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Zhang C, Chen H, Zhu Y, Zhang Y, Li X, Wang F. Saccharomyces cerevisiae cell surface display technology: Strategies for improvement and applications. Front Bioeng Biotechnol 2022; 10:1056804. [PMID: 36568309 PMCID: PMC9767963 DOI: 10.3389/fbioe.2022.1056804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial cell surface display technology provides a powerful platform for engineering proteins/peptides with enhanced properties. Compared to the classical intracellular and extracellular expression (secretion) systems, this technology avoids enzyme purification, substrate transport processes, and is an effective solution to enzyme instability. Saccharomyces cerevisiae is well suited to cell surface display as a common cell factory for the production of various fuels and chemicals, with the advantages of large cell size, being a Generally Regarded As Safe (GRAS) organism, and post-translational processing of secreted proteins. In this review, we describe various strategies for constructing modified S. cerevisiae using cell surface display technology and outline various applications of this technology in industrial processes, such as biofuels and chemical products, environmental pollution treatment, and immunization processes. The approaches for enhancing the efficiency of cell surface display are also discussed.
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Affiliation(s)
- Chenmeng Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Hongyu Chen
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yiping Zhu
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yu Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China,*Correspondence: Fei Wang,
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Adaptive evolution of Kluyveromyces marxianus MTCC1389 for high ethanol tolerance. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Beer production potentiality of some non-Saccharomyces yeast obtained from a traditional beer starter emao. Braz J Microbiol 2022; 53:1515-1531. [PMID: 35488168 PMCID: PMC9433491 DOI: 10.1007/s42770-022-00765-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/16/2022] [Indexed: 11/02/2022] Open
Abstract
The recent realisation regarding the potentiality of the long-neglected non-Saccharomyces yeasts in improving the flavour profile and functionality of alcoholic beverages has pushed researchers to search for such potent strains in many sources. We studied the fungal diversity and the rice beer production capability of the fungal strains isolated from emao-a traditional rice beer starter culture of the Boro community. Fifty distinct colonies were picked from mixed-culture plates, of which ten representative morphotypes were selected for species identification, and simultaneous saccharification and beer fermentation (SSBF) assay. The representative isolates were identified as Hyphopichia burtonii (Hbur-FI38, Hbur-FI44, Hbur-FI47 & Hbur-FI68), Saccharomyces cerevisiae (Scer-FI51), Wickerhamomyces anomalus (Wano-FI52), Candida carpophila (Ccar-FI53), Mucor circinelloides (Mcir-FI60), and Saccharomycopsis malanga (Smal-FI77 and Smal-FI84). The non-Saccharomyces yeast strains Hbur-FI38, Hbur-FI44, Ccar-FI53, and Smal-FI77 showed SSBF capacity on rice substrate producing beer that contained 7-10% (v/v) ethanol. A scaled-up fermentation assay was performed to assess the strain-wise fermentation behaviour in large-scale production. The nutritional, functional, and sensory qualities of the SSBF strain fermented beer were compared to the beer produced by emao. All the strains produced beer with reduced alcohol and energy value while compared to the traditional starter emao. Beer produced by both the strains of H. burtonii stood out with higher ascorbic acid, phenol, and antioxidant property, and improved sensory profile in addition to reduced alcohol and energy value. Such SSBF strains are advantageous over the non-SSBF S. cerevisiae strains as the former can be used for direct beer production from rice substrates.
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Narzary D, Boro N, Borah A, Okubo T, Takami H. Community structure and metabolic potentials of the traditional rice beer starter 'emao'. Sci Rep 2021; 11:14628. [PMID: 34272462 PMCID: PMC8285430 DOI: 10.1038/s41598-021-94059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/06/2021] [Indexed: 01/02/2023] Open
Abstract
The emao, a traditional beer starter used in the North-East regions of India produces a high quality of beer from rice substrates; however, its microbial community structure and functional metabolic modules remain unknown. To address this gap, we have used shot-gun whole-metagenome sequencing technology; accordingly, we have detected several enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao. The abundance of eukaryotic microorganisms, specifically the members of Mucoromycota and Ascomycota, dominated over the prokaryotes in the emao compared to previous metagenomic studies on such traditional starters where the relative abundance of prokaryotes occurred higher than the eukaryotes. The family Rhizopodaceae (64.5%) and its genus Rhizopus (64%) were the most dominant ones, followed by Phaffomycetaceae (11.14%) and its genus Wickerhamomyces (10.03%). The family Leuconostocaceae (6.09%) represented by two genera (Leuconostoc and Weissella) was dominant over the other bacteria, and it was the third-highest in overall relative abundance in the emao. The comprehensive microbial species diversity, community structure, and metabolic modules found in the emao are of practical value in the formulation of mixed-microbial cultures for biofuel production from plant-based feedstocks.
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Affiliation(s)
- Diganta Narzary
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India.
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan.
| | - Nitesh Boro
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Ashis Borah
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Takashi Okubo
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan
- Macrogen Japan Corp., 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideto Takami
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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Cripwell RA, Favaro L, Viljoen-Bloom M, van Zyl WH. Consolidated bioprocessing of raw starch to ethanol by Saccharomyces cerevisiae: Achievements and challenges. Biotechnol Adv 2020; 42:107579. [PMID: 32593775 DOI: 10.1016/j.biotechadv.2020.107579] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/30/2022]
Abstract
Recent advances in amylolytic strain engineering for starch-to-ethanol conversion have provided a platform for the development of raw starch consolidated bioprocessing (CBP) technologies. Several proof-of-concept studies identified improved enzyme combinations, alternative feedstocks and novel host strains for evaluation and application under fermentation conditions. However, further research efforts are required before this technology can be scaled up to an industrial level. In this review, different CBP approaches are defined and discussed, also highlighting the role of auxiliary enzymes for a supplemented CBP process. Various achievements in the development of amylolytic Saccharomyces cerevisiae strains for CBP of raw starch and the remaining challenges that need to be tackled/pursued to bring yeast raw starch CBP to industrial realization, are described. Looking towards the future, it provides potential solutions to develop more cost-effective processes that include cheaper substrates, integration of the 1G and 2G economies and implementing a biorefinery concept where high-value products are also derived from starchy substrates.
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Affiliation(s)
- Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
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Xu Y, Zhou T, Tang H, Li X, Chen Y, Zhang L, Zhang J. Probiotic potential and amylolytic properties of lactic acid bacteria isolated from Chinese fermented cereal foods. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Cripwell RA, Rose SH, Viljoen-Bloom M, van Zyl WH. Improved raw starch amylase production by Saccharomyces cerevisiae using codon optimisation strategies. FEMS Yeast Res 2019; 19:5237704. [PMID: 30535120 DOI: 10.1093/femsyr/foy127] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Amylases are used in a variety of industries that have a specific need for alternative enzymes capable of hydrolysing raw starch. Five α-amylase and five glucoamylase-encoding genes were expressed in the Saccharomyces cerevisiae Y294 laboratory strain to select for recombinant strains that best hydrolysed raw corn starch. Gene variants of four amylases were designed using codon optimisation and different secretion signals. The significant difference in activity levels among the gene variants confirms that codon optimisation of fungal genes for expression in S. cerevisiae does not guarantee improved recombinant protein production. The codon-optimised glucoamylase variant from Talaromyces emersonii (temG_Opt) yielded 3.3-fold higher extracellular activity relative to the native temG, whereas the codon-optimised T. emersonii α-amylase (temA_Opt) yielded 1.6-fold more extracellular activity than the native temA. The effect of four terminator sequences was also investigated using temG and temG_Opt as reporter genes, with the ALY2T terminator resulting in a 14% increase in glucoamylase activity relative to the gene cassettes containing the ENO1T terminator. This is the first report of engineered S. cerevisiae strains to express T. emersonii amylase variants, and these enzymes may have potential applications in the industrial conversion of raw starch under fermentation conditions.
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Affiliation(s)
- Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, JC Smuts Building, De Beer Street, Stellenbosch, 7600, South Africa
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Cunha-Pereira FD, Hickert LR, Rech R, Dillon AP, Ayub MAZ. Fermentation of hexoses and pentoses from hydrolyzed soybean hull into ethanol and xylitol by Candida guilliermondii BL 13. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2017. [DOI: 10.1590/0104-6632.20170344s20160005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | | | - R. Rech
- Federal University of Rio Grande do Sul, Brazil
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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10
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Hasunuma T, Kondo A. Production of Fuels and Chemicals from Biomass by Integrated Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Tomohisa Hasunuma
- Kobe University; Graduate School of Science, Technology and Innovation; 1-1 Rokkodai Nada Kobe 657-8501 Japan
| | - Akihiko Kondo
- RIKEN; Biomass Engineering Program; 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan
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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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Favaro L, Viktor MJ, Rose SH, Viljoen-Bloom M, van Zyl WH, Basaglia M, Cagnin L, Casella S. Consolidated bioprocessing of starchy substrates into ethanol by industrial Saccharomyces cerevisiae strains secreting fungal amylases. Biotechnol Bioeng 2015; 112:1751-60. [PMID: 25786804 DOI: 10.1002/bit.25591] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/03/2015] [Accepted: 03/09/2015] [Indexed: 01/16/2023]
Abstract
The development of a yeast strain that converts raw starch to ethanol in one step (called Consolidated Bioprocessing, CBP) could significantly reduce the commercial costs of starch-based bioethanol. An efficient amylolytic Saccharomyces cerevisiae strain suitable for industrial bioethanol production was developed in this study. Codon-optimized variants of the Thermomyces lanuginosus glucoamylase (TLG1) and Saccharomycopsis fibuligera α-amylase (SFA1) genes were δ-integrated into two S. cerevisiae yeast with promising industrial traits, i.e., strains M2n and MEL2. The recombinant M2n[TLG1-SFA1] and MEL2[TLG1-SFA1] yeast displayed high enzyme activities on soluble and raw starch (up to 8118 and 4461 nkat/g dry cell weight, respectively) and produced about 64 g/L ethanol from 200 g/L raw corn starch in a bioreactor, corresponding to 55% of the theoretical maximum ethanol yield (g of ethanol/g of available glucose equivalent). Their starch-to-ethanol conversion efficiencies were even higher on natural sorghum and triticale substrates (62 and 73% of the theoretical yield, respectively). This is the first report of direct ethanol production from natural starchy substrates (without any pre-treatment or commercial enzyme addition) using industrial yeast strains co-secreting both a glucoamylase and α-amylase.
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Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - Marko J Viktor
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marina Basaglia
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro (PD), Italy.
| | - Lorenzo Cagnin
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - Sergio Casella
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020, Legnaro (PD), Italy
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Tanaka T, Kondo A. Cell surface engineering of industrial microorganisms for biorefining applications. Biotechnol Adv 2015; 33:1403-11. [PMID: 26070720 DOI: 10.1016/j.biotechadv.2015.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/19/2022]
Abstract
In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan
| | - Akihiko Kondo
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan.
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Sun J, Alper HS. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production. ACTA ACUST UNITED AC 2015; 42:423-36. [DOI: 10.1007/s10295-014-1539-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022]
Abstract
Abstract
A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5–50 g/L), and lab-scale (0–5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.
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Affiliation(s)
- Jie Sun
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
| | - Hal S Alper
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
- grid.89336.37 0000000419369924 Institute for Cellular and Molecular Biology The University of Texas at Austin 2500 Speedway Avenue 78712 Austin TX USA
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Arumugam A, Ponnusami V. Ethanol Production from Cashew Apple Juice Using ImmobilizedSaccharomyces cerevisiaeCells on Silica Gel Matrix Synthesized from Sugarcane Leaf Ash. CHEM ENG COMMUN 2015. [DOI: 10.1080/00986445.2013.867256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Tanaka T, Kondo A. Cell-surface display of enzymes by the yeast Saccharomyces cerevisiae for synthetic biology. FEMS Yeast Res 2015; 15:1-9. [PMID: 25243459 DOI: 10.1111/1567-1364.12212] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/09/2014] [Accepted: 09/15/2014] [Indexed: 01/26/2023] Open
Abstract
In yeast cell-surface displays, functional proteins, such as cellulases, are genetically fused to an anchor protein and expressed on the cell surface. Saccharomyces cerevisiae, which is often utilized as a cell factory for the production of fuels, chemicals, and proteins, is the most commonly used yeast for cell-surface display. To construct yeast cells with a desired function, such as the ability to utilize cellulose as a substrate for bioethanol production, cell-surface display techniques for the efficient expression of enzymes on the cell membrane need to be combined with metabolic engineering approaches for manipulating target pathways within cells. In this Minireview, we summarize the recent progress of biorefinery fields in the development and application of yeast cell-surface displays from a synthetic biology perspective and discuss approaches for further enhancing cell-surface display efficiency.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Nada, Kobe, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Nada, Kobe, Japan
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Lomthong T, Chotineeranat S, Kitpreechavanich V. Production and characterization of raw starch degrading enzyme from a newly isolated thermophilic filamentous bacterium,Laceyella sacchariLP175. STARCH-STARKE 2014. [DOI: 10.1002/star.201400150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thanasak Lomthong
- Department of Microbiology, Faculty of Science; Kasetsart University; Bangkok Thailand
| | - Sunee Chotineeranat
- Cassava and Starch Technology Research Unit (CSTRU), National Center for Genetic Engineering and Biotechnology (BIOTEC); Kasetsart University; Bangkok Thailand
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Chakraborty S, Rusli H, Nath A, Sikder J, Bhattacharjee C, Curcio S, Drioli E. Immobilized biocatalytic process development and potential application in membrane separation: a review. Crit Rev Biotechnol 2014; 36:43-58. [DOI: 10.3109/07388551.2014.923373] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Görgens JF, Bressler DC, van Rensburg E. EngineeringSaccharomyces cerevisiaefor direct conversion of raw, uncooked or granular starch to ethanol. Crit Rev Biotechnol 2014; 35:369-91. [DOI: 10.3109/07388551.2014.888048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Buschke N, Schäfer R, Becker J, Wittmann C. Metabolic engineering of industrial platform microorganisms for biorefinery applications--optimization of substrate spectrum and process robustness by rational and evolutive strategies. BIORESOURCE TECHNOLOGY 2013; 135:544-554. [PMID: 23260271 DOI: 10.1016/j.biortech.2012.11.047] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 06/01/2023]
Abstract
Bio-based production promises a sustainable route to myriads of chemicals, materials and fuels. With regard to eco-efficiency, its future success strongly depends on a next level of bio-processes using raw materials beyond glucose. Such renewables, i.e., polymers, complex substrate mixtures and diluted waste streams, often cannot be metabolized naturally by the producing organisms. This particularly holds for well-known microorganisms from the traditional sugar-based biotechnology, including Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae which have been engineered successfully to produce a broad range of products from glucose. In order to make full use of their production potential within the bio-refinery value chain, they have to be adapted to various feed-stocks of interest. This review focuses on the strategies to be applied for this purpose which combine rational and evolutive approaches. Hereby, the three industrial platform microorganisms, E. coli, C. glutamicum and S. cerevisiae are highlighted due to their particular importance.
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Affiliation(s)
- Nele Buschke
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Germany
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Fan C, Qi K, Xia XX, Zhong JJ. Efficient ethanol production from corncob residues by repeated fermentation of an adapted yeast. BIORESOURCE TECHNOLOGY 2013; 136:309-15. [PMID: 23567696 DOI: 10.1016/j.biortech.2013.03.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 05/26/2023]
Abstract
For economically feasible lignocellulosic ethanol production, it is crucial to obtain a robust strain and develop an efficient fermentation process. An earlier-screened yeast strain Pichia guilliermondii was adapted to corncob residues (CCR) hydrolysate and used for high titer ethanol production without any detoxification or external nutrient supplementation. With an optimized fed-batch strategy, the maximum ethanol titer and productivity reached 56.3 g/l and 0.47 g l(-1) h(-1), respectively. To further increase the ethanol productivity, the fed-batch process was repeated three times with cell reuse, and the maximum ethanol titer and productivity reached 51.2 g/l and 1.11 g l(-1) h(-1), respectively. The results demonstrated that the combination of fed-batch with repeated fermentation was effective in improving the fermentation efficiency and achieving high ethanol productivity from CCR. The reported system is considered promising for commercial production of bioethanol from biomass hydrolysate in the future.
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Affiliation(s)
- Chao Fan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-chuan Road, Shanghai 200240, China
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Adachi D, Koda R, Hama S, Yamada R, Nakashima K, Ogino C, Kondo A. An integrative process model of enzymatic biodiesel production through ethanol fermentation of brown rice followed by lipase-catalyzed ethanolysis in a water-containing system. Enzyme Microb Technol 2013; 52:118-22. [DOI: 10.1016/j.enzmictec.2012.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
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van Zyl WH, Bloom M, Viktor MJ. Engineering yeasts for raw starch conversion. Appl Microbiol Biotechnol 2012; 95:1377-88. [PMID: 22797599 DOI: 10.1007/s00253-012-4248-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 11/29/2022]
Abstract
Next to cellulose, starch is the most abundant hexose polymer in plants, an import food and feed source and a preferred substrate for the production of many industrial products. Efficient starch hydrolysis requires the activities of both α-1,4 and α-1,6-debranching hydrolases, such as endo-amylases, exo-amylases, debranching enzymes, and transferases. Although amylases are widely distributed in nature, only about 10 % of amylolytic enzymes are able to hydrolyse raw or unmodified starch, with a combination of α-amylases and glucoamylases as minimum requirement for the complete hydrolysis of raw starch. The cost-effective conversion of raw starch for the production of biofuels and other important by-products requires the expression of starch-hydrolysing enzymes in a fermenting yeast strain to achieve liquefaction, hydrolysis, and fermentation (Consolidated Bioprocessing, CBP) by a single organism. The status of engineering amylolytic activities into Saccharomyces cerevisiae as fermentative host is highlighted and progress as well as challenges towards a true CBP organism for raw starch is discussed. Conversion of raw starch by yeast secreting or displaying α-amylases and glucoamylases on their surface has been demonstrated, although not at high starch loading or conversion rates that will be economically viable on industrial scale. Once efficient conversion of raw starch can be demonstrated at commercial level, engineering of yeast to utilize alternative substrates and produce alternative chemicals as part of a sustainable biorefinery can be pursued to ensure the rightful place of starch converting yeasts in the envisaged bio-economy of the future.
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Affiliation(s)
- W H van Zyl
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Olson DG, McBride JE, Joe Shaw A, Lynd LR. Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 2012; 23:396-405. [DOI: 10.1016/j.copbio.2011.11.026] [Citation(s) in RCA: 370] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/08/2011] [Accepted: 11/23/2011] [Indexed: 12/30/2022]
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Recent developments in yeast cell surface display toward extended applications in biotechnology. Appl Microbiol Biotechnol 2012; 95:577-91. [DOI: 10.1007/s00253-012-4175-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/13/2012] [Accepted: 05/14/2012] [Indexed: 10/28/2022]
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Repeated fermentation from raw starch using Saccharomyces cerevisiae displaying both glucoamylase and α-amylase. Enzyme Microb Technol 2012; 50:343-7. [DOI: 10.1016/j.enzmictec.2012.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/12/2012] [Accepted: 03/12/2012] [Indexed: 11/21/2022]
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Kotarska K, Kłosowski G, Czupryński B. Characterization of technological features of dry yeast (strain I-7-43) preparation, product of electrofusion between Saccharomyces cerevisiae and Saccharomyces diastaticus, in industrial application. Enzyme Microb Technol 2011; 49:38-43. [DOI: 10.1016/j.enzmictec.2011.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
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Yamada R, Taniguchi N, Tanaka T, Ogino C, Fukuda H, Kondo A. Direct ethanol production from cellulosic materials using a diploid strain of Saccharomyces cerevisiae with optimized cellulase expression. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:8. [PMID: 21496218 PMCID: PMC3095537 DOI: 10.1186/1754-6834-4-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 04/15/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND Hydrolysis of cellulose requires the action of the cellulolytic enzymes endoglucanase, cellobiohydrolase and β-glucosidase. The expression ratios and synergetic effects of these enzymes significantly influence the extent and specific rate of cellulose degradation. In this study, using our previously developed method to optimize cellulase-expression levels in yeast, we constructed a diploid Saccharomyces cerevisiae strain optimized for expression of cellulolytic enzymes, and attempted to improve the cellulose-degradation activity and enable direct ethanol production from rice straw, one of the most abundant sources of lignocellulosic biomass. RESULTS The engineered diploid strain, which contained multiple copies of three cellulase genes integrated into its genome, was precultured in molasses medium (381.4 mU/g wet cell), and displayed approximately six-fold higher phosphoric acid swollen cellulose (PASC) degradation activity than the parent haploid strain (63.5 mU/g wet cell). When used to ferment PASC, the diploid strain produced 7.6 g/l ethanol in 72 hours, with an ethanol yield that achieved 75% of the theoretical value, and also produced 7.5 g/l ethanol from pretreated rice straw in 72 hours. CONCLUSIONS We have developed diploid yeast strain optimized for expression of cellulolytic enzymes, which is capable of directly fermenting from cellulosic materials. Although this is a proof-of-concept study, it is to our knowledge, the first report of ethanol production from agricultural waste biomass using cellulolytic enzyme-expressing yeast without the addition of exogenous enzymes. Our results suggest that combining multigene expression optimization and diploidization in yeast is a promising approach for enhancing ethanol production from various types of lignocellulosic biomass.
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Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Naho Taniguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Tsutomu Tanaka
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hideki Fukuda
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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