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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.
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Affiliation(s)
- Pieter De Brabander
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Evelien Uitterhaegen
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Karel De Winter
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
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Dynamic Interplay between O2 Availability, Growth Rates, and the Transcriptome of Yarrowia lipolytica. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps Yarrowia lipolytica-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h−1, the largest simulated volume (90 m3) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h−1. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that Y. lipolytica can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for Y. lipolytica-based strain engineering, thereby accelerating bioprocess development.
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Timoumi A, Nguyen TC, Le T, Kraiem H, Cescut J, Anne-Archard D, Gorret N, Molina-Jouve C, To KA, Fillaudeau L. Comparison of methods to explore the morphology and granulometry of biological particles with complex shapes: Interpretation and limitations. POWDER TECHNOL 2022. [DOI: 10.1016/j.powtec.2022.118067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Celińska E. "Fight-flight-or-freeze" - how Yarrowia lipolytica responds to stress at molecular level? Appl Microbiol Biotechnol 2022; 106:3369-3395. [PMID: 35488934 PMCID: PMC9151528 DOI: 10.1007/s00253-022-11934-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Yarrowia lipolytica is a popular yeast species employed in multiple biotechnological production processes. High resistance to extreme environmental conditions or metabolic burden triggered by synthetically forced over-synthesis of a target metabolite has its practical consequences. The proud status of an “industrial workhorse” that Y. lipolytica has gained is directly related to such a quality of this species. With the increasing amount of knowledge coming from detailed functional studies and comprehensive omics analyses, it is now possible to start painting the landscape of the molecular background behind stress response and adaptation in Y. lipolytica. This review summarizes the current state-of-art of a global effort in revealing how Y. lipolytica responds to both environmental threats and the intrinsic burden caused by the overproduction of recombinant secretory proteins at the molecular level. Detailed lists of genes, proteins, molecules, and biological processes deregulated upon exposure to external stress factors or affected by over-synthesis of heterologous proteins are provided. Specificities and universalities of Y. lipolytica cellular response to different extrinsic and intrinsic threats are highlighted. Key points • Y. lipolytica as an industrial workhorse is subjected to multiple stress factors. • Cellular responses together with involved genes, proteins, and molecules are reviewed. • Native stress response mechanisms are studied and inspire engineering strategies.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627, Poznan, Poland.
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Delfau-Bonnet G, Imatoukene N, Clément T, Lopez M, Allais F, Hantson AL. Evaluation of the Potential of Lipid-Extracted Chlorella vulgaris Residue for Yarrowia lipolytica Growth at Different pH Levels. Mar Drugs 2022; 20:md20040264. [PMID: 35447937 PMCID: PMC9024751 DOI: 10.3390/md20040264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Projections show that the cultivation of microalgae will extend to the production of bio-based compounds, such as biofuels, cosmetics, and medicines. This will generate co-products or residues that will need to be valorized to reduce the environmental impact and the cost of the process. This study explored the ability of lipid-extracted Chlorella vulgaris residue as a sole carbon and nitrogen source for growing oleaginous yeasts without any pretreatment. Both wild-type Yarrowia lipolytica W29 and mutant JMY3501 (which was designed to accumulate more lipids without their remobilization or degradation) showed a similar growth rate of 0.28 h−1 at different pH levels (3.5, 5.5, and 7.5). However, the W29 cell growth had the best cell number on microalgal residue at a pH of 7.5, while three times fewer cells were produced at all pH levels when JMY3501 was grown on microalgal residue. The JMY3501 growth curves were similar at pH 3.5, 5.5, and 7.5, while the fatty-acid composition differed significantly, with an accumulation of α-linolenic acid on microalgal residue at a pH of 7.5. Our results demonstrate the potential valorization of Chlorella vulgaris residue for Yarrowia lipolytica growth and the positive effect of a pH of 7.5 on the fatty acid profile.
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Affiliation(s)
- Guillaume Delfau-Bonnet
- Chemical and Biochemical Process Engineering Unit, Faculty of Engineering, University of Mons, 7000 Mons, Belgium;
- Unite Recherche et Developpement Agro-Biotechnologies Industrielles (URD ABI), Centre Europeen de Biotechnologie et Bieconomie (CEBB), AgroParisTech, 51110 Pomacle, France; (N.I.); (T.C.); (M.L.); (F.A.)
| | - Nabila Imatoukene
- Unite Recherche et Developpement Agro-Biotechnologies Industrielles (URD ABI), Centre Europeen de Biotechnologie et Bieconomie (CEBB), AgroParisTech, 51110 Pomacle, France; (N.I.); (T.C.); (M.L.); (F.A.)
| | - Tiphaine Clément
- Unite Recherche et Developpement Agro-Biotechnologies Industrielles (URD ABI), Centre Europeen de Biotechnologie et Bieconomie (CEBB), AgroParisTech, 51110 Pomacle, France; (N.I.); (T.C.); (M.L.); (F.A.)
| | - Michel Lopez
- Unite Recherche et Developpement Agro-Biotechnologies Industrielles (URD ABI), Centre Europeen de Biotechnologie et Bieconomie (CEBB), AgroParisTech, 51110 Pomacle, France; (N.I.); (T.C.); (M.L.); (F.A.)
| | - Florent Allais
- Unite Recherche et Developpement Agro-Biotechnologies Industrielles (URD ABI), Centre Europeen de Biotechnologie et Bieconomie (CEBB), AgroParisTech, 51110 Pomacle, France; (N.I.); (T.C.); (M.L.); (F.A.)
| | - Anne-Lise Hantson
- Chemical and Biochemical Process Engineering Unit, Faculty of Engineering, University of Mons, 7000 Mons, Belgium;
- Correspondence: ; Tel.: +32-65374419
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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: 3.0] [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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7
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Solid-state fermentation enhances inulinase and invertase production by Aspergillus brasiliensis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
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Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
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9
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Lesage J, Timoumi A, Cenard S, Lombard E, Lee HLT, Guillouet SE, Gorret N. Accelerostat study in conventional and microfluidic bioreactors to assess the key role of residual glucose in the dimorphic transition of Yarrowia lipolytica in response to environmental stimuli. N Biotechnol 2021; 64:37-45. [PMID: 34058397 DOI: 10.1016/j.nbt.2021.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 11/19/2022]
Abstract
Yarrowia lipolytica, with a diverse array of biotechnological applications, is able to grow as ovoid yeasts or filamentous hyphae depending on environmental conditions. This study has explored the relationship between residual glucose levels and dimorphism in Y. lipolytica. Under pH stress conditions, the morphological and physiological characteristics of the yeast were examined during well-controlled accelerostat cultures using both a 1 L-laboratory scale and a 1 mL-microfluidic bioreactor. The accelerostat mode, via a smooth increase of dilution rate (D), enabled the cell growth rate to increase gradually up to the cell wash-out (D ≥μmax of the strain), which was accompanied by a progressive increase in residual glucose concentration. The results showed that Y. lipolytica maintained an ovoid morphology when residual glucose concentration was below a threshold value of around 0.35-0.37 mg L-1. Transitions towards more elongated forms were triggered at this threshold and progressively intensified with the increase in residual glucose levels. The effect of cAMP on the dimorphic transition was assessed by the exogenous addition of cAMP and the quantification of its intracellular levels during the accelerostat. cAMP has been reported to be an important mediator of environmental stimuli that inhibit filamentous growth in Y. lipolytica by activating the cAMP-PKA regulatory pathway. It was confirmed that the exogenous addition of cAMP inhibited the mycelial morphology of Y. lipolytica, even with glucose concentrations exceeding the threshold level. The results suggest that dimorphic responses in Y. lipolytica are regulated by sugar signaling pathways, most likely via the cAMP-PKA dependent pathway.
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Affiliation(s)
- Julie Lesage
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France
| | - Asma Timoumi
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France
| | - Stéphanie Cenard
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France
| | - Eric Lombard
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France
| | - Harry L T Lee
- Erbi Bio, Inc, 325 New Boston Stress, Unit 6, Woburn, MA, 01801, USA
| | - Stéphane E Guillouet
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France
| | - Nathalie Gorret
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil. 35077, Toulouse Cedex, France.
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Oleaginous Yeasts as Cell Factories for the Sustainable Production of Microbial Lipids by the Valorization of Agri-Food Wastes. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020050] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The agri-food industry annually produces huge amounts of crops residues and wastes, the suitable management of these products is important to increase the sustainability of agro-industrial production by optimizing the entire value chain. This is also in line with the driving principles of the circular economy, according to which residues can become feedstocks for novel processes. Oleaginous yeasts represent a versatile tool to produce biobased chemicals and intermediates. They are flexible microbial factories able to grow on different side-stream carbon sources such as those deriving from agri-food wastes, and this characteristic makes them excellent candidates for integrated biorefinery processes through the production of microbial lipids, known as single cell oils (SCOs), for different applications. This review aims to present an extensive overview of research progress on the production and use of oleaginous yeasts and present discussions on the current bottlenecks and perspectives of their exploitation in different sectors, such as foods, biofuels and fine chemicals.
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Carsanba E, Papanikolaou S, Fickers P, Erten H. Lipids by Yarrowia lipolytica Strains Cultivated on Glucose in Batch Cultures. Microorganisms 2020; 8:microorganisms8071054. [PMID: 32679918 PMCID: PMC7409262 DOI: 10.3390/microorganisms8071054] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Oleaginous microorganisms, such as Yarrowia lipolytica, accumulate lipids that can have interesting applications in food biotechnology or the synthesis of biodiesel. Y. lipolytica yeast can have many advantages such as wide substrate range usage and robustness to extreme conditions, while under several culture conditions it can produce high lipid productivity. Based on this assumption, in this study, 12 different Yarrowia lipolytica strains were used to investigate microbial lipid production using a glucose-based medium under nitrogen-limited conditions in shake-flask cultivations. Twelve wild-type or mutant strains of Yarrowia lipolytica which were newly isolated or belonged to official culture collections were tested, and moderate lipid quantities (up to 1.30 g/L) were produced; in many instances, nitrogen limitation led to citric acid production in the medium. Lipids were mainly composed of C16 and C18 fatty acids. Most of the fatty acids of the microbial lipid were unsaturated and corresponded mainly to oleic, palmitic and linoleic acids. Linolenic acid (C18:3) was produced in significant quantities (between 10% and 20%, wt/wt of dry cell weight (DCW)) by strains H917 and Po1dL.
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Affiliation(s)
- Erdem Carsanba
- Food Engineering Department, Faculty of Agriculture, Cukurova University, 01330 Adana, Turkey; or
- Amyris Bioproducts Portugal, Unipessoal, Lda, 4169-005 Porto, Portugal
| | - Seraphim Papanikolaou
- Department of Food Science& Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège-Gembloux Agro-Bio Tech, B-5030 Gembloux, Belgium;
| | - Huseyin Erten
- Food Engineering Department, Faculty of Agriculture, Cukurova University, 01330 Adana, Turkey; or
- Correspondence:
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12
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Cell Factories for Industrial Production Processes: Current Issues and Emerging Solutions. Processes (Basel) 2020. [DOI: 10.3390/pr8070768] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Despite all the progresses made by metabolic engineering, still only a few biotechnological processes are running at an industrial level. In order to boost the biotechnological sector, integration strategies as well as long-term views are needed. The aim of the present review is to identify the main drawbacks in biotechnological processes, and to propose possible solutions to overcome the issues in question. Novel cell factories and bioreactor design are discussed as possible solutions. In particular, the following microorganisms: Yarrowia lipolytica, Trichosporon oleaginosus, Ustilago cynodontis, Debaryomyces hansenii along with sequential bioreactor configurations are presented as possible cell factories and bioreactor design solutions, respectively.
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13
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Gorczyca M, Kaźmierczak J, Steels S, Fickers P, Celińska E. Impact of oxygen availability on heterologous geneexpression and polypeptide secretion dynamics in Yarrowia lipolytica-based protein production platforms. Yeast 2020; 37:559-568. [PMID: 32445214 DOI: 10.1002/yea.3499] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/04/2020] [Accepted: 05/14/2020] [Indexed: 11/09/2022] Open
Abstract
Industrially relevant traits of Yarrowia lipolytica, like high growth rate, capacity to grow at high cell density or to synthesize biomolecules with high productivities, strongly rely on sufficient oxygen provision. Although the impact of oxygen availability (OA) on the physiology of Y. lipolytica has been already studied, its influence on recombinant protein (rProt) synthesis and secretion has been largely neglected to date. With the aim to fill this gap, a fluorescent reporter protein (yellow fluorescent protein [YFP]) was used herein as a proxy to follow simultaneously rProt synthesis and secretion in Y. lipolytica under different OAs. This study covers the analysis of the reporter gene expression through reverse transcription quantitative polymerase chain reaction, polypeptide synthesis and its retention-to-secretion ratio using flow cytometry and fluorymetry during shake flasks and bioreactor cultivations under different OA. The results gathered demonstrate that OA has a dramatic impact on the kinetics of intracellular and extracellular YFP accumulation. Higher rProt production and secretion were favoured under high OA, and were largely related to OA and not to cell growth. Our observations also suggest the existence of some upper limit of secretory protein accumulation inside the cells above which massive secretion is initiated. Moreover, at low OA, the first bottleneck in rProt synthesis occurs as early as at transcription level, which could results from a lower availability of transcriptional machinery elements. Finally, using flow cytometry and bioreactor cultivations, we highlighted that ovoid cells are generally more efficient in terms of rProt synthesis.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, Poznań, 60-627, Poland
| | - Jan Kaźmierczak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, Poznań, 60-627, Poland
| | - Sebastien Steels
- TERRA Teaching and Research Centre, Microbial Process and Interaction, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Process and Interaction, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, Poznań, 60-627, Poland
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14
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Comparison and Analysis of Published Genome-scale Metabolic Models of Yarrowia lipolytica. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0208-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Wang Y, Tang LJ, Peng X, Zhang ZB, Yang HL, Yan RM, Zhu D. Transcriptome analysis of the dimorphic transition induced by pH change and lipid biosynthesis in Trichosporon cutaneum. J Ind Microbiol Biotechnol 2019; 47:49-61. [PMID: 31834585 DOI: 10.1007/s10295-019-02244-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/26/2019] [Indexed: 11/27/2022]
Abstract
Trichosporon cutaneum, a dimorphic oleaginous yeast, has immense biotechnological potential, which can use lignocellulose hydrolysates to accumulate lipids. Our preliminary studies on its dimorphic transition suggested that pH can significantly induce its morphogenesis. However, researches on dimorphic transition correlating with lipid biosynthesis in oleaginous yeasts are still limited. In this study, the unicellular yeast cells induced under pH 6.0-7.0 shake flask cultures resulted in 54.32% lipid content and 21.75 g/L dry cell weight (DCW), so lipid production was over threefold than that in hypha cells induced by acidic condition (pH 3.0-4.0). Furthermore, in bioreactor batch cultivation, the DCW and lipid content in unicellular yeast cells can reach 21.94 g/L and 58.72%, respectively, both of which were also more than twofold than that in hypha cells. Moreover, the activities of isocitrate dehydrogenase (IDH), malic enzyme (MAE), isocitrate lyase (ICL) and ATP citrate lyase (ACL) in unicellular cells were all higher than in the hyphal cells. In the meanwhile, the transcriptome data showed that the genes related to fatty acid biosynthesis, carbon metabolism and encoded Rim101 and cAMP-PKA signaling transduction pathways were significantly up-regulated in unicellular cells, which may play an important role in enhancing the lipid accumulation. In conclusion, our results provided insightful information focused on the molecular mechanism of dimorphic transition and process optimization for enhancing lipid accumulation in T. cutaneum.
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Affiliation(s)
- Ya Wang
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
- State Key Laboratory of Microbial Metabolism & School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China
| | - Li Juan Tang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China
| | - Xuan Peng
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhi Bin Zhang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China
| | - Hui Lin Yang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China
| | - Ri Ming Yan
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China
| | - Du Zhu
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China.
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Vandermies M, Fickers P. Bioreactor-Scale Strategies for the Production of Recombinant Protein in the Yeast Yarrowia lipolytica. Microorganisms 2019; 7:E40. [PMID: 30704141 PMCID: PMC6406515 DOI: 10.3390/microorganisms7020040] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 01/02/2023] Open
Abstract
Recombinant protein production represents a multibillion-dollar market. Therefore, it constitutes an important research field both in academia and industry. The use of yeast as a cell factory presents several advantages such as ease of genetic manipulation, growth at high cell density, and the possibility of post-translational modifications. Yarrowia lipolytica is considered as one of the most attractive hosts due to its ability to metabolize raw substrate, to express genes at a high level, and to secrete protein in large amounts. In recent years, several reviews have been dedicated to genetic tools developed for this purpose. Though the construction of efficient cell factories for recombinant protein synthesis is important, the development of an efficient process for recombinant protein production in a bioreactor constitutes an equally vital aspect. Indeed, a sports car cannot drive fast on a gravel road. The aim of this review is to provide a comprehensive snapshot of process tools to consider for recombinant protein production in bioreactor using Y. lipolytica as a cell factory, in order to facilitate the decision-making for future strain and process engineering.
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Affiliation(s)
- Marie Vandermies
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, University of Liège⁻Gembloux AgroBio Tech, 5030 Gembloux, Belgium.
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, University of Liège⁻Gembloux AgroBio Tech, 5030 Gembloux, Belgium.
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17
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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: 109] [Impact Index Per Article: 18.2] [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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18
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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: 0.8] [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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19
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Carsanba E, Papanikolaou S, Erten H. Production of oils and fats by oleaginous microorganisms with an emphasis given to the potential of the nonconventional yeast Yarrowia lipolytica. Crit Rev Biotechnol 2018; 38:1230-1243. [DOI: 10.1080/07388551.2018.1472065] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- E. Carsanba
- Cukurova University, Faculty of Agriculture, Food Engineering Department, Adana, Turkey
- Mustafa Kemal University, Altınozu Agricultural Sciences Vocational School, Hatay, Turkey
| | - S. Papanikolaou
- Agricultural University of Athens, Department of Food Science and Human Nutrition, Athens, Greece
| | - H. Erten
- Cukurova University, Faculty of Agriculture, Food Engineering Department, Adana, Turkey
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20
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Timoumi A, Guillouet SE, Molina-Jouve C, Fillaudeau L, Gorret N. Impacts of environmental conditions on product formation and morphology of Yarrowia lipolytica. Appl Microbiol Biotechnol 2018. [DOI: 10.1007/s00253-018-8870-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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21
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Cavallo E, Charreau H, Cerrutti P, Foresti ML. Yarrowia lipolytica: a model yeast for citric acid production. FEMS Yeast Res 2017; 17:4587737. [DOI: 10.1093/femsyr/fox084] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/01/2017] [Indexed: 11/12/2022] Open
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22
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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: 1.4] [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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