1
|
Minnaar L, den Haan R. Engineering natural isolates of Saccharomyces cerevisiae for consolidated bioprocessing of cellulosic feedstocks. Appl Microbiol Biotechnol 2023; 107:7013-7028. [PMID: 37688599 PMCID: PMC10589140 DOI: 10.1007/s00253-023-12729-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 09/11/2023]
Abstract
Saccharomyces cerevisiae has gained much attention as a potential host for cellulosic bioethanol production using consolidated bioprocessing (CBP) methodologies, due to its high-ethanol-producing titres, heterologous protein production capabilities, and tolerance to various industry-relevant stresses. Since the secretion levels of heterologous proteins are generally low in domesticated strains of S. cerevisiae, natural isolates may offer a more diverse genetic background for improved heterologous protein secretion, while also displaying greater robustness to process stresses. In this study, the potential of natural and industrial S. cerevisiae strains to secrete a core set of cellulases (CBH1, CBH2, EG2, and BGL1), encoded by genes integrated using CRISPR/Cas9 tools, was evaluated. High levels of heterologous protein production were associated with a reduced maximal growth rate and with slight changes in overall strain robustness, compared to the parental strains. The natural isolate derivatives YI13_BECC and YI59_BECC displayed superior secretion capacity for the heterologous cellulases at high incubation temperature and in the presence of acetic acid, respectively, compared to the reference industrial strain MH1000_BECC. These strains also exhibited multi-tolerance to several fermentation-associated and secretion stresses. Cultivation of the strains on crystalline cellulose in oxygen-limited conditions yielded ethanol concentrations in the range of 4-4.5 g/L, representing 35-40% of the theoretical maximum ethanol yield after 120 h, without the addition of exogenous enzymes. This study therefore highlights the potential of these natural isolates to be used as chassis organisms in CBP bioethanol production. KEY POINTS: • Process-related fermentation stresses influence heterologous protein production. • Transformants produced up to 4.5 g/L ethanol, ~ 40% of the theoretical yield in CBP. • CRISPR/Cas9 was feasible for integrating genes in natural S. cerevisiae isolates.
Collapse
Affiliation(s)
- Letitia Minnaar
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| |
Collapse
|
2
|
Wu Y, Feng S, Sun Z, Hu Y, Jia X, Zeng B. An outlook to sophisticated technologies and novel developments for metabolic regulation in the Saccharomyces cerevisiae expression system. Front Bioeng Biotechnol 2023; 11:1249841. [PMID: 37869712 PMCID: PMC10586203 DOI: 10.3389/fbioe.2023.1249841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/24/2023] Open
Abstract
Saccharomyces cerevisiae is one of the most extensively used biosynthetic systems for the production of diverse bioproducts, especially biotherapeutics and recombinant proteins. Because the expression and insertion of foreign genes are always impaired by the endogenous factors of Saccharomyces cerevisiae and nonproductive procedures, various technologies have been developed to enhance the strength and efficiency of transcription and facilitate gene editing procedures. Thus, the limitations that block heterologous protein secretion have been overcome. Highly efficient promoters responsible for the initiation of transcription and the accurate regulation of expression have been developed that can be precisely regulated with synthetic promoters and double promoter expression systems. Appropriate codon optimization and harmonization for adaption to the genomic codon abundance of S. cerevisiae are expected to further improve the transcription and translation efficiency. Efficient and accurate translocation can be achieved by fusing a specifically designed signal peptide to an upstream foreign gene to facilitate the secretion of newly synthesized proteins. In addition to the widely applied promoter engineering technology and the clear mechanism of the endoplasmic reticulum secretory pathway, the innovative genome editing technique CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated system) and its derivative tools allow for more precise and efficient gene disruption, site-directed mutation, and foreign gene insertion. This review focuses on sophisticated engineering techniques and emerging genetic technologies developed for the accurate metabolic regulation of the S. cerevisiae expression system.
Collapse
Affiliation(s)
| | | | | | | | | | - Bin Zeng
- College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong, China
| |
Collapse
|
3
|
Smuts IE, Blakeway NJ, Rose SH, den Haan R, Viljoen-Bloom M, van Zyl WH. Supplementation of recombinant cellulases with LPMOs and CDHs improves consolidated bioprocessing of cellulose. Enzyme Microb Technol 2023; 164:110171. [PMID: 36549094 DOI: 10.1016/j.enzmictec.2022.110171] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/15/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
The increased demand for energy has sparked a global search for renewable energy sources that could partly replace fossil fuel resources and help mitigate climate change. Cellulosic biomass is an ideal feedstock for renewable bioethanol production, but the process is not currently economically feasible due to the high cost of pretreatment and enzyme cocktails to release fermentable sugars. Lytic polysaccharide monooxygenases (LPMOs) and cellobiose dehydrogenases (CDHs) are auxiliary enzymes that can enhance cellulose hydrolysis. In this study, four LPMO and two CDH genes were subcloned and expressed in the Saccharomyces cerevisiae Y294 laboratory strain. SDS-PAGE analysis confirmed the extracellular production of the LPMOs and CDHs in the laboratory S. cerevisiae Y294 strain. A rudimentary cellulase cocktail (cellobiohydrolase 1 and 2, endoglucanase and β-glucosidase) was expressed in the commercial CelluX™ 4 strain and extracellular production of the individual cellulases was confirmed by SDS-PAGE analysis. In vitro cooperation of the CDHs and LPMOs with the rudimentary cellulases produced by strain CelluX™ 4[F4-1] was demonstrated on Whatman filter paper. The significant levels of soluble sugars released from this crystalline cellulose substrate indicated that these auxiliary enzymes could be important components of the CBP yeast cellulolytic system.
Collapse
Affiliation(s)
- Ivy E Smuts
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Nicole J Blakeway
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa.
| |
Collapse
|
4
|
Abbate E, Andrion J, Apel A, Biggs M, Chaves J, Cheung K, Ciesla A, Clark-ElSayed A, Clay M, Contridas R, Fox R, Hein G, Held D, Horwitz A, Jenkins S, Kalbarczyk K, Krishnamurthy N, Mirsiaghi M, Noon K, Rowe M, Shepherd T, Tarasava K, Tarasow TM, Thacker D, Villa G, Yerramsetty K. Optimizing the strain engineering process for industrial-scale production of bio-based molecules. J Ind Microbiol Biotechnol 2023; 50:kuad025. [PMID: 37656881 PMCID: PMC10548853 DOI: 10.1093/jimb/kuad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.
Collapse
Affiliation(s)
- Eric Abbate
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Jennifer Andrion
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Amanda Apel
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Matthew Biggs
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Julie Chaves
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Kristi Cheung
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Anthony Ciesla
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Alia Clark-ElSayed
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Michael Clay
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Riarose Contridas
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Richard Fox
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Glenn Hein
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Dan Held
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Andrew Horwitz
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Stefan Jenkins
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | | | | | - Mona Mirsiaghi
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katherine Noon
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Mike Rowe
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Tyson Shepherd
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katia Tarasava
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Theodore M Tarasow
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Drew Thacker
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Gladys Villa
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | | |
Collapse
|
5
|
Madhavan A, Arun KB, Sindhu R, Nair BG, Pandey A, Awasthi MK, Szakacs G, Binod P. Design and genome engineering of microbial cell factories for efficient conversion of lignocellulose to fuel. BIORESOURCE TECHNOLOGY 2023; 370:128555. [PMID: 36586428 DOI: 10.1016/j.biortech.2022.128555] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The gradually increasing need for fossil fuels demands renewable biofuel substitutes. This has fascinated an increasing investigation to design innovative energy fuels that have comparable Physico-chemical and combustion characteristics with fossil-derived fuels. The efficient microbes for bioenergy synthesis desire the proficiency to consume a large quantity of carbon substrate, transfer various carbohydrates through efficient metabolic pathways, capability to withstand inhibitory components and other degradation compounds, and improve metabolic fluxes to synthesize target compounds. Metabolically engineered microbes could be an efficient methodology for synthesizing biofuel from cellulosic biomass by cautiously manipulating enzymes and metabolic pathways. This review offers a comprehensive perspective on the trends and advances in metabolic and genetic engineering technologies for advanced biofuel synthesis by applying various heterologous hosts. Probable technologies include enzyme engineering, heterologous expression of multiple genes, CRISPR-Cas technologies for genome editing, and cell surface display.
Collapse
Affiliation(s)
- Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India.
| | - K B Arun
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, Karnataka, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 689 122, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248007, Uttarkhand, India; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - George Szakacs
- Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science, 1111 Budapest, Szent Gellert ter 4, Hungary
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| |
Collapse
|
6
|
Li J, Zeng Y, Wang WB, Wan QQ, Liu CG, den Haan R, van Zyl WH, Zhao XQ. Increasing extracellular cellulase activity of the recombinant Saccharomyces cerevisiae by engineering cell wall-related proteins for improved consolidated processing of carbon neutral lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 365:128132. [PMID: 36252752 DOI: 10.1016/j.biortech.2022.128132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Sustainable bioproduction usingcarbon neutral feedstocks, especially lignocellulosic biomass, has attracted increasing attention due to concern over climate change and carbon reduction. Consolidated bioprocessing (CBP) of lignocellulosic biomass using recombinantyeast of Saccharomyces cerevisiaeis a promising strategy forlignocellulosic biorefinery. However, the economic viability is restricted by low enzyme secretion levels.For more efficient CBP, MIG1spsc01isolated from the industrial yeast which encodes the glucose repression regulator derivative was overexpressed. Increased extracellular cellobiohydrolase (CBH) activity was observed with unexpectedly decreased cell wall integrity. Further studies revealed that disruption ofCWP2, YGP1, andUTH1,which are functionally related toMIG1spsc01, also enhanced CBH secretion. Subsequently, improved cellulase production was achieved by simultaneous disruption ofYGP1and overexpression ofSED5, which remarkably increased extracellular CBH activity of 2.2-fold over the control strain. These results provide a novel strategy to improve the CBP yeast for bioconversion of carbon neutral biomass.
Collapse
Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zeng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing-Qing Wan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Willem H van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
7
|
Overexpression of LAS21 in Cellulase-Displaying Saccharomyces cerevisiae for High-Yield Ethanol Production from Pretreated Sugarcane Bagasse. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The valorization of lignocellulosic feedstocks into biofuels and biochemicals has received much attention due to its environmental friendliness and sustainability. However, engineering an ideal microorganism that can both produce sufficient cellulases and ferment ethanol is highly challenging. In this study, we have tested seven different genes that are involved in glycosylphosphatidylinositol (GPI) biosynthesis and remodeling for the improvement of cellulase activity tethered on the S. cerevisiae cell surface. It was found that the overexpression of LAS21 can improve β-glucosidase activity by 48.8% compared to the original strain. Then, the three cellulase genes (cellobiohydrolase, endoglucanase, and β-glucosidase) and the LAS21 gene were co-introduced into a diploid thermotolerant S. cerevisiae strain by a multiple-round transformation approach, resulting in the cellulolytic ECBLCCE5 strain. Further optimization of the bioprocess parameters was found to enhance the ethanol yield of the ECBLCCE5 strain. Scaling up the valorization of pretreated sugarcane bagasses in a 1 L bioreactor resulted in a maximum ethanol concentration of 28.0 g/L (86.5% of theoretical yield). Our study provides a promising way to improve the economic viability of second-generation ethanol production. Moreover, the engineering of genes involved in GPI biosynthesis and remodeling can be applied to other yeast cell surface display applications.
Collapse
|
8
|
Chetty BJ, Inokuma K, Hasunuma T, van Zyl WH, den Haan R. Improvement of cell-tethered cellulase activity in recombinant strains of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2022; 106:6347-6361. [PMID: 35951080 DOI: 10.1007/s00253-022-12114-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
Consolidated bioprocessing (CBP) remains an attractive option for the production of commodity products from pretreated lignocellulose if a process-suitable organism can be engineered. The yeast Saccharomyces cerevisiae requires engineered cellulolytic activity to enable its use in CBP production of second-generation (2G) bioethanol. A promising strategy for heterologous cellulase production in yeast entails displaying enzymes on the cell surface by means of glycosylphosphatidylinositol (GPI) anchors. While strains producing a core set of cell-adhered cellulases that enabled crystalline cellulose hydrolysis have been created, secreted levels of enzyme were insufficient for complete cellulose hydrolysis. In fact, all reported recombinant yeast CBP candidates must overcome the drawback of generally low secretion titers. Rational strain engineering can be applied to enhance the secretion phenotype. This study aimed to improve the amount of cell-adhered cellulase activities of recombinant S. cerevisiae strains expressing a core set of four cellulases, through overexpression of genes that were previously shown to enhance cellulase secretion. Results showed significant increases in cellulolytic activity for all cell-adhered cellulase enzyme types. Cell-adhered cellobiohydrolase activity was improved by up to 101%, β-glucosidase activity by up to 99%, and endoglucanase activity by up to 231%. Improved hydrolysis of crystalline cellulose of up to 186% and improved ethanol yields from this substrate of 40-50% in different strain backgrounds were also observed. In addition, improvement in resistance to fermentation stressors was noted in some strains. These strains represent a step towards more efficient organisms for use in 2G biofuel production. KEY POINTS: • Cell-surface-adhered cellulase activity was improved in strains engineered for CBP. • Levels of improvement of activity were strain and enzyme dependent. • Crystalline cellulose conversion to ethanol could be improved up to 50%.
Collapse
Affiliation(s)
- Bronwyn Jean Chetty
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | | | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| |
Collapse
|
9
|
Kim SR, Eckert CA, Mazzoli R. Editorial: Microorganisms for Consolidated 2nd Generation Biorefining. Front Microbiol 2022; 13:940610. [PMID: 35783433 PMCID: PMC9248810 DOI: 10.3389/fmicb.2022.940610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Soo Rin Kim
- School of Food Science and Biotechnology, Research Institute of Tailored Food Technology, Kyungpook National University, Daegu, South Korea
| | - Carrie A. Eckert
- Synthetic Biology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- *Correspondence: Roberto Mazzoli
| |
Collapse
|
10
|
Cho JS, Oh HJ, Jang YE, Kim HJ, Kim A, Song JA, Lee EJ, Lee J. Synthetic pro-peptide design to enhance the secretion of heterologous proteins by Saccharomyces cerevisiae. Microbiologyopen 2022; 11:e1300. [PMID: 35765186 PMCID: PMC9178654 DOI: 10.1002/mbo3.1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 12/02/2022] Open
Abstract
Heterologous protein production in Saccharomyces cerevisiae is a useful and effective strategy with many advantages, including the secretion of proteins that require posttranslational processing. However, heterologous proteins in S. cerevisiae are often secreted at comparatively low levels. To improve the production of the heterologous protein, human granulocyte colony‐stimulating factor (hG‐CSF) in S. cerevisiae, a secretion‐enhancing peptide cassette including an hIL‐1β‐derived propeptide, was added and used as a secretion enhancer to alleviate specific bottlenecks in the yeast secretory pathway. The effects of three key parameters—N‐glycosylation, net negative charge balance, and glycine‐rich flexible linker—were investigated in batch cultures of S. cerevisiae. Using a three‐stage design involving screening, selection, and optimization, the production and secretion of hG‐CSF by S. cerevisiae were significantly increased. The amount of extracellular mature hG‐CSF produced by the optimized propeptide after the final stage increased by 190% compared to that of the original propeptide. Although hG‐CSF was used as the model protein in the current study, this strategy applies to the enhanced production of other heterologous proteins, using S. cerevisiae as the host.
Collapse
Affiliation(s)
- Ji Sung Cho
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Hye Ji Oh
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Young Eun Jang
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Hyun Jin Kim
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Areum Kim
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Jong-Am Song
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical Engineering, Kyungpook National University, Daegu, Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Seoul, Korea
| |
Collapse
|
11
|
Kroukamp H, Peng K, Paulsen IT, den Haan R. Fluorescence-Based Biosensors for the Detection of the Unfolded Protein Response. Methods Mol Biol 2022; 2378:19-30. [PMID: 34985691 DOI: 10.1007/978-1-0716-1732-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The unfolded protein response (UPR) is a highly conserved protein quality control mechanism of eukaryotic cells. Aberrations in this response have been linked to several human diseases, including retinitis pigmentosa and several cancers, and have been shown to have a drastic impact on recombinant protein yields in fungal, insect, and mammalian cell lines. Here, we describe the use of in vivo biosensors to measure and characterize this dynamic cellular response, specifically for detecting the UPR induced by protein overproduction stress in the model cell factory Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Heinrich Kroukamp
- Department of Molecular Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Kai Peng
- Department of Molecular Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| |
Collapse
|
12
|
den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
Collapse
Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
| |
Collapse
|
13
|
Peng K, Kroukamp H, Pretorius IS, Paulsen IT. Yeast Synthetic Minimal Biosensors for Evaluating Protein Production. ACS Synth Biol 2021; 10:1640-1650. [PMID: 34126009 DOI: 10.1021/acssynbio.0c00633] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The unfolded protein response (UPR) is a highly conserved cellular response in eukaryotic cells to counteract endoplasmic reticulum (ER) stress, typically triggered by unfolded protein accumulation. In addition to its relevance to human diseases like cancer, the induction of the UPR has a significant impact on the recombinant protein production in eukaryotic cell factories, including the industrial workhorseSaccharomyces cerevisiae. Being able to accurately detect and measure this ER stress response in single cells, enables the rapid optimization of protein production conditions and high-throughput strain selection strategies. Current methodologies to monitor the UPR in S. cerevisiae are often temporally and spatially removed from the cultivation stage or lack updated systematic evaluation. To this end, we constructed and systematically evaluated a series of high-throughput UPR sensors by different designs, incorporating either yeast native UPR promoters or novel synthetic minimal UPR promoters. The native promoters of DER1 and ERO1 were identified to have suitable UPR biosensor properties and served as an expression level guide for orthogonal sensor benchmarking. Our best synthetic minimal sensor is only 98 bp in length, has minimal homology to other native yeast sequences and displayed superior sensor characteristics. The synthetic minimal UPR sensor was able to accurately distinguish between cells expressing different heterologous proteins and between the different secretion levels of the same protein. This work demonstrated the potential of synthetic UPR biosensors as high-throughput tools to predict the protein production capacity of strains, interrogate protein properties hampering their secretion, and guide rational engineering strategies for optimal heterologous protein production.
Collapse
Affiliation(s)
- Kai Peng
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Heinrich Kroukamp
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Ian T. Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
14
|
Catalyst derived from wastes for biofuel production: a critical review and patent landscape analysis. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01948-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
15
|
Suntara C, Cherdthong A, Wanapat M, Uriyapongson S, Leelavatcharamas V, Sawaengkaew J, Chanjula P, Foiklang S. Isolation and Characterization of Yeasts from Rumen Fluids for Potential Use as Additives in Ruminant Feeding. Vet Sci 2021; 8:vetsci8030052. [PMID: 33808746 PMCID: PMC8003577 DOI: 10.3390/vetsci8030052] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Saccharomyces cerevisiae is a yeast strain often used to improve the feed quality of ruminants. However, S. cerevisiae has limited capacity to provide biomass when inoculated with carbon sources and a low ability to produce cellulase enzymes. Here, we hypothesized that yeast in the rumen produces a large amount of biomass and could release cellulase enzymes to break down fiber content. Therefore, the aim of this study was to screen, isolate and identify yeast from the rumen fluids of Holstein Friesian steers and measure the efficiency of biomass production and cellulase activity. A fermentation medium containing sugarcane molasses as a carbon source and urea as a nitrogen source was optimized. Two fistulated–crossbred Holstein Friesian steers averaging 350 ± 20 kg body weight were used to screen and isolate the ruminal yeast. Two experiments were designed: First, a 12 × 3 × 3 factorial was used in a completely randomized design to determine biomass and carboxymethyl cellulase activity. Factor A was the isolated yeast and S. cerevisiae. Factor B was sugarcane molasses (M) concentration. Factor C was urea (U) concentration. In the second experiment, potential yeasts were selected, identified, and analyzed for 7 × 4 factorial use in a completely randomized design. Factor A was the incubation times. Factor B was the isolated yeast strains, including codes H-Khon Kaen University (KKU) 20 (as P. kudriavzevii-KKU20), I-KKU20 (C. tropicalis-KKU20), and C-KKU20 (as Galactomyces sp.-KKU20). Isolation was imposed under aerobic conditions, resulting in a total of 11 different colonies. Two appearances of colonies including asymmetric colonies of isolated yeast (indicated as A, B, C, E, and J) and ovoid colonies (coded as D, F, G, H, I, and K) were noted. Isolated yeast from the rumen capable of providing a high amount of biomass when inoculant consisted of the molasses 15% + urea 3% (M15 + U3), molasses 25% + urea 1% (M25 + U1), molasses 25% + urea 3% (M25 + U3), and molasses 25% + urea 5% (M25 + U5) when compared to the other media solution (p < 0.01). In addition, 11 isolated biomass-producing yeasts were found in the media solution of M25 + U1. There were 4 isolates cellulase producing yeasts discovered in the media solution of M25 + U1 and M25 + U5 whereas molasses 5% + urea 1% (M5 + U1), molasses 5% + urea 3% (M5 + U3), molasses 5% + urea 5% (M5 + U5), molasses 15% + urea 1% (M15 + U1), molasses 15% + urea 3% (M5 + U3), and M25 + U3 were found with 2, 3, 1, 2, 1, and 2 isolates, respectively. Ruminal yeast strains H-KKU20, I-KKU20, and C-KKU20 were selected for their ability to produce biomass. Identification of isolates H-KKU20 and I-KKU20 revealed that those isolates belonged to Pichia kudriavzevii-KKU20 and Candida tropicalis-KKU20 while C-KKU20 was identified as Galactomyces sp.-KKU20. Two strains provided maximum cell growth: P. kudriavzevii-KKU20 (9.78 and 10.02 Log cell/mL) and C. tropicalis-KKU20 (9.53 and 9.6 Log cells/mL) at 60 and 72 h of incubation time, respectively. The highest ethanol production was observed in S. cerevisiae at 76.4, 77.8, 78.5, and 78.6 g/L at 36, 48, 60, and 72 h of incubation time, respectively (p < 0.01). The P. kudriavzevii-KKU20 yielded the least reducing sugar at about 30.6 and 29.8 g/L at 60 and 72 h of incubation time, respectively. The screening and isolation of yeasts from rumen fluids resulted in 11 different yeasts being obtained. The potential yeasts discovered in the rumen fluid of cattle were Pichia kudriavzevii-KKU20, Candida tropicalis-KKU20, and Galactomyces sp.-KKU20. P. kudriavzevii-KKU20 had higher results than the other yeasts in terms of biomass production, cellulase enzyme activity, and cell number.
Collapse
Affiliation(s)
- Chanon Suntara
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (C.S.); (M.W.); (S.U.)
| | - Anusorn Cherdthong
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (C.S.); (M.W.); (S.U.)
- Correspondence: ; Tel.: +66-43-202362
| | - Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (C.S.); (M.W.); (S.U.)
| | - Suthipong Uriyapongson
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (C.S.); (M.W.); (S.U.)
| | - Vichai Leelavatcharamas
- Fermentation Research Center for Value Added Agricultural Products (FerVAAP), Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Jutaporn Sawaengkaew
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Pin Chanjula
- Animal Production Innovation and Management Division, Faculty of Natural Resources, Hat Yai Campus, Prince of Songkla University, Songkhla 90112, Thailand;
| | - Suban Foiklang
- Faculty of Animal Science and Technology, Maejo University, Chiangmai 50290, Thailand;
| |
Collapse
|
16
|
Novel Crabtree negative yeast from rumen fluids can improve rumen fermentation and milk quality. Sci Rep 2021; 11:6236. [PMID: 33737628 PMCID: PMC7973541 DOI: 10.1038/s41598-021-85643-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
Upgrading the nutritive value of rice straw (RS) is necessary to increase its contribution to enhancing meat and milk production. Present work verified whether novel Crabtree negative yeast inoculant could promote RS utilization, rumen fermentation, and milk quality in tropical crossbred lactating Holstein cows. The new stain of Crabtree negative yeasts (Pichia kudriavzevii KKU20 and Candida tropicalis KKU20) was isolated from the rumen of dairy cattle. This study used 6 multiparous crossbreds between Holstein Frisian × Zebu dairy cows in their mid-lactation period. Dairy cows were randomly allocated to three ensiled RS with various yeast stains including Saccharomyces cerevisiae, P. kudriavzevii KKU20, and C. tropicalis KKU20 according to a 3 × 3 replicated Latin square design. Crabtree-negative yeast (P. kudriavzevii and C. tropicalis) increased the apparent digestibility of dry matter by about 6.9% when compared with Crabtree-positive yeast (S. cerevisiae). Bacterial populations were highest with ensiled RS by C. tropicalis KKU20. Ensiled RS with Crabtree-negative yeasts were significantly increased with total volatile fatty acids, but they did not affect volatile fatty acid profiles. Milk protein precentage was highest at 35.6 g/kg when C. tropicalis was fed, and lowest when applied with S. cerevisiae and P. kudriavzevii KKU20 in ensiled RS at 34.5 and 34.1 g/kg, respectively. Thus, feeding ensiled RS with novel Crabtree negative yeast could improve RS digestion, rumen fermentation, and milk protein content in dairy cows.
Collapse
|
17
|
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: 2] [Impact Index Per Article: 0.7] [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.
Collapse
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.
| |
Collapse
|
18
|
Wightman ELI, Kroukamp H, Pretorius IS, Paulsen IT, Nevalainen HKM. Rapid optimisation of cellulolytic enzymes ratios in Saccharomyces cerevisiae using in vitro SCRaMbLE. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:182. [PMID: 33292481 PMCID: PMC7607656 DOI: 10.1186/s13068-020-01823-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/23/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND For the economic production of biofuels and other valuable products from lignocellulosic waste material, a consolidated bioprocessing (CBP) organism is required. With efficient fermentation capability and attractive industrial qualities, Saccharomyces cerevisiae is a preferred candidate and has been engineered to produce enzymes that hydrolyze cellulosic biomass. Efficient cellulose hydrolysis requires the synergistic action of several enzymes, with the optimum combined activity ratio dependent on the composition of the substrate. RESULTS In vitro SCRaMbLE generated a library of plasmids containing different ratios of a β-glucosidase gene (CEL3A) from Saccharomycopsis fibuligera and an endoglucanase gene (CEL5A) from Trichoderma reesei. S. cerevisiae, transformed with the plasmid library, displayed a range of individual enzyme activities and synergistic capabilities. Furthermore, we show for the first time that 4,6-O-(3-ketobutylidene)-4-nitrophenyl-β-D-cellopentaoside (BPNPG5) is a suitable substrate to determine synergistic Cel3A and Cel5A action and an accurate predictive model for this synergistic action was devised. Strains with highest BPNPG5 activity had an average CEL3A and CEL5A gene cassette copy number of 1.3 ± 0.6 and 0.8 ± 0.2, respectively (ratio of 1.6:1). CONCLUSIONS Here, we describe a synthetic biology approach to rapidly optimise gene copy numbers to achieve efficient synergistic substrate hydrolysis. This study demonstrates how in vitro SCRaMbLE can be applied to rapidly combine gene constructs in various ratios to allow screening of synergistic enzyme activities for efficient substrate hydrolysis.
Collapse
Affiliation(s)
- Elizabeth L I Wightman
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Heinrich Kroukamp
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
| | | | - Ian T Paulsen
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Helena K M Nevalainen
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| |
Collapse
|
19
|
Microbial lignin peroxidases: Applications, production challenges and future perspectives. Enzyme Microb Technol 2020; 141:109669. [DOI: 10.1016/j.enzmictec.2020.109669] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
|
20
|
Methods for Metabolic Engineering of a Filamentous Trichoderma reesei. Methods Mol Biol 2020. [PMID: 32720145 DOI: 10.1007/978-1-0716-0195-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this work, we describe genetic tools and techniques for engineering Trichoderma reesei for the production of farnesene. Enhanced production of farnesene was used as an example of this methodology; as were the overexpression of a key enzyme, HMGS, in the MVA pathway.
Collapse
|
21
|
Factors affecting yeast ethanol tolerance and fermentation efficiency. World J Microbiol Biotechnol 2020; 36:114. [DOI: 10.1007/s11274-020-02881-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
|
22
|
Enzymatic Hydrolysis of Softwood Derived Paper Sludge by an In Vitro Recombinant Cellulase Cocktail for the Production of Fermentable Sugars. Catalysts 2020. [DOI: 10.3390/catal10070775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Paper sludge is an attractive biomass feedstock for bioconversion to ethanol due to its low cost and the lack of pretreatment required for its bioprocessing. This study assessed the use of a recombinant cellulase cocktail (mono-components: S. cerevisiae-derived PcBGL1B (BGL), TeCel7A (CBHI), ClCel6A (CBHII) and TrCel5A (EGII) mono-component cellulase enzymes) for the efficient saccharification of softwood-derived paper sludge to produce fermentable sugars. The paper sludge mainly contained 74.3% moisture and 89.7% (per dry mass (DM)) glucan with a crystallinity index of 91.5%. The optimal protein ratio for paper sludge hydrolysis was observed at 9.4: 30.2: 30.2: 30.2% for BGL: CBHI: CBHII: EGII. At a protein loading of 7.5 mg/g DW paper sludge, the yield from hydrolysis was approximately 80%, based on glucan, with scanning electron microscopy micrographs indicating a significant alteration in the microfibril size (length reduced from ≥ 2 mm to 93 µm) of the paper sludge. The paper sludge hydrolysis potential of the Opt CelMix (formulated cellulase cocktail) was similar to the commercial Cellic CTec2® and Celluclast® 1.5 L cellulase preparations and better than Viscozyme® L. Low enzyme loadings (15 mg/g paper sludge) of the Opt CelMix and solid loadings ranging between 1 to 10% (w/v) rendered over 80% glucan conversion. The high glucose yields attained on the paper sludge by the low enzyme loading of the Opt CelMix demonstrated the value of enzyme cocktail optimisation on specific substrates for efficient cellulose conversion to fermentable sugars.
Collapse
|
23
|
Lamour J, Wan C, Zhang M, Zhao X, Den Haan R. Overexpression of endogenous stress-tolerance related genes in Saccharomyces cerevisiae improved strain robustness and production of heterologous cellobiohydrolase. FEMS Yeast Res 2020; 19:5479884. [PMID: 31073597 DOI: 10.1093/femsyr/foz035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
To enable Saccharomyces cerevisiae to produce renewable fuels from lignocellulose in a consolidated bioprocess, a heterologous cellulase system must be engineered into this yeast. In addition, inherently low secretion titers and sensitivity to adverse environmental conditions must be overcome. Here, two native S. cerevisiae genes related to yeast stress tolerance, YHB1 and SET5, were overexpressed under transcriptional control of the constitutive PGK1 promoter and their effects on heterologous secretion of Talaromyces emersonii cel7A cellobiohydrolase was investigated. Transformants showed increased secreted enzyme activity that ranged from 22% to 55% higher compared to the parental strains and this did not lead to deleterious growth effects. The recombinant strains overexpressing either YHB1 or SET5 also demonstrated multi-tolerant characteristics desirable in bioethanol production, i.e. improved tolerance to osmotic and heat stress. Quantitative reverse transcriptase PCR analysis in these strains showed decreased transcription of secretion pathway genes. However, decreased unfolded protein response was also observed, suggesting novel mechanisms for enhancing enzyme production through stress modulation. Overexpression of YHB1 in an unrelated diploid strain also enhanced stress tolerance and improved ethanol productivity in medium containing acetic acid. To our knowledge, this is the first demonstration that improved heterologous secretion and environmental stress tolerance could be engineered into yeast simultaneously.
Collapse
Affiliation(s)
- Jarryd Lamour
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Chun Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan Den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| |
Collapse
|
24
|
Claes A, Deparis Q, Foulquié-Moreno MR, Thevelein JM. Simultaneous secretion of seven lignocellulolytic enzymes by an industrial second-generation yeast strain enables efficient ethanol production from multiple polymeric substrates. Metab Eng 2020; 59:131-141. [DOI: 10.1016/j.ymben.2020.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/01/2020] [Accepted: 02/18/2020] [Indexed: 01/22/2023]
|
25
|
Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
Collapse
|
26
|
Mazzoli R. Metabolic engineering strategies for consolidated production of lactic acid from lignocellulosic biomass. Biotechnol Appl Biochem 2020; 67:61-72. [DOI: 10.1002/bab.1869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/05/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Roberto Mazzoli
- Structural and Functional BiochemistryLaboratory of Proteomics and Metabolic Engineering of ProkaryotesDepartment of Life Sciences and Systems BiologyUniversity of Torino Torino Italy
| |
Collapse
|
27
|
Cedras G, Kroukamp H, Van Zyl WH, Den Haan R. The
in vivo
detection and measurement of the unfolded protein response in recombinant cellulase producing
Saccharomyces cerevisiae
strains. Biotechnol Appl Biochem 2020; 67:82-94. [DOI: 10.1002/bab.1819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/16/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Gillian Cedras
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
| | - Heinrich Kroukamp
- Department of Molecular SciencesMacquarie University North Ryde NSW Australia
| | | | - Riaan Den Haan
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
| |
Collapse
|
28
|
Improved cellulase expression in diploid yeast strains enhanced consolidated bioprocessing of pretreated corn residues. Enzyme Microb Technol 2019; 131:109382. [DOI: 10.1016/j.enzmictec.2019.109382] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/27/2019] [Accepted: 07/12/2019] [Indexed: 01/12/2023]
|
29
|
Emerging technologies for the pretreatment of lignocellulosic materials for bio-based products. Appl Microbiol Biotechnol 2019; 104:455-473. [DOI: 10.1007/s00253-019-10158-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
|
30
|
Tarraran L, Mazzoli R. Alternative strategies for lignocellulose fermentation through lactic acid bacteria: the state of the art and perspectives. FEMS Microbiol Lett 2019; 365:4995910. [PMID: 30007320 DOI: 10.1093/femsle/fny126] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022] Open
Abstract
Lactic acid bacteria (LAB) have a long history in industrial processes as food starters and biocontrol agents, and also as producers of high-value compounds. Lactic acid, their main product, is among the most requested chemicals because of its multiple applications, including the synthesis of biodegradable plastic polymers. Moreover, LAB are attractive candidates for the production of ethanol, polyhydroalkanoates, sweeteners and exopolysaccharides. LAB generally have complex nutritional requirements. Furthermore, they cannot directly ferment inexpensive feedstocks such as lignocellulose. This significantly increases the cost of LAB fermentation and hinders its application in the production of high volumes of low-cost chemicals. Different strategies have been explored to extend LAB fermentation to lignocellulosic biomass. Fermentation of lignocellulose hydrolysates by LAB has been frequently reported and is the most mature technology. However, current economic constraints of this strategy have driven research for alternative approaches. Co-cultivation of LAB with native cellulolytic microorganisms may reduce the high cost of exogenous cellulase supplementation. Special attention is given in this review to the construction of recombinant cellulolytic LAB by metabolic engineering, which may generate strains able to directly ferment plant biomass. The state of the art of these strategies is illustrated along with perspectives of their applications to industrial second generation biorefinery processes.
Collapse
Affiliation(s)
- Loredana Tarraran
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy
| |
Collapse
|
31
|
Davison SA, den Haan R, van Zyl WH. Identification of superior cellulase secretion phenotypes in haploids derived from natural Saccharomyces cerevisiae isolates. FEMS Yeast Res 2019; 19:5154912. [PMID: 30388213 DOI: 10.1093/femsyr/foy117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is considered an important host for consolidated bioprocessing and the production of high titres of recombinant cellulases is required for efficient hydrolysis of lignocellulosic substrates to fermentable sugars. Since recombinant protein secretion profiles vary highly among different strain backgrounds, careful selection of robust strains with optimal secretion profiles is of crucial importance. Here, we construct and screen sets of haploid derivatives, derived from natural strain isolates YI13, FINI and YI59, for improved general cellulase secretion. This report details a novel approach that combines secretion profiles of strains and phenotypic responses to stresses known to influence the secretion pathway for the development of a phenotypic screen to isolate strains with improved secretory capacities. A clear distinction was observed between the YI13 haploid derivatives and industrial and laboratory counterparts, Ethanol Red and S288c, respectively. By using sub-lethal concentrations of the secretion stressor tunicamycin and cell wall stressor Congo Red, YI13 haploid derivative strains demonstrated tolerance profiles related to their heterologous secretion profiles. Our results demonstrated that a new screening technique combined with a targeted mating approach could produce a pool of novel strains capable of high cellulase secretion.
Collapse
Affiliation(s)
- Steffi A Davison
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Willem Heber van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
32
|
Favaro L, Jansen T, van Zyl WH. Exploring industrial and naturalSaccharomyces cerevisiaestrains for the bio-based economy from biomass: the case of bioethanol. Crit Rev Biotechnol 2019; 39:800-816. [DOI: 10.1080/07388551.2019.1619157] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Trudy Jansen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | |
Collapse
|
33
|
Song X, Li Y, Wu Y, Cai M, Liu Q, Gao K, Zhang X, Bai Y, Xu H, Qiao M. Metabolic engineering strategies for improvement of ethanol production in cellulolytic Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5071949. [PMID: 30107496 DOI: 10.1093/femsyr/foy090] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/09/2018] [Indexed: 01/31/2023] Open
Abstract
As a traditional ethanol-producing microorganism, Saccharomyces cerevisiae is an ideal host for consolidated bioprocessing. However, expression of heterologous cellulase increases the metabolic burden in yeast, which results in low cellulase activity and poor cellulose degradation efficiency. In this study, cellulase-expressing yeast strains that could efficiently degrade different cellulosic substrates were created by optimizing cellulase ratios through a POT1-mediated δ-integration strategy. Metabolic engineering strategies, including optimization of codon usage, promoter and signal peptide, were also included in this system. We also confirmed that heterologous cellulase expression in cellulosic yeast induced the unfolded protein response. To enhance protein folding capacity, the endoplasmic reticulum chaperone protein BiP and the disulfide isomerase Pdi1p were overexpressed, and the Golgi membrane protein Ca2+/Mn2+ ATPase Pmr1p was disrupted to decrease the glycosylation of cellulase. The resultant strain, SK18-3, could produce 5.4 g L-1 ethanol with carboxymethyl-cellulose. Strain SK12-50 achieved 4.7 g L-1 ethanol production with phosphoric acid swollen cellulose hydrolysis. When Avicel was used as the substrate, 3.8 g L-1 ethanol (75% of the theoretical maximum yield) was produced in SK13-34. This work will significantly increase our knowledge of how to engineer optimal yeast strains for biofuel production from cellulosic biomass.
Collapse
Affiliation(s)
- Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuzhen Wu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Quanli Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Kai Gao
- Tianjin Academy of Environmental Sciences, No. 17 Fukang Road, Nankai District, Tianjin 300071, China
| | - Xiuming Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yanling Bai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Haijin Xu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| |
Collapse
|
34
|
Zhang W, Yang Y, Liu X, Liu C, Bai Z. Development of a secretory expression system with high compatibility between expression elements and an optimized host for endoxylanase production in Corynebacterium glutamicum. Microb Cell Fact 2019; 18:72. [PMID: 30995928 PMCID: PMC6471998 DOI: 10.1186/s12934-019-1116-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In terms of protein production, the internal environment of the host influences the activity of expression elements, thus affecting the expression level of the target protein. Native expression elements from a specific strain always function well in the original host. In the present study, to enhance the endoxylanase (XynA) production level in Corynebacterium glutamicum CGMCC1.15647 with its native expression elements, approaches to reduce host expression obstacles and to promote expression were evaluated. RESULTS We identified the signal peptide of CspB2 in C. glutamicum CGMCC1.15647 by MALDI-TOF and applied it along with its promoter for the production of endoxylanase (XynA) in this strain. The native cspB2 promoter and cspB2 signal peptide are superior to the well-used cspB1 promoter and cspA signal peptide for XynA expression in C. glutamicum CGMCC1.15647, and expression in this strain is superior to the expression in C. glutamicum ATCC13032. The highest XynA secretion efficiency level in deep 24-well plates level (2492.88 U/mL) was achieved by disruption of the cell wall protein CspB2 and the protease ClpS, chromosomal integration of xynA and coexisting plasmid expression, which increased expression 11.43- and 1.35-fold compared to that of chromosomal expression and pXMJ19-xynA-mediated expression in the original strain, respectively. In fed-batch cultivation, the highest XynA accumulation (1.77 g/L) was achieved in the culture supernatant after 44 h of cultivation. CONCLUSION Adaptation between the expression elements and the host is crucial for XynA production in C. glutamicum CGMCC1.15647. Strategies including host optimization, chromosomal integration, and coexistence of plasmids were useful for efficient protein production in C. glutamicum.
Collapse
Affiliation(s)
- Wei Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Chunli Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Kumar N, Sudan SK, Garg R, Sahni G. Enhanced production of novel halostable recombinant endoglucanase derived from the metagenomic library using fed-batch fermentation. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.12.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
Collapse
Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
40
|
de Paiva DP, Rocha TB, Rubini MR, Nicola AM, Reis VCB, Torres FAG, de Moraes LMP. A study on the use of strain-specific and homologous promoters for heterologous expression in industrial Saccharomyces cerevisiae strains. AMB Express 2018; 8:82. [PMID: 29785587 PMCID: PMC5962522 DOI: 10.1186/s13568-018-0613-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/12/2018] [Indexed: 02/08/2023] Open
Abstract
Polymorphism is well known in Saccharomyces cerevisiae strains used for different industrial applications, however little is known about its effects on promoter efficiency. In order to test this, five different promoters derived from an industrial and a laboratory (S288c) strain were used to drive the expression of eGFP reporter gene in both cells. The ADH1 promoter (PADH1) in particular, which showed more polymorphism among the promoters analyzed, also exhibited the highest differences in intracellular fluorescence production. This was further confirmed by Northern blot analysis. The same behavior was also observed when the gene coding for secreted α-amylase from Cryptococcus flavus was placed under the control of either PADH1. These results underline the importance of the careful choice of the source of the promoter to be used in industrial yeast strains for heterologous expression.
Collapse
|
41
|
Chang JJ, Lin YJ, Lay CH, Thia C, Wu YC, Hou YH, Huang CC, Li WH. Constructing a cellulosic yeast host with an efficient cellulase cocktail. Biotechnol Bioeng 2017; 115:751-761. [PMID: 29197184 DOI: 10.1002/bit.26507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 10/26/2017] [Accepted: 11/28/2017] [Indexed: 01/13/2023]
Abstract
Cellulose is a renewable feedstock for green industry. It is therefore important to develop a technique to construct a host with a high cellulolytic efficiency to digest cellulose. In this study, we developed a convenient host-engineering technique to adjust the expression levels of heterologous genes in the host by promoter rearrangement and gene copy number adjustment. Using genes from different glycoside hydrolase (GH) families including GH2, GH3, GH5, GH6, GH7, and GH12 from Aspergillus niger, Trichoderma reesei, and Neocallimastix patriciarum, we constructed a cellulolytic Kluyveromyces marxianus with eight cellulase gene-cassettes that produced a cellulase cocktail with a high cellulolytic efficiency, leading to a significant reduction in enzyme cost in a rice straw saccharification process. Our technique can be used to design a host that can efficiently convert biomass feedstock to biofuel.
Collapse
Affiliation(s)
- Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chyi-How Lay
- Master Program of Green Energy Science and Technology, Feng Chia University, Taichung, Taiwan.,Green Energy Development Center, Feng Chia University, Taichung, Taiwan
| | - Caroline Thia
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yueh-Chin Wu
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Han Hou
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
42
|
Kroukamp H, den Haan R, la Grange DC, Sibanda N, Foulquié‐Moreno MR, Thevelein JM, van Zyl WH. Strain Breeding Enhanced Heterologous Cellobiohydrolase Secretion by
Saccharomyces cerevisiae
in a Protein Specific Manner. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/10/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Heinrich Kroukamp
- Department of MicrobiologyUniversity of StellenboschStellenboschSouth Africa
| | - Riaan den Haan
- Department of BiotechnologyUniversity of Western CapeBellvilleSouth Africa
| | - Daniël C. la Grange
- Unit of Environmental Sciences and ManagementNorth‐West UniversityPotchefstroomSouth Africa
| | - Ntsako Sibanda
- Department of Biochemistry, Microbiology and BiotechnologyUniversity of LimpopoSovengaSouth Africa
| | - Maria R. Foulquié‐Moreno
- Institute of Botany and MicrobiologyKU LeuvenLeuven‐HeverleeBelgium
- Department of Molecular Microbiology, VIBLeuven‐HeverleeBelgium
| | - Johan M. Thevelein
- Institute of Botany and MicrobiologyKU LeuvenLeuven‐HeverleeBelgium
- Department of Molecular Microbiology, VIBLeuven‐HeverleeBelgium
| | - Willem H. van Zyl
- Department of MicrobiologyUniversity of StellenboschStellenboschSouth Africa
| |
Collapse
|
43
|
Gandini C, Tarraran L, Kalemasi D, Pessione E, Mazzoli R. RecombinantLactococcus lactisfor efficient conversion of cellodextrins into L-lactic acid. Biotechnol Bioeng 2017; 114:2807-2817. [DOI: 10.1002/bit.26400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Chiara Gandini
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Loredana Tarraran
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Denis Kalemasi
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Roberto Mazzoli
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| |
Collapse
|
44
|
Song X, Liu Q, Mao J, Wu Y, Li Y, Gao K, Zhang X, Bai Y, Xu H, Qiao M. POT1-mediated δ-integration strategy for high-copy, stable expression of heterologous proteins in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:4083647. [DOI: 10.1093/femsyr/fox064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Quanli Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Jiwei Mao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Yuzhen Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Kai Gao
- Tianjin Academy of Environmental Sciences, No. 17 Fukang Road, Nankai District, Tianjin, China
| | - Xiuming Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Yanling Bai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, China
| |
Collapse
|
45
|
Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT. Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 2017; 17:3868933. [PMID: 28899031 PMCID: PMC5812533 DOI: 10.1093/femsyr/fox044] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.
Collapse
Affiliation(s)
- Mickel L. A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Hans de Bruijn
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
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.
Collapse
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.
| |
Collapse
|
48
|
Cripwell RA, Rose SH, van Zyl WH. Expression and comparison of codon optimised Aspergillus tubingensis amylase variants in Saccharomyces cerevisiae. FEMS Yeast Res 2017. [DOI: 10.1093/femsyr/fox040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
49
|
Makhuvele R, Ncube I, Jansen van Rensburg EL, La Grange DC. Isolation of fungi from dung of wild herbivores for application in bioethanol production. Braz J Microbiol 2017. [PMID: 28629967 PMCID: PMC5628305 DOI: 10.1016/j.bjm.2016.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Producing biofuels such as ethanol from non-food plant material has the potential to meet transportation fuel requirements in many African countries without impacting directly on food security. The current shortcomings in biomass processing are inefficient fermentation of plant sugars, such as xylose, especially at high temperatures, lack of fermenting microbes that are able to resist inhibitors associated with pre-treated plant material and lack of effective lignocellulolytic enzymes for complete hydrolysis of plant polysaccharides. Due to the presence of residual partially degraded lignocellulose in the gut, the dung of herbivores can be considered as a natural source of pre-treated lignocellulose. A total of 101 fungi were isolated (36 yeast and 65 mould isolates). Six yeast isolates produced ethanol during growth on xylose while three were able to grow at 42 °C. This is a desirable growth temperature as it is closer to that which is used during the cellulose hydrolysis process. From the yeast isolates, six isolates were able to tolerate 2 g/L acetic acid and one tolerated 2 g/L furfural in the growth media. These inhibitors are normally generated during the pre-treatment step. When grown on pre-treated thatch grass, Aspergillus species were dominant in secretion of endo-glucanase, xylanase and mannanase.
Collapse
Affiliation(s)
- Rhulani Makhuvele
- University of Limpopo, Department of Biochemistry, Microbiology, and Biotechnology, Sovenga, South Africa
| | - Ignatious Ncube
- University of Limpopo, Department of Biochemistry, Microbiology, and Biotechnology, Sovenga, South Africa
| | | | - Daniël Coenrad La Grange
- Unit of Environmental Sciences and Management, North-West University, Potchefstroom Campus, Potchefstroom, South Africa.
| |
Collapse
|
50
|
Liu Z, Inokuma K, Ho SH, den Haan R, van Zyl WH, Hasunuma T, Kondo A. Improvement of ethanol production from crystalline cellulose via optimizing cellulase ratios in cellulolytic Saccharomyces cerevisiae. Biotechnol Bioeng 2017; 114:1201-1207. [PMID: 28112385 DOI: 10.1002/bit.26252] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/28/2016] [Accepted: 01/15/2017] [Indexed: 12/30/2022]
Abstract
Crystalline cellulose is one of the major contributors to the recalcitrance of lignocellulose to degradation, necessitating high dosages of cellulase to digest, thereby impeding the economic feasibility of cellulosic biofuels. Several recombinant cellulolytic yeast strains have been developed to reduce the cost of enzyme addition, but few of these strains are able to efficiently degrade crystalline cellulose due to their low cellulolytic activities. Here, by combining the cellulase ratio optimization with a novel screening strategy, we successfully improved the cellulolytic activity of a Saccharomyces cerevisiae strain displaying four different synergistic cellulases on the cell surface. The optimized strain exhibited an ethanol yield from Avicel of 57% of the theoretical maximum, and a 60% increase of ethanol titer from rice straw. To our knowledge, this work is the first optimization of the degradation of crystalline cellulose by tuning the cellulase ratio in a cellulase cell-surface display system. This work provides key insights in engineering the cellulase cocktail in a consolidated bioprocessing yeast strain. Biotechnol. Bioeng. 2017;114: 1201-1207. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Zhuo Liu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Willem H van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.,Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| |
Collapse
|