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Xiong L, Wang YT, Zhou MH, Takagi H, Qin J, Zhao XQ. Overexpression of arginase gene CAR1 renders yeast Saccharomyces cerevisiae acetic acid tolerance. Synth Syst Biotechnol 2024; 9:723-732. [PMID: 38882181 PMCID: PMC11178985 DOI: 10.1016/j.synbio.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/12/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Acetic acid is a common inhibitor present in lignocellulose hydrolysate, which inhibits the ethanol production by yeast strains. Therefore, the cellulosic ethanol industry requires yeast strains that can tolerate acetic acid stress. Here we demonstrate that overexpressing a yeast native arginase-encoding gene, CAR1, renders Saccharomyces cerevisiae acetic acid tolerance. Specifically, ethanol yield increased by 27.3% in the CAR1-overexpressing strain compared to the control strain under 5.0 g/L acetic acid stress. The global intracellular amino acid level and compositions were further analyzed, and we found that CAR1 overexpression reduced the total amino acid content in response to acetic acid stress. Moreover, the CAR1 overexpressing strain showed increased ATP level and improved cell membrane integrity. Notably, we demonstrated that the effect of CAR1 overexpression was independent of the spermidine and proline metabolism, which indicates novel mechanisms for enhancing yeast stress tolerance. Our studies also suggest that CAR1 is a novel genetic element to be used in synthetic biology of yeast for efficient production of fuel ethanol.
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Affiliation(s)
- Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming-Hai Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hiroshi Takagi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Choi B, Tafur Rangel A, Kerkhoven EJ, Nygård Y. Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass. Metab Eng 2024; 84:23-33. [PMID: 38788894 DOI: 10.1016/j.ymben.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Metabolic engineering for high productivity and increased robustness is needed to enable sustainable biomanufacturing of lactic acid from lignocellulosic biomass. Lactic acid is an important commodity chemical used for instance as a monomer for production of polylactic acid, a biodegradable polymer. Here, rational and model-based optimization was used to engineer a diploid, xylose fermenting Saccharomyces cerevisiae strain to produce L-lactic acid. The metabolic flux was steered towards lactic acid through the introduction of multiple lactate dehydrogenase encoding genes while deleting ERF2, GPD1, and CYB2. A production of 93 g/L of lactic acid with a yield of 0.84 g/g was achieved using xylose as the carbon source. To increase xylose utilization and reduce acetic acid synthesis, PHO13 and ALD6 were also deleted from the strain. Finally, CDC19 encoding a pyruvate kinase was overexpressed, resulting in a yield of 0.75 g lactic acid/g sugars consumed, when the substrate used was a synthetic lignocellulosic hydrolysate medium, containing hexoses, pentoses and inhibitors such as acetate and furfural. Notably, modeling also provided leads for understanding the influence of oxygen in lactic acid production. High lactic acid production from xylose, at oxygen-limitation could be explained by a reduced flux through the oxidative phosphorylation pathway. On the contrast, higher oxygen levels were beneficial for lactic acid production with the synthetic hydrolysate medium, likely as higher ATP concentrations are needed for tolerating the inhibitors therein. The work highlights the potential of S. cerevisiae for industrial production of lactic acid from lignocellulosic biomass.
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Affiliation(s)
- Bohyun Choi
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Albert Tafur Rangel
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden; VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
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Cámara E, Mormino M, Siewers V, Nygård Y. Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses. Appl Environ Microbiol 2024; 90:e0233023. [PMID: 38587374 PMCID: PMC11107148 DOI: 10.1128/aem.02330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness. IMPORTANCE The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.
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Affiliation(s)
- Elena Cámara
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Maurizio Mormino
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- VTT Technical Research Centre of Finland, Espoo, Finland
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Liu C, Choi B, Efimova E, Nygård Y, Santala S. Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:61. [PMID: 38711153 DOI: 10.1186/s13068-024-02510-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/23/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Lignocellulosic biomass as feedstock has a huge potential for biochemical production. Still, efficient utilization of hydrolysates derived from lignocellulose is challenged by their complex and heterogeneous composition and the presence of inhibitory compounds, such as furan aldehydes. Using microbial consortia where two specialized microbes complement each other could serve as a potential approach to improve the efficiency of lignocellulosic biomass upgrading. RESULTS This study describes the simultaneous inhibitor detoxification and production of lactic acid and wax esters from a synthetic lignocellulosic hydrolysate by a defined coculture of engineered Saccharomyces cerevisiae and Acinetobacter baylyi ADP1. A. baylyi ADP1 showed efficient bioconversion of furan aldehydes present in the hydrolysate, namely furfural and 5-hydroxymethylfurfural, and did not compete for substrates with S. cerevisiae, highlighting its potential as a coculture partner. Furthermore, the remaining carbon sources and byproducts of S. cerevisiae were directed to wax ester production by A. baylyi ADP1. The lactic acid productivity of S. cerevisiae was improved approximately 1.5-fold (to 0.41 ± 0.08 g/L/h) in the coculture with A. baylyi ADP1, compared to a monoculture of S. cerevisiae. CONCLUSION The coculture of yeast and bacterium was shown to improve the consumption of lignocellulosic substrates and the productivity of lactic acid from a synthetic lignocellulosic hydrolysate. The high detoxification capacity and the ability to produce high-value products by A. baylyi ADP1 demonstrates the strain to be a potential candidate for coculture to increase production efficiency and economics of S. cerevisiae fermentations.
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Affiliation(s)
- Changshuo Liu
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland
| | - Bohyun Choi
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Elena Efimova
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Suvi Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Tampere, Finland.
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Parmaki S, Vasquez MI, Patsalou M, Gomes RFA, Simeonov SP, Afonso CAM, Koutinas M. Ecotoxicological assessment of biomass-derived furan platform chemicals using aquatic and terrestrial bioassays. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:686-699. [PMID: 38372577 DOI: 10.1039/d3em00552f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
An environmental toxicological assessment of fourteen furanic compounds serving as valuable building blocks produced from biomass was performed. The molecules selected included well studied compounds serving as control examples to compare the toxicity exerted against a variety of highly novel furans which have been additionally targeted as potential or current alternatives to biofuels, building blocks and polymer monomers. The impact of the furan platform chemicals targeted on widely applied ecotoxicity model organisms was determined employing the marine bioluminescent bacterium Aliivibrio fischeri and the freshwater green microalgae Raphidocelis subcapitata, while their ecotoxicity effects on plants were assessed using dicotyledonous plants Sinapis alba and Lepidium sativum. Regarding the specific endpoints evaluated, the furans tested were slightly toxic or practically nontoxic for A. fischeri following 5 and 15 min of exposure. Moreover, most of the building blocks did not affect the growth of L. sativum and S. alba at 150 mg L-1 for 72 h of exposure. Specifically, 9 and 11 out of the 14 furan platform chemicals tested were non-effective or stimulant for L. sativum and S. alba respectively. Given that furans comprise common inhibitors in biorefinery fermentations, the growth inhibition of the specific building blocks was studied using the industrial workhorse yeast Saccharomyces cerevisiae, demonstrating insignificant inhibition on eukaryotic cell growth following 6, 12 and 16 h of exposure at a concentration of 500 mg L-1. The study provides baseline information to unravel the ecotoxic effects and to confirm the green aspects of a range of versatile biobased platform molecules.
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Affiliation(s)
- Stella Parmaki
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
| | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
- European University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus
| | - Maria Patsalou
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
| | - Rafael F A Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Svilen P Simeonov
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl. 9, 1113, Sofia, Bulgaria
| | - Carlos A M Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Michalis Koutinas
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
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Yuan B, Wang WB, Wang YT, Zhao XQ. Regulatory mechanisms underlying yeast chemical stress response and development of robust strains for bioproduction. Curr Opin Biotechnol 2024; 86:103072. [PMID: 38330874 DOI: 10.1016/j.copbio.2024.103072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Yeast is widely studied in producing biofuels and biochemicals using renewable biomass. Among various yeasts, Saccharomyces cerevisiae has been particularly recognized as an important yeast cell factory. However, economic bioproduction using S. cerevisiae is challenged by harsh environments during fermentation, among which inhibitory chemicals in the culture media or toxic products are common experiences. Understanding the stress-responsive mechanisms is conducive to developing robust yeast strains. Here, we review recent progress in mechanisms underlying yeast stress response, including regulation of cell wall integrity, membrane transport, antioxidative system, and gene transcription. We highlight epigenetic regulation of stress response and summarize manipulation of yeast stress tolerance for improved bioproduction. Prospects in the application of machine learning to improve production efficiency are also discussed.
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Affiliation(s)
- Bing Yuan
- 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
| | - Wei-Bin Wang
- 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
| | - Ya-Ting Wang
- 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
| | - Xin-Qing 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.
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7
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Zhao XQ, Liu CG, Bai FW. Making the biochemical conversion of lignocellulose more robust. Trends Biotechnol 2024; 42:418-430. [PMID: 37858385 DOI: 10.1016/j.tibtech.2023.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Lignocellulose is an alternative to fossil resources, but its biochemical conversion is not economically competitive. While decentralized processing can reduce logistical cost for this feedstock, sugar platforms need to be developed with energy-saving pretreatment technologies and cost-effective cellulases, and products must be selected correctly. Anaerobic fermentation with less energy consumption and lower contamination risk is preferred, particularly for producing biofuels. Great effort has been devoted to producing cellulosic ethanol, but CO2 released with large quantities during ethanol fermentation must be utilized in situ for credit. Unless titer and yield are improved substantially, butanol cannot be produced as an advanced biofuel. Microbial lipids produced through aerobic fermentation with low yield and intensive energy consumption are not affordable as feedstocks for biodiesel production.
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Affiliation(s)
- Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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8
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Ravn JL, Manfrão-Netto JHC, Schaubeder JB, Torello Pianale L, Spirk S, Ciklic IF, Geijer C. Engineering Saccharomyces cerevisiae for targeted hydrolysis and fermentation of glucuronoxylan through CRISPR/Cas9 genome editing. Microb Cell Fact 2024; 23:85. [PMID: 38493086 PMCID: PMC10943827 DOI: 10.1186/s12934-024-02361-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The abundance of glucuronoxylan (GX) in agricultural and forestry residual side streams positions it as a promising feedstock for microbial conversion into valuable compounds. By engineering strains of the widely employed cell factory Saccharomyces cerevisiae with the ability to directly hydrolyze and ferment GX polymers, we can avoid the need for harsh chemical pretreatments and costly enzymatic hydrolysis steps prior to fermentation. However, for an economically viable bioproduction process, the engineered strains must efficiently express and secrete enzymes that act in synergy to hydrolyze the targeted polymers. RESULTS The aim of this study was to equip the xylose-fermenting S. cerevisiae strain CEN.PK XXX with xylanolytic enzymes targeting beechwood GX. Using a targeted enzyme approach, we matched hydrolytic enzyme activities to the chemical features of the GX substrate and determined that besides endo-1,4-β-xylanase and β-xylosidase activities, α-methyl-glucuronidase activity was of great importance for GX hydrolysis and yeast growth. We also created a library of strains expressing different combinations of enzymes, and screened for yeast strains that could express and secrete the enzymes and metabolize the GX hydrolysis products efficiently. While strains engineered with BmXyn11A xylanase and XylA β-xylosidase could grow relatively well in beechwood GX, strains further engineered with Agu115 α-methyl-glucuronidase did not display an additional growth benefit, likely due to inefficient expression and secretion of this enzyme. Co-cultures of strains expressing complementary enzymes as well as external enzyme supplementation boosted yeast growth and ethanol fermentation of GX, and ethanol titers reached a maximum of 1.33 g L- 1 after 48 h under oxygen limited condition in bioreactor fermentations. CONCLUSION This work underscored the importance of identifying an optimal enzyme combination for successful engineering of S. cerevisiae strains that can hydrolyze and assimilate GX. The enzymes must exhibit high and balanced activities, be compatible with the yeast's expression and secretion system, and the nature of the hydrolysis products must be such that they can be taken up and metabolized by the yeast. The engineered strains, particularly when co-cultivated, display robust growth and fermentation of GX, and represent a significant step forward towards a sustainable and cost-effective bioprocessing of GX-rich biomass. They also provide valuable insights for future strain and process development targets.
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Affiliation(s)
- Jonas L Ravn
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden.
| | - João H C Manfrão-Netto
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biorenewables National Laboratory (LNBR), Campinas, 13083-100, Brazil
| | - Jana B Schaubeder
- Institute of Bioproducts and Paper Technology (BPTI), Graz University of Technology, Inffeldgasse 23, Graz, 8010, Austria
| | - Luca Torello Pianale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Stefan Spirk
- Institute of Bioproducts and Paper Technology (BPTI), Graz University of Technology, Inffeldgasse 23, Graz, 8010, Austria
| | - Iván F Ciklic
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden
- Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria (INTA), 5507 Luján de Cuyo, San Martín, Mendoza, 3853, Argentina
| | - Cecilia Geijer
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden.
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Luo L, Wei H, Kong D, Wan L, Jiang Y, Qin S, Suo Y. Efficient production of butyric acid from lignocellulosic biomass by revealing the mechanisms of Clostridium tyrobutyricum tolerance to phenolic inhibitors. BIORESOURCE TECHNOLOGY 2024; 396:130427. [PMID: 38336212 DOI: 10.1016/j.biortech.2024.130427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Phenolic compounds (PCs) generated during pretreatment of lignocellulosic biomass severely hinder the biorefinery by Clostridia. As a hyperbutyrate-producing strain, Clostridium tyrobutyricum has excellent tolerance to PCs, but its tolerance mechanism is poorly understood. In this study, a comprehensive transcriptome analysis was applied to elucidate the response of C. tyrobutyricum to four typical PCs. The findings revealed that the expression levels of genes associated with PC reduction, HSPs, and membrane transport were significantly altered under PC stress. Due to PCs being reduced to low-toxicity alcohols/acids by C. tyrobutyricum, enhancing the reduction of PCs by overexpressing reductase genes could enhance the strain's tolerance to PCs. Under 1.0 g/L p-coumaric acid stress, compared with the wild-type strain, ATCC 25755/sdr1 exhibited a 31.2 % increase in butyrate production and a 38.5 % increase in productivity. These insights contribute to the construction of PC-tolerant Clostridia, which holds promise for improving biofuel and chemical production from lignocellulosic biomass.
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Affiliation(s)
- Linshuang Luo
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Hailing Wei
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Deting Kong
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Liqiong Wan
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Yuntao Jiang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Shiwen Qin
- School of Agriculture, Yunnan University, Kunming 650500, China.
| | - Yukai Suo
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China; Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming 650031, China.
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10
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Lu P, Bai R, Gao T, Chen J, Jiang K, Zhu Y, Lu Y, Zhang S, Xu F, Zhao H. Systemic metabolic engineering of Enterobacter aerogenes for efficient 2,3-butanediol production. Appl Microbiol Biotechnol 2024; 108:146. [PMID: 38240862 PMCID: PMC10798932 DOI: 10.1007/s00253-023-12911-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024]
Abstract
2,3-Butanediol (2,3-BDO) is an important gateway molecule for many chemical derivatives. Currently, microbial production is gradually being recognized as a green and sustainable alternative to petrochemical synthesis, but the titer, yield, and productivity of microbial 2,3-BDO remain suboptimal. Here, we used systemic metabolic engineering strategies to debottleneck the 2,3-BDO production in Enterobacter aerogenes. Firstly, the pyruvate metabolic network was reconstructed by deleting genes for by-product synthesis to improve the flux toward 2,3-BDO synthesis, which resulted in a 90% increase of the product titer. Secondly, the 2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose, 20% higher than that from glucose, and the yield of 2,3-BDO reached 0.49 g/g. Finally, the titer of 2,3-BDO of IAM1183-LPCT/D in a 5-L fermenter reached 22.93 g/L, 85% higher than the wild-type strain, and the titer of by-products except ethanol was very low. KEY POINTS: Deletion of five key genes in E. aerogenes improved 2,3-BDO production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity.
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Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiale Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yalun Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ye Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Liaoning Province Key Laboratory of Cordyceps Militaris With Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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11
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Li M, Chu Y, Dong X, Ji H. General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts. World J Microbiol Biotechnol 2023; 40:49. [PMID: 38133718 DOI: 10.1007/s11274-023-03875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
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Affiliation(s)
- Mengmeng Li
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Yunfei Chu
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, PR China.
| | - Hao Ji
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
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12
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Cingiz MÖ. k- Strong Inference Algorithm: A Hybrid Information Theory Based Gene Network Inference Algorithm. Mol Biotechnol 2023:10.1007/s12033-023-00929-2. [PMID: 37950851 DOI: 10.1007/s12033-023-00929-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/05/2023] [Indexed: 11/13/2023]
Abstract
Gene networks allow researchers to understand the underlying mechanisms between diseases and genes while reducing the need for wet lab experiments. Numerous gene network inference (GNI) algorithms have been presented in the literature to infer accurate gene networks. We proposed a hybrid GNI algorithm, k-Strong Inference Algorithm (ksia), to infer more reliable and robust gene networks from omics datasets. To increase reliability, ksia integrates Pearson correlation coefficient (PCC) and Spearman rank correlation coefficient (SCC) scores to determine mutual information scores between molecules to increase diversity of relation predictions. To infer a more robust gene network, ksia applies three different elimination steps to remove redundant and spurious relations between genes. The performance of ksia was evaluated on microbe microarrays database in the overlap analysis with other GNI algorithms, namely ARACNE, C3NET, CLR, and MRNET. Ksia inferred less number of relations due to its strict elimination steps. However, ksia generally performed better on Escherichia coli (E.coli) and Saccharomyces cerevisiae (yeast) gene expression datasets due to F- measure and precision values. The integration of association estimator scores and three elimination stages slightly increases the performance of ksia based gene networks. Users can access ksia R package and user manual of package via https://github.com/ozgurcingiz/ksia .
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Affiliation(s)
- Mustafa Özgür Cingiz
- Computer Engineering Department, Faculty of Engineering and Natural Sciences, Bursa Technical University, Mimar Sinan Campus, Yildirim, 16310, Bursa, Turkey.
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13
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Llamas M, Greses S, Magdalena JA, González-Fernández C, Tomás-Pejó E. Microbial co-cultures for biochemicals production from lignocellulosic biomass: A review. BIORESOURCE TECHNOLOGY 2023; 386:129499. [PMID: 37460020 DOI: 10.1016/j.biortech.2023.129499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Global reliance on fossil oil should shift to cleaner alternatives to get a decarbonized society. One option to achieve this ambitious goal is the use of biochemicals produced from lignocellulosic biomass (LCB). The inherent low biodegradability of LCB and the inhibitory compounds that might be released during pretreatment are two main challenges for LCB valorization. At microbiological level, constraints are mostly linked to the need for axenic cultures and the preference for certain carbon sources (i.e., glucose). To cope with these issues, this review focuses on efficient LCB conversion via the sugar platform as well as an innovative carboxylate platform taking advantage of the co-cultivation of microorganisms. This review discusses novel trends in the use of microbial communities and co-cultures aiming at different bioproducts co-generation in single reactors as well as in sequential bioprocess combination. The outlook and further perspectives of these alternatives have been outlined for future successful development.
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Affiliation(s)
- Mercedes Llamas
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Silvia Greses
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Jose Antonio Magdalena
- LBE, Univ Montpellier, INRAE, 102 avenue des Étangs, F-11100 Narbonne, France; Vicerrectorado de Investigación y Transferencia de la Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Cristina González-Fernández
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, Valladolid 47011, Spain; Institute of Sustainable Processes, Dr. Mergelina, s/n, Valladolid 47011, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain.
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14
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Ndubuisi IA, Amadi CO, Nwagu TN, Murata Y, Ogbonna JC. Non-conventional yeast strains: Unexploited resources for effective commercialization of second generation bioethanol. Biotechnol Adv 2023; 63:108100. [PMID: 36669745 DOI: 10.1016/j.biotechadv.2023.108100] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The conventional yeast (Saccharomyces cerevisiae) is the most studied yeast and has been used in many important industrial productions, especially in bioethanol production from first generation feedstock (sugar and starchy biomass). However, for reduced cost and to avoid competition with food, second generation bioethanol, which is produced from lignocellulosic feedstock, is now being investigated. Production of second generation bioethanol involves pre-treatment and hydrolysis of lignocellulosic biomass to sugar monomers containing, amongst others, d-glucose and D-xylose. Intrinsically, S. cerevisiae strains lack the ability to ferment pentose sugars and genetic engineering of S. cerevisiae to inculcate the ability to ferment pentose sugars is ongoing to develop recombinant strains with the required stability and robustness for commercial second generation bioethanol production. Furthermore, pre-treatment of these lignocellulosic wastes leads to the release of inhibitory compounds which adversely affect the growth and fermentation by S. cerevisae. S. cerevisiae also lacks the ability to grow at high temperatures which favour Simultaneous Saccharification and Fermentation of substrates to bioethanol. There is, therefore, a need for robust yeast species which can co-ferment hexose and pentose sugars and can tolerate high temperatures and the inhibitory substances produced during pre-treatment and hydrolysis of lignocellulosic materials. Non-conventional yeast strains are potential solutions to these problems due to their abilities to ferment both hexose and pentose sugars, and tolerate high temperature and stress conditions encountered during ethanol production from lignocellulosic hydrolysate. This review highlights the limitations of the conventional yeast species and the potentials of non-conventional yeast strains in commercialization of second generation bioethanol.
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Affiliation(s)
| | - Chioma O Amadi
- Department of Microbiology, University of Nigeria Nsukka, Nigeria
| | - Tochukwu N Nwagu
- Department of Microbiology, University of Nigeria Nsukka, Nigeria
| | - Y Murata
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - James C Ogbonna
- Department of Microbiology, University of Nigeria Nsukka, Nigeria.
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15
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Zhao F, Zhang Y, Hu J, Shi C, Ao X, Wang S, Lin Y, Sun Z, Han S. Disruption of phosphate metabolism and sterol transport-related genes conferring yeast resistance to vanillin and rapid ethanol production. BIORESOURCE TECHNOLOGY 2023; 369:128489. [PMID: 36528179 DOI: 10.1016/j.biortech.2022.128489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Vanillin is a potent growth-inhibiting factor in Saccharomyces cerevisiae during lignocellulose biorefineries. Here, a haploid gene-deletion library was screened to search for vanillin-tolerant mutants and explain the possible tolerance mechanisms. Twenty-two deletion mutants were identified. The deleted genes in these mutants were involved in phosphate and inositol polyphosphate metabolism and intracellular sterol transport. Activation of the phosphate signaling pathway is not conducive to yeast against the pressure of vanillin. Furthermore, the findings indicate the role of inositol polyphosphates in altering vanillin tolerance by regulating phosphate metabolism. Meanwhile, reducing the transport of sterols from the plasma membrane enhanced tolerance to vanillin. In the presence of vanillin, the representative yeast deletions, pho84Δ and lam3Δ, showed good growth performance and promoted rapid ethanol production. Overall, this study identifies robust yeast strain alternatives for ethanol fermentation of cellulose and provides guidance for further genomic reconstruction of yeast strains.
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Affiliation(s)
- Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yaping Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jian Hu
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ce Shi
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xiang Ao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Shengding Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zhongwei Sun
- Fleming Biological Pharmaceutical Limited Company, Nanning, 530031, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China.
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16
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Li Z, Gao C, Ye C, Guo L, Liu J, Chen X, Song W, Wu J, Liu L. Systems engineering of Escherichia coli for high-level shikimate production. Metab Eng 2023; 75:1-11. [PMID: 36328295 DOI: 10.1016/j.ymben.2022.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
To further increase the production efficiency of microbial shikimate, a valuable compound widely used in the pharmaceutical and chemical industries, ten key target genes contributing to shikimate production were identified by exploiting the enzyme constraint model ec_iML1515, and subsequently used for promoting metabolic flux towards shikimate biosynthesis in the tryptophan-overproducing strain Escherichia coli TRP0. The engineered E. coli SA05 produced 78.4 g/L shikimate via fed-batch fermentation. Deletion of quinate dehydrogenase and introduction of the hydroaromatic equilibration-alleviating shikimate dehydrogenase mutant AroET61W/L241I reduced the contents of byproducts quinate (7.5 g/L) and 3-dehydroshikimic acid (21.4 g/L) by 89.1% and 52.1%, respectively. Furthermore, a high concentration shikimate responsive promoter PrpoS was recruited to dynamically regulate the expression of the tolerance target ProV to enhance shikimate productivity by 23.2% (to 2 g/L/h). Finally, the shikimate titer was increased to 126.4 g/L, with a yield of 0.50 g/g glucose and productivity of 2.63 g/L/h, using a 30-L fermenter and the engineered strain E. coli SA09. This is, to the best of our knowledge, the highest reported shikimate titer and productivity in E. coli.
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Affiliation(s)
- Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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17
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Han X, Liu J, Tian S, Tao F, Xu P. Microbial cell factories for bio-based biodegradable plastics production. iScience 2022; 25:105462. [DOI: 10.1016/j.isci.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Mormino M, Lenitz I, Siewers V, Nygård Y. Identification of acetic acid sensitive strains through biosensor-based screening of a Saccharomyces cerevisiae CRISPRi library. Microb Cell Fact 2022; 21:214. [PMID: 36243715 PMCID: PMC9571444 DOI: 10.1186/s12934-022-01938-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background Acetic acid tolerance is crucial for the development of robust cell factories for conversion of lignocellulosic hydrolysates that typically contain high levels of acetic acid. Screening mutants for growth in medium with acetic acid is an attractive way to identify sensitive variants and can provide novel insights into the complex mechanisms regulating the acetic acid stress response. Results An acetic acid biosensor based on the Saccharomyces cerevisiae transcription factor Haa1, was used to screen a CRISPRi yeast strain library where dCas9-Mxi was set to individually repress each essential or respiratory growth essential gene. Fluorescence-activated cell sorting led to the enrichment of a population of cells with higher acetic acid retention. These cells with higher biosensor signal were demonstrated to be more sensitive to acetic acid. Biosensor-based screening of the CRISPRi library strains enabled identification of strains with increased acetic acid sensitivity: strains with gRNAs targeting TIF34, MSN5, PAP1, COX10 or TRA1. Conclusions This study demonstrated that biosensors are valuable tools for screening and monitoring acetic acid tolerance in yeast. Fine-tuning the expression of essential genes can lead to altered acetic acid tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01938-7.
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Affiliation(s)
- Maurizio Mormino
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ibai Lenitz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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19
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Guo H, Zhao Y, Chang JS, Lee DJ. Inhibitor formation and detoxification during lignocellulose biorefinery: A review. BIORESOURCE TECHNOLOGY 2022; 361:127666. [PMID: 35878776 DOI: 10.1016/j.biortech.2022.127666] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
For lignocellulose biorefinery, pretreatment is needed to maximize the cellulose accessibility, frequently generating excess inhibitory substances to decline the efficiency of the subsequent fermentation processes. This mini-review updates the current research efforts to detoxify the adverse impacts of generated inhibitors on the performance of biomass biorefinery. The lignocellulose pretreatment processes are first reviewed. The generation of inhibitors, furans, furfural, phenols, formic acid, and acetic acid, from the lignocellulose, with their action mechanisms, are listed. Then the detoxification processes are reviewed, from which the biological detoxification processes are noted as promising and worth further study. The challenges and prospects for applying biological detoxification in lignocellulose biorefinery are outlined. Integrated studies considering the entire biorefinery should be performed on a case-by-case basis.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan.
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20
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Pangestu R, Kahar P, Kholida LN, Perwitasari U, Thontowi A, Fahrurrozi, Lisdiyanti P, Yopi, Ogino C, Prasetya B, Kondo A. Harnessing originally robust yeast for rapid lactic acid bioproduction without detoxification and neutralization. Sci Rep 2022; 12:13645. [PMID: 35953496 PMCID: PMC9372150 DOI: 10.1038/s41598-022-17737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022] Open
Abstract
Acidic and chemical inhibitor stresses undermine efficient lactic acid bioproduction from lignocellulosic feedstock. Requisite coping treatments, such as detoxification and neutralizing agent supplementation, can be eliminated if a strong microbial host is employed in the process. Here, we exploited an originally robust yeast, Saccharomyces cerevisiae BTCC3, as a production platform for lactic acid. This wild-type strain exhibited a rapid cell growth in the presence of various chemical inhibitors compared to laboratory and industrial strains, namely BY4741 and Ethanol-red. Pathway engineering was performed on the strain by introducing an exogenous LDH gene after disrupting the PDC1 and PDC5 genes. Facilitated by this engineered strain, high cell density cultivation could generate lactic acid with productivity at 4.80 and 3.68 g L−1 h−1 under semi-neutralized and non-neutralized conditions, respectively. Those values were relatively higher compared to other studies. Cultivation using real lignocellulosic hydrolysate was conducted to assess the performance of this engineered strain. Non-neutralized fermentation using non-detoxified hydrolysate from sugarcane bagasse as a medium could produce lactic acid at 1.69 g L−1 h−1, which was competitive to the results from other reports that still included detoxification and neutralization steps in their experiments. This strategy could make the overall lactic acid bioproduction process simpler, greener, and more cost-efficient.
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Affiliation(s)
- Radityo Pangestu
- Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.,National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Prihardi Kahar
- Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Lutfi Nia Kholida
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Urip Perwitasari
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Ahmad Thontowi
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Fahrurrozi
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Puspita Lisdiyanti
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Yopi
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia.,National Standardization Agency of Indonesia (BSN), Gedung Badan Pengkajian Dan Penerapan Teknologi (BPPT), Jl. M.H. Thamrin No. 8, Jakarta, 10340, Indonesia
| | - Chiaki Ogino
- Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.
| | - Bambang Prasetya
- National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia.,National Standardization Agency of Indonesia (BSN), Gedung Badan Pengkajian Dan Penerapan Teknologi (BPPT), Jl. M.H. Thamrin No. 8, Jakarta, 10340, Indonesia
| | - Akihiko Kondo
- Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.,Graduate School of Science, Technology, and Innovation (STIN), Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
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21
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Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 2022; 21:6650360. [PMID: 35883225 PMCID: PMC9508847 DOI: 10.1093/femsyr/foac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.
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Affiliation(s)
- Elena Vanacloig-Pedros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Kaitlin J Fisher
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Megan K M Young
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Trey K Sato
- Corresponding author: Trey K. Sato, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 4117 Wisconsin Energy Institute, 1552 University Ave, Madison, WI 53726. Tel: (608) 890-2546; E-mail:
| | - Audrey P Gasch
- Corresponding author: Audrey P. Gasch, Center for Genomic Science Innovation, University of Wisconsin-Madison, 3422 Genetics-Biotechnology Center, 425 Henry Mall, Madison, WI 53704, United States. Tel: (608)265-0859; E-mail:
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22
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:jof8070687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Correspondence:
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Improving Lipid Production of Yarrowia lipolytica by the Aldehyde Dehydrogenase-Mediated Furfural Detoxification. Int J Mol Sci 2022; 23:ijms23094761. [PMID: 35563152 PMCID: PMC9102794 DOI: 10.3390/ijms23094761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 02/01/2023] Open
Abstract
Yarrowia lipolytica, the non-conventional yeast capable of high lipogenesis, is a microbial chassis for producing lipid-based biofuels and chemicals from renewable resources such as lignocellulosic biomass. However, the low tolerance of Y. lipolytica against furfural, a major inhibitory furan aldehyde derived from the pretreatment processes of lignocellulosic biomass, has restricted the efficient conversion of lignocellulosic hydrolysates. In this study, the furfural tolerance of Y. lipolytica has been improved by supporting its endogenous detoxification mechanism. Specifically, the endogenous genes encoding the aldehyde dehydrogenase family proteins were overexpressed in Y. lipolytica to support the conversion of furfural to furoic acid. Among them, YALI0E15400p (FALDH2) has shown the highest conversion rate of furfural to furoic acid and resulted in two-fold increased cell growth and lipid production in the presence of 0.4 g/L of furfural. To our knowledge, this is the first report to identify the native furfural detoxification mechanism and increase furfural resistance through rational engineering in Y. lipolytica. Overall, these results will improve the potential of Y. lipolytica to produce lipids and other value-added chemicals from a carbon-neutral feedstock of lignocellulosic biomass.
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