipolytica for efficient growth and erythritol synthesis from glycerol in low-oxygen conditions. Erythritol is a natural sweetener produced by Y. lipolytica under high osmotic pressure and at low pH, and this process requires high oxygen demand. Results Under these conditions the VHb overexpressing strain showed mostly yeast-type cells resulting in 83% higher erythritol titer in shake-flask experiments. During a bioreactor study the engineered strain showed higher erythritol productivity (QERY = 0.38 g/l h) and yield (YERY = 0.37 g/g) in comparison to the control strain (QERY = 0.30 g/l h, YERY = 0.29 g/g). Moreover, low stirring during the fermentation process resulted in modest foam formation. Conclusions This study showed that overexpression of VHb in Y. lipolytica allows for dynamic growth and efficient production of a value-added product from a low-value substrate.
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Affiliation(s)
- Aleksandra M Mirończuk
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland.
| | - Katarzyna E Kosiorowska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland
| | - Anna Biegalska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland
| | - Magdalena Rakicka-Pustułka
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland
| | - Mateusz Szczepańczyk
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland
| | - Adam Dobrowolski
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630, Wrocław, Poland
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Zahoor A, Küttner FTF, Blank LM, Ebert BE. Evaluation of pyruvate decarboxylase-negative Saccharomyces cerevisiae strains for the production of succinic acid. Eng Life Sci 2019; 19:711-720. [PMID: 32624964 PMCID: PMC6999389 DOI: 10.1002/elsc.201900080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/19/2019] [Accepted: 08/07/2019] [Indexed: 01/06/2023] Open
Abstract
Dicarboxylic acids are important bio‐based building blocks, and Saccharomyces cerevisiae is postulated to be an advantageous host for their fermentative production. Here, we engineered a pyruvate decarboxylase‐negative S. cerevisiae strain for succinic acid production to exploit its promising properties, that is, lack of ethanol production and accumulation of the precursor pyruvate. The metabolic engineering steps included genomic integration of a biosynthesis pathway based on the reductive branch of the tricarboxylic acid cycle and a dicarboxylic acid transporter. Further modifications were the combined deletion of GPD1 and FUM1 and multi‐copy integration of the native PYC2 gene, encoding a pyruvate carboxylase required to drain pyruvate into the synthesis pathway. The effect of increased redox cofactor supply was tested by modulating oxygen limitation and supplementing formate. The physiologic analysis of the differently engineered strains focused on elucidating metabolic bottlenecks. The data not only highlight the importance of a balanced activity of pathway enzymes and selective export systems but also shows the importance to find an optimal trade‐off between redox cofactor supply and energy availability in the form of ATP.
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Affiliation(s)
- Ahmed Zahoor
- Institute of Applied Microbiology - iAMB Aachen Biology and Biotechnology - ABBt RWTH Aachen University Aachen Germany
| | - Felix T F Küttner
- Institute of Applied Microbiology - iAMB Aachen Biology and Biotechnology - ABBt RWTH Aachen University Aachen Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB Aachen Biology and Biotechnology - ABBt RWTH Aachen University Aachen Germany
| | - Birgitta E Ebert
- Institute of Applied Microbiology - iAMB Aachen Biology and Biotechnology - ABBt RWTH Aachen University Aachen Germany
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23
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Biodiesel-Derived Glycerol Obtained from Renewable Biomass-A Suitable Substrate for the Growth of Candida zeylanoides Yeast Strain ATCC 20367. Microorganisms 2019; 7:microorganisms7080265. [PMID: 31426397 PMCID: PMC6722897 DOI: 10.3390/microorganisms7080265] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Used kitchen oil represents a feasible and renewable biomass to produce green biofuels such as biodiesel. Biodiesel production generates large amounts of by-products such as the crude glycerol fraction, which can be further used biotechnologically as a valuable nutrient for many microorganisms. In this study, we transesterified used kitchen oil with methanol and sodium hydroxide in order to obtain biodiesel and crude glycerol fractions. The crude glycerol fraction consisting of 30% glycerol was integrated into a bioreactor cultivation process as a nutrient source for the growth of Candida zeylanoides ATCC 20367. Cell viability and biomass production were similar to those obtained with batch cultivations on pure glycerol or glucose as the main nutrient substrates. However, the biosynthesis of organic acids (e.g., citric and succinic) was significantly different compared to pure glycerol and glucose used as main carbon sources.
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Pleissner D, Dietz D, van Duuren JBJH, Wittmann C, Yang X, Lin CSK, Venus J. Biotechnological Production of Organic Acids from Renewable Resources. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 166:373-410. [PMID: 28265703 DOI: 10.1007/10_2016_73] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Biotechnological processes are promising alternatives to petrochemical routes for overcoming the challenges of resource depletion in the future in a sustainable way. The strategies of white biotechnology allow the utilization of inexpensive and renewable resources for the production of a broad range of bio-based compounds. Renewable resources, such as agricultural residues or residues from food production, are produced in large amounts have been shown to be promising carbon and/or nitrogen sources. This chapter focuses on the biotechnological production of lactic acid, acrylic acid, succinic acid, muconic acid, and lactobionic acid from renewable residues, these products being used as monomers for bio-based material and/or as food supplements. These five acids have high economic values and the potential to overcome the "valley of death" between laboratory/pilot scale and commercial/industrial scale. This chapter also provides an overview of the production strategies, including microbial strain development, used to convert renewable resources into value-added products.
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Affiliation(s)
- Daniel Pleissner
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Donna Dietz
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Xiaofeng Yang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Joachim Venus
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.
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Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica H222. Microbiol Resour Announc 2019; 8:MRA01547-18. [PMID: 30701247 PMCID: PMC6346196 DOI: 10.1128/mra.01547-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/18/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. This genomic resource will help integrate intraspecies diversity into synthetic biology projects that utilize Yarrowia as a biotechnological chassis for value-added chemical productions.
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Yu Q, Cui Z, Zheng Y, Huo H, Meng L, Xu J, Gao C. Exploring succinic acid production by engineered Yarrowia lipolytica strains using glucose at low pH. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Succinic acid production using a glycerol-based medium by an engineered strain of Yarrowia lipolytica: Statistical optimization and preliminary economic feasibility study. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng 2018; 50:192-208. [PMID: 30056205 DOI: 10.1016/j.ymben.2018.07.016] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.
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Affiliation(s)
- Ahmad M Abdel-Mawgoud
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States.
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The role of laboratory-scale bioreactors at the semi-continuous and continuous microbiological and biotechnological processes. Appl Microbiol Biotechnol 2018; 102:7293-7308. [DOI: 10.1007/s00253-018-9194-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022]
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Engineering Yarrowia lipolytica for Use in Biotechnological Applications: A Review of Major Achievements and Recent Innovations. Mol Biotechnol 2018; 60:621-635. [DOI: 10.1007/s12033-018-0093-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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31
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Li C, Gao S, Yang X, Lin CSK. Green and sustainable succinic acid production from crude glycerol by engineered Yarrowia lipolytica via agricultural residue based in situ fibrous bed bioreactor. BIORESOURCE TECHNOLOGY 2018; 249:612-619. [PMID: 29091845 DOI: 10.1016/j.biortech.2017.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
In situ fibrous bed bioreactor (isFBB) for efficient succinic acid (SA) production by Yarrowia lipolytica was firstly developed in our former study. In this study, agricultural residues including wheat straw, corn stalk and sugarcane bagasse were investigated for the improvement of isFBB, and sugarcane bagasse was demonstrated to be the best immobilization material. With crude glycerol as the sole carbon source, optimization for isFBB batch fermentation was carried out. Under the optimal conditions of 20g sugarcane bagasse as immobilization material, 120gL-1 crude glycerol as carbon source and 4Lmin-1 of aeration rate, the resultant SA concentration was 53.6gL-1 with an average productivity of 1.45gL-1h-1 and a SA yield of 0.45gg-1. By feeding crude glycerol, SA titer up to 209.7gL-1 was obtained from fed batch fermentation, which was the highest value that ever reported.
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Affiliation(s)
- Chong Li
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Shi Gao
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Xiaofeng Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong.
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Li C, Gao S, Li X, Yang X, Lin CSK. Efficient metabolic evolution of engineered Yarrowia lipolytica for succinic acid production using a glucose-based medium in an in situ fibrous bioreactor under low-pH condition. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:236. [PMID: 30181775 PMCID: PMC6116362 DOI: 10.1186/s13068-018-1233-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/22/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Alkali used for pH control during fermentation and acidification for downstream recovery of succinic acid (SA) are the two largest cost contributors for bio-based SA production. To promote the commercialization process of fermentative SA, the development of industrially important microorganisms that can tolerate low pH has emerged as a crucial issue. RESULTS In this study, an in situ fibrous bed bioreactor (isFBB) was employed for the metabolic evolution for selection of Y. lipolytica strain that can produce SA at low pH using glucose-based medium. An evolved strain named Y. lipolytica PSA3.0 that could produce SA with a titer of 19.3 g/L, productivity of 0.52 g/L/h, and yield of 0.29 g/g at pH 3.0 from YPD was achieved. The enzyme activity analysis demonstrated that the pathway from pyruvate to acetate was partially blocked in Y. lipolytica PSA3.0 after the evolution, which is beneficial to cell growth and SA production at low pH. When free-cell batch fermentations were performed using the parent and evolved strains separately, the evolved strain PSA3.0 produced 18.4 g/L SA with a yield of 0.23 g/g at pH 3.0. Although these values were lower than that obtained by the parent strain PSA02004 at its optimal pH 6.0, which were 25.2 g/L and 0.31 g/g, respectively, they were 4.8 and 4.6 times higher than that achieved by PSA02004 at pH 3.0. By fed-batch fermentation, the resultant SA titer of 76.8 g/L was obtained, which is the highest value that ever achieved from glucose-based medium at low pH, to date. When using mixed food waste (MFW) hydrolysate as substrate, 18.9 g/L SA was produced with an SA yield of 0.38 g/g, which demonstrates the feasibility of using low-cost glucose-based hydrolysate for SA production by Y. lipolytica in a low-pH environment. CONCLUSIONS This study presents an effective and efficient strategy for the evolution of Y. lipolytica for SA production under low-pH condition for the first time. The isFBB was demonstrated to improve the metabolic evolution efficiency of Y. lipolytica to the acidic condition. Moreover, the acetate accumulation was found to be the major reason for the inhibition of SA production at low pH by Y. lipolytica, which suggested the direction for further metabolic modification of the strain for improved SA production. Furthermore, the evolved strain Y. lipolytica PSA3.0 was demonstrated to utilize glucose-rich hydrolysate from MFW for fermentative SA production at low pH. Similarly, Y. lipolytica PSA3.0 is expected to utilize the glucose-rich hydrolysate generated from other carbohydrate-rich waste streams for SA production. This study paves the way for the commercialization of bio-based SA and contributes to the sustainable development of a green economy.
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Affiliation(s)
- Chong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 Guangdong People’s Republic of China
| | - Shi Gao
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaotong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 People’s Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Influence of oxygen availability on the metabolism and morphology of Yarrowia lipolytica: insights into the impact of glucose levels on dimorphism. Appl Microbiol Biotechnol 2017; 101:7317-7333. [DOI: 10.1007/s00253-017-8446-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 10/18/2022]
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Cui Z, Gao C, Li J, Hou J, Lin CSK, Qi Q. Engineering of unconventional yeast Yarrowia lipolytica for efficient succinic acid production from glycerol at low pH. Metab Eng 2017. [PMID: 28627452 DOI: 10.1016/j.ymben.2017.06.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Yarrowia lipolytica is considered as a potential candidate for succinic acid production because of its innate ability to accumulate citric acid cycle intermediates and its tolerance to acidic pH. Previously, a succinate-production strain was obtained through the deletion of succinate dehydrogenase subunit encoding gene Ylsdh5. However, the accumulation of by-product acetate limited further improvement of succinate production. Meanwhile, additional pH adjustment procedure increased the downstream cost in industrial application. In this study, we identified for the first time that acetic acid overflow is caused by CoA-transfer reaction from acetyl-CoA to succinate in mitochondria rather than pyruvate decarboxylation reaction in SDH negative Y. lipolytica. The deletion of CoA-transferase gene Ylach eliminated acetic acid formation and improved succinic acid production and the cell growth. We then analyzed the effect of overexpressing the key enzymes of oxidative TCA, reductive carboxylation and glyoxylate bypass on succinic acid yield and by-products formation. The best strain with phosphoenolpyruvate carboxykinase (ScPCK) from Saccharomyces cerevisiae and endogenous succinyl-CoA synthase beta subunit (YlSCS2) overexpression improved succinic acid titer by 4.3-fold. In fed-batch fermentation, this strain produced 110.7g/L succinic acid with a yield of 0.53g/g glycerol without pH control. This is the highest succinic acid titer achieved at low pH by yeast reported worldwide, to date, using defined media. This study not only revealed the mechanism of acetic acid overflow in SDH negative Y. lipolytica, but it also reported the development of an efficient succinic acid production strain with great industrial prospects.
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Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Cuijuan Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China; School of Life Science, Linyi University, Linyi 276000, China
| | - Jiaojiao Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China.
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Yang X, Wang H, Li C, Lin CSK. Restoring of Glucose Metabolism of Engineered Yarrowia lipolytica for Succinic Acid Production via a Simple and Efficient Adaptive Evolution Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4133-4139. [PMID: 28474529 DOI: 10.1021/acs.jafc.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Succinate dehydrogenase inactivation in Yarrowia lipolytica has been demonstrated for robust succinic acid production, whereas the inefficient glucose metabolism has hindered its practical application. In this study, a simple and efficient adaptive evolution strategy via cell immobilization was conducted in shake flasks, with an aim to restore the glucose metabolism of Y. lipolytica mutant PGC01003. After 21 days with 14 generations evolution, glucose consumption rate increased to 0.30 g/L/h in YPD medium consisting of 150 g/L initial glucose concentration, while poor yeast growth was observed in the same medium using the initial strain without adaptive evolution. Succinic acid productivity of the evolved strain also increased by 2.3-fold, with stable cell growth in YPD medium with high initial glucose concentration. Batch fermentations resulted in final succinic acid concentrations of 65.7 g/L and 87.9 g/L succinic acid using YPD medium and food waste hydrolysate, respectively. The experimental results in this study show that a simple and efficient strategy could facilitate the glucose uptake rate in succinic acid fermentation using glucose-rich substrates.
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Affiliation(s)
- Xiaofeng Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology , Guangzhou 510006, People's Republic of China
- School of Energy and Environment, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
| | - Huaimin Wang
- School of Energy and Environment, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
| | - Chong Li
- School of Energy and Environment, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
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Li C, Yang X, Gao S, Wang H, Lin CSK. High efficiency succinic acid production from glycerol via in situ fibrous bed bioreactor with an engineered Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2017; 225:9-16. [PMID: 27875768 DOI: 10.1016/j.biortech.2016.11.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 05/02/2023]
Abstract
In this study, in situ fibrous bed bioreactor (isFBB) was developed at the first time for efficient succinic acid (SA) production by Yarrowia lipolytica. After optimization, SA titer, productivity and yield of 51.9g/L, 1.46g/L/h and 0.42g/g were obtained respectively via isFBB fermentation under conditions of 750cm2 cotton towel, 120g/L initial glycerol and 3L/min aeration rate. By fed batch strategy, SA titer raised up to 198.2g/L was achieved, which was the highest value ever reported. In operation stability study, SA productivity showed no obvious decrease after 12 repeated batches of 460h fermentation, and cell viability even recovered within two repeated batches after intentional interruption. This study successfully attained a highly efficient and stable isFBB for enhanced SA production by Y. lipolytica.
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Affiliation(s)
- Chong Li
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Xiaofeng Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Shi Gao
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Huaimin Wang
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong.
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Egermeier M, Russmayer H, Sauer M, Marx H. Metabolic Flexibility of Yarrowia lipolytica Growing on Glycerol. Front Microbiol 2017; 8:49. [PMID: 28174563 PMCID: PMC5258708 DOI: 10.3389/fmicb.2017.00049] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/06/2017] [Indexed: 12/24/2022] Open
Abstract
The yeast Yarrowia lipolytica is a fascinating microorganism with an amazing metabolic flexibility. This yeast grows very well on a wide variety of carbon sources from alkanes over lipids, to sugars and glycerol. Y. lipolytica accumulates a wide array of industrially relevant metabolites. It is very tolerant to many environmental factors, above all the pH value. It grows perfectly well over a wide pH range, but it has been described, that the pH has a decisive influence on the metabolite pattern accumulated by this yeast. Here, we set out to characterize the metabolism of different Y. lipolytica strains, isolated from various environments, growing on glycerol at different pH values. The conditions applied for strain characterization are of utmost importance. Shake flask cultures lead to very different results, when compared to controlled conditions in bioreactors regarding pH and aeration. Only one of the tested strains was able to accumulate high amounts of citric acid in shake flask experiments, whereas a group of six strains turned out to accumulate citric acid efficiently under controlled conditions. The present study shows that strains isolated from dairy products predominantly accumulate sugar alcohols at any given pH, when grown on glycerol under nitrogen-limitation.
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Affiliation(s)
- Michael Egermeier
- Christian Doppler-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
- Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
| | - Hannes Russmayer
- Christian Doppler-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
- Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
| | - Michael Sauer
- Christian Doppler-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
- Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
- ACIB GmbH, Austrian Centre of Industrial BiotechnologyVienna, Austria
| | - Hans Marx
- Christian Doppler-Laboratory for Biotechnology of Glycerol, Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
- Department of Biotechnology, BOKU-Vienna Institute of Bio Technology (VIBT), University of Natural Resources and Life SciencesVienna, Austria
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38
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Mirończuk AM, Biegalska A, Dobrowolski A. Functional overexpression of genes involved in erythritol synthesis in the yeast Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:77. [PMID: 28352301 PMCID: PMC5366165 DOI: 10.1186/s13068-017-0772-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Erythritol, a four-carbon polyol synthesized by microorganisms as an osmoprotectant, is a natural sweetener produced on an industrial scale for decades. Despite the fact that the yeast Yarrowia lipolytica has been reported since the 1970s as an erythritol producer, the metabolic pathway of this polyol has never been characterized. It was shown that erythritol synthesis in yeast occurs via the pentose phosphate pathway (PPP). The oleaginous yeast Y. lipolytica is a good host for converting inexpensive glycerol into a value-added product such as erythritol. Glycerol is a renewable feedstock which is produced on a large scale as a waste product by many branches of industry. RESULTS In this study, we functionally overexpressed four genes involved in the pentose phosphate pathway (PPP): gene YALI0E06479g encoding transketolase (TKL1), gene YALI0F15587g encoding transaldolase (TAL1), gene YALI0E22649g encoding glucose-6-phosphate dehydrogenase (ZWF1), and gene YALI0B15598g encoding 6-phosphogluconate dehydrogenase (GND1). Here, we show that the crucial gene for erythritol synthesis in Y. lipolytica is transketolase. Overexpression of this gene results in a twofold improvement in erythritol synthesis during a shake-flask experiment (58 g/L). Moreover, overexpression of TKL1 allows for efficient production of erythritol independently from the supplied dissolved oxygen. Fermentation conducted in a 5-L bioreactor at low agitation results in almost 70% higher titer of erythritol over the control strain. CONCLUSION This work presents the importance of the PPP in erythritol synthesis and the feasibility for economic production of erythritol from glycerol by the yeast Y. lipolytica.
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Affiliation(s)
- Aleksandra M. Mirończuk
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Anna Biegalska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Adam Dobrowolski
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
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Morgunov IG, Kamzolova SV, Dedyukhina EG, Chistyakova TI, Lunina JN, Mironov AA, Stepanova NN, Shemshura ON, Vainshtein MB. Application of organic acids for plant protection against phytopathogens. Appl Microbiol Biotechnol 2016; 101:921-932. [PMID: 28040844 DOI: 10.1007/s00253-016-8067-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022]
Abstract
The basic tendency in the field of plant protection concerns with reducing the use of pesticides and their replacement by environmentally acceptable biological preparations. The most promising approach to plant protection is application of microbial metabolites. In the last years, bactericidal, fungicidal, and nematodocidal activities were revealed for citric, succinic, α-ketoglutaric, palmitoleic, and other organic acids. It was shown that application of carboxylic acids resulted in acceleration of plant development and the yield increase. Of special interest is the use of arachidonic acid in very low concentrations as an inductor (elicitor) of protective functions in plants. The bottleneck in practical applications of these simple, nontoxic, and moderately priced preparations is the absence of industrial production of the mentioned organic acids of required quality since even small contaminations of synthetic preparations decrease their quality and make them dangerous for ecology and toxic for plants, animals, and human. This review gives a general conception on the use of organic acids for plant protection against the most dangerous pathogens and pests, as well as focuses on microbiological processes for production of these microbial metabolites of high quality from available, inexpensive, and renewable substrates.
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Affiliation(s)
- Igor G Morgunov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290. .,Pushchino State Institute of Natural Sciences, Pushchino, Russia, 142290.
| | - Svetlana V Kamzolova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290
| | - Emilia G Dedyukhina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290
| | - Tatiana I Chistyakova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290
| | - Julia N Lunina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290
| | - Alexey A Mironov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290
| | - Nadezda N Stepanova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290.,Pushchino State Institute of Natural Sciences, Pushchino, Russia, 142290
| | - Olga N Shemshura
- Institute of Microbiology and Virology, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan, 050510
| | - Mikhail B Vainshtein
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow region, Russia, 142290.,Pushchino State Institute of Natural Sciences, Pushchino, Russia, 142290
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Pleissner D, Qi Q, Gao C, Rivero CP, Webb C, Lin CSK, Venus J. Valorization of organic residues for the production of added value chemicals: A contribution to the bio-based economy. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.12.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Enhanced succinic acid productivity by expression of mgtCB gene in Escherichia coli mutant. ACTA ACUST UNITED AC 2016; 43:505-16. [DOI: 10.1007/s10295-015-1720-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/10/2015] [Indexed: 01/02/2023]
Abstract
Abstract
In this study, a novel engineering Escherichia coli strain (CBMG111) with the expression of mgtCB gene was constructed for the enhanced fermentative production of succinic acid by utilizing the synergetic effect of mgtC gene to improve the growth of strains at the environment of low Mg2+ concentration and mgtB to enhance the transport of Mg2+ into cells. After the effect of the expression of the individual genes (mgtA, mgtB, mgtC) on the growth of E. coli was clarified, the fermentative production of succinic acid by CBMG111 was studied with the low-price mixture of Mg(OH)2 and NH3·H2O as the alkaline neutralizer and the biomass hydrolysates as the carbon sources, which demonstrated that the expression of mgtCB gene can significantly increase the productivity of succinic acid (2.97 g L−1 h−1) compared with that by using the engineering strain with the overexpression of mgtA gene.
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Gao C, Yang X, Wang H, Rivero CP, Li C, Cui Z, Qi Q, Lin CSK. Robust succinic acid production from crude glycerol using engineered Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:179. [PMID: 27579143 PMCID: PMC5004273 DOI: 10.1186/s13068-016-0597-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/19/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Integrating waste management with fuels and chemical production is considered to address the food waste problem and oil crisis. Approximately, 600 million tonnes crude glycerol is produced from the biodiesel industry annually, which is a top renewable feedstock for succinic acid production. To meet the increasing demand for succinic acid production, the development of more efficient and cost-effective production methods is urgently needed. Herein, we have proposed a new strategy for integration of both biodiesel and SA production in a biorefinery unit by construction of an aerobic yeast Yarrowia lipolytica with a deletion in the gene coding succinate dehydrogenase subunit 5. RESULTS Robust succinic acid production by an engineered yeast Y. lipolytica from crude glycerol without pre-treatment was demonstrated. Diversion of metabolic flow from tricarboxylic acid cycle led to the success in generating a succinic acid producer Y. lipolytica PGC01003. The fermentation media and conditions were optimized, which resulted in 43 g L(-1) succinic acid production from crude glycerol. Using the fed-batch strategy in 2.5 L fermenter, up to 160 g L(-1) SA was yielded, indicating the great industrial potential. CONCLUSIONS Inactivation of SDH5 in Y. lipolytica Po1f led to succinic acid accumulation and secretion significantly. To our best knowledge, this is the highest titer obtained in fermentation on succinic acid production. In addition, the performance of batch and fed-batch fermentation showed high tolerance and yield on biodiesel by-product crude glycerol. All these results indicated that PGC01003 is a promising microbial factorial cell for the highly efficient strategy solving the environmental problem in connection with the production of value-added product.
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Affiliation(s)
- Cuijuan Gao
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
- School of Life Science, Linyi University, Linyi, 276005 People’s Republic of China
| | - Xiaofeng Yang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 People’s Republic of China
| | - Huaimin Wang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Cristina Perez Rivero
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, UK
| | - Chong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering. Appl Microbiol Biotechnol 2015; 99:4559-77. [PMID: 25947247 DOI: 10.1007/s00253-015-6624-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/13/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica has become a recognized system for expression/secretion of heterologous proteins. This non-conventional yeast is currently being developed as a workhorse for biotechnology by several research groups throughout the world, especially for single-cell oil production, whole cell bioconversion and upgrading of industrial wastes. This mini-review presents established tools for protein expression in Y. lipolytica and highlights novel developments in the areas of promoter design, surface display, and host strain or metabolic pathway engineering. An overview of the industrial and commercial biotechnological applications of Y. lipolytica is also presented.
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Zhang T, Ge C, Deng L, Tan T, Wang F. C4-dicarboxylic acid production by overexpressing the reductive TCA pathway. FEMS Microbiol Lett 2015; 362:fnv052. [DOI: 10.1093/femsle/fnv052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2015] [Indexed: 01/30/2023] Open
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