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Qin J, Kurt E, LBassi T, Sa L, Xie D. Biotechnological production of omega-3 fatty acids: current status and future perspectives. Front Microbiol 2023; 14:1280296. [PMID: 38029217 PMCID: PMC10662050 DOI: 10.3389/fmicb.2023.1280296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body's inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.
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Affiliation(s)
| | | | | | | | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
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2
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Yin W, Wang X, Liao Y, Ma L, Qiao J, Liu H, Song X, Liu Y. Encapsulating IM7-Displaying Yeast Cells in Calcium Alginate Beads for One-Step Protein Purification and Multienzyme Biocatalysis. Front Bioeng Biotechnol 2022; 10:849542. [PMID: 35372292 PMCID: PMC8969745 DOI: 10.3389/fbioe.2022.849542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
There are several commercial chromatographic systems for protein purification; however, development of cost-effective 3H-grade (high yield, high purity, and high activity) purification approaches is highly demanded. Here, we establish a methodology for encapsulating the IM7-displaying yeast cells in calcium alginate beads. Taking advantage of this biomaterial-based affinity chromatography, rapid and cost-effective purification of proteins with over 90% purity in a single step is achieved. Moreover, our system enables coating the multienzyme complex to produce reusable immobilized cells for efficient cascade biotransformation. Together, the present method has great application potentials not only in the laboratory but also in the industry for production of protein products as well as biocatalysis.
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Affiliation(s)
- Wenhao Yin
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Henan, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Ying Liao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Jie Qiao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Henan, China
- *Correspondence: Jie Qiao, ; Xin Song, ; Hui Liu, ; Yi Liu,
| | - Hui Liu
- Department of Hematology, Renmin Hospital of Wuhan University, Hubei, China
- *Correspondence: Jie Qiao, ; Xin Song, ; Hui Liu, ; Yi Liu,
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Henan, China
- *Correspondence: Jie Qiao, ; Xin Song, ; Hui Liu, ; Yi Liu,
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- BravoVax Co., Ltd., Hubei, China
- *Correspondence: Jie Qiao, ; Xin Song, ; Hui Liu, ; Yi Liu,
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3
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Wei H, Wang W, Knoshaug EP, Chen X, Van Wychen S, Bomble YJ, Himmel ME, Zhang M. Disruption of the Snf1 Gene Enhances Cell Growth and Reduces the Metabolic Burden in Cellulase-Expressing and Lipid-Accumulating Yarrowia lipolytica. Front Microbiol 2022; 12:757741. [PMID: 35003001 PMCID: PMC8733397 DOI: 10.3389/fmicb.2021.757741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/19/2021] [Indexed: 12/01/2022] Open
Abstract
Yarrowia lipolytica is known to be capable of metabolizing glucose and accumulating lipids intracellularly; however, it lacks the cellulolytic enzymes needed to break down cellulosic biomass directly. To develop Y. lipolytica as a consolidated bioprocessing (CBP) microorganism, we previously expressed the heterologous CBH I, CBH II, and EG II cellulase enzymes both individually and collectively in this microorganism. We concluded that the coexpression of these cellulases resulted in a metabolic drain on the host cells leading to reduced cell growth and lipid accumulation. The current study aims to build a new cellulase coexpressing platform to overcome these hinderances by (1) knocking out the sucrose non-fermenting 1 (Snf1) gene that represses the energetically expensive lipid and protein biosynthesis processes, and (2) knocking in the cellulase cassette fused with the recyclable selection marker URA3 gene in the background of a lipid-accumulating Y. lipolytica strain overexpressing ATP citrate lyase (ACL) and diacylglycerol acyltransferase 1 (DGA1) genes. We have achieved a homologous recombination insertion rate of 58% for integrating the cellulases-URA3 construct at the disrupted Snf1 site in the genome of host cells. Importantly, we observed that the disruption of the Snf1 gene promoted cell growth and lipid accumulation and lowered the cellular saturated fatty acid level and the saturated to unsaturated fatty acid ratio significantly in the transformant YL163t that coexpresses cellulases. The result suggests a lower endoplasmic reticulum stress in YL163t, in comparison with its parent strain Po1g ACL-DGA1. Furthermore, transformant YL163t increased in vitro cellulolytic activity by 30%, whereas the “total in vivo newly formed FAME (fatty acid methyl esters)” increased by 16% in comparison with a random integrative cellulase-expressing Y. lipolytica mutant in the same YNB-Avicel medium. The Snf1 disruption platform demonstrated in this study provides a potent tool for the further development of Y. lipolytica as a robust host for the expression of cellulases and other commercially important proteins.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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4
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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5
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Larroude M, Nicaud J, Rossignol T. Yarrowia lipolytica chassis strains engineered to produce aromatic amino acids via the shikimate pathway. Microb Biotechnol 2021; 14:2420-2434. [PMID: 33438818 PMCID: PMC8601196 DOI: 10.1111/1751-7915.13745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
Yarrowia lipolytica is widely used as a microbial producer of lipids and lipid derivatives. Here, we exploited this yeast's potential to generate aromatic amino acids by developing chassis strains optimized for the production of phenylalanine, tyrosine and tryptophan. We engineered the shikimate pathway to overexpress a combination of Y. lipolytica and heterologous feedback-insensitive enzyme variants. Our best chassis strain displayed high levels of de novo Ehrlich metabolite production (up to 0.14 g l-1 in minimal growth medium), which represented a 93-fold increase compared to the wild-type strain (0.0015 g l-1 ). Production was further boosted to 0.48 g l-1 when glycerol, a low-cost carbon source, was used, concomitantly to high secretion of phenylalanine precursor (1 g l-1 ). Among these metabolites, 2-phenylethanol is of particular interest due to its rose-like flavour. We also established a production pathway for generating protodeoxyviolaceinic acid, a dye derived from tryptophan, in a chassis strain optimized for chorismate, the precursor of tryptophan. We have thus demonstrated that Y. lipolytica can serve as a platform for the sustainable de novo bio-production of high-value aromatic compounds, and we have greatly improved our understanding of the potential feedback-based regulation of the shikimate pathway in this yeast.
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Affiliation(s)
- Macarena Larroude
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
| | - Jean‐Marc Nicaud
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
| | - Tristan Rossignol
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
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Chattopadhyay A, Maiti MK. Lipid production by oleaginous yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2021; 116:1-98. [PMID: 34353502 DOI: 10.1016/bs.aambs.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbial lipid production has been studied extensively for years; however, lipid metabolic engineering in many of the extraordinarily high lipid-accumulating yeasts was impeded by inadequate understanding of the metabolic pathways including regulatory mechanisms defining their oleaginicity and the limited genetic tools available. The aim of this review is to highlight the prominent oleaginous yeast genera, emphasizing their oleaginous characteristics, in conjunction with diverse other features such as cheap carbon source utilization, withstanding the effect of inhibitory compounds, commercially favorable fatty acid composition-all supporting their future development as economically viable lipid feedstock. The unique aspects of metabolism attributing to their oleaginicity are accentuated in the pretext of outlining the various strategies successfully implemented to improve the production of lipid and lipid-derived metabolites. A large number of in silico data generated on the lipid accumulation in certain oleaginous yeasts have been carefully curated, as suggestive evidences in line with the exceptional oleaginicity of these organisms. The different genetic elements developed in these yeasts to execute such strategies have been scrupulously inspected, underlining the major types of newly-found and synthetically constructed promoters, transcription terminators, and selection markers. Additionally, there is a plethora of advanced genetic toolboxes and techniques described, which have been successfully used in oleaginous yeasts in the recent years, promoting homologous recombination, genome editing, DNA assembly, and transformation at remarkable efficiencies. They can accelerate and effectively guide the rational designing of system-wide metabolic engineering approaches pinpointing the key targets for developing industrially suitable yeast strains.
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Affiliation(s)
- Atrayee Chattopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
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7
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Celińska E, Nicaud JM, Białas W. Hydrolytic secretome engineering in Yarrowia lipolytica for consolidated bioprocessing on polysaccharide resources: review on starch, cellulose, xylan, and inulin. Appl Microbiol Biotechnol 2021; 105:975-989. [PMID: 33447867 PMCID: PMC7843476 DOI: 10.1007/s00253-021-11097-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 10/25/2022]
Abstract
Consolidated bioprocessing (CBP) featuring concomitant hydrolysis of renewable substrates and microbial conversion into value-added biomolecules is considered to bring substantial benefits to the overall process efficiency. The biggest challenge in developing an economically feasible CBP process is identification of bifunctional biocatalyst merging the ability to utilize the substrate and convert it to value-added product with high efficiency. Yarrowia lipolytica is known for its exceptional performance in hydrophobic substrates assimilation and storage. On the other hand, its capacity to grow on plant-derived biomass is strongly limited. Still, its high potential to simultaneously overproduce several secretory proteins makes Y. lipolytica a platform of choice for expanding its substrate range to complex polysaccharides by engineering its hydrolytic secretome. This review provides an overview of different genetic engineering strategies advancing development of Y. lipolytica strains able to grow on the following four complex polysaccharides: starch, cellulose, xylan, and inulin. Much attention has been paid to genome mining studies uncovering native potential of this species to assimilate untypical sugars, as in many cases it turns out that dormant pathways are present in Y. lipolytica's genome. In addition, the magnitude of the economic gain by CBP processing is here discussed and supported with adequate calculations based on simulated process models. KEY POINTS: • The mini-review updates the knowledge on polysaccharide-utilizing Yarrowia lipolytica. • Insight into molecular bases founding new biochemical qualities is provided. • Model industrial processes were simulated and the associated costs were calculated.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Jean-Marc Nicaud
- Micalis Institute, INRAE-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Domaine de Vilvert, 78352, Jouy-en-Josas, France
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
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8
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Alahuhta M, Xu Q, Knoshaug EP, Wang W, Wei H, Amore A, Baker JO, Vander Wall T, Himmel ME, Zhang M. Chimeric cellobiohydrolase I expression, activity, and biochemical properties in three oleaginous yeast. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:6. [PMID: 33407766 PMCID: PMC7789491 DOI: 10.1186/s13068-020-01856-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/10/2020] [Indexed: 05/16/2023]
Abstract
Consolidated bioprocessing using oleaginous yeast is a promising modality for the economic conversion of plant biomass to fuels and chemicals. However, yeast are not known to produce effective biomass degrading enzymes naturally and this trait is essential for efficient consolidated bioprocessing. We expressed a chimeric cellobiohydrolase I gene in three different oleaginous, industrially relevant yeast: Yarrowia lipolytica, Lipomyces starkeyi, and Saccharomyces cerevisiae to study the biochemical and catalytic properties and biomass deconstruction potential of these recombinant enzymes. Our results showed differences in glycosylation, surface charge, thermal and proteolytic stability, and efficacy of biomass digestion. L. starkeyi was shown to be an inferior active cellulase producer compared to both the Y. lipolytica and S. cerevisiae enzymes, whereas the cellulase expressed in S. cerevisiae displayed the lowest activity against dilute-acid-pretreated corn stover. Comparatively, the chimeric cellobiohydrolase I enzyme expressed in Y. lipolytica was found to have a lower extent of glycosylation, better protease stability, and higher activity against dilute-acid-pretreated corn stover.
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Affiliation(s)
- Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Antonella Amore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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9
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Dong C, Qiao J, Wang X, Sun W, Chen L, Li S, Wu K, Ma L, Liu Y. Engineering Pichia pastoris with surface-display minicellulosomes for carboxymethyl cellulose hydrolysis and ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:108. [PMID: 32549912 PMCID: PMC7296672 DOI: 10.1186/s13068-020-01749-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUNDS Engineering yeast as a consolidated bioprocessing (CBP) microorganism by surface assembly of cellulosomes has been aggressively utilized for cellulosic ethanol production. However, most of the previous studies focused on Saccharomyces cerevisiae, achieving efficient conversion of phosphoric acid-swollen cellulose (PASC) or microcrystalline cellulose (Avicel) but not carboxymethyl cellulose (CMC) to ethanol, with an average titer below 2 g/L. RESULTS Harnessing an ultra-high-affinity IM7/CL7 protein pair, here we describe a method to engineer Pichia pastoris with minicellulosomes by in vitro assembly of three recombinant cellulases including an endoglucanase (EG), an exoglucanase (CBH) and a β-glucosidase (BGL), as well as a carbohydrate-binding module (CBM) on the cell surface. For the first time, the engineered yeasts enable efficient and direct conversion of CMC to bioethanol, observing an impressive ethanol titer of 5.1 g/L. CONCLUSIONS The research promotes the application of P. pastoris as a CBP cell factory in cellulosic ethanol production and provides a promising platform for screening the cellulases from different species to construct surface-assembly celluosome.
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Affiliation(s)
- Ce Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Jie Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Wenli Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Lixia Chen
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Shuntang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Ke Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- BravoVax Co., Ltd., Wuhan, 430000 Hubei China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
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Engineering of industrially important microorganisms for assimilation of cellulosic biomass: towards consolidated bioprocessing. Biochem Soc Trans 2020; 47:1781-1794. [PMID: 31845725 DOI: 10.1042/bst20190293] [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: 08/02/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 01/01/2023]
Abstract
Conversion of cellulosic biomass (non-edible plant material) to products such as chemical feedstocks and liquid fuels is a major goal of industrial biotechnology and an essential component of plans to move from an economy based on fossil carbon to one based on renewable materials. Many microorganisms can effectively degrade cellulosic biomass, but attempts to engineer this ability into industrially useful strains have met with limited success, suggesting an incomplete understanding of the process. The recent discovery and continuing study of enzymes involved in oxidative depolymerisation, as well as more detailed study of natural cellulose degradation processes, may offer a way forward.
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11
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Ganesan V, Spagnuolo M, Agrawal A, Smith S, Gao D, Blenner M. Advances and opportunities in gene editing and gene regulation technology for Yarrowia lipolytica. Microb Cell Fact 2019; 18:208. [PMID: 31783869 PMCID: PMC6884833 DOI: 10.1186/s12934-019-1259-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/25/2019] [Indexed: 12/18/2022] Open
Abstract
Yarrowia lipolytica has emerged as a biomanufacturing platform for a variety of industrial applications. It has been demonstrated to be a robust cell factory for the production of renewable chemicals and enzymes for fuel, feed, oleochemical, nutraceutical and pharmaceutical applications. Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR-Cas9, transposons, and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica. In this review we summarize the work to develop these tools and their demonstrated uses in engineering Y. lipolytica, discuss important subtleties and challenges to using these tools, and give our perspective on important gaps in gene/genome editing tools in Y. lipolytica.
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Affiliation(s)
- Vijaydev Ganesan
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Michael Spagnuolo
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Ayushi Agrawal
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Spencer Smith
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Difeng Gao
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC 29634 USA
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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Wei H, Wang W, Alper HS, Xu Q, Knoshaug EP, Van Wychen S, Lin CY, Luo Y, Decker SR, Himmel ME, Zhang M. Ameliorating the Metabolic Burden of the Co-expression of Secreted Fungal Cellulases in a High Lipid-Accumulating Yarrowia lipolytica Strain by Medium C/N Ratio and a Chemical Chaperone. Front Microbiol 2019; 9:3276. [PMID: 30687267 PMCID: PMC6333634 DOI: 10.3389/fmicb.2018.03276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Yarrowia lipolytica, known to accumulate lipids intracellularly, lacks the cellulolytic enzymes needed to break down solid biomass directly. This study aimed to evaluate the potential metabolic burden of expressing core cellulolytic enzymes in an engineered high lipid-accumulating strain of Y. lipolytica. Three fungal cellulases, Talaromyces emersonii-Trichoderma reesei chimeric cellobiohydrolase I (chimeric-CBH I), T. reesei cellobiohydrolase II (CBH II), and T. reesei endoglucanase II (EG II) were expressed using three constitutive strong promoters as a single integrative expression block in a recently engineered lipid hyper-accumulating strain of Y. lipolytica (HA1). In yeast extract-peptone-dextrose (YPD) medium, the resulting cellulase co-expressing transformant YL165-1 had the chimeric-CBH I, CBH II, and EG II secretion titers being 26, 17, and 132 mg L-1, respectively. Cellulase co-expression in YL165-1 in culture media with a moderate C/N ratio of ∼4.5 unexpectedly resulted in a nearly two-fold reduction in cellular lipid accumulation compared to the parental control strain, a sign of cellular metabolic drain. Such metabolic drain was ameliorated when grown in media with a high C/N ratio of 59 having a higher glucose utilization rate that led to approximately twofold more cell mass and threefold more lipid production per liter culture compared to parental control strain, suggesting cross-talk between cellulase and lipid production, both of which involve the endoplasmic reticulum (ER). Most importantly, we found that the chemical chaperone, trimethylamine N-oxide dihydride increased glucose utilization, cell mass and total lipid titer in the transformants, suggesting further amelioration of the metabolic drain. This is the first study examining lipid production in cellulase-expressing Y. lipolytica strains under various C/N ratio media and with a chemical chaperone highlighting the metabolic complexity for developing robust, cellulolytic and lipogenic yeast strains.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yonghua Luo
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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14
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Xu Q, Alahuhta M, Wei H, Knoshaug EP, Wang W, Baker JO, Vander Wall T, Himmel ME, Zhang M. Expression of an endoglucanase-cellobiohydrolase fusion protein in Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:322. [PMID: 30524504 PMCID: PMC6278004 DOI: 10.1186/s13068-018-1301-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 05/28/2023]
Abstract
The low secretion levels of cellobiohydrolase I (CBHI) in yeasts are one of the key barriers preventing yeast from directly degrading and utilizing lignocellulose. To overcome this obstacle, we have explored the approach of genetically linking an easily secreted protein to CBHI, with CBHI being the last to be folded. The Trichoderma reesei eg2 (TrEGII) gene was selected as the leading gene due to its previously demonstrated outstanding secretion in yeast. To comprehensively characterize the effects of this fusion protein, we tested this hypothesis in three industrially relevant yeasts: Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. Our initial assays with the L. starkeyi secretome expressing differing TrEGII domains fused to a chimeric Talaromyces emersonii-T. reesei CBHI (TeTrCBHI) showed that the complete TrEGII enzyme, including the glycoside hydrolase (GH) 5 domain is required for increased expression level of the fusion protein when linked to CBHI. We found that this new construct (TrEGII-TeTrCBHI, Fusion 3) had an increased secretion level of at least threefold in L. starkeyi compared to the expression level of the chimeric TeTrCBHI. However, the same improvements were not observed when Fusion 3 construct was expressed in S. cerevisiae and Y. lipolytica. Digestion of pretreated corn stover with the secretomes of Y. lipolytica and L. starkeyi showed that conversion was much better using Y. lipolytica secretomes (50% versus 29%, respectively). In Y. lipolytica, TeTrCBHI performed better than the fusion construct. Furthermore, S. cerevisiae expression of Fusion 3 construct was poor and only minimal activity was observed when acting on the substrate, pNP-cellobiose. No activity was observed for the pNP-lactose substrate. Clearly, this approach is not universally applicable to all yeasts, but works in specific cases. With purified protein and soluble substrates, the exoglucanase activity of the GH7 domain embedded in the Fusion 3 construct in L. starkeyi was significantly higher than that of the GH7 domain in TeTrCBHI expressed alone. It is probable that a higher fraction of fusion construct CBHI is in an active form in Fusion 3 compared to just TeTrCBHI. We conclude that the strategy of leading TeTrCBHI expression with a linked TrEGII module significantly improved the expression of active CBHI in L. starkeyi.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Eric P. Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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15
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Pi HW, Anandharaj M, Kao YY, Lin YJ, Chang JJ, Li WH. Engineering the oleaginous red yeast Rhodotorula glutinis for simultaneous β-carotene and cellulase production. Sci Rep 2018; 8:10850. [PMID: 30022171 PMCID: PMC6052021 DOI: 10.1038/s41598-018-29194-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/22/2018] [Indexed: 02/05/2023] Open
Abstract
Rhodotorula glutinis, an oleaginous red yeast, intrinsically produces several bio-products (i.e., lipids, carotenoids and enzymes) and is regarded as a potential host for biorefinery. In view of the limited available genetic engineering tools for this yeast, we have developed a useful genetic transformation method and transformed the β-carotene biosynthesis genes (crtI, crtE, crtYB and tHMG1) and cellulase genes (CBHI, CBHII, EgI, EgIII, EglA and BGS) into R. glutinis genome. The transformant P4-10-9-63Y-14B produced significantly higher β-carotene (27.13 ± 0.66 mg/g) than the wild type and also exhibited cellulase activity. Furthermore, the lipid production and salt tolerance ability of the transformants were unaffected. This is the first study to engineer the R. glutinis for simultaneous β-carotene and cellulase production. As R. glutinis can grow in sea water and can be engineered to utilize the cheaper substrates (i.e. biomass) for the production of biofuels or valuable compounds, it is a promising host for biorefinery.
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Affiliation(s)
- Hong-Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Marimuthu Anandharaj
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yi-Ying Kao
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, No. 91 Hsueh-Shih Road, Taichung, 402, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan. .,Biotechnology center, National Chung Hsing University, Taichung, 40227, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA.
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16
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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: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Spagnuolo M, Shabbir Hussain M, Gambill L, Blenner M. Alternative Substrate Metabolism in Yarrowia lipolytica. Front Microbiol 2018; 9:1077. [PMID: 29887845 PMCID: PMC5980982 DOI: 10.3389/fmicb.2018.01077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.
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Affiliation(s)
- Michael Spagnuolo
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
- Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, United States
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
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18
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Guo ZP, Robin J, Duquesne S, O’Donohue MJ, Marty A, Bordes F. Developing cellulolytic Yarrowia lipolytica as a platform for the production of valuable products in consolidated bioprocessing of cellulose. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:141. [PMID: 29785208 PMCID: PMC5952637 DOI: 10.1186/s13068-018-1144-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/07/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND Both industrial biotechnology and the use of cellulosic biomass as feedstock for the manufacture of various commercial goods are prominent features of the bioeconomy. In previous work, with the aim of developing a consolidated bioprocess for cellulose bioconversion, we conferred cellulolytic activity of Yarrowia lipolytica, one of the most widely studied "nonconventional" oleaginous yeast species. However, further engineering this strain often leads to the loss of previously introduced heterologous genes due to the presence of multiple LoxP sites when using Cre-recombinase to remove previously employed selection markers. RESULTS In the present study, we first optimized the strategy of expression of multiple cellulases and rescued selection makers to obtain an auxotrophic cellulolytic Y. lipolytica strain. Then we pursued the quest, exemplifying how this cellulolytic Y. lipolytica strain can be used as a CBP platform for the production of target products. Our results reveal that overexpression of SCD1 gene, encoding stearoyl-CoA desaturase, and DGA1, encoding acyl-CoA:diacylglycerol acyltransferase, confers the obese phenotype to the cellulolytic Y. lipolytica. When grown in batch conditions and minimal medium, the resulting strain consumed 12 g/L cellulose and accumulated 14% (dry cell weight) lipids. Further enhancement of lipid production was achieved either by the addition of glucose or by enhancing cellulose consumption using a commercial cellulase cocktail. Regarding the latter option, although the addition of external cellulases is contrary to the concept of CBP, the amount of commercial cocktail used remained 50% lower than that used in a conventional process (i.e., without internalized production of cellulases). The introduction of the LIP2 gene into cellulolytic Y. lipolytica led to the production of a strain capable of producing lipase 2 while growing on cellulose. Remarkably, when the strain was grown on glucose, the expression of six cellulases did not alter the level of lipase production. When grown in batch conditions on cellulose, the engineered strain consumed 16 g/L cellulose and produced 9.0 U/mL lipase over a 96-h period. The lipase yield was 562 U lipase/g cellulose, which represents 60% of that obtained on glucose. Finally, expression of the hydroxylase from Claviceps purpurea (CpFAH12) in cellulolytic Y. lipolytica procured a strain that can produce ricinoleic acid (RA). Using this strain in batch cultures revealed that the consumption of 11 g/L cellulose sustained the production of 2.2 g/L RA in the decane phase, 69% of what was obtained on glucose. CONCLUSIONS In summary, this study has further demonstrated the potential of cellulolytic Y. lipolytica as a microbial platform for the bioconversion of cellulose into target products. Its ability to be used in consolidated process designs has been exemplified and clues revealing how cellulose consumption can be further enhanced using commercial cellulolytic cocktails are provided.
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Affiliation(s)
- Zhong-peng Guo
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Julien Robin
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Sophie Duquesne
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Michael Joseph O’Donohue
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Alain Marty
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Florence Bordes
- LISBP, CNRS, INSA/INRA UMR 792, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
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19
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Larroude M, Celinska E, Back A, Thomas S, Nicaud JM, Ledesma-Amaro R. A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene. Biotechnol Bioeng 2017; 115:464-472. [PMID: 28986998 DOI: 10.1002/bit.26473] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/11/2017] [Accepted: 10/05/2017] [Indexed: 12/17/2022]
Abstract
The increasing market demands of β-carotene as colorant, antioxidant and vitamin precursor, requires novel biotechnological production platforms. Yarrowia lipolytica, is an industrial organism unable to naturally synthesize carotenoids but with the ability to produce high amounts of the precursor Acetyl-CoA. We first found that a lipid overproducer strain was capable of producing more β-carotene than a wild type after expressing the heterologous pathway. Thereafter, we developed a combinatorial synthetic biology approach base on Golden Gate DNA assembly to screen the optimum promoter-gene pairs for each transcriptional unit expressed. The best strain reached a production titer of 1.5 g/L and a maximum yield of 0.048 g/g of glucose in flask. β-carotene production was further increased in controlled conditions using a fed-batch fermentation. A total production of β-carotene of 6.5 g/L and 90 mg/g DCW with a concomitant production of 42.6 g/L of lipids was achieved. Such high titers suggest that engineered Y. lipolytica is a competitive producer organism of β-carotene.
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Affiliation(s)
- Macarena Larroude
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ewelina Celinska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Alexandre Back
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stephan Thomas
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Department of Bioengineering, Imperial College London, London, UK
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20
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Xu Q, Knoshaug EP, Wang W, Alahuhta M, Baker JO, Yang S, Vander Wall T, Decker SR, Himmel ME, Zhang M, Wei H. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi. Microb Cell Fact 2017; 16:126. [PMID: 28738851 PMCID: PMC5525229 DOI: 10.1186/s12934-017-0742-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/13/2017] [Indexed: 11/29/2022] Open
Abstract
Background Lipomyces starkeyi is one of the leading lipid-producing microorganisms reported to date; its genetic transformation was only recently reported. Our aim is to engineer L. starkeyi to serve in consolidated bioprocessing (CBP) to produce lipid or fatty acid-related biofuels directly from abundant and low-cost lignocellulosic substrates. Results To evaluate L. starkeyi in this role, we first conducted a genome analysis, which revealed the absence of key endo- and exocellulases in this yeast, prompting us to select and screen four signal peptides for their suitability for the overexpression and secretion of cellulase genes. To compensate for the cellulase deficiency, we chose two prominent cellulases, Trichoderma reesei endoglucanase II (EG II) and a chimeric cellobiohydrolase I (TeTrCBH I) formed by fusion of the catalytic domain from Talaromyces emersonii CBH I with the linker peptide and cellulose-binding domain from T. reesei CBH I. The systematically tested signal peptides included three peptides from native L. starkeyi and one from Yarrowia lipolytica. We found that all four signal peptides permitted secretion of active EG II. We also determined that three of these signal peptides worked for expression of the chimeric CBH I; suggesting that our design criteria for selecting these signal peptides was effective. Encouragingly, the Y. lipolytica signal peptide was able to efficiently guide secretion of the chimeric TeTrCBH I protein from L. starkeyi. The purified chimeric TeTrCBH I showed high activity against the cellulose in pretreated corn stover and the purified EG II showed high endocellulase activity measured by the CELLG3 (Megazyme) method. Conclusions Our results suggest that L. starkeyi is capable of expressing and secreting core fungal cellulases. Moreover, the purified EG II and chimeric TeTrCBH I displayed significant and potentially useful enzymatic activities, demonstrating that engineered L. starkeyi has the potential to function as an oleaginous CBP strain for biofuel production. The effectiveness of the tested secretion signals will also benefit future secretion of other heterologous proteins in L. starkeyi and, given the effectiveness of the cross-genus secretion signal, possibly other oleaginous yeasts as well. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0742-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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21
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Lee CR, Sung BH, Lim KM, Kim MJ, Sohn MJ, Bae JH, Sohn JH. Co-fermentation using Recombinant Saccharomyces cerevisiae Yeast Strains Hyper-secreting Different Cellulases for the Production of Cellulosic Bioethanol. Sci Rep 2017; 7:4428. [PMID: 28667330 PMCID: PMC5493647 DOI: 10.1038/s41598-017-04815-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/19/2017] [Indexed: 01/02/2023] Open
Abstract
To realize the economical production of ethanol and other bio-based chemicals from lignocellulosic biomass by consolidated bioprocessing (CBP), various cellulases from different sources were tested to improve the level of cellulase secretion in the yeast Saccharomyces cerevisiae by screening an optimal translational fusion partner (TFP) as both a secretion signal and fusion partner. Among them, four indispensable cellulases for cellulose hydrolysis, including Chaetomium thermophilum cellobiohydrolase (CtCBH1), Chrysosporium lucknowense cellobiohydrolase (ClCBH2), Trichoderma reesei endoglucanase (TrEGL2), and Saccharomycopsis fibuligera β-glucosidase (SfBGL1), were identified to be highly secreted in active form in yeast. Despite variability in the enzyme levels produced, each recombinant yeast could secrete approximately 0.6–2.0 g/L of cellulases into the fermentation broth. The synergistic effect of the mixed culture of the four strains expressing the essential cellulases with the insoluble substrate Avicel and several types of cellulosic biomass was demonstrated to be effective. Co-fermentation of these yeast strains produced approximately 14 g/L ethanol from the pre-treated rice straw containing 35 g/L glucan with 3-fold higher productivity than that of wild type yeast using a reduced amount of commercial cellulases. This process will contribute to the cost-effective production of bioenergy such as bioethanol and biochemicals from cellulosic biomass.
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Affiliation(s)
- Cho-Ryong Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Kwang-Mook Lim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Min Jeong Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Bae
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea. .,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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22
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Guo ZP, Duquesne S, Bozonnet S, Cioci G, Nicaud JM, Marty A, O’Donohue MJ. Conferring cellulose-degrading ability to Yarrowia lipolytica to facilitate a consolidated bioprocessing approach. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:132. [PMID: 28533816 PMCID: PMC5438512 DOI: 10.1186/s13068-017-0819-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/13/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Yarrowia lipolytica, one of the most widely studied "nonconventional" oleaginous yeast species, is unable to grow on cellulose. Recently, we identified and overexpressed two endogenous β-glucosidases in Y. lipolytica, thus enabling this yeast to use cello-oligosaccharides as a carbon source for growth. Using this engineered yeast platform, we have now gone further toward building a fully cellulolytic Y. lipolytica for use in consolidated bioprocessing of cellulose. RESULTS Initially, different essential enzyme components of a cellulase cocktail (i.e,. cellobiohydrolases and endoglucanases) were individually expressed in Y. lipolytica in order to ascertain the viability of the strategy. Accordingly, the Trichoderma reesei endoglucanase I (TrEG I) and II (TrEG II) were secreted as active proteins in Y. lipolytica, with the secretion yield of EG II being twice that of EG I. Characterization of the purified His-tagged recombinant EG proteins (rhTrEGs) revealed that rhTrEG I displayed higher specific activity than rhTrEG II on both cellotriose and insoluble cellulosic substrates, such as Avicel, β-1, 3 glucan, β-1, 4 glucan, and PASC. Similarly, cellobiohydrolases, such as T. reesei CBH I and II (TrCBH I and II), and the CBH I from Neurospora crassa (NcCBH I) were successfully expressed in Y. lipolytica. However, the yield of the expressed TrCBH I was low, so work on this was not pursued. Contrastingly, rhNcCBH I was not only well expressed, but also highly active on PASC and more active on Avicel (0.11 U/mg) than wild-type TrCBH I (0.065 U/mg). Therefore, work was pursued using a combination of NcCBH I and TrCBH II. The quantification of enzyme levels in culture supernatants revealed that the use of a hybrid promoter instead of the primarily used TEF promoter procured four and eight times more NcCBH I and TrCBH II expressions, respectively. Finally, the coexpression of the previously described Y. lipolytica β-glucosidases, the CBH II, and EG I and II from T. reesei, and the N. crassa CBH I procured an engineered Y. lipolytica strain that was able to grow both on model cellulose substrates, such as highly crystalline Avicel, and on industrial cellulose pulp, such as that obtained using an organosolv process. CONCLUSIONS A Y. lipolytica strain coexpressing six cellulolytic enzyme components has been successfully developed. In addition, the results presented show how the recombinant strain can be optimized, for example, using artificial promoters to tailor expression levels. Most significantly, this study has provided a demonstration of how the strain can grow on a sample of industrial cellulose as sole carbon source, thus revealing the feasibility of Yarrowia-based consolidated bioprocess for the production of fuel and chemical precursors. Further, enzyme and strain optimization, coupled to appropriate process design, will undoubtedly lead to much better performances in the future.
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Affiliation(s)
- Zhong-peng Guo
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Sophie Duquesne
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Sophie Bozonnet
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Gianluca Cioci
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Marty
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
| | - Michael Joseph O’Donohue
- Biocatalysis Group, INSA/INRA UMR 792, CNRS, LISBP, Université de Toulouse, 135, Avenue de Rangueil, 31077 Toulouse, France
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Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels. Appl Microbiol Biotechnol 2017; 101:2603-2618. [PMID: 28078400 DOI: 10.1007/s00253-017-8091-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
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Applying pathway engineering to enhance production of alpha-ketoglutarate in Yarrowia lipolytica. Appl Microbiol Biotechnol 2016; 100:9875-9884. [DOI: 10.1007/s00253-016-7913-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/29/2022]
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25
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Huang R, Guo H, Su R, Qi W, He Z. Enhanced cellulase recovery without β-glucosidase supplementation for cellulosic ethanol production using an engineered strain and surfactant. Biotechnol Bioeng 2016; 114:543-551. [DOI: 10.1002/bit.26194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Renliang Huang
- Tianjin Engineering Center of Bio Gas/Oil Technology; School of Environmental Science and Engineering; Tianjin University; Tianjin China
| | - Hong Guo
- State Key Laboratory of Chemical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology; Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology; Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 China
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Ledesma-Amaro R, Nicaud JM. Metabolic Engineering for Expanding the Substrate Range of Yarrowia lipolytica. Trends Biotechnol 2016; 34:798-809. [DOI: 10.1016/j.tibtech.2016.04.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
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Comparison of Nitrogen Depletion and Repletion on Lipid Production in Yeast and Fungal Species. ENERGIES 2016. [DOI: 10.3390/en9090685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components. Appl Environ Microbiol 2016; 82:5174-85. [PMID: 27316952 DOI: 10.1128/aem.00713-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus Ustilago maydis for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process. IMPORTANCE This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus Ustilago maydis As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future.
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Ledesma-Amaro R, Lazar Z, Rakicka M, Guo Z, Fouchard F, Coq AMCL, Nicaud JM. Metabolic engineering of Yarrowia lipolytica to produce chemicals and fuels from xylose. Metab Eng 2016; 38:115-124. [PMID: 27396355 DOI: 10.1016/j.ymben.2016.07.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/17/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Abstract
Yarrowia lipolytica is a biotechnological chassis for the production of a range of products, such as microbial oils and organic acids. However, it is unable to consume xylose, the major pentose in lignocellulosic hydrolysates, which are considered a preferred carbon source for bioprocesses due to their low cost, wide abundance and high sugar content. Here, we engineered Y. lipolytica to metabolize xylose to produce lipids or citric acid. The overexpression of xylose reductase and xylitol dehydrogenase from Scheffersomyces stipitis were necessary but not sufficient to permit growth. The additional overexpression of the endogenous xylulokinase enabled identical growth as the wild type strain in glucose. This mutant was able to produce up to 80g/L of citric acid from xylose. Transferring these modifications to a lipid-overproducing strain boosted the production of lipids from xylose. This is the first step towards a consolidated bioprocess to produce chemicals and fuels from lignocellulosic materials.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Zbigniew Lazar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Magdalena Rakicka
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Zhongpeng Guo
- LISBP-Biocatalysis Group, INSA/INRA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France
| | - Florian Fouchard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Ledesma-Amaro R, Dulermo R, Niehus X, Nicaud JM. Combining metabolic engineering and process optimization to improve production and secretion of fatty acids. Metab Eng 2016; 38:38-46. [PMID: 27301328 DOI: 10.1016/j.ymben.2016.06.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/10/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022]
Abstract
Microbial oils are sustainable alternatives to petroleum for the production of chemicals and fuels. Oleaginous yeasts are promising source of oils and Yarrowia lipolytica is the most studied and engineered one. Nonetheless the commercial production of biolipids is so far limited to high value products due to the elevated production and extraction costs. In order to contribute to overcoming these limitations we exploited the possibility of secreting lipids to the culture broth, uncoupling production and biomass formation and facilitating the extraction. We therefore considered two synthetic approaches, Strategy I where fatty acids are produced by enhancing the flux through neutral lipid formation, as typically occurs in eukaryotic systems and Strategy II where the bacterial system to produce free fatty acids is mimicked. The engineered strains, in a coupled fermentation and extraction process using alkanes, secreted the highest titer of lipids described so far, with a content of 120% of DCW.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Remi Dulermo
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xochitl Niehus
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), A.C. 44270 Guadalajara, Jalisco, Mexico
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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Lamers D, van Biezen N, Martens D, Peters L, van de Zilver E, Jacobs-van Dreumel N, Wijffels RH, Lokman C. Selection of oleaginous yeasts for fatty acid production. BMC Biotechnol 2016; 16:45. [PMID: 27233820 PMCID: PMC4884388 DOI: 10.1186/s12896-016-0276-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 05/23/2016] [Indexed: 12/03/2022] Open
Abstract
Background Oleaginous yeast species are an alternative for the production of lipids or triacylglycerides (TAGs). These yeasts are usually non-pathogenic and able to store TAGs ranging from 20 % to 70 % of their cell mass depending on culture conditions. TAGs originating from oleaginous yeasts can be used as the so-called second generation biofuels, which are based on non-food competing “waste carbon sources”. Results In this study the selection of potentially new interesting oleaginous yeast strains is described. Important selection criteria were: a broad maximum temperature and pH range for growth (robustness of the strain), a broad spectrum of carbon sources that can be metabolized (preferably including C-5 sugars), a high total fatty acid content in combination with a low glycogen content and genetic accessibility. Conclusions Based on these selection criteria, among 24 screened species, Schwanniomyces occidentalis (Debaromyces occidentalis) CBS2864 was selected as a promising strain for the production of high amounts of lipids. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0276-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dennis Lamers
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands. .,Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands.
| | - Nick van Biezen
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | - Dirk Martens
- Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands
| | - Linda Peters
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | - Eric van de Zilver
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | | | - René H Wijffels
- Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands.,University of Nordland, Faculty of Biosciences and Aquaculture, N-8049, Bodø, Norway
| | - Christien Lokman
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
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Celińska E, Borkowska M, Białas W. Evaluation of heterologous α-amylase production in two expression platforms dedicated for Yarrowia lipolytica: commercial Po1g-pYLSC (php4d) and custom-made A18-pYLTEF (pTEF). Yeast 2016; 33:165-81. [PMID: 26694961 DOI: 10.1002/yea.3149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/25/2015] [Accepted: 12/14/2015] [Indexed: 11/10/2022] Open
Abstract
In view of the constantly increasing demand for cost-effective, low-energy and environmentally friendly industrial processes and household care products, enzyme production occupies an essential place in the field of biotechnology. Along with increasing demand for industrial and household care enzymes, the demand for heterologous expression platforms has also increased. Apart from the conventional hosts, e.g. Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris, routinely used in heterologous protein expression, the non-conventional ones have become more and more exploited in this field. Among the available yeast host systems, Yarrowia lipolytica appears to be an attractive alternative. The aim of this study was to compare efficiency of two Yarrowia-based expression platforms, commercial Po1g-pYLSC and custom-made A18-pYLTEF, in expression of an insect-derived, raw-starch-digesting α-amylase, to select the 'champion' system for further studies on this valuable enzyme. Both expression platforms were compared with respect to copy number of the integrated expression cassette/transformed genome, and the recombinant strains performance (Po1g-pYLSC-derived 4.29 strain, and A18-pYLTEF-derived B9 strain) during batch bioreactor cultures. Our results demonstrate that the average number of integration events into the recipient's genome was comparable for both expression systems under investigation, but with varying distribution of the multicopy integrants; and the number of the recombinant gene copies was highly correlated with the acquired amylolytic activity of the strains. Due to severe susceptibility of the recombinant AMY1 polypeptide to native proteases of the custom-made expression system, the final yield of the enzyme was substantially lower when compared to the commercial Po1g-pYLSC (reaching a maximum level of 142.84 AU/l). Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Poland
| | - Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Poland
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Friedlander J, Tsakraklides V, Kamineni A, Greenhagen EH, Consiglio AL, MacEwen K, Crabtree DV, Afshar J, Nugent RL, Hamilton MA, Joe Shaw A, South CR, Stephanopoulos G, Brevnova EE. Engineering of a high lipid producing Yarrowia lipolytica strain. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:77. [PMID: 27034715 PMCID: PMC4815080 DOI: 10.1186/s13068-016-0492-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/21/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Microbial lipids are produced by many oleaginous organisms including the well-characterized yeast Yarrowia lipolytica, which can be engineered for increased lipid yield by up-regulation of the lipid biosynthetic pathway and down-regulation or deletion of competing pathways. RESULTS We describe a strain engineering strategy centered on diacylglycerol acyltransferase (DGA) gene overexpression that applied combinatorial screening of overexpression and deletion genetic targets to construct a high lipid producing yeast biocatalyst. The resulting strain, NS432, combines overexpression of a heterologous DGA1 enzyme from Rhodosporidium toruloides, a heterlogous DGA2 enzyme from Claviceps purpurea, and deletion of the native TGL3 lipase regulator. These three genetic modifications, selected for their effect on lipid production, enabled a 77 % lipid content and 0.21 g lipid per g glucose yield in batch fermentation. In fed-batch glucose fermentation NS432 produced 85 g/L lipid at a productivity of 0.73 g/L/h. CONCLUSIONS The yields, productivities, and titers reported in this study may further support the applied goal of cost-effective, large -scale microbial lipid production for use as biofuels and biochemicals.
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Affiliation(s)
| | | | | | | | | | - Kyle MacEwen
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | | | | | - Rebecca L. Nugent
- />Total New Energies, 5858 Horton Street, Emeryville, CA 94610 USA
- />Twist Bioscience, 455 Mission Bay Blvd South, San Francisco, CA 94158 USA
| | | | - A. Joe Shaw
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | - Colin R. South
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
| | - Gregory Stephanopoulos
- />Novogy, Inc., 85 Bolton Street, Cambridge, MA 02140 USA
- />Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 USA
| | - Elena E. Brevnova
- />Total New Energies, 5858 Horton Street, Emeryville, CA 94610 USA
- />Evelo Therapeutics, 620 Memorial Dr., Cambridge, MA 02139 USA
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Ledesma-Amaro R, Nicaud JM. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. Prog Lipid Res 2016; 61:40-50. [DOI: 10.1016/j.plipres.2015.12.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
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Zhu Q, Jackson EN. Metabolic engineering of Yarrowia lipolytica for industrial applications. Curr Opin Biotechnol 2015; 36:65-72. [DOI: 10.1016/j.copbio.2015.08.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/18/2015] [Accepted: 08/09/2015] [Indexed: 01/01/2023]
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Ledesma-Amaro R, Dulermo T, Nicaud JM. Engineering Yarrowia lipolytica to produce biodiesel from raw starch. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:148. [PMID: 26379779 PMCID: PMC4571081 DOI: 10.1186/s13068-015-0335-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/03/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND In the last year, the worldwide concern about the abuse of fossil fuels and the seeking for alternatives sources to produce energy have found microbial oils has potential candidates for diesel substitutes. Yarrowia lipolytica has emerged as a paradigm organism for the production of bio-lipids in white biotechnology. It accumulates high amounts of lipids from glucose as sole carbon sources. Nonetheless, to lower the cost of microbial oil production and rival plant-based fuels, the use of raw and waste materials as fermentation substrate is required. Starch is one of the most abundant carbohydrates in nature and it is constituted by glucose monomers. Y. lipolytica lacks the capacity to breakdown this polymer and thus expensive enzymatic and/or physical pre-treatments are needed. RESULTS In this work, we express heterologous alpha-amylase and glucoamylase enzymes in Y. lipolytica. The modified strains were able to produce and secrete high amounts of active form of both proteins in the culture media. These strains were able to grow on starch as sole carbon source and produce certain amount of lipids. Thereafter, we expressed both enzymes in an engineered strain able to overaccumulate lipids. This strain was able to produce up to 21 % of DCW as fatty acids from soluble starch, 5.7 times more than the modified strain in the wild-type background. Media optimization to increase the C/N ratio to 90 increased total lipid content up to 27 % of DCW. We also tested these strains in industrial raw starch as a proof of concept of the feasibility of the consolidated bioprocess. Lipid production from raw starch was further enhanced by the expression of a second copy of each enzyme. Finally, we determined in silico that the properties of a biodiesel produced by this strain from raw starch would fit the established standards. CONCLUSIONS In this work, we performed a strain engineering approach to obtain a consolidated bioprocess to directly produce biolipids from raw starch. Additionally, we proved that lipid production from starch can be enhanced by both metabolic engineering and culture condition optimization, setting up the basis for further studies.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip, Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
| | - Thierry Dulermo
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Jean Marc Nicaud
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip, Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
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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: 150] [Impact Index Per Article: 16.7] [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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