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Nawab S, Zhang Y, Ullah MW, Lodhi AF, Shah SB, Rahman MU, Yong YC. Microbial host engineering for sustainable isobutanol production from renewable resources. Appl Microbiol Biotechnol 2024; 108:33. [PMID: 38175234 DOI: 10.1007/s00253-023-12821-9] [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: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Due to the limited resources and environmental problems associated with fossil fuels, there is a growing interest in utilizing renewable resources for the production of biofuels through microbial fermentation. Isobutanol is a promising biofuel that could potentially replace gasoline. However, its production efficiency is currently limited by the use of naturally isolated microorganisms. These naturally isolated microorganisms often encounter problems such as a limited range of substrates, low tolerance to solvents or inhibitors, feedback inhibition, and an imbalanced redox state. This makes it difficult to improve their production efficiency through traditional process optimization methods. Fortunately, recent advancements in genetic engineering technologies have made it possible to enhance microbial hosts for the increased production of isobutanol from renewable resources. This review provides a summary of the strategies and synthetic biology approaches that have been employed in the past few years to improve naturally isolated or non-natural microbial hosts for the enhanced production of isobutanol by utilizing different renewable resources. Furthermore, it also discusses the challenges that are faced by engineered microbial hosts and presents future perspectives to enhancing isobutanol production. KEY POINTS: • Promising potential of isobutanol to replace gasoline • Engineering of native and non-native microbial host for isobutanol production • Challenges and opportunities for enhanced isobutanol production.
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Affiliation(s)
- Said Nawab
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - YaFei Zhang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Adil Farooq Lodhi
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Syed Bilal Shah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mujeeb Ur Rahman
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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2
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Montes-Peña KD, Fonseca-Aguiñaga R, Warren-Vega WM, Romero-Cano LA. Decoding of the isotopic fingerprint of tequila 100% agave silver class and image analysis to evaluate differences between spirits. Food Chem 2024; 460:140735. [PMID: 39111035 DOI: 10.1016/j.foodchem.2024.140735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
This communication shows the decoding of Isotopic Fingerprint of Tequila 100% agave silver class (IFTequila100% agave) in three areas corresponding to isotopic variations due to: plant used as raw material, fermentation and distillation process, and hydrolysis process. Isotopic tracers that make them up correspond to the δ13CVPDB ethanol-δ13CVPDB ethyl acetate-δ13CVPDB isoamyl alcohol, δ13CVPDB ethyl acetate-δ13CVPDB isoamyl alcohol-δ13CVPDB n-propanol and δ13CVPDB ethyl acetate-δ13CVPDB n-propanol-δ13CVPDB methanol, respectively. Once the IFTequila100%agave has been decoded, an image comparison was performed against isotopic fingerprints of spirits (Tequila, Bacanora, Raicilla, Sotol, and Mezcal). Results show that it is possible classifies 100% of samples analyzed. Likewise, from decoding it is possible to determine the critical process stage to determine variations with respect to the IFTequila100%agave. The chemometric analysis developed corresponds to an auxiliary analytical tool useful for the inspection processes currently carried out by the authorities to determine the authenticity of the beverage.
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Affiliation(s)
- Kevin D Montes-Peña
- Grupo de Investigación en Materiales y Fenómenos de Superficie. Departamento de Biotecnológicas y Ambientales. Universidad Autónoma de Guadalajara. Av. Patria 1201, C.P. 45129. Zapopan, Jalisco. Mexico
| | - Rocío Fonseca-Aguiñaga
- Grupo de Investigación en Materiales y Fenómenos de Superficie. Departamento de Biotecnológicas y Ambientales. Universidad Autónoma de Guadalajara. Av. Patria 1201, C.P. 45129. Zapopan, Jalisco. Mexico.; Laboratorio de Isotopía. Consejo Regulador del Tequila A.C. Av. Patria 723, Zapopan, 45030, Mexico
| | - Walter M Warren-Vega
- Grupo de Investigación en Materiales y Fenómenos de Superficie. Departamento de Biotecnológicas y Ambientales. Universidad Autónoma de Guadalajara. Av. Patria 1201, C.P. 45129. Zapopan, Jalisco. Mexico.; Laboratorio de Isotopía. Consejo Regulador del Tequila A.C. Av. Patria 723, Zapopan, 45030, Mexico
| | - Luis A Romero-Cano
- Grupo de Investigación en Materiales y Fenómenos de Superficie. Departamento de Biotecnológicas y Ambientales. Universidad Autónoma de Guadalajara. Av. Patria 1201, C.P. 45129. Zapopan, Jalisco. Mexico..
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3
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Rua AJ, Mitchell W, Claypool SM, Alder NN, Alexandrescu AT. Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study. J Biol Chem 2024; 300:107746. [PMID: 39236875 PMCID: PMC11470594 DOI: 10.1016/j.jbc.2024.107746] [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: 06/19/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
Mitochondria are central to cellular metabolism; hence, their dysfunction contributes to a wide array of human diseases. Cardiolipin, the signature phospholipid of the mitochondrion, affects proper cristae morphology, bioenergetic functions, and metabolic reactions carried out in mitochondrial membranes. To match tissue-specific metabolic demands, cardiolipin typically undergoes an acyl tail remodeling process with the final step carried out by the phospholipid-lysophospholipid transacylase tafazzin. Mutations in tafazzin are the primary cause of Barth syndrome. Here, we investigated how defects in cardiolipin biosynthesis and remodeling impacts metabolic flux through the TCA cycle and associated yeast pathways. Nuclear magnetic resonance was used to monitor in real-time the metabolic fate of 13C3-pyruvate in isolated mitochondria from three isogenic yeast strains. We compared mitochondria from a WT strain to mitochondria from a Δtaz1 strain that lacks tafazzin and contains lower amounts of unremodeled cardiolipin and mitochondria from a Δcrd1 strain that lacks cardiolipin synthase and cannot synthesize cardiolipin. We found that the 13C-label from the pyruvate substrate was distributed through twelve metabolites. Several of the metabolites were specific to yeast pathways including branched chain amino acids and fusel alcohol synthesis. While most metabolites showed similar kinetics among the different strains, mevalonate concentrations were significantly increased in Δtaz1 mitochondria. Additionally, the kinetic profiles of α-ketoglutarate, as well as NAD+ and NADH measured in separate experiments, displayed significantly lower concentrations for Δtaz1 and Δcrd1 mitochondria at most time points. Taken together, the results show how cardiolipin remodeling influences pyruvate metabolism, tricarboxylic acid cycle flux, and the levels of mitochondrial nucleotides.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Wayne Mitchell
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nathan N Alder
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA.
| | - Andrei T Alexandrescu
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA.
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4
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Schulz-Mirbach H, Krüsemann JL, Andreadaki T, Nerlich JN, Mavrothalassiti E, Boecker S, Schneider P, Weresow M, Abdelwahab O, Paczia N, Dronsella B, Erb TJ, Bar-Even A, Klamt S, Lindner SN. Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nat Commun 2024; 15:6725. [PMID: 39112480 PMCID: PMC11306353 DOI: 10.1038/s41467-024-51029-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
Anaerobic microbial fermentations provide high product yields and are a cornerstone of industrial bio-based processes. However, the need for redox balancing limits the array of fermentable substrate-product combinations. To overcome this limitation, here we design an aerobic fermentative metabolism that allows the introduction of selected respiratory modules. These can use oxygen to re-balance otherwise unbalanced fermentations, hence achieving controlled respiro-fermentative growth. Following this design, we engineer and characterize an obligate fermentative Escherichia coli strain that aerobically ferments glucose to stoichiometric amounts of lactate. We then re-integrate the quinone-dependent glycerol 3-phosphate dehydrogenase and demonstrate glycerol fermentation to lactate while selectively transferring the surplus of electrons to the respiratory chain. To showcase the potential of this fermentation mode, we direct fermentative flux from glycerol towards isobutanol production. In summary, our design permits using oxygen to selectively re-balance fermentations. This concept is an advance freeing highly efficient microbial fermentation from the limitations imposed by traditional redox balancing.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jan Lukas Krüsemann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Theofania Andreadaki
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jana Natalie Nerlich
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Eleni Mavrothalassiti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Simon Boecker
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Berliner Hochschule für Technik (BHT), Seestr. 64, 13347, Berlin, Germany
| | - Philipp Schneider
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Moritz Weresow
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Omar Abdelwahab
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany.
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5
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Rua AJ, Mitchell W, Claypool SM, Alder NN, Alexandrescu AT. Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599628. [PMID: 38948727 PMCID: PMC11212973 DOI: 10.1101/2024.06.18.599628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mitochondria are central to cellular metabolism; hence, their dysfunction contributes to a wide array of human diseases including cancer, cardiopathy, neurodegeneration, and heritable pathologies such as Barth syndrome. Cardiolipin, the signature phospholipid of the mitochondrion promotes proper cristae morphology, bioenergetic functions, and directly affects metabolic reactions carried out in mitochondrial membranes. To match tissue-specific metabolic demands, cardiolipin typically undergoes an acyl tail remodeling process with the final step carried out by the phospholipid-lysophospholipid transacylase tafazzin. Mutations in the tafazzin gene are the primary cause of Barth syndrome. Here, we investigated how defects in cardiolipin biosynthesis and remodeling impact metabolic flux through the tricarboxylic acid cycle and associated pathways in yeast. Nuclear magnetic resonance was used to monitor in real-time the metabolic fate of 13C3-pyruvate in isolated mitochondria from three isogenic yeast strains. We compared mitochondria from a wild-type strain to mitochondria from a Δtaz1 strain that lacks tafazzin and contains lower amounts of unremodeled cardiolipin, and mitochondria from a Δcrd1 strain that lacks cardiolipin synthase and cannot synthesize cardiolipin. We found that the 13C-label from the pyruvate substrate was distributed through about twelve metabolites. Several of the identified metabolites were specific to yeast pathways, including branched chain amino acids and fusel alcohol synthesis. Most metabolites showed similar kinetics amongst the different strains but mevalonate and α-ketoglutarate, as well as the NAD+/NADH couple measured in separate nuclear magnetic resonance experiments, showed pronounced differences. Taken together, the results show that cardiolipin remodeling influences pyruvate metabolism, tricarboxylic acid cycle flux, and the levels of mitochondrial nucleotides.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Wayne Mitchell
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan N. Alder
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrei T. Alexandrescu
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
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6
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Alkalbani NS, Alam MZ, Al-Nabulsi A, Osaili TM, Obaid RR, Liu SQ, Kamal-Eldin A, Ayyash M. Unraveling the potential nutritional benefits of fermented date syrup waste: Untargeted metabolomics and carbohydrate metabolites of in vitro digested fraction. Food Chem 2024; 442:138483. [PMID: 38241989 DOI: 10.1016/j.foodchem.2024.138483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/09/2023] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Valorization of fruit by-products is a crucial area of research for the development of innovative bio-based products. This study investigated the physicochemical properties and health-promoting benefits of date syrup waste, both fermented by Pichia cecembensis or Pichia kudriavzevii (FDSW), and unfermented (CDSW). Metabolomics profiles of these samples were identified post in vitro digestion. FDSW exhibited 42 volatile compounds, including 9 new ones, and contained (-)-epicatechin, tyrosol, and gallic acid. Bioaccessible fractions of FDSW demonstrated substantial α-amylase inhibition, with percentages of 40.7 % and 53.9 %, respectively. FDSW displayed superior cytotoxicity against Caco2 and MCF-7 cancer cell lines, with an average of ∼75 % and 56 %, respectively. Untargeted metabolomics analysis revealed an increase in secondary metabolites, totaling 27 metabolites. LC-QTOF analysis of bioaccessible carbohydrate metabolites in FDSW identified two phytochemical groups, alkaloids, and terpenoids. This study underscores the potential of FDSW for producing value-added bio-based products with desirable characteristics and health benefits.
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Affiliation(s)
- Nadia S Alkalbani
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Muneeba Zubair Alam
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Anas Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 21121, Jordan
| | - Tareq M Osaili
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 21121, Jordan; Department Clinical Nutrition and Dietetics, University of Sharjah, Sharjah, P.O. Box 27272, UAE
| | - Reyad R Obaid
- Department Clinical Nutrition and Dietetics, University of Sharjah, Sharjah, P.O. Box 27272, UAE
| | - Shao-Quan Liu
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore 117542, Singapore
| | - Afaf Kamal-Eldin
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Mutamed Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates; Zayed Center for Health Sciences, United Arab Emirates University (UAEU), Al-Ain, P.O. Box 15551, United Arab Emirates.
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7
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Ali SA, Songdech P, Samakkarn W, Duangphakdee O, Soontorngun N. New regulatory role of Znf1 in transcriptional control of pentose phosphate pathway and ATP synthesis for enhanced isobutanol and acid tolerance. Yeast 2024; 41:401-417. [PMID: 38708451 DOI: 10.1002/yea.3940] [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: 09/30/2023] [Revised: 02/20/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
To develop a cost-effective microbial cell factory for the production of biofuels and biochemicals, an understanding of tolerant mechanisms is vital for the construction of robust host strains. Here, we characterized a new function of a key metabolic transcription factor named Znf1 and its involvement in stress response in Saccharomyces cerevisiae to enhance tolerance to advanced biofuel, isobutanol. RNA-sequencing analysis of the wild-type versus the znf1Δ deletion strains in glucose revealed a new role for transcription factor Znf1 in the pentose phosphate pathway (PPP) and energy generation. The gene expression analysis confirmed that isobutanol induces an adaptive cell response, resulting in activation of ATP1-3 and COX6 expression. These genes were Znf1 targets that belong to the electron transport chain, important to produce ATPs. Znf1 also activated PPP genes, required for the generation of key amino acids, cellular metabolites, and maintenance of NADP/NADPH redox balance. In glucose, Znf1 also mediated the upregulation of valine biosynthetic genes of the Ehrlich pathway, namely ILV3, ILV5, and ARO10, associated with the generation of key intermediates for isobutanol production. Using S. cerevisiae knockout collection strains, cells with deleted transcriptional regulatory gene ZNF1 or its targets displayed hypersensitivity to isobutanol and acid inhibitors; in contrast, overexpression of ZNF1 enhanced cell survival. Thus, the transcription factor Znf1 functions in the maintenance of energy homeostasis and redox balance at various checkpoints of yeast metabolic pathways. It ensures the rapid unwiring of gene transcription in response to toxic products/by-products generated during biofuel production. Importantly, we provide a new approach to enhance strain tolerance during the conversion of glucose to biofuels.
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Affiliation(s)
- Syed Azhar Ali
- Excellent Research Laboratory for Yeast Innovation, School of Bioresources and Technology, Division of Biochemical Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pattanan Songdech
- Excellent Research Laboratory for Yeast Innovation, School of Bioresources and Technology, Division of Biochemical Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Wiwan Samakkarn
- Excellent Research Laboratory for Yeast Innovation, School of Bioresources and Technology, Division of Biochemical Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Orawan Duangphakdee
- Native Honeybee and Pollinator Research Center, King Mongkut's University of Technology Thonburi, Ratchaburi, Thailand
| | - Nitnipa Soontorngun
- Excellent Research Laboratory for Yeast Innovation, School of Bioresources and Technology, Division of Biochemical Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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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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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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10
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Ren X, Wei Y, Zhao H, Shao J, Zeng F, Wang Z, Li L. A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli. Front Bioeng Biotechnol 2023; 11:1261832. [PMID: 38116200 PMCID: PMC10729320 DOI: 10.3389/fbioe.2023.1261832] [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: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
L-tryptophan and its derivatives are widely used in the chemical, pharmaceutical, food, and feed industries. Microbial fermentation is the most commonly used method to produce L-tryptophan, which calls for an effective cell factory. The mechanism of L-tryptophan biosynthesis in Escherichia coli, the widely used producer of L-tryptophan, is well understood. Saccharomyces cerevisiae also plays a significant role in the industrial production of biochemicals. Because of its robustness and safety, S. cerevisiae is favored for producing pharmaceuticals and food-grade biochemicals. However, the biosynthesis of L-tryptophan in S. cerevisiae has been rarely summarized. The synthetic pathways and engineering strategies of L-tryptophan in E. coli and S. cerevisiae have been reviewed and compared in this review. Furthermore, the information presented in this review pertains to the existing understanding of how L-tryptophan affects S. cerevisiae's stress fitness, which could aid in developing a novel plan to produce more resilient industrial yeast and E. coli cell factories.
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Affiliation(s)
- Xinru Ren
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Yue Wei
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Honglu Zhao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Juanjuan Shao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Zhen Wang
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Li Li
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
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11
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Fonseca-Aguiñaga R, Navarro-Arteaga UE, Muñoz-Sánchez M, Gómez-Ruiz H, Warren-Vega WM, Romero-Cano LA. Design of a Novel Auxiliary Diagnostic Test for the Determination of Authenticity of Tequila 100% Agave Silver Class Based on Chemometrics Analysis of the Isotopic Fingerprint of the Beverage. Foods 2023; 12:2605. [PMID: 37444343 DOI: 10.3390/foods12132605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The present research shows a robust isotopic ratio characterization of Carbon-13 (δ13CVPDB) in congeneric compounds such as methanol, n-propanol, isoamyl alcohol, ethyl lactate, ethyl acetate, ethanol, and acetaldehyde in representative samples (n = 69) of Tequila 100% agave silver class (TSC), employing gas chromatography/combustion/isotope-ratio mass spectrometry (GC/C/IRMS). From the information obtained, the construction of a radial plot attributable to the isotopic fingerprint of TSC was achieved. With this information, a diagnostic test was designed to determine the authenticity of TSC, comparing alcoholic beverages from other agave species as non-authentic samples. The sensitivity of the test was 94.2%; the specificity was 83.3%. Additionally, non-authentic samples were analyzed that meet all the criteria established in the regulations. The results obtained show that the GC/C/IRMS analytical technique and designed diagnostic test are useful as auxiliary parameters to determine the authenticity of the beverage, thus managing to determine the adulteration or falsification of the product.
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Affiliation(s)
- Rocío Fonseca-Aguiñaga
- Grupo de Investigación en Materiales y Fenómenos de Superficie, Departamento de Biotecnológicas y Ambientales, Universidad Autónoma de Guadalajara, Av. Patria 1201, Zapopan 45129, Mexico
- Laboratorio de Isotopía, Consejo Regulador del Tequila A. C., Av. Patria 723, Zapopan 45030, Mexico
| | - Uriel E Navarro-Arteaga
- Grupo de Investigación en Materiales y Fenómenos de Superficie, Departamento de Biotecnológicas y Ambientales, Universidad Autónoma de Guadalajara, Av. Patria 1201, Zapopan 45129, Mexico
- Laboratorio de Isotopía, Consejo Regulador del Tequila A. C., Av. Patria 723, Zapopan 45030, Mexico
| | | | - Humberto Gómez-Ruiz
- Departamento de Química Analítica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Walter M Warren-Vega
- Grupo de Investigación en Materiales y Fenómenos de Superficie, Departamento de Biotecnológicas y Ambientales, Universidad Autónoma de Guadalajara, Av. Patria 1201, Zapopan 45129, Mexico
| | - Luis A Romero-Cano
- Grupo de Investigación en Materiales y Fenómenos de Superficie, Departamento de Biotecnológicas y Ambientales, Universidad Autónoma de Guadalajara, Av. Patria 1201, Zapopan 45129, Mexico
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12
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Garces Daza F, Haitz F, Born A, Boles E. An optimized reverse β-oxidation pathway to produce selected medium-chain fatty acids in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:71. [PMID: 37101299 PMCID: PMC10134560 DOI: 10.1186/s13068-023-02317-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Medium-chain fatty acids are molecules with applications in different industries and with growing demand. However, the current methods for their extraction are not environmentally sustainable. The reverse β-oxidation pathway is an energy-efficient pathway that produces medium-chain fatty acids in microorganisms, and its use in Saccharomyces cerevisiae, a broadly used industrial microorganism, is desired. However, the application of this pathway in this organism has so far either led to low titers or to the predominant production of short-chain fatty acids. RESULTS We genetically engineered Saccharomyces cerevisiae to produce the medium-chain fatty acids hexanoic and octanoic acid using novel variants of the reverse β-oxidation pathway. We first knocked out glycerolphosphate dehydrogenase GPD2 in an alcohol dehydrogenases knock-out strain (△adh1-5) to increase the NADH availability for the pathway, which significantly increased the production of butyric acid (78 mg/L) and hexanoic acid (2 mg/L) when the pathway was expressed from a plasmid with BktB as thiolase. Then, we tested different enzymes for the subsequent pathway reactions: the 3-hydroxyacyl-CoA dehydrogenase PaaH1 increased hexanoic acid production to 33 mg/L, and the expression of enoyl-CoA hydratases Crt2 or Ech was critical to producing octanoic acid, reaching titers of 40 mg/L in both cases. In all cases, Ter from Treponema denticola was the preferred trans-enoyl-CoA reductase. The titers of hexanoic acid and octanoic acid were further increased to almost 75 mg/L and 60 mg/L, respectively, when the pathway expression cassette was integrated into the genome and the fermentation was performed in a highly buffered YPD medium. We also co-expressed a butyryl-CoA pathway variant to increase the butyryl-CoA pool and support the chain extension. However, this mainly increased the titers of butyric acid and only slightly increased that of hexanoic acid. Finally, we also tested the deletion of two potential medium-chain acyl-CoA depleting reactions catalyzed by the thioesterase Tes1 and the medium-chain fatty acyl CoA synthase Faa2. However, their deletion did not affect the production titers. CONCLUSIONS By engineering the NADH metabolism and testing different reverse β-oxidation pathway variants, we extended the product spectrum and obtained the highest titers of octanoic acid and hexanoic acid reported in S. cerevisiae. Product toxicity and enzyme specificity must be addressed for the industrial application of the pathway in this organism.
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Affiliation(s)
- Fernando Garces Daza
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Fabian Haitz
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Alice Born
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe-Universität Frankfurt Am Main, Max-von-Laue-Str.9, 60438, Frankfurt am Main, Germany.
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13
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Dinh HV, Maranas CD. Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis. Metab Eng 2023; 77:242-255. [PMID: 37080482 DOI: 10.1016/j.ymben.2023.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (kapp) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Overall, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.
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Affiliation(s)
- Hoang V Dinh
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA.
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Maurya R, Gohil N, Nixon S, Kumar N, Noronha SB, Dhali D, Trabelsi H, Alzahrani KJ, Reshamwala SMS, Awasthi MK, Ramakrishna S, Singh V. Rewiring of metabolic pathways in yeasts for sustainable production of biofuels. BIORESOURCE TECHNOLOGY 2023; 372:128668. [PMID: 36693507 DOI: 10.1016/j.biortech.2023.128668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/17/2023]
Abstract
The ever-increasing global energy demand has led world towards negative repercussions such as depletion of fossil fuels, pollution, global warming and climate change. Designing microbial cell factories for the sustainable production of biofuels is therefore an active area of research. Different yeast cells have been successfully engineered using synthetic biology and metabolic engineering approaches for the production of various biofuels. In the present article, recent advancements in genetic engineering strategies for production of bioalcohols, isoprenoid-based biofuels and biodiesels in different yeast chassis designs are reviewed, along with challenges that must be overcome for efficient and high titre production of biofuels.
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Affiliation(s)
- Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Snovia Nixon
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Nilesh Kumar
- M.Tech. Programme in Bioprocess Engineering, Institute of Chemical Technology, Mumbai, India; DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Santosh B Noronha
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Debarun Dhali
- EV Biotech BV, Zernikelaan 8, 9747 AA Groningen, The Netherlands
| | - Heykel Trabelsi
- Carbocode GmbH, Byk-Gulden-Strasse 2, 78467 Konstanz, Germany
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Suresh Ramakrishna
- College of Medicine, Hanyang University, Seoul, South Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India.
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15
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Wang M, Qiao J, Sheng Y, Wei J, Cui H, Li X, Yue G. Bioconversion of corn fiber to bioethanol: Status and perspectives. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 157:256-268. [PMID: 36577277 DOI: 10.1016/j.wasman.2022.12.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Due to the rising demand for green energy, bioethanol has attracted increasing attention from academia and industry. Limited by the bottleneck of bioethanol yield in traditional corn starch dry milling processes, an increasing number of studies focus on fully utilizing all corn ingredients, especially kernel fiber, to further improve the bioethanol yield. This mini-review addresses the technological challenges and opportunities on the way to achieving the efficient conversion of corn fiber. Significant advances during the review period include the detailed characterization of different forms of corn kernel fiber and the development of off-line and in-situ conversion strategies. Lessons from cellulosic ethanol technologies offer new ways to utilize corn fiber in traditional processes. However, the commercialization of corn kernel fiber conversion may be hampered by enzyme cost, conversion efficiency, and overall process economics. Thus, future studies should address these technical limitations.
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Affiliation(s)
- Minghui Wang
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Jie Qiao
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Yijie Sheng
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Junnan Wei
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Xiujuan Li
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China.
| | - Guojun Yue
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China; SDIC Biotech Investment Co., Ltd., Beijing 100034, China
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16
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Salas-Millán JÁ, Aguayo E, Conesa-Bueno A, Aznar A. Revalorization of Melon By-Product to Obtain a Novel Sparkling Fruity-Based Wine. Foods 2023; 12:foods12030491. [PMID: 36766020 PMCID: PMC9914186 DOI: 10.3390/foods12030491] [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: 12/07/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Fresh melons not meeting cosmetic standards were revaluated into sparkling melon-based wine. Firstly, still melon wine was elaborated and bottled into 750 mL bottles, closed with a crown seal, and stored for 10-weeks at 14 °C. The oenological parameters and polar compounds in must, still wine, and during the sparkling process were evaluated during the experiment. The volatile profile was qualified by GC-MS, and the odor activity value (OAV) and relative odor contribution (ROC) were measured for aroma characterization. Results show that sparkling wine resulted in 12% v/v ethanol. Certain amino acids contributed to the transformation and increase of volatile compounds via Ehrlich's pathway: leucine to isoamyl alcohol; valine to iso-butyl alcohol; and phenylalanine to phenethyl alcohol. The volatile compounds also increased after the first fermentation, principally in acetate and ethyl esters, and higher alcohols. Isoamyl acetate, ethyl decanoate, 3,6-nonadienyl acetate, and (E,Z)-nonadien-1-ol had the highest OAV and ROC values among the volatiles; this contributed to the sweet, fruity, banana, tropical, nutty and melon aroma in this sparkling wine. Sensory evaluation (100 to 40) was evaluated according to International Organisation of Vine and Wine compendium, the final product (10-week) scored 92 points, with great visual, nose, and taste values. This study demonstrates how by-products revalorization can provide new products such as this novel sparkling wine with a characteristic and distinctive aroma, good sensory acceptance and market potential.
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Affiliation(s)
- José Ángel Salas-Millán
- Postharvest and Refrigeration Group, Universidad Politécnica de Cartagena (UPCT), 30202 Cartagena, Spain
- Food Quality and Health Group, Institute of Plant Biotechnology (UPCT), Campus Muralla del Mar, 30202 Cartagena, Spain
- JimboFresh International SLL, C/Mina Buena Suerte, 1, La Unión, 30360 Murcia, Spain
| | - Encarna Aguayo
- Postharvest and Refrigeration Group, Universidad Politécnica de Cartagena (UPCT), 30202 Cartagena, Spain
- Food Quality and Health Group, Institute of Plant Biotechnology (UPCT), Campus Muralla del Mar, 30202 Cartagena, Spain
- Correspondence: (E.A.); (A.A.)
| | - Andrés Conesa-Bueno
- JimboFresh International SLL, C/Mina Buena Suerte, 1, La Unión, 30360 Murcia, Spain
| | - Arantxa Aznar
- Department of Agronomical Engineering, Institute of Plant Biotechnology, UPCT, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
- Correspondence: (E.A.); (A.A.)
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17
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Gambacorta FV, Dietrich JJ, Baerwald JJ, Brown SJ, Su Y, Pfleger BF. Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:1080024. [PMID: 36532572 PMCID: PMC9755324 DOI: 10.3389/fbioe.2022.1080024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and a preferred host for production of other biofuels. That said, rewiring the metabolism of S. cerevisiae to produce other fermentation products, such as isobutanol, remains an academic challenge. Many studies report aerobic production of isobutanol, but ethanol remains a substantial by-product under these conditions due to the Crabtree effect. These studies indicate that the native isobutanol pathway is incapable of carrying sufficient flux to displace ethanol. In this report, we screened a combinatorial library of pathway enzymes to identify an isobutanol pathway cassette capable of supporting the growth of a non-ethanol producing S. cerevisiae. We began by identifying a diverse set of isobutanol pathway enzyme homologs and combined each open reading frame with varied-strength promoters in a combinatorial, pooled fashion. We applied a growth-coupled screen where a functional isobutanol pathway restored NAD+ regeneration during glucose catabolism that is otherwise repressed via the Crabtree effect. Using this screen, we isolated a cassette consisting of a mosaic of bacterial and cytosol-localized fungal enzymes that conferred under aerobic conditions the ability to produce 364 mg/L isobutanol (8.8% of the theoretical maximum yield). We next shifted the cofactor usage of the isolated ketol-acid reductoisomerase enzyme in the cassette from NADPH to NADH-preferring to improve redox balance. The approach used herein isolated isobutanol producing strains that approach the best in the literature without producing substantial ethanol titers. Still, the best isolated cassette was insufficient to support anaerobic growth in the absence of ethanol fermentation - indicating the presence of further fundamental gaps in our understanding of yeast fermentation.
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Affiliation(s)
- Francesca V. Gambacorta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Joshua J. Dietrich
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Justin J. Baerwald
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Stephanie J. Brown
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian F. Pfleger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Brian F. Pfleger,
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Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:41. [PMID: 35501883 PMCID: PMC9063327 DOI: 10.1186/s13068-022-02144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2022] [Indexed: 11/15/2022]
Abstract
Background Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. Results Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. Conclusions This research provides a new way to improve the efficiency of the biological route of isobutanol production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02144-8. Kp-IpdC is more efficient than KivD for 2-ketoisovalerate decarboxylation. Pyruvate decarboxylase activity is a limitation of Kp-IpdC. T290L variant exhibits a decreased pyruvate decarboxylase activity. Isobutanol production by K. pneumoniae T290L was improved.
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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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Cui D, Liu L, Zhang X, Lin L, Li X, Cheng T, Wei C, Zhang Y, Zhou Z, Li W, Zhang C. Using transcriptomics to reveal the molecular mechanism of higher alcohol metabolism in Saccharomyces cerevisiae. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins. FERMENTATION 2022. [DOI: 10.3390/fermentation8110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.
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Liang B, Fu R, Ma Y, Hu L, Fei Q, Xing XH. Turning C1-gases to isobutanol towards great environmental and economic sustainability via innovative biological routes: two birds with one stone. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:107. [PMID: 36221148 PMCID: PMC9555204 DOI: 10.1186/s13068-022-02202-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The dramatic increase in greenhouse gas (GHG) emissions, which causes serious global environmental issues and severe climate changes, has become a global problem of concern in recent decades. Currently, native and/or non-native C1-utilizing microbes have been modified to be able to effectively convert C1-gases (biogas, natural gas, and CO2) into isobutanol via biological routes. Even though the current experimental results are satisfactory in lab-scale research, the techno-economic feasibility of C1 gas-derived isobutanol production at the industrial scale still needs to be analyzed and evaluated, which will be essential for the future industrialization of C1-gas bioconversion. Therefore, techno-economic analyses were conducted in this study with comparisons of capital cost (CAPEX), operating cost (OPEX), and minimum isobutanol selling price (MISP) derived from biogas (scenario #1), natural gas (scenario #2), and CO2 (scenario #3) with systematic economic assessment. RESULTS By calculating capital investments and necessary expenses, the highest CAPEX ($317 MM) and OPEX ($67 MM) were projected in scenario #1 and scenario #2, respectively. Because of the lower CAPEX and OPEX from scenario #3, the results revealed that bioconversion of CO2 into isobutanol temporally exhibited the best economic performance with an MISP of $1.38/kg isobutanol. Furthermore, a single sensitivity analysis with nine different parameters was carried out for the production of CO2-derived isobutanol. The annual plant capacity, gas utilization rate, and substrate cost are the three most important economic-driving forces on the MISP of CO2-derived isobutanol. Finally, a multiple-point sensitivity analysis considering all five parameters simultaneously was performed using ideal targets, which presented the lowest MISP of $0.99/kg in a long-term case study. CONCLUSIONS This study provides a comprehensive assessment of the bioconversion of C1-gases into isobutanol in terms of the bioprocess design, mass/energy calculation, capital investment, operating expense, sensitivity analysis, and minimum selling price. Compared with isobutanol derived from biogas and natural gas, the CO2-based isobutanol showed better economic feasibility. A market competitive isobutanol derived from CO2 is predicable with lower CO2 cost, better isobutanol titer, and higher annual capacity. This study will help researchers and decision-makers explore innovative and effective approaches to neutralizing GHGs and focus on key economic-driving forces to improve techno-economic performance.
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Affiliation(s)
- Bobo Liang
- grid.43169.390000 0001 0599 1243Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Rongzhan Fu
- grid.412262.10000 0004 1761 5538Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi’an, 710069 China
| | - Yingqun Ma
- grid.43169.390000 0001 0599 1243Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Lizhen Hu
- grid.43169.390000 0001 0599 1243Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Qiang Fei
- grid.43169.390000 0001 0599 1243Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Xin-Hui Xing
- grid.12527.330000 0001 0662 3178MOE Key Lab of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
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Chen H, Wang J, Li Q, Xu X, Niu C, Zheng F, Liu C. Fed-Batch Fermentation of Saccharomyces pastorianus with High Ribonucleic Acid Yield. Foods 2022; 11:foods11182742. [PMID: 36140869 PMCID: PMC9497889 DOI: 10.3390/foods11182742] [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: 07/18/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The degradation products of ribonucleic acid (RNA)are widely used in the food and pharmaceutical industry for their flavoring and nutritional enhancement functions. Yeast is the main source for commercial RNA production, and an efficient strain is the key to reducing production costs; (2) Methods: A mutant Saccharomyces pastorianus G03H8 with a high RNA yield was developed via ARTP mutagenesis and fed-batch fermentation was applied to optimize production capacity. Genome sequencing analysis was used to reveal the underlying mechanism of higher RNA production genetic differences in the preferred mutant; (3) Results: Compared with the highest RNA content of the mutant strain, G03H8 increased by 40% compared with the parental strain G03 after response surface model optimization. Meanwhile, in fed-batch fermentation, G03H8′s dry cell weight (DCW) reached 60.58 g/L in 5 L fermenter by molasses flowing and RNA production reached up to 3.58 g/L. Genome sequencing showed that the ribosome biogenesis, yeast meiosis, RNA transport, and longevity regulating pathway were closely related to the metabolism of high RNA production; (4) Conclusion: S. pastorianus G03H8 was developed for RNA production and had the potential to greatly reduce the cost of RNA production and shorten the fermentation cycle. This work lays the foundation for efficient RNA content using S. pastorianus.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-0510-85918176
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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24
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [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: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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25
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Gambacorta FV, Wagner ER, Jacobson TB, Tremaine M, Muehlbauer LK, McGee MA, Baerwald JJ, Wrobel RL, Wolters JF, Place M, Dietrich JJ, Xie D, Serate J, Gajbhiye S, Liu L, Vang-Smith M, Coon JJ, Zhang Y, Gasch AP, Amador-Noguez D, Hittinger CT, Sato TK, Pfleger BF. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 2022; 7:738-749. [PMID: 35387233 PMCID: PMC8938195 DOI: 10.1016/j.synbio.2022.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketol-acid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.
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Affiliation(s)
- Francesca V. Gambacorta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ellen R. Wagner
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin J. Baerwald
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Russell L. Wrobel
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Mike Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Dietrich
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose Serate
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Shabda Gajbhiye
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F. Pfleger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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26
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Muratovska N, Silva P, Pozdniakova T, Pereira H, Grey C, Johansson B, Carlquist M. Towards engineered yeast as production platform for capsaicinoids. Biotechnol Adv 2022; 59:107989. [PMID: 35623491 DOI: 10.1016/j.biotechadv.2022.107989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/23/2022]
Abstract
Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.
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Affiliation(s)
- Nina Muratovska
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden
| | - Paulo Silva
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Tatiana Pozdniakova
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Humberto Pereira
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Carl Grey
- Division of Biotechnology, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden.
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27
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Joshi S, Mishra S. Recent advances in biofuel production through metabolic engineering. BIORESOURCE TECHNOLOGY 2022; 352:127037. [PMID: 35318143 DOI: 10.1016/j.biortech.2022.127037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Rising global energy demands and climate crisis has created an unprecedented need for the bio-based circular economy to ensure sustainable development with the minimized carbon footprint. Along with conventional biofuels such as ethanol, microbes can be used to produce advanced biofuels which are equivalent to traditional fuels in their energy efficiencies and are compatible with already established infrastructure and hence can be directly blended in higher proportions without overhauling of the pre-existing setup. Metabolic engineering is at the frontiers to develop microbial chassis for biofuel bio-foundries to meet the industrial needs for clean energy. This review does a thorough inquiry of recent developments in metabolic engineering for increasing titers, rates, and yields (TRY) of biofuel production by engineered microorganisms.
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Affiliation(s)
- Swati Joshi
- ICMR-National Institute of Occupational Health (NIOH), Ahmedabad, Gujarat, India; Central University of Gujarat, Gandhinagar, Gujarat, India.
| | - SukhDev Mishra
- ICMR-National Institute of Occupational Health (NIOH), Ahmedabad, Gujarat, India
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28
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Ohtsuka H, Shimasaki T, Aiba H. Response to leucine in Schizosaccharomyces pombe (fission yeast). FEMS Yeast Res 2022; 22:6553821. [PMID: 35325114 PMCID: PMC9041340 DOI: 10.1093/femsyr/foac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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29
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Ziegler M, Hägele L, Gäbele T, Takors R. CRISPRi enables fast growth followed by stable aerobic pyruvate formation in Escherichia coli without auxotrophy. Eng Life Sci 2022; 22:70-84. [PMID: 35140555 PMCID: PMC8811725 DOI: 10.1002/elsc.202100021] [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: 02/15/2021] [Revised: 10/06/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR interference (CRISPRi) was applied to enable the aerobic production of pyruvate in Escherichia coli MG1655 under glucose excess conditions by targeting the promoter regions of aceE or pdhR. Knockdown strains were cultivated in aerobic shaking flasks and the influence of inducer concentration and different sgRNA binding sites on the production of pyruvate was measured. Targeting the promoter regions of aceE or pdhR triggered pyruvate production during the exponential phase and reduced expression of aceE. In lab-scale bioreactor fermentations, an aceE silenced strain successfully produced pyruvate under fully aerobic conditions during the exponential phase, but loss of productivity occurred during a subsequent nitrogen-limited phase. Targeting the promoter region of pdhR enabled pyruvate production during the growth phase of cultivations, and a continued low-level accumulation during the nitrogen-limited production phase. Combinatorial targeting of the promoter regions of both aceE and pdhR in E. coli MG1655 pdCas9 psgRNA_aceE_234_pdhR_329 resulted in the stable aerobic production of pyruvate with non-growing cells at YP/S = 0.36 ± 0.029 gPyruvate/gGlucose in lab-scale bioreactors throughout an extended nitrogen-limited production phase.
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Affiliation(s)
- Martin Ziegler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Lorena Hägele
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Teresa Gäbele
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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30
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Lu H, Yadav V, Zhong M, Bilal M, Taherzadeh MJ, Iqbal HMN. Bioengineered microbial platforms for biomass-derived biofuel production - A review. CHEMOSPHERE 2022; 288:132528. [PMID: 34637864 DOI: 10.1016/j.chemosphere.2021.132528] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 10/08/2021] [Indexed: 02/08/2023]
Abstract
Global warming issues, rapid fossil fuel diminution, and increasing worldwide energy demands have diverted accelerated attention in finding alternate sources of biofuels and energy to combat the energy crisis. Bioconversion of lignocellulosic biomass has emerged as a prodigious way to produce various renewable biofuels such as biodiesel, bioethanol, biogas, and biohydrogen. Ideal microbial hosts for biofuel synthesis should be capable of using high substrate quantity, tolerance to inhibiting substances and end-products, fast sugar transportation, and amplified metabolic fluxes to yielding enhanced fermentative bioproduct. Genetic manipulation and microbes' metabolic engineering are fascinating strategies for the economical production of next-generation biofuel from lignocellulosic feedstocks. Metabolic engineering is a rapidly developing approach to construct robust biofuel-producing microbial hosts and an important component for future bioeconomy. This approach has been widely adopted in the last decade for redirecting and revamping the biosynthetic pathways to obtain a high titer of target products. Biotechnologists and metabolic scientists have produced a wide variety of new products with industrial relevance through metabolic pathway engineering or optimizing native metabolic pathways. This review focuses on exploiting metabolically engineered microbes as promising cell factories for the enhanced production of advanced biofuels.
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Affiliation(s)
- Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Mengyuan Zhong
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China.
| | | | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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31
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High-level Production of Isoleucine and Fusel alcohol by expression of the Feedback Inhibition-insensitive Threonine deaminase in Saccharomyces cerevisiae. Appl Environ Microbiol 2022; 88:e0213021. [PMID: 35020456 PMCID: PMC8904041 DOI: 10.1128/aem.02130-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A variety of the yeast Saccharomyces cerevisiae with intracellular accumulation of isoleucine (Ile) would be a promising strain for developing a distinct kind of sake, a traditional Japanese alcoholic beverage, because Ile-derived volatile compounds have a great impact on the flavor and taste of fermented foods. In this study, we isolated an Ile-accumulating mutant (strain K9-I48) derived from a diploid sake yeast of S. cerevisiae by conventional mutagenesis. Strain K9-I48 carries a novel mutation in the ILV1 gene encoding the His480Tyr variant of threonine deaminase (TD). Interestingly, the TD activity of the His480Tyr variant was markedly insensitive to feedback inhibition by Ile, but was not upregulated by valine, leading to intracellular accumulation of Ile and extracellular overproduction of 2-methyl-1-butanol, a fusel alcohol derived from Ile, in yeast cells. The present study demonstrated for the first time that the conserved histidine residue located in a linker region between two regulatory domains is involved in allosteric regulation of TD. Moreover, sake brewed with strain K9-I48 contained 2 to 3 times more 2-methyl-1-butanol and 2-methylbutyl acetate than sake brewed with the parent strain. These findings are valuable for the engineering of TD to increase the productivity of Ile and its derived fusel alcohols. IMPORTANCE Fruit-like flavors of isoleucine-derived volatile compounds, 2-methyl-1-butanol (2MB) and its acetate ester, contribute to a variety of the flavors and tastes of alcoholic beverages. Besides its value as aroma components in foods and cosmetics, 2MB has attracted significant attention as second-generation biofuels. Threonine deaminase (TD) catalyzes the first step in isoleucine biosynthesis and its activity is subject to feedback inhibition by isoleucine. Here, we isolated an isoleucine-accumulating sake yeast mutant and identified a mutant gene encoding a novel variant of TD. The variant TD exhibited much less sensitivity to isoleucine, leading to higher production of 2MB as well as isoleucine than the wild-type TD. Furthermore, sake brewed with a mutant yeast expressing the variant TD contained more 2MB and its acetate ester than that brewed with the parent strain. These findings will contribute to the development of superior industrial yeast strains for high-level production of isoleucine and its related fusel alcohols.
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Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun 2022; 13:270. [PMID: 35022416 PMCID: PMC8755756 DOI: 10.1038/s41467-021-27852-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Branched-chain amino acid (BCAA) metabolism fulfills numerous physiological roles and can be harnessed to produce valuable chemicals. However, the lack of eukaryotic biosensors specific for BCAA-derived products has limited the ability to develop high-throughput screens for strain engineering and metabolic studies. Here, we harness the transcriptional regulator Leu3p from Saccharomyces cerevisiae to develop a genetically encoded biosensor for BCAA metabolism. In one configuration, we use the biosensor to monitor yeast production of isobutanol, an alcohol derived from valine degradation. Small modifications allow us to redeploy Leu3p in another biosensor configuration that monitors production of the leucine-derived alcohol, isopentanol. These biosensor configurations are effective at isolating high-producing strains and identifying enzymes with enhanced activity from screens for branched-chain higher alcohol (BCHA) biosynthesis in mitochondria as well as cytosol. Furthermore, this biosensor has the potential to assist in metabolic studies involving BCAA pathways, and offers a blueprint to develop biosensors for other products derived from BCAA metabolism. There are a lack of eukaryotic biosensors specific for branched-chain amino acid (BCAA)-derived products. Here the authors report a genetically encoded biosensor for BCAA metabolism based on the Leu3p transcriptional regulator; they use this to monitor yeast production of isobutanol and isopentanol.
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Ho PW, Piampongsant S, Gallone B, Del Cortona A, Peeters PJ, Reijbroek F, Verbaet J, Herrera B, Cortebeeck J, Nolmans R, Saels V, Steensels J, Jarosz DF, Verstrepen KJ. Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:211. [PMID: 34727964 PMCID: PMC8564995 DOI: 10.1186/s13068-021-02059-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The brewer's yeast Saccharomyces cerevisiae is exploited in several industrial processes, ranging from food and beverage fermentation to the production of biofuels, pharmaceuticals and complex chemicals. The large genetic and phenotypic diversity within this species offers a formidable natural resource to obtain superior strains, hybrids, and variants. However, most industrially relevant traits in S. cerevisiae strains are controlled by multiple genetic loci. Over the past years, several studies have identified some of these QTLs. However, because these studies only focus on a limited set of traits and often use different techniques and starting strains, a global view of industrially relevant QTLs is still missing. RESULTS Here, we combined the power of 1125 fully sequenced inbred segregants with high-throughput phenotyping methods to identify as many as 678 QTLs across 18 different traits relevant to industrial fermentation processes, including production of ethanol, glycerol, isobutanol, acetic acid, sulfur dioxide, flavor-active esters, as well as resistance to ethanol, acetic acid, sulfite and high osmolarity. We identified and confirmed several variants that are associated with multiple different traits, indicating that many QTLs are pleiotropic. Moreover, we show that both rare and common variants, as well as variants located in coding and non-coding regions all contribute to the phenotypic variation. CONCLUSIONS Our findings represent an important step in our understanding of the genetic underpinnings of industrially relevant yeast traits and open new routes to study complex genetics and genetic interactions as well as to engineer novel, superior industrial yeasts. Moreover, the major role of rare variants suggests that there is a plethora of different combinations of mutations that can be explored in genome editing.
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Affiliation(s)
- Ping-Wei Ho
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Supinya Piampongsant
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Brigida Gallone
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Andrea Del Cortona
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Pieter-Jan Peeters
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Frank Reijbroek
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jules Verbaet
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jeroen Cortebeeck
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Robbe Nolmans
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jan Steensels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Kevin J. Verstrepen
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
- Labo VIB-CMPG, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Heverlee Belgium
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Aamer Mehmood M, Shahid A, Malik S, Wang N, Rizwan Javed M, Nabeel Haider M, Verma P, Umer Farooq Ashraf M, Habib N, Syafiuddin A, Boopathy R. Advances in developing metabolically engineered microbial platforms to produce fourth-generation biofuels and high-value biochemicals. BIORESOURCE TECHNOLOGY 2021; 337:125510. [PMID: 34320777 DOI: 10.1016/j.biortech.2021.125510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Producing bio-based chemicals is imperative to establish an eco-friendly circular bioeconomy. However, the compromised titer of these biochemicals hampers their commercial implementation. Advances in genetic engineering tools have enabled researchers to develop robust strains producing desired titers of the next-generation biofuels and biochemicals. The native and non-native pathways have been extensively engineered in various host strains via pathway reconstruction and metabolic flux redirection of lipid metabolism and central carbon metabolism to produce myriad biomolecules including alcohols, isoprenoids, hydrocarbons, fatty-acids, and their derivatives. This review has briefly covered the research efforts made during the previous decade to produce advanced biofuels and biochemicals through engineered microbial platforms along with the engineering approaches employed. The efficiency of the various techniques along with their shortcomings is also covered to provide a comprehensive overview of the progress and future directions to achieve higher titer of fourth-generation biofuels and biochemicals while keeping environmental sustainability intact.
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Affiliation(s)
- Muhammad Aamer Mehmood
- School of Bioengineering, Sichuan University of Science and Engineering, Zigong, China; Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ayesha Shahid
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sana Malik
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ning Wang
- School of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Muhammad Rizwan Javed
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Nabeel Haider
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Pradeep Verma
- Department of Microbiology, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer-305801, Rajasthan, India
| | - Muhammad Umer Farooq Ashraf
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nida Habib
- Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Achmad Syafiuddin
- Department of Public Health, Universitas Nahdlatul Ulama Surabaya, 60237 Surabaya, East Java, Indonesia
| | - Raj Boopathy
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA.
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Fu C, Li Z, Zhang Y, Yi C, Xie S. Assessment of extraction options for a next-generation biofuel: Recovery of bio-isobutanol from aqueous solutions. Eng Life Sci 2021; 21:653-665. [PMID: 34690636 PMCID: PMC8518583 DOI: 10.1002/elsc.202000090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/02/2021] [Accepted: 05/31/2021] [Indexed: 11/15/2022] Open
Abstract
Isobutanol is a widely used platform compound and a raw material for synthesizing many high value-added compounds. It also has excellent fuel properties and is an ideal gasoline additive or substitute with a very broad development space. Isobutanol production by biological fermentation has the advantages of a comprehensive source of raw materials, low cost, environmental protection, and sustainability. However, it also has disadvantages such as many impurities, low isobutanol concentration, and difficulty separating the water + isobutanol azeotrope. Thus, it is necessary to explore an appropriate downstream separation process for the water + isobutanol azeotrope. K2CO3 with a strong salting-out effect was used as the salting-out agent, and the salting-out of isobutanol from aqueous solutions was investigated at 298.15 K. The effect of the initial salt concentration in the aqueous solution, the recovery of isobutanol, and the effect of dehydration were investigated in detail. The e-NRTL-RK model was employed to generate the binary parameters for isobutanol and water, and electrolyte pair parameters for water/isobutanol and ions to reproduce the phase diagram with high accuracy. The processes of solvent extractive distillation, and salting-out + distillation were simulated by Aspen Plus. The energy consumptions for the solvent-based and salting-out-based processes were compared. The salting-out + distillation process turned out to be more energy-saving than the solvent extraction process.
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Affiliation(s)
- Chuhan Fu
- The Gene and Linda Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWAUSA
| | - Zhuoxi Li
- School of PharmacyGuangzhou Xinhua UniversityGuangzhouP. R. China
| | - Yulei Zhang
- School of Chemistry & Chemical EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Conghua Yi
- School of Chemistry & Chemical EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Shaoqu Xie
- The Gene and Linda Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWAUSA
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Wang L, Upadhyay V, Maranas CD. dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLoS Comput Biol 2021; 17:e1009448. [PMID: 34570771 PMCID: PMC8496854 DOI: 10.1371/journal.pcbi.1009448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/07/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
Group contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs energy change (ΔrG′o) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has comparable prediction accuracy compared to existing GC methods and can capture Gibbs energy changes for isomerase and transferase reactions, which exhibit no overall group changes. We also demonstrate dGPredictor’s ability to predict the Gibbs energy change for novel reactions and seamless integration within de novo metabolic pathway design tools such as novoStoic for safeguarding against the inclusion of reaction steps with infeasible directionalities. To facilitate easy access to dGPredictor, we developed a graphical user interface to predict the standard Gibbs energy change for reactions at various pH and ionic strengths. The tool allows customized user input of known metabolites as KEGG IDs and novel metabolites as InChI strings (https://github.com/maranasgroup/dGPredictor). The standard Gibbs energy change is commonly used to check for the feasibility of enzyme-catalyzed reactions as thermodynamics plays a crucial role in pathway design for biochemical synthesis. The group contribution methods using expert-defined functional groups have been extensively used for estimating standard Gibbs energy change. Here, we introduce a molecular fingerprint-based thermodynamic tool, dGPredictor, that enables distinguishing between (stereo)isomers in metabolic reactions leading to improved reaction coverage and comparable prediction accuracy as GC methods. dGPredictor can also be used alongside de novo pathway design tools to ensure the correct directionality of chosen reaction steps. We applied and tested dGPredictor on reactions from the KEGG database and applied it to screen an isobutanol synthesis pathway design. An open-source, user-friendly web interface is provided to facilitate easy access for standard Gibbs energy change of reactions at different pH values. (https://github.com/maranasgroup/dGPredictor).
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Affiliation(s)
- Lin Wang
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America
| | - Vikas Upadhyay
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America
- * E-mail:
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Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
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Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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38
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Co-Production of Isobutanol and Ethanol from Prairie Grain Starch Using Engineered Saccharomyces cerevisiae. FERMENTATION 2021. [DOI: 10.3390/fermentation7030150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Isobutanol is an important and valuable platform chemical and an appealing biofuel that is compatible with contemporary combustion engines and existing fuel distribution infrastructure. The present study aimed to compare the potential of triticale, wheat and barley starch as feedstock for isobutanol production using an engineered strain of Saccharomyces cerevisiae. A simultaneous saccharification and fermentation (SSF) approach showed that all three starches were viable feedstock for co-production of isobutanol and ethanol and could produce titres similar to that produced using purified sugar as feedstock. A fed-batch process using triticale starch yielded 0.006 g isobutanol and 0.28 g ethanol/g starch. Additionally, it is demonstrated that Fusarium graminearum infected grain starch contaminated with mycotoxin can be used as an effective feedstock for isobutanol and ethanol co-production. These findings demonstrate the potential for triticale as a purpose grown energy crop and show that mycotoxin-contaminated grain starch can be used as feedstock for isobutanol biosynthesis, thus adding value to a grain that would otherwise be of limited use.
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Shewanella oneidensis MR-1 as a bacterial platform for electro-biotechnology. Essays Biochem 2021; 65:355-364. [PMID: 33769488 PMCID: PMC8314016 DOI: 10.1042/ebc20200178] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
The genus Shewanella comprises over 70 species of heterotrophic bacteria with versatile respiratory capacities. Some of these bacteria are known to be pathogens of fishes and animals, while many are non-pathogens considered to play important roles in the global carbon cycle. A representative strain is Shewanella oneidensis MR-1 that has been intensively studied for its ability to respire diverse electron acceptors, such as oxygen, nitrate, sulfur compounds, metals, and organics. In addition, studies have been focused on its ability as an electrochemically active bacterium that is capable of discharging electrons to and receiving electrons from electrodes in bioelectrochemical systems (BESs) for balancing intracellular redox states. This ability is expected to be applied to electro-fermentation (EF) for producing value-added chemicals that conventional fermentation technologies are difficult to produce efficiently. Researchers are also attempting to utilize its electrochemical ability for controlling gene expression, for which electro-genetics (EG) has been coined. Here we review fundamental knowledge on this bacterium and discuss future directions of studies on its applications to electro-biotechnology (EB).
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40
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Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19. Synth Syst Biotechnol 2021; 6:135-143. [PMID: 34151035 PMCID: PMC8200311 DOI: 10.1016/j.synbio.2021.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2, the causative agent for COVID-19, infect human mainly via respiratory tract, which is heavily inhabited by local microbiota. However, the interaction between SARS-CoV-2 and nasopharyngeal microbiota, and the association with metabolome has not been well characterized. Here, metabolomic analysis of blood, urine, and nasopharyngeal swabs from a group of COVID-19 and non-COVID-19 patients, and metagenomic analysis of pharyngeal samples were used to identify the key features of COVID-19. Results showed lactic acid, l-proline, and chlorogenic acid methyl ester (CME) were significantly reduced in the sera of COVID-19 patients compared with non-COVID-19 ones. Nasopharyngeal commensal bacteria including Gemella morbillorum, Gemella haemolysans and Leptotrichia hofstadii were notably depleted in the pharynges of COVID-19 patients, while Prevotella histicola, Streptococcus sanguinis, and Veillonella dispar were relatively increased. The abundance of G. haemolysans and L. hofstadii were significantly positively associated with serum CME, which might be an anti-SARS-CoV-2 bacterial metabolite. This study provides important information to explore the linkage between nasopharyngeal microbiota and disease susceptibility. The findings were based on a very limited number of patients enrolled in this study; a larger size of cohort will be appreciated for further investigation.
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Felczak MM, Bowers RM, Woyke T, TerAvest MA. Zymomonas diversity and potential for biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:112. [PMID: 33933155 PMCID: PMC8088579 DOI: 10.1186/s13068-021-01958-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Zymomonas mobilis is an aerotolerant α-proteobacterium, which has been genetically engineered for industrial purposes for decades. However, a comprehensive comparison of existing strains on the genomic level in conjunction with phenotype analysis has yet to be carried out. We here performed whole-genome comparison of 17 strains including nine that were sequenced in this study. We then compared 15 available Zymomonas strains for their natural abilities to perform under conditions relevant to biofuel synthesis. We tested their growth in anaerobic rich media, as well as growth, ethanol production and xylose utilization in lignocellulosic hydrolysate. We additionally compared their tolerance to isobutanol, flocculation characteristics, and ability to uptake foreign DNA by electroporation and conjugation. RESULTS Using clustering based on 99% average nucleotide identity (ANI), we classified 12 strains into four clusters based on sequence similarity, while five strains did not cluster with any other strain. Strains belonging to the same 99% ANI cluster showed similar performance while significant variation was observed between the clusters. Overall, conjugation and electroporation efficiencies were poor across all strains, which was consistent with our finding of coding potential for several DNA defense mechanisms, such as CRISPR and restriction-modification systems, across all genomes. We found that strain ATCC31821 (ZM4) had a more diverse plasmid profile than other strains, possibly leading to the unique phenotypes observed for this strain. ZM4 also showed the highest growth of any strain in both laboratory media and lignocellulosic hydrolysate and was among the top 3 strains for isobutanol tolerance and electroporation and conjugation efficiency. CONCLUSIONS Our findings suggest that strain ZM4 has a unique combination of genetic and phenotypic traits that are beneficial for biofuel production and propose investing future efforts in further engineering of ZM4 for industrial purposes rather than exploring new Zymomonas isolates.
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Affiliation(s)
- Magdalena M Felczak
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert M Bowers
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michaela A TerAvest
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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Weitz S, Hermann M, Linder S, Bengelsdorf FR, Takors R, Dürre P. Isobutanol Production by Autotrophic Acetogenic Bacteria. Front Bioeng Biotechnol 2021; 9:657253. [PMID: 33912549 PMCID: PMC8072342 DOI: 10.3389/fbioe.2021.657253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
Two different isobutanol synthesis pathways were cloned into and expressed in the two model acetogenic bacteria Acetobacterium woodii and Clostridium ljungdahlii. A. woodii is specialized on using CO2 + H2 gas mixtures for growth and depends on sodium ions for ATP generation by a respective ATPase and Rnf system. On the other hand, C. ljungdahlii grows well on syngas (CO + H2 + CO2 mixture) and depends on protons for energy conservation. The first pathway consisted of ketoisovalerate ferredoxin oxidoreductase (Kor) from Clostridium thermocellum and bifunctional aldehyde/alcohol dehydrogenase (AdhE2) from C. acetobutylicum. Three different kor gene clusters are annotated in C. thermocellum and were all tested. Only in recombinant A. woodii strains, traces of isobutanol could be detected. Additional feeding of ketoisovalerate increased isobutanol production to 2.9 mM under heterotrophic conditions using kor3 and to 1.8 mM under autotrophic conditions using kor2. In C. ljungdahlii, isobutanol could only be detected upon additional ketoisovalerate feeding under autotrophic conditions. kor3 proved to be the best suited gene cluster. The second pathway consisted of ketoisovalerate decarboxylase from Lactococcus lactis and alcohol dehydrogenase from Corynebacterium glutamicum. For increasing the carbon flux to ketoisovalerate, genes encoding ketol-acid reductoisomerase, dihydroxy-acid dehydratase, and acetolactate synthase from C. ljungdahlii were subcloned downstream of adhA. Under heterotrophic conditions, A. woodii produced 0.2 mM isobutanol and 0.4 mM upon additional ketoisovalerate feeding. Under autotrophic conditions, no isobutanol formation could be detected. Only upon additional ketoisovalerate feeding, recombinant A. woodii produced 1.5 mM isobutanol. With C. ljungdahlii, no isobutanol was formed under heterotrophic conditions and only 0.1 mM under autotrophic conditions. Additional feeding of ketoisovalerate increased these values to 1.5 mM and 0.6 mM, respectively. A further increase to 2.4 mM and 1 mM, respectively, could be achieved upon inactivation of the ilvE gene in the recombinant C. ljungdahlii strain. Engineering the coenzyme specificity of IlvC of C. ljungdahlii from NADPH to NADH did not result in improved isobutanol production.
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Affiliation(s)
- Sandra Weitz
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Maria Hermann
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Sonja Linder
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Frank R Bengelsdorf
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
| | - Ralf Takors
- Institut für Bioverfahrenstechnik, Universität Stuttgart, Stuttgart, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Ulm, Germany
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Elucidating the differences in oxidation of high-performance α- and β- diisobutylene biofuels via Synchrotron photoionization mass spectrometry. Sci Rep 2020; 10:21776. [PMID: 33311537 PMCID: PMC7733457 DOI: 10.1038/s41598-020-76462-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/21/2020] [Indexed: 11/09/2022] Open
Abstract
Biofuels are a promising ecologically viable and renewable alternative to petroleum fuels, with the potential to reduce net greenhouse gas emissions. However, biomass sourced fuels are often produced as blends of hydrocarbons and their oxygenates. Such blending complicates the implementation of these fuels in combustion applications. Variations in a biofuel's composition will dictate combustion properties such as auto ignition temperature, reaction delay time, and reaction pathways. A handful of novel drop-in replacement biofuels for conventional transportation fuels have recently been down selected from a list of over 10,000 potential candidates as part of the U.S. Department of Energy's (DOE) Co-Optimization of Fuels and Engines (Co-Optima) initiative. Diisobutylene (DIB) is one such high-performing hydrocarbon which can readily be produced from the dehydration and dimerization of isobutanol, produced from the fermentation of biomass-derived sugars. The two most common isomers realized, from this process, are 2,4,4-trimethyl-1-pentene (α-DIB) and 2,4,4-trimethyl-2-pentene (β-DIB). Due to a difference in olefinic bond location, the α- and β- isomer exhibit dramatically different ignition temperatures at constant pressure and equivalence ratio. This may be attributed to different fragmentation pathways enabled by allylic versus vinylic carbons. For optimal implementation of these biofuel candidates, explicit identification of the intermediates formed during the combustion of each of the isomers is needed. To investigate the combustion pathways of these molecules, tunable vacuum ultraviolet (VUV) light (in the range 8.1-11.0 eV) available at the Lawrence Berkeley National Laboratory's Advanced Light Source (ALS) has been used in conjunction with a jet stirred reactor (JSR) and time-of-flight mass spectrometry to probe intermediates formed. Relative intensity curves for intermediate mass fragments produced during this process were obtained. Several important unique intermediates were identified at the lowest observable combustion temperature with static pressure of 93,325 Pa and for 1.5 s residence time. As this relatively short residence time is just after ignition, this study is targeted at the fuels' ignition events. Ignition characteristics for both isomers were found to be strongly dependent on the kinetics of C4 and C7 fragment production and decomposition, with the tert-butyl radical as a key intermediate species. However, the ignition of α-DIB exhibited larger concentrations of C4 compounds over C7, while the reverse was true for β-DIB. These identified species will allow for enhanced engineering modeling of fuel blending and engine design.
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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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Cui DY, Wei YN, Lin LC, Chen SJ, Feng PP, Xiao DG, Lin X, Zhang CY. Increasing Yield of 2,3,5,6-Tetramethylpyrazine in Baijiu Through Saccharomyces cerevisiae Metabolic Engineering. Front Microbiol 2020; 11:596306. [PMID: 33324376 PMCID: PMC7726194 DOI: 10.3389/fmicb.2020.596306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Baijiu is a traditional distilled beverage in China with a rich variety of aroma substances. 2,3,5,6-tetramethylpyrazine (TTMP) is an important component in Baijiu and has the function of promoting cardiovascular and cerebrovascular health. During the brewing of Baijiu, the microorganisms in jiuqu produce acetoin and then synthesize TTMP, but the yield of TTMP is very low. In this work, 2,3-butanediol dehydrogenase (BDH) coding gene BDH1 and another BDH2 gene were deleted or overexpressed to evaluate the effect on the content of acetoin and TTMP in Saccharomyces cerevisiae. The results showed that the acetoin synthesis of strain α5-D1B2 was significantly enhanced by disrupting BDH1 and overexpressing BDH2, leading to a 2.6-fold increase of TTMP production up to 10.55 mg/L. To further improve the production level of TTMP, the α-acetolactate synthase (ALS) of the pyruvate decomposition pathway was overexpressed to enhance the synthesis of diacetyl. However, replacing the promoter of the ILV2 gene with a strong promoter (PGK1p) to increase the expression level of the ILV2 gene did not result in further increased diacetyl, acetoin and TTMP production. Based on these evidences, we constructed the diploid strains AY-SB1 (ΔBDH1:loxP/ΔBDH1:loxP) and AY-SD1B2 (ΔBDH1:loxP-PGK1p-BDH2-PGK1t/ΔBDH1:loxP-PGK1p-BDH2-PGK1t) to ensure the fermentation performance of the strain is more stable in Baijiu brewing. The concentration of TTMP in AY-SB1 and AY-SD1B2 was 7.58 and 9.47 mg/L, respectively, which represented a 2.3- and 2.87-fold increase compared to the parental strain. This work provides an example for increasing TTMP production in S. cerevisiae by genetic engineering, and highlight a novel method to improve the quality and beneficial health attributes of Baijiu.
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Affiliation(s)
- Dan-Yao Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Ya-Nan Wei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Liang-Cai Lin
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Shi-Jia Chen
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Peng-Peng Feng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Dong-Guang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Xue Lin
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Cui-Ying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Yibin, China
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Lacerda MP, Oh EJ, Eckert C. The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels. Life (Basel) 2020; 10:E299. [PMID: 33233378 PMCID: PMC7700301 DOI: 10.3390/life10110299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.
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Affiliation(s)
- Maria Priscila Lacerda
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
| | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Carrie Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
- National Renewable Energy Laboratory (NREL), Biosciences Center, Golden, CO 80401, USA
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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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Engineering cofactor supply and NADH-dependent D-galacturonic acid reductases for redox-balanced production of L-galactonate in Saccharomyces cerevisiae. Sci Rep 2020; 10:19021. [PMID: 33149263 PMCID: PMC7642425 DOI: 10.1038/s41598-020-75926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
D-Galacturonic acid (GalA) is the major constituent of pectin-rich biomass, an abundant and underutilized agricultural byproduct. By one reductive step catalyzed by GalA reductases, GalA is converted to the polyhydroxy acid L-galactonate (GalOA), the first intermediate of the fungal GalA catabolic pathway, which also has interesting properties for potential applications as an additive to nutrients and cosmetics. Previous attempts to establish the production of GalOA or the full GalA catabolic pathway in Saccharomyces cerevisiae proved challenging, presumably due to the inefficient supply of NADPH, the preferred cofactor of GalA reductases. Here, we tested this hypothesis by coupling the reduction of GalA to the oxidation of the sugar alcohol sorbitol that has a higher reduction state compared to glucose and thereby yields the necessary redox cofactors. By choosing a suitable sorbitol dehydrogenase, we designed yeast strains in which the sorbitol metabolism yields a "surplus" of either NADPH or NADH. By biotransformation experiments in controlled bioreactors, we demonstrate a nearly complete conversion of consumed GalA into GalOA and a highly efficient utilization of the co-substrate sorbitol in providing NADPH. Furthermore, we performed structure-guided mutagenesis of GalA reductases to change their cofactor preference from NADPH towards NADH and demonstrated their functionality by the production of GalOA in combination with the NADH-yielding sorbitol metabolism. Moreover, the engineered enzymes enabled a doubling of GalOA yields when glucose was used as a co-substrate. This significantly expands the possibilities for metabolic engineering of GalOA production and valorization of pectin-rich biomass in general.
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Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Appl Microbiol Biotechnol 2020; 104:7915-7925. [PMID: 32776205 DOI: 10.1007/s00253-020-10800-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.
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50
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Verhagen KJA, van Gulik WM, Wahl SA. Dynamics in redox metabolism, from stoichiometry towards kinetics. Curr Opin Biotechnol 2020; 64:116-123. [DOI: 10.1016/j.copbio.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
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