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Songdech P, Butkinaree C, Yingchutrakul Y, Promdonkoy P, Runguphan W, Soontorngun N. Increased production of isobutanol from xylose through metabolic engineering of Saccharomyces cerevisiae overexpressing transcription factor Znf1 and exogenous genes. FEMS Yeast Res 2024; 24:foae006. [PMID: 38331422 PMCID: PMC10878408 DOI: 10.1093/femsyr/foae006] [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: 09/23/2023] [Revised: 01/21/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024] Open
Abstract
Only trace amount of isobutanol is produced by the native Saccharomyces cerevisiae via degradation of amino acids. Despite several attempts using engineered yeast strains expressing exogenous genes, catabolite repression of glucose must be maintained together with high activity of downstream enzymes, involving iron-sulfur assimilation and isobutanol production. Here, we examined novel roles of nonfermentable carbon transcription factor Znf1 in isobutanol production during xylose utilization. RNA-seq analysis showed that Znf1 activates genes in valine biosynthesis, Ehrlich pathway and iron-sulfur assimilation while coupled deletion or downregulated expression of BUD21 further increased isobutanol biosynthesis from xylose. Overexpression of ZNF1 and xylose-reductase/dehydrogenase (XR-XDH) variants, a xylose-specific sugar transporter, xylulokinase, and enzymes of isobutanol pathway in the engineered S. cerevisiae pho13gre3Δ strain resulted in the superb ZNXISO strain, capable of producing high levels of isobutanol from xylose. The isobutanol titer of 14.809 ± 0.400 g/L was achieved, following addition of 0.05 g/L FeSO4.7H2O in 5 L bioreactor. It corresponded to 155.88 mg/g xylose consumed and + 264.75% improvement in isobutanol yield. This work highlights a new regulatory control of alternative carbon sources by Znf1 on various metabolic pathways. Importantly, we provide a foundational step toward more sustainable production of advanced biofuels from the second most abundant carbon source xylose.
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Affiliation(s)
- Pattanan Songdech
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Chutikarn Butkinaree
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Peerada Promdonkoy
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Nitnipa Soontorngun
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
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Stanchev LD, Møller-Hansen I, Lojko P, Rocha C, Borodina I. Screening of Saccharomyces cerevisiae metabolite transporters by 13C isotope substrate labeling. Front Microbiol 2023; 14:1286597. [PMID: 38116525 PMCID: PMC10729909 DOI: 10.3389/fmicb.2023.1286597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
The transportome of Saccharomyces cerevisiae comprises approximately 340 membrane-bound proteins, of which very few are well-characterized. Elucidating transporter proteins' function is essential not only for understanding central cellular processes in metabolite exchange with the external milieu but also for optimizing the production of value-added compounds in microbial cell factories. Here, we describe the application of 13C-labeled stable isotopes and detection by targeted LC-MS/MS as a screening tool for identifying Saccharomyces cerevisiae metabolite transporters. We compare the transport assay's sensitivity, reproducibility, and accuracy in yeast transporter mutant cell lines and Xenopus oocytes. As proof of principle, we analyzed the transport profiles of five yeast amino acid transporters. We first cultured yeast transporter deletion or overexpression mutants on uniformly labeled 13C-glucose and then screened their ability to facilitate the uptake or export of an unlabeled pool of amino acids. Individual transporters were further studied by heterologous expression in Xenopus oocytes, followed by an uptake assay with 13C labeled yeast extract. Uptake assays in Xenopus oocytes showed higher reproducibility and accuracy. Although having lower accuracy, the results from S. cerevisiae indicated the system's potential for initial high-throughput screening for native metabolite transporters. We partially confirmed previously reported substrates for all five amino acid transporters. In addition, we propose broader substrate specificity for two of the transporter proteins. The method presented here demonstrates the application of a comprehensive screening platform for the knowledge expansion of the transporter-substrate relationship for native metabolites in S. cerevisiae.
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Affiliation(s)
| | | | | | | | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Willers VP, Beer B, Sieber V. Integrating Carbohydrate and C1 Utilization for Chemicals Production. CHEMSUSCHEM 2023; 16:e202202122. [PMID: 36520644 DOI: 10.1002/cssc.202202122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO2 and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO2 and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L-1 ethanol or 2 g L-1 isobutanol from 7.5 g L-1 xylose and 1.6 g L-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO2 and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO2 or sugars.
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Affiliation(s)
- Vivian Pascal Willers
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Current address: CASCAT GmbH, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Technical University of Munich, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
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Sibirny AA. Metabolic engineering of non-conventional yeasts for construction of the advanced producers of biofuels and high-value chemicals. BBA ADVANCES 2022; 3:100071. [PMID: 37082251 PMCID: PMC10074886 DOI: 10.1016/j.bbadva.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Non-conventional yeasts, i.e. yeasts different from Saccharomyces cerevisiae, represent heterogenous group of unicellular fungi consisting of near 1500 species. Some of these species have interesting and sometimes unique properties like ability to grow on methanol, n-alkanes, ferment pentose sugars xylose and l-arabinose, grow at high temperatures (50°С and more), overproduce riboflavin (vitamin B2) and others. These unique properties are important for development of basic science; moreover, some of them possess also significant applied interest for elaboration of new biotechnologies. Current paper represents review of the recent own results and of those of other authors in the field of non-conventional yeast study for construction of the advanced producers of biofuels (ethanol, isobutanol) from lignocellulosic sugars glucose and xylose or crude glycerol (Ogataea polymorpha, Magnusiomyces magnusii) and vitamin B2 (riboflavin) from glucose and cheese whey (Candida famata).
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Affiliation(s)
- Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine
- University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601 Poland
- Corresponding author at: Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine.
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Liu HL, Wang CHT, Chiang EPI, Huang CC, Li WH. Tryptophan plays an important role in yeast's tolerance to isobutanol. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:200. [PMID: 34645498 PMCID: PMC8513309 DOI: 10.1186/s13068-021-02048-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Isobutanol is considered a potential biofuel, thanks to its high-energy content and octane value, limited water solubility, and compatibility with gasoline. As its biosynthesis pathway is known, a microorganism, such as Saccharomyces cerevisiae, that inherently produces isobutanol, can serve as a good engineering host. Isobutanol's toxicity, however, is a major obstacle for bioproduction. This study is to understand how yeast tolerates isobutanol. RESULTS A S. cerevisiae gene-deletion library with 5006 mutants was used to screen genes related to isobutanol tolerance. Image recognition was efficiently used for high-throughput screening via colony size on solid media. In enrichment analysis of the 161 isobutanol-sensitive clones identified, more genes than expected were mapped to tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP). Interestingly, adding exogenous tryptophan enabled both tryptophan biosynthesis and PPP mutant strains to overcome the stress. In transcriptomic analysis, cluster analysis of differentially expressed genes revealed the relationship between tryptophan and isobutanol stress through some specific cellular functions, such as biosynthesis and transportation of amino acids, PPP, tryptophan metabolism, nicotinate/nicotinamide metabolism (e.g., nicotinamide adenine dinucleotide biosynthesis), and fatty acid metabolism. CONCLUSIONS The importance of tryptophan in yeast's tolerance to isobutanol was confirmed by the recovery of isobutanol tolerance in defective strains by adding exogenous tryptophan to the growth medium. Transcriptomic analysis showed that amino acid biosynthesis- and transportation-related genes in a tryptophan biosynthesis-defective host were up-regulated under conditions similar to nitrogen starvation. This may explain why ubiquitination was required for the protein turnover. PPP metabolites may serve as precursors and cofactors in tryptophan biosynthesis to enhance isobutanol tolerance. Furthermore, the tolerance mechanism may also be linked to tryptophan downstream metabolism, including the kynurenine pathway and nicotinamide adenine dinucleotide biosynthesis. Both pathways are responsible for cellular redox balance and anti-oxidative ability. Our study highlights the central role of tryptophan in yeast's isobutanol tolerance and offers new clues for engineering a yeast host with strong isobutanol tolerance.
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Affiliation(s)
- Hsien-Lin Liu
- Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei, 115, Taiwan
- Department of Life Sciences, National Chung Hsing University, No. 145, Xingda Rd., Taichung, 402, Taiwan
| | - Christine H-T Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei, 115, Taiwan
| | - En-Pei Isabel Chiang
- Department of Food Science and Biotechnology, National Chung Hsing University, No. 145, Xingda Rd., Taichung, 402, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, No. 145, Xingda Rd. , Taichung, 402, Taiwan
| | - Chieh-Chen Huang
- Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.
- Department of Life Sciences, National Chung Hsing University, No. 145, Xingda Rd., Taichung, 402, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, No. 145, Xingda Rd. , Taichung, 402, Taiwan.
| | - Wen-Hsiung Li
- Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei, 115, Taiwan.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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Ramamurthy PC, Singh S, Kapoor D, Parihar P, Samuel J, Prasad R, Kumar A, Singh J. Microbial biotechnological approaches: renewable bioprocessing for the future energy systems. Microb Cell Fact 2021; 20:55. [PMID: 33653344 PMCID: PMC7923469 DOI: 10.1186/s12934-021-01547-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
The accelerating energy demands of the increasing global population and industrialization has become a matter of great concern all over the globe. In the present scenario, the world is witnessing a considerably huge energy crisis owing to the limited availability of conventional energy resources and rapid depletion of non-renewable fossil fuels. Therefore, there is a dire need to explore the alternative renewable fuels that can fulfil the energy requirements of the growing population and overcome the intimidating environmental issues like greenhouse gas emissions, global warming, air pollution etc. The use of microorganisms such as bacteria has captured significant interest in the recent era for the conversion of the chemical energy reserved in organic compounds into electrical energy. The versatility of the microorganisms to generate renewable energy fuels from multifarious biological and biomass substrates can abate these ominous concerns to a great extent. For instance, most of the microorganisms can easily transform the carbohydrates into alcohol. Establishing the microbial fuel technology as an alternative source for the generation of renewable energy sources can be a state of art technology owing to its reliability, high efficiency, cleanliness and production of minimally toxic or inclusively non-toxic byproducts. This review paper aims to highlight the key points and techniques used for the employment of bacteria to generate, biofuels and bioenergy, and their foremost benefits.
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Affiliation(s)
- Praveen C Ramamurthy
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, India
| | - Simranjeet Singh
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, India
| | - Dhriti Kapoor
- Department of Botany, Lovely Professional University, Phagwara, Punjab, India
| | - Parul Parihar
- Department of Botany, Lovely Professional University, Phagwara, Punjab, India
| | - Jastin Samuel
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab, India
- Waste Valorization Research Lab, Lovely Professional University, Phagwara, Punjab, India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar, India.
| | - Alok Kumar
- School of Plant Sciences, College of Agriculture and Environmental Sciences, Haramaya University, Box-138, Dire Dawa, Ethiopia.
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab, India.
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Choi KR, Jiao S, Lee SY. Metabolic engineering strategies toward production of biofuels. Curr Opin Chem Biol 2020; 59:1-14. [DOI: 10.1016/j.cbpa.2020.02.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
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Biorefinery: The Production of Isobutanol from Biomass Feedstocks. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10228222] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Environmental issues have prompted the vigorous development of biorefineries that use agricultural waste and other biomass feedstock as raw materials. However, most current biorefinery products are cellulosic ethanol. There is an urgent need for biorefineries to expand into new bioproducts. Isobutanol is an important bulk chemical with properties that are close to gasoline, making it a very promising biofuel. The use of microorganisms to produce isobutanol has been extensively studied, but there is still a considerable gap to achieving the industrial production of isobutanol from biomass. This review summarizes current metabolic engineering strategies that have been applied to biomass isobutanol production and recent advances in the production of isobutanol from different biomass feedstocks.
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Promdonkoy P, Mhuantong W, Champreda V, Tanapongpipat S, Runguphan W. Improvement in d-xylose utilization and isobutanol production in S. cerevisiae by adaptive laboratory evolution and rational engineering. ACTA ACUST UNITED AC 2020; 47:497-510. [DOI: 10.1007/s10295-020-02281-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022]
Abstract
Abstract
As the effects of climate change become apparent, metabolic engineers and synthetic biologists are exploring sustainable sources for transportation fuels. The design and engineering of microorganisms to produce gasoline, diesel, and jet fuel compounds from renewable feedstocks can significantly reduce our dependence on fossil fuels as well as lower the emissions of greenhouse gases. Over the past 2 decades, a considerable amount of work has led to the development of microbial strains for the production of advanced fuel compounds from both C5 and C6 sugars. In this work, we combined two strategies—adaptive laboratory evolution and rational metabolic engineering—to improve the yeast Saccharomyces cerevisiae’s ability to utilize d-xylose, a major C5 sugar in biomass, and produce the advanced biofuel isobutanol. Whole genome resequencing of several evolved strains followed by reverse engineering identified two single nucleotide mutations, one in CCR4 and another in TIF1, that improved the yeast’s specific growth rate by 23% and 14%, respectively. Neither one of these genes has previously been implicated to play a role in utilization of d-xylose. Fine-tuning the expression levels of the bottleneck enzymes in the isobutanol pathway further improved the evolved strain’s isobutanol titer to 92.9 ± 4.4 mg/L (specific isobutanol production of 50.2 ± 2.6 mg/g DCW), a 90% improvement in titer and a 110% improvement in specific production over the non-evolved strain. We hope that our work will set the stage for an economic route to the advanced biofuel isobutanol and enable efficient utilization of xylose-containing biomass.
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Affiliation(s)
- Peerada Promdonkoy
- grid.419250.b National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park, Paholyothin Road, Klong 1 12120 Klong Luang Pathumthani Thailand
| | - Wuttichai Mhuantong
- grid.419250.b National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park, Paholyothin Road, Klong 1 12120 Klong Luang Pathumthani Thailand
| | - Verawat Champreda
- grid.419250.b National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park, Paholyothin Road, Klong 1 12120 Klong Luang Pathumthani Thailand
| | - Sutipa Tanapongpipat
- grid.419250.b National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park, Paholyothin Road, Klong 1 12120 Klong Luang Pathumthani Thailand
| | - Weerawat Runguphan
- grid.419250.b National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park, Paholyothin Road, Klong 1 12120 Klong Luang Pathumthani Thailand
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