51
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Cai G, Lin Z, Shi S. Development and expansion of the CRISPR/Cas9 toolboxes for powerful genome engineering in yeast. Enzyme Microb Technol 2022; 159:110056. [PMID: 35561628 DOI: 10.1016/j.enzmictec.2022.110056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 01/09/2023]
Abstract
Yeasts represent a group of the microorganisms most frequently seen in biotechnology. Recently, the class 2 type II CRISPR system (CRISPR/Cas9) has become the principal toolbox for genome editing. By efficiently implementing genetic manipulations such as gene integration/knockout, base editor, and transcription regulation, the development of biotechnological applications in yeasts has been extensively promoted. The genome-level tools based on CRISPR/Cas9, used for screening and identifying functional genes/gene clusters, are also advancing. In general, CRISPR/Cas9-assisted editing tools have gradually become standardized and function as host-orthogonal genetic systems, which results in time-saving for strain engineering and biotechnological application processes. In this review, we summarize the key points of the basic elements in the CRISPR/Cas9 system, including Cas9 variants, guide RNA, donors, and effectors. With a focus on yeast, we have also introduced the development of various CRISPR/Cas9 systems and discussed their future possibilities.
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Affiliation(s)
- Guang Cai
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhenquan Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
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52
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Controlling gene expression with deep generative design of regulatory DNA. Nat Commun 2022; 13:5099. [PMID: 36042233 PMCID: PMC9427793 DOI: 10.1038/s41467-022-32818-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random DNA libraries, which limits the designs to span merely a short section of the promoter and restricts their control of gene expression. Here, we prototype a deep learning strategy based on generative adversarial networks (GAN) by learning directly from genomic and transcriptomic data. Our ExpressionGAN can traverse the entire regulatory sequence-expression landscape in a gene-specific manner, generating regulatory DNA with prespecified target mRNA levels spanning the whole gene regulatory structure including coding and adjacent non-coding regions. Despite high sequence divergence from natural DNA, in vivo measurements show that 57% of the highly-expressed synthetic sequences surpass the expression levels of highly-expressed natural controls. This demonstrates the applicability and relevance of deep generative design to expand our knowledge and control of gene expression regulation in any desired organism, condition or tissue. Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Here the authors present EspressionGAN, a generative adversarial network that uses genomic and transcriptomic data to generate regulatory sequences.
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53
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Kong S, Yu W, Gao N, Zhai X, Zhou YJ. Expanding the neutral sites for integrated gene expression in Saccharomyces cerevisiae. FEMS Microbiol Lett 2022; 369:6671531. [PMID: 35981819 DOI: 10.1093/femsle/fnac081] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Construction of efficient microbial cell factories always requires assembling biosynthetic pathways and rewiring cellular metabolism with overexpression of multiple genes. Genomic integration is considered to be helpful for stable gene expression in compared with the episomal plasmids. However, the limited availability of suitable loci hinders the extensive metabolic engineering. We here characterized 30 neutral sites in Saccharomyces cerevisiae genome that did not affect cellular fitness by using expression cassettes of green fluorescent protein (eGFP) and fatty acyl-CoA reductase (MaFAR1) with the aid of efficient CRISPR-Cas9 technique. We found that integration of gene expression cassettes to different genome loci resulted a varied GFP signal and fatty alcohol production, which showed that genomic loci could be used for tuning gene expression. The characterized set of neutral sites should be helpful for extensively metabolic engineering of S. cerevisiae for chemical production and other purposes.
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Affiliation(s)
- Sijia Kong
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ning Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiaoxin Zhai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
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54
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Zhang G, Zhang C, Wang Z, Wang Q, Nielsen J, Dai Z. Dual β-oxidation pathway and transcription factor engineering for methyl ketones production in Saccharomyces cerevisiae. Metab Eng 2022; 73:225-234. [PMID: 35987431 DOI: 10.1016/j.ymben.2022.08.004] [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: 05/14/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Methyl ketones (MK) are highly valuable fatty acid derivatives with broad applications. Microbes based biosynthesis represents an alternative route for production of these usually fossil based chemicals. In this study, we reported metabolic engineering of Saccharomyces cerevisiae to produce MK, including 2-nonanone, 2-undecanone, 2-tridecanone and 2-pentadecanone. Besides enhancing inherent peroxisomal fatty acids β-oxidation cycle, a novel heterologous cytosolic fatty acids β-oxidation pathway was constructed, and this resulted in an increased production of MK by 2-fold. To increase carbon fluxes to methyl ketones, the supply of precursors was enhanced by engineering lipid metabolism, including improving the intracellular biosynthesis of acyl-CoAs, weakening the consumption of acyl-CoAs for lipids storage, and reinforcing activation of free fatty acids to acyl-CoAs. Hereby the titer of MK was improved by 7-fold, reaching 143.72 mg/L. Finally, transcription factor engineering was employed to increase the biosynthesis of methyl ketones and it was found that overexpression of ADR1 can mimic the oleate activated biogenesis and proliferation of peroxisomes, which resulted in a further increased production of MK by 28%. With these modifications and optimization, up to 845 mg/L total MK were produced from glucose in fed-batch fermentation, which is the highest titer of methyl ketones reported produced by fungi.
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Affiliation(s)
- Ge Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Chao Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zheng Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Department of Biology and Biological Engineering, Chalmers University of Technology, SE 412 96, Gothenburg, Sweden.
| | - Zongjie Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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55
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Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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56
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The Dicarboxylate Transporters from the AceTr Family and Dct-02 Oppositely Affect Succinic Acid Production in S. cerevisiae. J Fungi (Basel) 2022; 8:jof8080822. [PMID: 36012810 PMCID: PMC9409672 DOI: 10.3390/jof8080822] [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: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane transporters are important targets in metabolic engineering to establish and improve the production of chemicals such as succinic acid from renewable resources by microbial cell factories. We recently provided a Saccharomyces cerevisiae strain able to strongly overproduce succinic acid from glycerol and CO2 in which the Dct-02 transporter from Aspergillus niger, assumed to be an anion channel, was used to export succinic acid from the cells. In a different study, we reported a new group of succinic acid transporters from the AceTr family, which were also described as anion channels. Here, we expressed these transporters in a succinic acid overproducing strain and compared their impact on extracellular succinic acid accumulation with that of the Dct-02 transporter. The results show that the tested transporters of the AceTr family hinder succinic acid accumulation in the extracellular medium at low pH, which is in strong contrast to Dct-02. Data suggests that the AceTr transporters prefer monovalent succinate, whereas Dct-02 prefers divalent succinate anions. In addition, the results provided deeper insights into the characteristics of Dct-02, showing its ability to act as a succinic acid importer (thus being bidirectional) and verifying its capability of exporting malate.
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57
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Ramos-Viana V, Møller-Hansen I, Kempen P, Borodina I. Modulation of the cell wall protein Ecm33p in yeast Saccharomyces cerevisiae improves the production of small metabolites. FEMS Yeast Res 2022; 22:6654878. [PMID: 35922083 PMCID: PMC9440718 DOI: 10.1093/femsyr/foac037] [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: 03/07/2022] [Revised: 07/15/2022] [Accepted: 08/01/2022] [Indexed: 11/12/2022] Open
Abstract
The cell wall is a dynamic organelle that determines the shape and provides the cell with mechanical strength. This study investigated whether modulation of cell wall composition can influence the production or secretion of small metabolites by yeast cell factories. We deleted and upregulated several cell wall-related genes KRE2, CWP1, CWP2, ECM33, PUN1, and LAS21 in yeast Saccharomyces cerevisiae engineered for p-coumaric acid or β-carotene production. Deletions of las21∆ and ecm33∆ impaired the yeast growth on medium with cell wall stressors, calcofluor white, and caffeine. Both overexpression and deletion of ECM33 significantly improved the specific yield of p-coumaric acid and β-carotene. We observed no change in secretion in any cell wall altered mutants, suggesting the cell wall is not a limiting factor for small molecule secretion at the current production levels. We evaluated the cell wall morphology of the ECM33 mutant strains using transmission electron microscopy. The ecm33∆ mutants had an increased chitin deposition and a less structured cell wall, while the opposite was observed in ECM33-overexpressing strains. Our results point at the cell wall-related gene ECM33 as a potential target for improving production in engineered yeast cell factories.
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Affiliation(s)
- Verónica Ramos-Viana
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Paul Kempen
- Department of Health Technology, Section for Biotherapeutic Engineering and Drug Targeting, Technical University of Denmark, Lyngby, Denmark.,National Centre for Nano Fabrication and Characterization, Technical University of Denmark, Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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58
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Bean BDM, Whiteway M, Martin VJJ. The MyLO CRISPR-Cas9 toolkit: a markerless yeast localization and overexpression CRISPR-Cas9 toolkit. G3 (BETHESDA, MD.) 2022; 12:jkac154. [PMID: 35708612 PMCID: PMC9339301 DOI: 10.1093/g3journal/jkac154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 12/28/2022]
Abstract
The genetic tractability of the yeast Saccharomyces cerevisiae has made it a key model organism for basic research and a target for metabolic engineering. To streamline the introduction of tagged genes and compartmental markers with powerful Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) - CRISPR-associated protein 9 (Cas9)-based genome editing tools, we constructed a Markerless Yeast Localization and Overexpression (MyLO) CRISPR-Cas9 toolkit with 3 components: (1) a set of optimized Streptococcus pyogenes Cas9-guide RNA expression vectors with 5 selectable markers and the option to either preclone or cotransform the gRNAs; (2) vectors for the one-step construction of integration cassettes expressing an untagged or green fluorescent protein/red fluorescent protein/hemagglutinin-tagged gene of interest at one of 3 levels, supporting localization and overexpression studies; and (3) integration cassettes containing moderately expressed green fluorescent protein- or red fluorescent protein-tagged compartmental markers for colocalization experiments. These components allow rapid, high-efficiency genomic integrations and modifications with only transient selection for the Cas9 vector, resulting in markerless transformations. To demonstrate the ease of use, we applied our complete set of compartmental markers to colabel all target subcellular compartments with green fluorescent protein and red fluorescent protein. Thus, the MyLO toolkit packages CRISPR-Cas9 technology into a flexible, optimized bundle that allows the stable genomic integration of DNA with the ease of use approaching that of transforming plasmids.
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Affiliation(s)
- Björn D M Bean
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC H4B1R6, Canada
| | - Malcolm Whiteway
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC H4B1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC H4B1R6, Canada
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59
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Sáez Moreno D, Udi Q, Azeredo J, Domingues L. Towards T7 RNA polymerase (T7RNAP)-based expression system in yeast: challenges and opportunities. Bioengineered 2022; 13:14947-14959. [PMID: 37105766 DOI: 10.1080/21655979.2023.2180579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
During the last decades, we have witnessed unprecedented advances in biological engineering and synthetic biology. These disciplines aim to take advantage of gene pathway regulation and gene expression in different organisms, to enable cells to perform desired functions. Yeast has been widely utilized as a model for the study of eukaryotic protein expression while bacteriophage T7RNAP and its promoter constitute the preferred system for prokaryotic protein expression (such as pET-based expression systems). The ability to integrate a T7RNAP-based expression system in yeast could allow for a better understanding of gene regulation in eukaryotic cells, and potentially increase the efficiency and processivity of yeast as an expression system. However, the attempts for the creation of such a system have been unsuccessful to date. This review aims to: (i) summarize the efforts that, for many years, have been devoted to the creation of a T7RNAP-based yeast expression system and ii) provide an overview of the latest advances in knowledge of eukaryotic transcription and translation that could lead to the construction of a successful T7RNAP expression system in yeast. The completion of this new expression system would allow to further expand the toolkit of yeast in synthetic biology and ultimately contribute to boost yeast usage as a key cell factory in sustainable biorefinery and circular economy.
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Affiliation(s)
- David Sáez Moreno
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Qimron Udi
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
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60
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Bao J, de Dios Mateos E, Scheller S. Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis. ACS Synth Biol 2022; 11:2496-2503. [PMID: 35730587 PMCID: PMC9295151 DOI: 10.1021/acssynbio.2c00137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The rapid-growing
and genetically tractable methanogen Methanococcus
maripaludis is a promising host organism
for the biotechnological conversion of carbon dioxide and renewable
hydrogen to fuels and value-added products. Expansion of its product
scope through metabolic engineering necessitates reliable and efficient
genetic tools, particularly for genome edits that affect the primary
metabolism and cell growth. Here, we have designed a genome-editing
toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair
machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up
to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (∼8.9 kbp)
was replaced by the Escherichia coli β-glucuronidase gene. To facilitate metabolic engineering
and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified
in the presence of two common growth substrates, either formate or
carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded
as a reliable and quick method for genome editing in a methanogen.
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Affiliation(s)
- Jichen Bao
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Enrique de Dios Mateos
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
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61
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Ylinen A, de Ruijter JC, Jouhten P, Penttilä M. PHB production from cellobiose with Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:124. [PMID: 35729556 PMCID: PMC9210708 DOI: 10.1186/s12934-022-01845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Replacement of petrochemical-based materials with microbially produced biodegradable alternatives calls for industrially attractive fermentation processes. Lignocellulosic materials offer non-edible alternatives for cultivated sugars, but require often use of expensive sugar releasing enzymes, such as β-glucosidases. These cellulose treatment costs could be reduced if microbial production hosts could use short cellodextrins such as cellobiose directly as their substrates. In this study, we demonstrate production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Yeast strains expressing PHB pathway genes from Cupriavidus necator and cellodextrin transporter gene CDT-1 from Neurospora crassa were complemented either with β-glucosidase gene GH1-1 from N. crassa or with cellobiose phosphorylase gene cbp from Ruminococcus flavefaciens. These cellobiose utilization routes either with Gh1-1 or Cbp enzymes differ in energetics and dynamics. However, both routes enabled higher PHB production per consumed sugar and higher PHB accumulation % of cell dry weight (CDW) than use of glucose as a carbon source. As expected, the strains with Gh1-1 consumed cellobiose faster than the strains with Cbp, both in flask and bioreactor batch cultures. In shake flasks, higher final PHB accumulation % of CDW was reached with Cbp route (10.0 ± 0.3%) than with Gh1-1 route (8.1 ± 0.2%). However, a higher PHB accumulation was achieved in better aerated and pH-controlled bioreactors, in comparison to shake flasks, and the relative performance of strains switched. In bioreactors, notable PHB accumulation levels per CDW of 13.4 ± 0.9% and 18.5 ± 3.9% were achieved with Cbp and Gh1-1 routes, respectively. The average molecular weights of accumulated PHB were similar using both routes; approximately 500 kDa and 450 kDa for strains expressing either cbp or GH1-1 genes, respectively. The formation of PHB with high molecular weights, combined with efficient cellobiose conversion, demonstrates a highly potential solution for improving attractiveness of sustainable polymer production using microbial cells.
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Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
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62
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Perruca-Foncillas R, Davidsson J, Carlquist M, Gorwa-Grauslund MF. Assessment of fluorescent protein candidates for multi-color flow cytometry analysis of Saccharomyces cerevisiae. BIOTECHNOLOGY REPORTS 2022; 34:e00735. [PMID: 35686015 PMCID: PMC9171426 DOI: 10.1016/j.btre.2022.e00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/25/2022]
Abstract
In vivo fluorescence of candidate fluorescent proteins was assessed in Saccharomyces cerevisiae. eEGFP, CyOFP1opt and mBeRFPopt were found to be suitable for multicolour flow cytometry. Successful protein selection and equipment configuration allowed potential tri-color flow cytometry with 488 nm single-laser excitation.
Transcription factor-based biosensors represent promising tools in the construction and evaluation of efficient cell factories for the sustainable production of fuels, chemicals and pharmaceuticals. They can notably be designed to follow the production of a target compound or to monitor key cellular properties, such as stress or starvation. In most cases, the biosensors are built with fluorescent protein (FP) genes as reporter genes because of the direct correlation between promoter activity and fluorescence level that can be measured using, for instance, flow cytometry or fluorometry. The expansion of available FPs offers the possibility of using several FPs - and biosensors – in parallel in one host, with simultaneous detection using multicolor flow cytometry. However, the technique is currently limited by the unavailability of combinations of FP whose genes can be successfully expressed in the host and whose fluorescence can be efficiently distinguished from each other. In the present study, the broad collection of available FPs was explored and four different FPs were successfully expressed in the yeast Saccharomyces cerevisiae: yEGFP, mEGFP, CyOFP1opt and mBeRFPopt. After studying their fluorescence signals, population heterogeneity and possible interactions, we recommend two original combinations of FPs for bi-color flow cytometry: mEGFP together with either CyOFP1opt or mBeRFPopt, as well as the combination of all three FPs mEGFP, CyOFP1opt and mBeRFPopt for tri-color flow cytometry. These combinations will allow to perform different types of bi-color or possibly tri-color flow cytometry and FACS experiments with yeast, such as phenotype evaluation, screening or sorting, by single-laser excitation with a standard 488 nm blue laser.
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Re-engineering of CUP1 promoter and Cup2/Ace1 transactivator to convert Saccharomyces cerevisiae into a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper. Biosens Bioelectron 2022; 214:114502. [DOI: 10.1016/j.bios.2022.114502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
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A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae. Synth Syst Biotechnol 2022; 7:657-663. [PMID: 35224233 PMCID: PMC8857431 DOI: 10.1016/j.synbio.2022.02.001] [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] [Received: 10/31/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/22/2022] Open
Abstract
The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.
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Engineering Saccharomyces cerevisiae for production of the capsaicinoid nonivamide. Microb Cell Fact 2022; 21:106. [PMID: 35643562 PMCID: PMC9148506 DOI: 10.1186/s12934-022-01831-3] [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: 01/20/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Background Capsaicinoids are produced by plants in the Capsicum genus and are the main reason for the pungency of chili pepper fruits. They are strong agonists of TRPV1 (the transient receptor potential cation channel subfamily V member 1) and used as active ingredients in pharmaceuticals for the treatment of pain. The use of bioengineered microorganisms in a fermentation process may be an efficient route for their preparation, as well as for the discovery of (bio-)synthetic capsaicinoids with improved or novel bioactivities. Results Saccharomyces cerevisiae was engineered to over-express a selection of amide-forming N-acyltransferase and CoA-ligase enzyme cascades using a combinatorial gene assembly method, and was screened for nonivamide production from supplemented vanillylamine and nonanoic acid. Data from this work demonstrate that Tyramine N-hydroxycinnamoyl transferase from Capsicum annuum (CaAT) was most efficient for nonivamide formation in yeast, outcompeting the other candidates including AT3 (Pun1) from Capsicum spp. The CoA-ligase partner with highest activity from the ones evaluated here were from Petunia hybrida (PhCL) and Spingomonas sp. Ibu-2 (IpfF). A yeast strain expressing CaAT and IpfF produced 10.6 mg L−1 nonivamide in a controlled bioreactor setup, demonstrating nonivamide biosynthesis by S. cerevisiae for the first time. Conclusions Baker’s yeast was engineered for production of nonivamide as a model capsaicinoid, by expressing N-acyltransferases and CoA-ligases of plant and bacterial origin. The constructed yeast platform holds potential for in vivo biocatalytic formation of capsaicinoids and could be a useful tool for the discovery of novel drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01831-3.
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Malubhoy Z, Bahia FM, de Valk SC, de Hulster E, Rendulić T, Ortiz JPR, Xiberras J, Klein M, Mans R, Nevoigt E. Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:102. [PMID: 35643577 PMCID: PMC9148483 DOI: 10.1186/s12934-022-01817-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Background The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO2). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO2-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol−1. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO2-fixation and SA yield. Results By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO3 to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol−1 was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol−1 at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO2-enriched gas-phase indicated that CO2 was fixed during the SA production phase. Conclusions The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO2. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO2. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01817-1.
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Lengger B, Hoch-Schneider EE, Jensen CN, Jakočiu̅nas T, Petersen AA, Frimurer TM, Jensen ED, Jensen MK. Serotonin G Protein-Coupled Receptor-Based Biosensing Modalities in Yeast. ACS Sens 2022; 7:1323-1335. [PMID: 35452231 PMCID: PMC9150182 DOI: 10.1021/acssensors.1c02061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
Abstract
Serotonin is a key neurotransmitter involved in numerous physiological processes and serves as an important precursor for manufacturing bioactive indoleamines and alkaloids used in the treatment of human pathologies. In humans, serotonin sensing and signaling can occur by 12 G protein-coupled receptors (GPCRs) coupled to Gα proteins. In yeast, human serotonin GPCRs coupled to Gα proteins have previously been shown to function as whole-cell biosensors of serotonin. However, systematic characterization of serotonin biosensing modalities between variant serotonin GPCRs and application thereof for high-resolution serotonin quantification is still awaiting. To systematically assess GPCR signaling in response to serotonin, we characterized reporter gene expression at two different pHs of a 144-sized library encoding all 12 human serotonin GPCRs in combination with 12 different Gα proteins engineered in yeast. From this screen, we observed changes in the biosensor sensitivities of >4 orders of magnitude. Furthermore, adopting optimal biosensing designs and pH conditions enabled high-resolution high-performance liquid chromatography-validated sensing of serotonin produced in yeast. Lastly, we used the yeast platform to characterize 19 serotonin GPCR polymorphisms found in human populations. While major differences in signaling were observed among the individual polymorphisms when studied in yeast, a cross-comparison of selected variants in mammalian cells showed both similar and disparate results. Taken together, our study highlights serotonin biosensing modalities of relevance to both biotechnological and potential human health applications.
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Affiliation(s)
- Bettina Lengger
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Emma E. Hoch-Schneider
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christina N. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tadas Jakočiu̅nas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Anja A. Petersen
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Thomas M. Frimurer
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Emil D. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system. Metab Eng Commun 2022; 14:e00199. [PMID: 35571351 PMCID: PMC9095885 DOI: 10.1016/j.mec.2022.e00199] [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] [Received: 12/13/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022] Open
Abstract
The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation in vivo at gene expression level, independent of cultivation conditions. We used the modified doxycycline-based Tet-On approach to adjust the expression of the stereospecific D-lactate dehydrogenase gene (ldhA) from Leuconostoc mesenteroides to control D-lactic acid formation in yeast Saccharomyces cerevisiae. The synthetic Tet-On transcription factor with a VP16 activation domain was continuously expressed and its binding to a synthetic promoter with eight transcription factor specific binding sites upstream of the ldhA gene was controlled with the doxycycline concentration in the media. The increase in doxycycline concentration correlated positively with ldhA expression, D-lactic acid production, poly(D-lactic acid) (PDLA) accumulation in vivo, and D-lactic acid content in the poly(D-lactate-co-3-hydroxybutyrate) P(LA-3HB) copolymer. We demonstrated that the D-lactic acid content of the P(LA-3HB) copolymer can be adjusted linearly from 6 mol% to 93 mol% in vivo in S. cerevisiae. These results highlight the power of controlling gene expression and monomer formation in the tuning of the polymer composition. In addition, we obtained 5.6% PDLA and 19% P(LA-3HB) of the cell dry weight (CDW), which are over two- and five-fold higher accumulation levels, respectively, than reported in the previous studies with yeast. We also compared two engineered PHA synthases and discovered that in S. cerevisiae the PHA synthase PhaC1437Ps6-19 produced P(LA-3HB) copolymers with lower D-lactic acid content, but with higher molecular weight, in comparison to the PHA synthase PhaC1Pre. P(LA-3HB) monomer structure was adjusted with controlled gene expression. Expression of D-lactate dehydrogenase (ldhA) was controlled with Tet-On approach. Lactic acid content in copolymer P(LA-3HB) was adjusted from 6 mol% up to 93 mol%. 5.6% PDLA and 19% P(LA-3HB) of cell dry weight (CDW) were obtained in S. cerevisiae. PhaC1437Ps6-19 P(LA-3HB) had lower D-lactic acid % than PhaC1Pre P(LA-3HB).
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Stovicek V, Dato L, Almqvist H, Schöpping M, Chekina K, Pedersen LE, Koza A, Figueira D, Tjosås F, Ferreira BS, Forster J, Lidén G, Borodina I. Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:22. [PMID: 35219341 PMCID: PMC8882276 DOI: 10.1186/s13068-022-02121-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/12/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids. RESULTS The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µmax) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µmax between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL. CONCLUSIONS The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.
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Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Laura Dato
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,River Stone Biotech ApS, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Henrik Almqvist
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Marie Schöpping
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark.,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ksenia Chekina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark
| | - Diogo Figueira
- Biotrend S.A., Biocant Park Núcleo 04, Lote 2, 3060-197, Cantanhede, Portugal
| | - Freddy Tjosås
- Borregaard ApS, Hjalmar Wessels vei 6, 1721, Sarpsborg, Norway
| | | | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.
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Tellechea-Luzardo J, Hobbs L, Velázquez E, Pelechova L, Woods S, de Lorenzo V, Krasnogor N. Versioning biological cells for trustworthy cell engineering. Nat Commun 2022; 13:765. [PMID: 35140226 PMCID: PMC8828774 DOI: 10.1038/s41467-022-28350-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
“Full-stack” biotechnology platforms for cell line (re)programming are on the horizon, thanks mostly to (a) advances in gene synthesis and editing techniques as well as (b) the growing integration of life science research with informatics, the internet of things and automation. These emerging platforms will accelerate the production and consumption of biological products. Hence, traceability, transparency, and—ultimately—trustworthiness is required from cradle to grave for engineered cell lines and their engineering processes. Here we report a cloud-based version control system for biotechnology that (a) keeps track and organizes the digital data produced during cell engineering and (b) molecularly links that data to the associated living samples. Barcoding protocols, based on standard genetic engineering methods, to molecularly link to the cloud-based version control system six species, including gram-negative and gram-positive bacteria as well as eukaryote cells, are shown. We argue that version control for cell engineering marks a significant step toward more open, reproducible, easier to trace and share, and more trustworthy engineering biology. Full traceability and transparency are important to establish trust in engineered cell lines. Here the authors argue that version control for cell engineering marks a significant step toward more open, reproducible, traceable and ultimately more trustworthy engineering biology.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Leanne Hobbs
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Elena Velázquez
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Lenka Pelechova
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Simon Woods
- Policy Ethics and Life Sciences (PEALS), Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK.
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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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Liu T, Gou Y, Zhang B, Gao R, Dong C, Qi M, Jiang L, Ding X, Li C, Lian J. Construction of Ajmalicine and Sanguinarine
de novo
Biosynthetic Pathways using Stable Integration Sites in Yeast. Biotechnol Bioeng 2022; 119:1314-1326. [DOI: 10.1002/bit.28040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 01/02/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Xuanwei Ding
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
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Gronchi N, De Bernardini N, Cripwell RA, Treu L, Campanaro S, Basaglia M, Foulquié-Moreno MR, Thevelein JM, Van Zyl WH, Favaro L, Casella S. Natural Saccharomyces cerevisiae Strain Reveals Peculiar Genomic Traits for Starch-to-Bioethanol Production: the Design of an Amylolytic Consolidated Bioprocessing Yeast. Front Microbiol 2022; 12:768562. [PMID: 35126325 PMCID: PMC8815085 DOI: 10.3389/fmicb.2021.768562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Natural yeast with superior fermentative traits can serve as a platform for the development of recombinant strains that can be used to improve the sustainability of bioethanol production from starch. This process will benefit from a consolidated bioprocessing (CBP) approach where an engineered strain producing amylases directly converts starch into ethanol. The yeast Saccharomyces cerevisiae L20, previously selected as outperforming the benchmark yeast Ethanol Red, was here subjected to a comparative genomic investigation using a dataset of industrial S. cerevisiae strains. Along with Ethanol Red, strain L20 was then engineered for the expression of α-amylase amyA and glucoamylase glaA genes from Aspergillus tubingensis by employing two different approaches (delta integration and CRISPR/Cas9). A correlation between the number of integrated copies and the hydrolytic abilities of the recombinants was investigated. L20 demonstrated important traits for the construction of a proficient CBP yeast. Despite showing a close relatedness to commercial wine yeast and the benchmark Ethanol Red, a unique profile of gene copy number variations (CNVs) was found in L20, mainly encoding membrane transporters and secretion pathway proteins but also the fermentative metabolism. Moreover, the genome annotation disclosed seven open reading frames (ORFs) in L20 that are absent in the reference S288C genome. Genome engineering was successfully implemented for amylase production. However, with equal amylase gene copies, L20 proved its proficiency as a good enzyme secretor by exhibiting a markedly higher amylolytic activity than Ethanol Red, in compliance to the findings of the genomic exploration. The recombinant L20 dT8 exhibited the highest amylolytic activity and produced more than 4 g/L of ethanol from 2% starch in a CBP setting without the addition of supplementary enzymes. Based on the performance of this strain, an amylase/glucoamylase ratio of 1:2.5 was suggested as baseline for further improvement of the CBP ability. Overall, L20 showed important traits for the future construction of a proficient CBP yeast. As such, this work shows that natural S. cerevisiae strains can be used for the expression of foreign secreted enzymes, paving the way to strain improvement for the starch-to-bioethanol route.
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Affiliation(s)
- Nicoletta Gronchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | | | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | | | - Marina Basaglia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | | | - Johan M Thevelein
- Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- NovelYeast Bv, Open Bio-Incubator, Erasmus High School, Jette, Belgium
| | - Willem H Van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Lorenzo Favaro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | - Sergio Casella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
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74
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Engineering precursor supply for the high-level production of ergothioneine in Saccharomyces cerevisiae. Metab Eng 2022; 70:129-142. [DOI: 10.1016/j.ymben.2022.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022]
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75
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Jakočiūnas T, Jensen MK, Keasling JD. CasPER: A CRISPR/Cas9-Based Method for Directed Evolution in Genomic Loci in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2513:23-37. [PMID: 35781198 DOI: 10.1007/978-1-0716-2399-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, in this chapter, we describe a detailed protocol for the method named Cas9-mediated protein evolution reaction or short CasPER. CasPER is based on the generation of large 300-600-bp mutagenized linear DNA fragments by error-prone PCR which are used as a donor for repair of double-strand break mediated by Cas9 and subsequently integrated to the genome. This method can be efficiently used for directed evolution of desired essential or nonessential genes in the genome and most importantly can be multiplexed. Altogether, the described method allows for heterogeneous DNA integration with successful transformation efficiencies of 98-100% for both single and multiplex targeting.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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76
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Otto M, Liu D, Siewers V. Saccharomyces cerevisiae as a Heterologous Host for Natural Products. Methods Mol Biol 2022; 2489:333-367. [PMID: 35524059 DOI: 10.1007/978-1-0716-2273-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell factories can provide a sustainable supply of natural products with applications as pharmaceuticals, food-additives or biofuels. Besides being an important model organism for eukaryotic systems, Saccharomyces cerevisiae is used as a chassis for the heterologous production of natural products. Its success as a cell factory can be attributed to the vast knowledge accumulated over decades of research, its overall ease of engineering and its robustness. Many methods and toolkits have been developed by the yeast metabolic engineering community with the aim of simplifying and accelerating the engineering process.In this chapter, a range of methodologies are highlighted, which can be used to develop novel natural product cell factories or to improve titer, rate and yields of an existing cell factory with the goal of developing an industrially relevant strain. The addressed topics are applicable for different stages of a cell factory engineering project and include the choice of a natural product platform strain, expression cassette design for heterologous or native genes, basic and advanced genetic engineering strategies, and library screening methods using biosensors. The many engineering methods available and the examples of yeast cell factories underline the importance and future potential of this host for industrial production of natural products.
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Affiliation(s)
- Maximilian Otto
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dany Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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77
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Moon HY, Sim GH, Kim HJ, Kim K, Kang HA. Assessment of Cre-lox and CRISPR-Cas9 as tools for recycling of multiple-integrated selection markers in Saccharomyces cerevisiae. J Microbiol 2022; 60:18-30. [PMID: 34964942 DOI: 10.1007/s12275-022-1580-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
We evaluated the Cre-lox and CRISPR-Cas9 systems as marker-recycling tools in Saccharomyces cerevisiae recombinants containing multiple-integrated expression cassettes. As an initial trial, we constructed rDNA-nontranscribed spacer- or Ty4-based multiple integration vectors containing the URA3 marker flanked by the loxP sequence. Integrants harboring multiple copies of tHMG1 and NNV-CP expression cassettes were obtained and subsequently transformed with the Cre plasmid. However, the simultaneous pop-out of the expression cassettes along with the URA3 marker hampered the use of Cre-lox as a marker-recycling tool in multiple integrants. As an alternative, we constructed a set of CRISPR-Cas9-gRNA vectors containing gRNA targeted to auxotrophic marker genes. Transformation of multiple integrants of tHMG1 and NNV-CP cassettes by the Cas9-gRNA vector in the presence of the URA3 (stop) donor DNA fragments generated the Ura- transformants retaining multiple copies of the expression cassettes. CRISPR-Cas9-based inactivation led to the recycling of the other markers, HIS3, LEU2, and TRP1, without loss of expression cassettes in the recombinants containing multiple copies of tHMG1, NNV-CP, and SfBGL1 cassettes, respectively. Reuse of the same selection marker in marker-inactivated S. cerevisiae was validated by multiple integrations of the TrEGL2 cassette into the S. cerevisiae strain expressing SfBGL1. These results demonstrate that introducing stop codons into selection marker genes using the CRISPR-Cas9 system with donor DNA fragments is an efficient strategy for markerrecycling in multiple integrants. In particular, the continual reuse of auxotrophic markers would facilitate the construction of a yeast cell factory containing multiple copies of expression cassettes without antibiotic resistance genes.
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Affiliation(s)
- Hye Yun Moon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Gyu Hun Sim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyeon Jin Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keunpil Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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78
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Liao B, Chen X, Zhou X, Zhou Y, Shi Y, Ye X, Liao M, Zhou Z, Cheng L, Ren B. Applications of CRISPR/Cas gene-editing technology in yeast and fungi. Arch Microbiol 2021; 204:79. [DOI: 10.1007/s00203-021-02723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/20/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
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79
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Otto M, Skrekas C, Gossing M, Gustafsson J, Siewers V, David F. Expansion of the Yeast Modular Cloning Toolkit for CRISPR-Based Applications, Genomic Integrations and Combinatorial Libraries. ACS Synth Biol 2021; 10:3461-3474. [PMID: 34860007 PMCID: PMC8689691 DOI: 10.1021/acssynbio.1c00408] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 01/04/2023]
Abstract
Standardisation of genetic parts has become a topic of increasing interest over the last decades. The promise of simplifying molecular cloning procedures, while at the same time making them more predictable and reproducible has led to the design of several biological standards, one of which is modular cloning (MoClo). The Yeast MoClo toolkit provides a large library of characterised genetic parts combined with a comprehensive and flexible assembly strategy. Here we aimed to (1) simplify the adoption of the standard by providing a simple design tool for including new parts in the MoClo library, (2) characterise the toolkit further by demonstrating the impact of a BglII site in promoter parts on protein expression, and (3) expand the toolkit to enable efficient construction of gRNA arrays, marker-less integration cassettes and combinatorial libraries. These additions make the toolkit more applicable for common engineering tasks and will further promote its adoption in the yeast biological engineering community.
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Affiliation(s)
- Maximilian Otto
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Christos Skrekas
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Michael Gossing
- Discovery
Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg SE-43150, Sweden
| | - Johan Gustafsson
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Wallenberg
Center for Protein Research, Chalmers University
of Technology, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Florian David
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-41296, Sweden
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80
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Okada S, Doi G, Nakagawa S, Kusumoto E, Ito T. Simple-to-use CRISPR-SpCas9/SaCas9/AsCas12a vector series for genome editing in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2021; 11:6359819. [PMID: 34739076 PMCID: PMC8664446 DOI: 10.1093/g3journal/jkab304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
Genome editing using the CRISPR/Cas system has been implemented for various organisms and becomes increasingly popular even in the genetically tractable budding yeast Saccharomyces cerevisiae. Because each CRISPR/Cas system recognizes only the sequences flanked by its unique protospacer adjacent motif (PAM), a certain single system often fails to target a region of interest due to the lack of PAM, thus necessitating the use of another system with a different PAM. Three CRISPR/Cas systems with distinct PAMs, namely SpCas9, SaCas9, and AsCas12a, have been successfully used in yeast genome editing. Their combined use should expand the repertoire of editable targets. However, currently available plasmids for these systems were individually developed under different design principles, thus hampering their seamless use in the practice of genome editing. Here, we report a series of Golden Gate Assembly-compatible backbone vectors designed under a unified principle to exploit the three CRISPR/Cas systems in yeast genome editing. We also created a program to assist the design of genome-editing plasmids for individual target sequences using the backbone vectors. Genome editing with these plasmids demonstrated practically sufficient efficiency in the insertion of gene fragments to essential genes (median 52.1%), the complete deletion of an open reading frame (median 78.9%), and the introduction of single amino acid substitutions (median 79.2%). The backbone vectors with the program would provide a versatile toolbox to facilitate the seamless use of SpCas9, SaCas9, and AsCas12a in various types of genome manipulation, especially those that are difficult to perform with conventional techniques in yeast genetics.
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Affiliation(s)
- Satoshi Okada
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Goro Doi
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Shitomi Nakagawa
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Emiko Kusumoto
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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81
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Wang G, Tavares A, Schmitz S, França L, Almeida H, Cavalheiro J, Carolas A, Øzmerih S, Blank LM, Ferreira BS, Borodina I. An integrated yeast-based process for cis,cis-muconic acid production. Biotechnol Bioeng 2021; 119:376-387. [PMID: 34786710 PMCID: PMC9299173 DOI: 10.1002/bit.27992] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022]
Abstract
Cis,cis‐muconic acid (CCM) is a promising polymer building block. CCM can be made by whole‐cell bioconversion of lignin hydrolysates or de novo biosynthesis from sugar feedstocks using engineered microorganisms. At present, however, there is no established process for large‐scale CCM production. In this study, we developed an integrated process for manufacturing CCM from glucose by yeast fermentation. We systematically engineered the CCM‐producing Saccharomyces cerevisiae strain by rewiring the shikimate pathway flux and enhancing phosphoenolpyruvate supply. The engineered strain ST10209 accumulated less biomass but produced 1.4 g/L CCM (70 mg CCM per g glucose) in microplate assay, 71% more than the previously engineered strain ST8943. The strain ST10209 produced 22.5 g/L CCM in a 2 L fermenter with a productivity of 0.19 g/L/h, compared to 0.14 g/L/h achieved by ST8943 in our previous report under the same fermentation conditions. The fermentation process was demonstrated at pilot scale in 10 and 50 L steel tanks. In 10 L fermenter, ST10209 produced 20.8 g/L CCM with a CCM yield of 0.1 g/g glucose and a productivity of 0.21 g/L/h, representing the highest to‐date CCM yield and productivity. We developed a CCM recovery and purification process by treating the fermentation broth with activated carbon at low pH and low temperature, achieving an overall CCM recovery yield of 66.3% and 95.4% purity. In summary, we report an integrated CCM production process employing engineered S. cerevisiae yeast.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Aline Tavares
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Simone Schmitz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Lucas França
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Hugo Almeida
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - João Cavalheiro
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Ana Carolas
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Süleyman Øzmerih
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars M Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Bruno S Ferreira
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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82
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Jensen ED, Ambri F, Bendtsen MB, Javanpour AA, Liu CC, Jensen MK, Keasling JD. Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast. Microb Biotechnol 2021; 14:2617-2626. [PMID: 33645919 PMCID: PMC8601171 DOI: 10.1111/1751-7915.13774] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.
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Affiliation(s)
- Emil D. Jensen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Marie B. Bendtsen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Alex A. Javanpour
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCA92697USA
| | - Chang C. Liu
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCA92697USA
- Department of ChemistryUniversity of California, IrvineIrvineCA92697USA
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCA92697USA
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
- Joint BioEnergy InstituteEmeryvilleCAUSA
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of Chemical and Biomolecular EngineeringDepartment of BioengineeringUniversity of CaliforniaBerkeleyCAUSA
- Center for Synthetic BiochemistryInstitute for Synthetic BiologyShenzhen Institutes of Advanced TechnologiesShenzhenChina
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83
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Munro LJ, Kell DB. Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Affiliation(s)
- Lachlan J. Munro
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Douglas B. Kell
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, U.K
- Mellizyme Biotechnology Ltd, IC1, Liverpool Science Park, 131 Mount Pleasant, Liverpool L3 5TF, U.K
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84
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den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
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Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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85
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Jensen ED, Laloux M, Lehka BJ, Pedersen LE, Jakočiūnas T, Jensen M, Keasling J. A synthetic RNA-mediated evolution system in yeast. Nucleic Acids Res 2021; 49:e88. [PMID: 34107026 PMCID: PMC8421215 DOI: 10.1093/nar/gkab472] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/13/2021] [Accepted: 05/18/2021] [Indexed: 11/19/2022] Open
Abstract
Laboratory evolution is a powerful approach to search for genetic adaptations to new or improved phenotypes, yet either relies on labour-intensive human-guided iterative rounds of mutagenesis and selection, or prolonged adaptation regimes based on naturally evolving cell populations. Here we present CRISPR- and RNA-assisted in vivo directed evolution (CRAIDE) of genomic loci using evolving chimeric donor gRNAs continuously delivered from an error-prone T7 RNA polymerase, and directly introduced as RNA repair donors into genomic targets under either Cas9 or dCas9 guidance. We validate CRAIDE by evolving novel functional variants of an auxotrophic marker gene, and by conferring resistance to a toxic amino acid analogue in baker's yeast Saccharomyces cerevisiae with a mutation rate >3,000-fold higher compared to spontaneous native rate, thus enabling the first demonstrations of in vivo delivery and information transfer from long evolving RNA donor templates into genomic context without the use of in vitro supplied and pre-programmed repair donors.
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Affiliation(s)
- Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marcos Laloux
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tadas Jakočiūnas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
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86
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Costa CE, Møller-Hansen I, Romaní A, Teixeira JA, Borodina I, Domingues L. Resveratrol Production from Hydrothermally Pretreated Eucalyptus Wood Using Recombinant Industrial Saccharomyces cerevisiae Strains. ACS Synth Biol 2021; 10:1895-1903. [PMID: 34304554 DOI: 10.1021/acssynbio.1c00120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Resveratrol is a phenolic compound with strong antioxidant activity, being promising for several applications in health, food, and cosmetics. It is generally extracted from plants or chemically synthesized, in both complex and not sustainable processes, but microbial biosynthesis of resveratrol can counter these drawbacks. In this work, resveratrol production by microbial biosynthesis from lignocellulosic materials was assessed. Three robust industrial Saccharomyces cerevisiae strains known for their thermotolerance and/or resistance to inhibitory compounds were identified as suitable hosts for de novo resveratrol production from glucose and ethanol. Through the CRISPR/Cas9 system, all industrial strains, and a laboratory one, were successfully engineered with the resveratrol biosynthetic pathway via the phenylalanine intermediate. All strains were further screened at 30 °C and 39 °C to evaluate thermotolerance, which is a key feature for Simultaneous Saccharification and Fermentation processes. Ethanol Red RBP showed the best performance at 39 °C, with more than 2.6-fold of resveratrol production in comparison with the other strains. This strain was then used to assess resveratrol production from glucose and ethanol. A maximum resveratrol titer of 187.07 ± 19.88 mg/L was attained from a medium with 2% glucose and 5% ethanol (w/v). Lastly, Ethanol Red RBP produced 151.65 ± 3.84 mg/L resveratrol from 2.95% of cellulose from hydrothermally pretreated Eucalyptus globulus wood, at 39 °C, in a Simultaneous Saccharification and Fermentation process. To the best of our knowledge, this is the first report of lignocellulosic resveratrol production, establishing grounds for the implementation of an integrated lignocellulose-to-resveratrol process in an industrial context.
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Affiliation(s)
- Carlos E. Costa
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Aloia Romaní
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - José A. Teixeira
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Lucília Domingues
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
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87
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Wagner JM, Palmer CM, Venkataraman MV, Lauffer LH, Wiggers JM, Williams EV, Yi X, Alper HS. Genome Engineering of Yarrowia lipolytica with the PiggyBac Transposon System. Methods Mol Biol 2021; 2307:1-24. [PMID: 33847979 DOI: 10.1007/978-1-0716-1414-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A mutant excision+/integration- piggyBac transposase can be used to seamlessly excise a chromosomally integrated, piggyBac-compatible selection marker cassette from the Yarrowia lipolytica genome. This piggyBac transposase-based genome engineering process allows for both positive selection of targeted homologous recombination events and scarless or footprint-free genome modifications after precise marker recovery. Residual non-native sequences left in the genome after marker excision can be minimized (0-4 nucleotides) or customized (user-defined except for a TTAA tetranucleotide). Both of these options reduce the risk of unintended homologous recombination events in strains with multiple genomic edits. A suite of dual positive/negative selection marker pairs flanked by piggyBac inverted terminal repeats (ITRs) have been constructed and are available for precise genome engineering in Y. lipolytica using this method. This protocol specifically describes the split marker homologous recombination-based disruption of Y. lipolytica ADE2 with a piggyBac ITR-flanked URA3 cassette, followed by piggyBac transposase-mediated excision of the URA3 marker to leave a 50 nucleotide synthetic barcode at the ADE2 locus. The resulting ade2 strain is auxotrophic for adenine, which enables the use of ADE2 as a selectable marker for further strain engineering.
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Affiliation(s)
- James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Maya V Venkataraman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lars H Lauffer
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Joshua M Wiggers
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Eden V Williams
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Xiunan Yi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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88
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Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites. Essays Biochem 2021; 65:277-291. [PMID: 34061167 PMCID: PMC8314005 DOI: 10.1042/ebc20200137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/17/2022]
Abstract
Fungal secondary metabolites (FSMs) represent a remarkable array of bioactive compounds, with potential applications as pharmaceuticals, nutraceuticals, and agrochemicals. However, these molecules are typically produced only in limited amounts by their native hosts. The native organisms may also be difficult to cultivate and genetically engineer, and some can produce undesirable toxic side-products. Alternatively, recombinant production of fungal bioactives can be engineered into industrial cell factories, such as aspergilli or yeasts, which are well amenable for large-scale manufacturing in submerged fermentations. In this review, we summarize the development of baker's yeast Saccharomyces cerevisiae to produce compounds derived from filamentous fungi and mushrooms. These compounds mainly include polyketides, terpenoids, and amino acid derivatives. We also describe how native biosynthetic pathways can be combined or expanded to produce novel derivatives and new-to-nature compounds. We describe some new approaches for cell factory engineering, such as genome-scale engineering, biosensor-based high-throughput screening, and machine learning, and how these tools have been applied for S. cerevisiae strain improvement. Finally, we prospect the challenges and solutions in further development of yeast cell factories to more efficiently produce FSMs.
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89
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Milne N, Tramontin LRR, Borodina I. A teaching protocol demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica. FEMS Yeast Res 2021; 20:5574399. [PMID: 31556952 PMCID: PMC8260333 DOI: 10.1093/femsyr/foz062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/19/2019] [Indexed: 11/14/2022] Open
Abstract
We present a teaching protocol suitable for demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of industrially relevant yeasts Saccharomyces cerevisiae and Yarrowia lipolytica, using β-carotene production as a case study. The protocol details all steps required to generate DNA parts, transform and genotype yeast, and perform a phenotypic screen to determine β-carotene production. The protocol is intended to be used as an instruction manual for a two-week practical course aimed at M.Sc. and Ph.D. students. The protocol details all necessary steps for students to engineer yeast to produce β-carotene and serves as a practical introduction to the principles of metabolic engineering including the concepts of boosting native precursor supply and alleviating rate-limiting steps. It also highlights key differences in the metabolism and heterologous production capacity of two industrially relevant yeast species. The protocol is divided into daily experiments covering a two-week period and provides detailed instructions for every step meaning this protocol can be used 'as is' for a teaching course or as a case study for how yeast can be engineered to produce value-added molecules.
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Affiliation(s)
- N Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - L R R Tramontin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - I Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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90
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Improving the Utilization of Isomaltose and Panose by Lager Yeast Saccharomyces pastorianus. FERMENTATION 2021. [DOI: 10.3390/fermentation7030107] [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
Approximately 25% of all carbohydrates in industrial worts are poorly, if at all, fermented by brewing yeast. This includes dextrins, β-glucans, arabinose, xylose, disaccharides such as isomaltose, nigerose, kojibiose, and trisaccharides such as panose and isopanose. As the efficient utilization of carbohydrates during the wort’s fermentation impacts the alcohol yield and the organoleptic traits of the product, developing brewing strains with enhanced abilities to ferment subsets of these sugars is highly desirable. In this study, we developed Saccharomyces pastorianus laboratory yeast strains with a superior capacity to grow on isomaltose and panose. First, we designed a plasmid toolbox for the stable integration of genes into lager strains. Next, we used the toolbox to elevate the levels of the α-glucoside transporter Agt1 and the major isomaltase Ima1. This was achieved by integrating synthetic AGT1 and IMA1 genes under the control of strong constitutive promoters into defined genomic sites. As a result, strains carrying both genes showed a superior capacity to grow on panose and isomaltose, indicating that Ima1 and Agt1 act in synergy to consume these sugars. Our study suggests that non-GMO strategies aiming to develop strains with improved isomaltose and panose utilization could include identifying strains that overexpress AGT1 and IMA1.
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91
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Babaei M, Sartori L, Karpukhin A, Abashkin D, Matrosova E, Borodina I. Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites. FEMS Yeast Res 2021; 21:foab027. [PMID: 33893795 PMCID: PMC8112480 DOI: 10.1093/femsyr/foab027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Biotechnological production requires genetically stable recombinant strains. To ensure genomic stability, recombinant DNA is commonly integrated into the genome of the host strain. Multiple genetic tools have been developed for genomic integration into baker's yeast Saccharomyces cerevisiae. Previously, we had developed a vector toolkit EasyClone-MarkerFree for stable integration into eleven sites on chromosomes X, XI, and XII of S. cerevisiae. The markerless integration was enabled by CRISPR-Cas9 system. In this study, we have expanded the kit with eight additional intergenic integration sites located on different chromosomes. The integration efficiency into the new sites was above 80%. The expression level of green fluorescence protein (gfp) for all eight sites was similar or above XI-2 site from the original EasyClone-MarkerFree toolkit. The cellular growth was not affected by the integration into any of the new eight locations. The eight-vector expansion kit is available from AddGene.
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Affiliation(s)
- Mahsa Babaei
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Luisa Sartori
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Alexey Karpukhin
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Dmitrii Abashkin
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Elena Matrosova
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
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92
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β-Ionone: Its Occurrence and Biological Function and Metabolic Engineering. PLANTS 2021; 10:plants10040754. [PMID: 33921545 PMCID: PMC8069406 DOI: 10.3390/plants10040754] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 12/03/2022]
Abstract
β-Ionone is a natural plant volatile compound, and it is the 9,10 and 9′,10′ cleavage product of β-carotene by the carotenoid cleavage dioxygenase. β-Ionone is widely distributed in flowers, fruits, and vegetables. β-Ionone and other apocarotenoids comprise flavors, aromas, pigments, growth regulators, and defense compounds; serve as ecological cues; have roles as insect attractants or repellants, and have antibacterial and fungicidal properties. In recent years, β-ionone has also received increased attention from the biomedical community for its potential as an anticancer treatment and for other human health benefits. However, β-ionone is typically produced at relatively low levels in plants. Thus, expressing plant biosynthetic pathway genes in microbial hosts and engineering the metabolic pathway/host to increase metabolite production is an appealing alternative. In the present review, we discuss β-ionone occurrence, the biological activities of β-ionone, emphasizing insect attractant/repellant activities, and the current strategies and achievements used to reconstruct enzyme pathways in microorganisms in an effort to to attain higher amounts of the desired β-ionone.
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93
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He X, Ding J, Xu Z, Li N, Yang J, Chen H, Lu D. Development of a new genetic reference material system based on Saccharomyces cerevisiae cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:473-482. [PMID: 33614823 PMCID: PMC7868937 DOI: 10.1016/j.omtm.2021.01.004] [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: 10/23/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
As an important quality control link of molecular diagnosis, genetic reference materials (RMs) are widely used in various gene detection platforms such as mutation detection, gene quantification, and second generation sequencing. However, contamination, construction, and storage of existing genetic RMs still remain challenges. Here, we established a new genetic RM system based on Saccharomyces cerevisiae. We chose the non-small cell lung cancer (NSCLC) mutation hotspots in Kirsten rat sarcoma viral oncogene (KRAS) and epidermal growth factor receptor (EGFR), using clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas9) system-mediated gene editing technology, combined with the high homologous recombination efficiency of Saccharomyces cerevisiae. A single copy of the target gene was inserted into the yeast genome, and the inserted target gene was stably inherited with the passage of yeast cells. The copy number calculation for the target gene can replays by cell counting. The RM system was evaluated by sequence, copy number, stability, and homogeneity. In summary, the recombinant yeast cell line has ease of construction and screening, stable genetic characteristics, accurate copy number calculation, and convenient culture and preservation. Our findings may provide new ideas and directions for the research and industrialization of genetic RMs.
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Affiliation(s)
- Xin He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jiaqi Ding
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhenhua Xu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Na Li
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingmin Yang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai 200438, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
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94
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Wang G, Møller-Hansen I, Babaei M, D'Ambrosio V, Christensen HB, Darbani B, Jensen MK, Borodina I. Transportome-wide engineering of Saccharomyces cerevisiae. Metab Eng 2021; 64:52-63. [PMID: 33465478 PMCID: PMC7970624 DOI: 10.1016/j.ymben.2021.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/16/2020] [Accepted: 01/10/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology enables the production of small molecules by recombinant microbes for pharma, food, and materials applications. The secretion of products reduces the cost of separation and purification, but it is challenging to engineer due to the limited understanding of the transporter proteins' functions. Here we describe a method for genome-wide transporter disruption that, in combination with a metabolite biosensor, enables the identification of transporters impacting the production of a given target metabolite in yeast Saccharomyces cerevisiae. We applied the method to study the transport of xenobiotic compounds, cis,cis-muconic acid (CCM), protocatechuic acid (PCA), and betaxanthins. We found 22 transporters that influenced the production of CCM or PCA. The transporter of the 12-spanner drug:H(+) antiporter (DHA1) family Tpo2p was further confirmed to import CCM and PCA in Xenopus expression assays. We also identified three transporter proteins (Qdr1p, Qdr2p, and Apl1p) involved in betaxanthins transport. In summary, the described method enables high-throughput transporter identification for small molecules in cell factories.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mahsa Babaei
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Vasil D'Ambrosio
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Hanne Bjerre Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Michael Krogh Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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95
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Baek S, Utomo JC, Lee JY, Dalal K, Yoon YJ, Ro DK. The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system. Metab Eng 2021; 64:111-121. [PMID: 33549837 DOI: 10.1016/j.ymben.2021.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/28/2020] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
Saccharomyces cerevisiae is a versatile microbial platform to build synthetic metabolic pathways for production of diverse chemicals. To expedite the construction of complex metabolic pathways by multiplex CRISPR-Cas9 genome-edit, eight desirable intergenic loci, located adjacent to highly expressed genes selected from top 100 expressers, were identified and fully characterized for three criteria after integrating green fluorescent protein (GFP) gene - CRISPR-mediated GFP integration efficiency, expression competency assessed by levels of GFP fluorescence, and assessing growth rates of GFP integrated strains. Five best performing intergenic loci were selected to build a multiplex CRISPR platform, and a synthetic 23-bp DNA comprised of 20-bp synthetic DNA with a protospacer adjacent motif (PAM) was integrated into the five loci using CRISPR-Cas9 in a sequential manner. This process resulted in five different yeast strains harbouring 1-5 synthetic gRNA-binding sites in their genomes. Using these pre-engineered yeast strains, simultaneous integrations of 2-, 3-, 4-, or 5-genes to the targeted loci were demonstrated with efficiencies from 85% to 98% using beet pigment betalain (3-gene pathway), hygromycin and geneticin resistance markers. Integrations of the multiple, foreign genes in the targeted loci with 100% precision were validated by genotyping. Finally, we further developed the strain to have 6th synthetic gRNA-binding site, and the resulting yeast strain was used to generate a yeast strain producing a sesquiterpene lactone, kauniolide by simultaneous 6-gene integrations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in yeast.
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Affiliation(s)
- Sihyun Baek
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | | | - Ji Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kunal Dalal
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada.
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96
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Kuivanen J, Kannisto M, Mojzita D, Rischer H, Toivari M, Jäntti J. Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production. Microb Cell Fact 2021; 20:34. [PMID: 33536025 PMCID: PMC7860014 DOI: 10.1186/s12934-021-01532-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Anthranilate is a platform chemical used by the industry in the synthesis of a broad range of high-value products, such as dyes, perfumes and pharmaceutical compounds. Currently anthranilate is produced via chemical synthesis from non-renewable resources. Biological synthesis would allow the use of renewable carbon sources and avoid accumulation of toxic by-products. Microorganisms produce anthranilate as an intermediate in the tryptophan biosynthetic pathway. Several prokaryotic microorganisms have been engineered to overproduce anthranilate but attempts to engineer eukaryotic microorganisms for anthranilate production are scarce. Results We subjected Saccharomyces cerevisiae, a widely used eukaryotic production host organism, to metabolic engineering for anthranilate production. A single gene knockout was sufficient to trigger anthranilate accumulation both in minimal and SCD media and the titer could be further improved by subsequent genomic alterations. The effects of the modifications on anthranilate production depended heavily on the growth medium used. By growing an engineered strain in SCD medium an anthranilate titer of 567.9 mg l−1 was obtained, which is the highest reported with an eukaryotic microorganism. Furthermore, the anthranilate biosynthetic pathway was extended by expression of anthranilic acid methyltransferase 1 from Medicago truncatula. When cultivated in YPD medium, this pathway extension enabled production of the grape flavor compound methyl anthranilate in S. cerevisiae at 414 mg l−1. Conclusions In this study we have engineered metabolism of S. cerevisiae for improved anthranilate production. The resulting strains may serve as a basis for development of efficient production host organisms for anthranilate-derived compounds. In order to demonstrate suitability of the engineered S. cerevisiae strains for production of such compounds, we successfully extended the anthranilate biosynthesis pathway to synthesis of methyl anthranilate.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,eniferBio Oy, Espoo, Finland
| | - Matti Kannisto
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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97
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Qi M, Zhang B, Jiang L, Xu S, Dong C, Du YL, Zhou Z, Huang L, Xu Z, Lian J. PCR & Go: A Pre-installed Expression Chassis for Facile Integration of Multi-Gene Biosynthetic Pathways. Front Bioeng Biotechnol 2021; 8:613771. [PMID: 33520963 PMCID: PMC7841387 DOI: 10.3389/fbioe.2020.613771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022] Open
Abstract
The introduction of multi-gene metabolic pathways is generally the first step for the construction of microbial cell factories and plays an essential role in metabolic engineering and synthetic biology. Here, we developed a “PCR & Go” system for facile integration and assembly of multi-gene pathways into the chromosome of Saccharomyces cerevisiae. The core component of the “PCR & Go” system was an expression chassis, where eight promoter/terminator pairs were pre-installed into the yeast chromosome and PCR amplified gene fragments could be inserted directly for functional expression. In combination with the CRISPR/Cas9 system and a gRNA plasmid library, the β-carotene (three genes), zeaxanthin (four genes), and astaxanthin (five genes) biosynthetic pathways were integrated and assembled into the yeast genome with an efficiency of ~93, ~85, and 69%, respectively, using PCR amplified gene fragments with ~40 bp homology arms in a single step. Therefore, the “PCR & Go” system can be used for fast construction of yeast cell factories harboring multi-gene pathways with high efficiency and flexibility.
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Affiliation(s)
- Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Saijuan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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98
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Baptista SL, Costa CE, Cunha JT, Soares PO, Domingues L. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv 2021; 47:107697. [PMID: 33508428 DOI: 10.1016/j.biotechadv.2021.107697] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal.
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99
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Adegboye MF, Ojuederie OB, Talia PM, Babalola OO. Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:5. [PMID: 33407786 PMCID: PMC7788794 DOI: 10.1186/s13068-020-01853-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/09/2020] [Indexed: 05/17/2023]
Abstract
The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.
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Affiliation(s)
- Mobolaji Felicia Adegboye
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
| | - Omena Bernard Ojuederie
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
- Department of Biological Sciences, Faculty of Science, Kings University, Ode-Omu, PMB 555, Osun State, Nigeria
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA CICVyA, CNIA, INTA Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, 1686) Hurlingham, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Buenos Aires, Provincia de Buenos Aires, Argentina
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa.
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Utomo JC, Hodgins CL, Ro DK. Multiplex Genome Editing in Yeast by CRISPR/Cas9 - A Potent and Agile Tool to Reconstruct Complex Metabolic Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:719148. [PMID: 34421973 PMCID: PMC8374951 DOI: 10.3389/fpls.2021.719148] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 05/22/2023]
Abstract
Numerous important pharmaceuticals and nutraceuticals originate from plant specialized metabolites, most of which are synthesized via complex biosynthetic pathways. The elucidation of these pathways is critical for the applicable uses of these compounds. Although the rapid progress of the omics technology has revolutionized the identification of candidate genes involved in these pathways, the functional characterization of these genes remains a major bottleneck. Baker's yeast (Saccharomyces cerevisiae) has been used as a microbial platform for characterizing newly discovered metabolic genes in plant specialized metabolism. Using yeast for the investigation of numerous plant enzymes is a streamlined process because of yeast's efficient transformation, limited endogenous specialized metabolism, partially sharing its primary metabolism with plants, and its capability of post-translational modification. Despite these advantages, reconstructing complex plant biosynthetic pathways in yeast can be time intensive. Since its discovery, CRISPR/Cas9 has greatly stimulated metabolic engineering in yeast. Yeast is a popular system for genome editing due to its efficient homology-directed repair mechanism, which allows precise integration of heterologous genes into its genome. One practical use of CRISPR/Cas9 in yeast is multiplex genome editing aimed at reconstructing complex metabolic pathways. This system has the capability of integrating multiple genes of interest in a single transformation, simplifying the reconstruction of complex pathways. As plant specialized metabolites usually have complex multigene biosynthetic pathways, the multiplex CRISPR/Cas9 system in yeast is suited well for functional genomics research in plant specialized metabolism. Here, we review the most advanced methods to achieve efficient multiplex CRISPR/Cas9 editing in yeast. We will also discuss how this powerful tool has been applied to benefit the study of plant specialized metabolism.
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