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Wei S, Li M, Lang X, Robertson NR, Park SY, Cutler SR, Wheeldon I. Repurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast. Metab Eng 2024; 83:102-109. [PMID: 38554744 DOI: 10.1016/j.ymben.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1ABA/HAB1 and PYR1*MANDI/HAB1*) for high dynamic-range gene activation and repression controlled by either abscisic acid (ABA) or mandipropamid (mandi). To redirect metabolic flux towards ethyl acetate biosynthesis, we simultaneously repress pyruvate dehydrogenase (PDA1) and activate pyruvate decarboxylase (PDC1) to enhance ethyl acetate titers. Thus, we have developed new tools for chemically tuning gene expression in K. marxianus and S. cerevisiae that should be deployable across many non-conventional eukaryotic hosts.
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Affiliation(s)
- Shuang Wei
- Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, USA
| | - Mengwan Li
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Xuye Lang
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Nicholas R Robertson
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Sang-Youl Park
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Sean R Cutler
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
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2
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Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
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Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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3
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Zhang Y, Guo X, Yang H, Shi S. The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters. Front Bioeng Biotechnol 2022; 9:799032. [PMID: 35087801 PMCID: PMC8787340 DOI: 10.3389/fbioe.2021.799032] [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: 10/21/2021] [Accepted: 11/19/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid alkyl esters have broad applications in biofuels, lubricant formulas, paints, coatings, and cosmetics. Traditionally, these esters are mostly produced through unsustainable and energy-intensive processes. In contrast, microbial production of esters from renewable and sustainable feedstocks may provide a promising alternative and has attracted widespread attention in recent years. At present, yeasts are used as ideal hosts for producing such esters, due to their availability for high-density fermentation, resistance to phage infection, and tolerance against toxic inhibitors. Here, we summarize recent development on the biosynthesis of alkyl esters, including fatty acid ethyl esters (FAEEs), fatty acid short-branched chain alkyl esters (FASBEs), and wax esters (WEs) by various yeast cell factories. We focus mainly on the enzyme engineering strategies of critical wax ester synthases, and the pathway engineering strategies employed for the biosynthesis of various ester products. The bottlenecks that limit productivity and their potential solutions are also discussed in this review.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huaiyi Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 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, China
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4
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Lee JW, Seo H, Young C, Trinh CT. Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high-throughput microbial screening platform. Biotechnol Bioeng 2021; 118:4655-4667. [PMID: 34436763 DOI: 10.1002/bit.27926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/13/2021] [Accepted: 08/22/2021] [Indexed: 11/07/2022]
Abstract
Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl-CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CATSa ) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only probe the alcohol substrate specificity of both native and engineered AATs but also identify the beneficial mutations in engineered AATs for enhanced ester synthesis. We anticipate the high-throughput microbial screening platform provides a useful tool to identify novel wildtype and engineered AATs that have important roles in nature and industrial biocatalysis for designer bioester production.
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Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hyeongmin Seo
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Caleb Young
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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5
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Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
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Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
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6
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Löser C, Kupsch C, Walther T, Hoffmann A. A new approach for balancing the microbial synthesis of ethyl acetate and other volatile metabolites during aerobic bioreactor cultivations. Eng Life Sci 2021; 21:137-153. [PMID: 33716613 PMCID: PMC7923609 DOI: 10.1002/elsc.202000047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Ethyl acetate is an organic solvent with many industrial applications, currently produced by energy-intensive chemical processes based on fossil carbon resources. Ethyl acetate can be synthesized from renewable sugars by yeasts like Kluyveromyces marxianus in aerobic processes. However, ethyl acetate is highly volatile and thus stripped from aerated cultivation systems which complicate the quantification of the produced ester. Synthesis of volatile metabolites is commonly monitored by repeated analysis of metabolite concentrations in both the gas and liquid phase. In this study, a model-based method for quantifying the synthesis and degradation of volatile metabolites was developed. This quantification of volatiles is solely based on repeatedly measured gas-phase concentrations and allows calculation of reaction rates and yields in high temporal resolution. Parameters required for these calculations were determined in abiotic stripping tests. The developed method was validated for ethyl acetate, ethanol and acetaldehyde which were synthesized by K. marxianus DSM 5422 during an iron-limited batch cultivation; it was shown that the presented method is more precise and less time-consuming than the conventional method. The biomass-specific synthesis rate and the yield of ethyl acetate varied over time and exhibited distinct momentary maxima of 0.50 g g‒1h‒1 and 0.38 g g‒1 at moderate iron limitation.
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Affiliation(s)
- Christian Löser
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Kupsch
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Thomas Walther
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Andreas Hoffmann
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
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7
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Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021; 47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using 13C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.
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Affiliation(s)
- Pradipta Patra
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manali Das
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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8
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Li M, Lang X, Moran Cabrera M, De Keyser S, Sun X, Da Silva N, Wheeldon I. CRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:3. [PMID: 33407831 PMCID: PMC7788952 DOI: 10.1186/s13068-020-01852-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND 2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material. RESULTS We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 33-factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7G141S, results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L. The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures. CONCLUSIONS The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.
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Affiliation(s)
- Mengwan Li
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xuye Lang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Marcos Moran Cabrera
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Sawyer De Keyser
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xiyan Sun
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Nancy Da Silva
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California Riverside, Riverside, CA, 92527, USA.
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Lang X, Besada-Lombana PB, Li M, Da Silva NA, Wheeldon I. Developing a broad-range promoter set for metabolic engineering in the thermotolerant yeast Kluyveromyces marxianus. Metab Eng Commun 2020; 11:e00145. [PMID: 32995271 PMCID: PMC7508702 DOI: 10.1016/j.mec.2020.e00145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/17/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
Kluyveromyces marxianus is an emerging host for metabolic engineering. This thermotolerant yeast is the fastest growing eukaryote, has high flux through the TCA cycle, and can metabolize a broad range of C5, C6, and C12 carbon sources. In comparison to the common host Saccharomyces cerevisiae, this non-conventional yeast suffers from a lack of metabolic engineering tools to control gene expression over a wide transcriptional range. To address this issue, we designed a library of 25 native-derived promoters from K. marxanius CBS6556 that spans 87-fold transcriptional strength under glucose metabolism. Six promoters from the library were further characterized in both glucose and xylose as well as across various temperatures from 30 to 45 °C. The temperature study revealed that in most cases EGFP expression decreased with elevating temperature; however, two promoters, P SSA3 and P ADH1 , increased expression above 40 °C in both xylose and glucose. The six-promoter set was also validated in xylose for triacetic acid lactone (TAL) production. By controlling the expression level of heterologous 2-pyrone synthase (2-PS), the specific TAL titer increased over 8-fold at 37 °C. Cultures at 41 °C exhibited a similar TAL biosynthesis capability, while at 30 °C TAL levels were lower. Taken together, these results advance the metabolic engineering tool set in K. marxianus and further develop this new host for chemical biosynthesis.
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Affiliation(s)
- Xuye Lang
- Department of Chemical and Environmental Engineering, UC Riverside, United States
| | | | - Mengwan Li
- Department of Chemical and Environmental Engineering, UC Riverside, United States
| | - Nancy A. Da Silva
- Department of Chemical and Biomolecular Engineering, UC Irvine, United States
- Corresponding author. Department of Chemical and Biomolecular Engineering, UC Irvine, United States.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, UC Riverside, United States
- Center for Industrial Biotechnology, UC Riverside, United States
- Corresponding author. Department of Chemical and Environmental Engineering, UC Riverside, United States.
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10
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Reyes-Sánchez FJ, Páez-Lerma JB, Rojas-Contreras JA, López-Miranda J, Soto-Cruz NÓ, Reinhart-Kirchmayr M. Study of the Enzymatic Capacity of Kluyveromyces marxianus for the Synthesis of Esters. J Mol Microbiol Biotechnol 2020; 29:1-9. [PMID: 32325454 DOI: 10.1159/000507551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
Recently, biotechnological opportunities have been found in non-Saccharomyces yeasts because they possess metabolic characteristics that lead to the production of compounds of interest. It has been observed that Kluyveromyces marxianus has a great potential in the production of esters, which are aromatic compounds of industrial importance. The genetic bases that govern the synthesis of esters include a large group of enzymes, among which the most important are alcohol acetyl transferases (AATases) and esterases (AEATases), and it is known that some are present in K. marxianus, because it has genetic characteristics like S. cerevisiae. It also has a physiology suitable for biotechnological use since it is the eukaryotic microorganism with the fastest growth rate and has a wide range of thermotolerance with respect to other yeasts. In this work, the enzymatic background of K. marxianus involved in the synthesis of esters is analyzed, based on the sequences reported in the NCBI database.
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Affiliation(s)
| | | | | | - Javier López-Miranda
- Chemistry and Biochemistry, TECNM/Instituto Tecnológico de Durango, Durango, Mexico
| | | | - Manuel Reinhart-Kirchmayr
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Guadalajara, Mexico
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11
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Drying of the Natural Fibers as A Solvent-Free Way to Improve the Cellulose-Filled Polymer Composite Performance. Polymers (Basel) 2020; 12:polym12020484. [PMID: 32098150 PMCID: PMC7077673 DOI: 10.3390/polym12020484] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/19/2020] [Indexed: 01/21/2023] Open
Abstract
When considering cellulose (UFC100) modification, most of the processes employ various solvents in the role of the reaction environment. The following article addresses a solvent-free method, thermal drying, which causes a moisture content decrease in cellulose fibers. Herein, the moisture content in UFC100 was analyzed with spectroscopic methods, thermogravimetric analysis, and differential scanning calorimetry. During water desorption, a moisture content drop from approximately 6% to 1% was evidenced. Moreover, drying may bring about a specific variation in cellulose's chemical structure. These changes affected the cellulose-filled polymer composite's properties, e.g., an increase in tensile strength from 17 MPa for the not-dried UFC100 to approximately 30 MPa (dried cellulose; 24 h, 100 °C) was observed. Furthermore, the obtained tensile test results were in good correspondence with Payne effect values, which changed from 0.82 MPa (not-dried UFC100) to 1.21 MPa (dried fibers). This raise proves the reinforcing nature of dried UFC100, as the Payne effect is dependent on the filler structure's development within a polymer matrix. This finding paves new opportunities for natural fiber applications in polymer composites by enabling a solvent-free and efficient cellulose modification approach that fulfils the sustainable development rules.
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12
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Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis. Nat Chem Biol 2020; 16:113-121. [DOI: 10.1038/s41589-019-0452-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
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13
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Kruis AJ, Bohnenkamp AC, Patinios C, van Nuland YM, Levisson M, Mars AE, van den Berg C, Kengen SW, Weusthuis RA. Microbial production of short and medium chain esters: Enzymes, pathways, and applications. Biotechnol Adv 2019; 37:107407. [DOI: 10.1016/j.biotechadv.2019.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/24/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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15
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Recent advancements in fungal-derived fuel and chemical production and commercialization. Curr Opin Biotechnol 2019; 57:1-9. [DOI: 10.1016/j.copbio.2018.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/15/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
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Zhu J, Schwartz C, Wheeldon I. Controlled intracellular trafficking alleviates an expression bottleneck in S. cerevisiae ester biosynthesis. Metab Eng Commun 2018; 8:e00085. [PMID: 30622894 PMCID: PMC6317282 DOI: 10.1016/j.mec.2018.e00085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 01/17/2023] Open
Abstract
In metabolic engineering, most available pathway engineering strategies aim to control enzyme expression by making changes at the transcriptional level with an underlying assumption that translation and functional expression follow suit. In this work, we engineer expression of a key reaction step in medium chain ester biosynthesis that does not follow this common assumption. The native Saccharomyces cerevisiae alcohol acyltransferses Eeb1 and Eht1 condense acyl-CoAs with ethanol to produce the corresponding ester, a reaction that is rate limiting in engineering ester biosynthesis pathways. By changing the N- and C-termini of Eeb1 to those of Eht1, Eeb1 localization is changed from the mitochondria to lipid droplets. The change has no significant effect on transcription, but increases protein expression by 23-fold thus enabling a 3-fold increase in enzyme activity. This system demonstrates one example of the impact of protein trafficking on functional pathway expression, and will guide future metabolic engineering of ester biosynthesis and, potentially, other pathways with critical membrane-bound enzymes. Intracellular localization can control membrane-associated enzyme expression. Terminal domain swapping of Eht1 and Eeb1 alters intracellular localization. Eeb1 expression and activity are increased with lipid droplet targeting.
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Affiliation(s)
- Jie Zhu
- Biochemistry, University of California Riverside, Riverside, CA 92521, USA
| | - Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521 USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521 USA.,Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, CA 92521, USA
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17
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Löbs AK, Schwartz C, Thorwall S, Wheeldon I. Highly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus. ACS Synth Biol 2018; 7:2647-2655. [PMID: 30354074 DOI: 10.1021/acssynbio.8b00331] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The emergence of CRISPR-Cas9 for targeted genome editing and regulation has enabled the manipulation of desired traits and enhanced strain development of nonmodel microorganisms. The natural capacity of the yeast Kluyveromyces marxianus to produce volatile esters at high rate and at elevated temperatures make it a potentially valuable production platform for industrial biotechnology. Here, we identify the native localization of ethyl acetate biosynthesis in K. marxianus and use this information to develop a multiplexed CRISPRi system for redirecting carbon flux along central metabolic pathways, increasing ethyl acetate productivity. First, we identified the primary pathways of precursor and acetate ester biosynthesis. A genetic knockout screen revealed that the alcohol acetyltransferase Eat1 is the critical enzyme for ethyl, isoamyl, and phenylethyl acetate production. Truncation studies revealed that high ester biosynthesis is contingent on Eat1 mitochondrial localization. As ethyl acetate is formed from the condensation of ethanol and acetyl-CoA, we modulated expression of the TCA cycle and electron transport chain genes using a highly multiplexed CRISPRi approach. The simultaneous knockdown of ACO2b, SDH2, RIP1, and MSS51 resulted in a 3.8-fold increase in ethyl acetate productivity over the already high natural capacity. This work demonstrates that multiplexed CRISPRi regulation of central carbon flux, supported by a fundamental understanding of pathway biochemistry, is a potent strategy for metabolic engineering in nonconventional microorganisms.
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Affiliation(s)
- Ann-Kathrin Löbs
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Sarah Thorwall
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, California 92521, United States
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18
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Lin JL, Ekas H, Markham K, Alper HS. An enzyme-coupled assay enables rapid protein engineering for geraniol production in yeast. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Serra Colomer M, Funch B, Forster J. The raise of Brettanomyces yeast species for beer production. Curr Opin Biotechnol 2018; 56:30-35. [PMID: 30173102 DOI: 10.1016/j.copbio.2018.07.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
Abstract
The adequate application of Brettanomyces species could raise a potential opportunity for the beer industry, generating new products and optimizing production processes. Several valuable properties like high ethanol yield, tolerance to low pH and production of unique flavors have brought this yeast species into the spotlight. Aroma and flavor production of Brettanomyces in beer is currently under discussion, and it can be adjusted if the mechanism insights are understood. This review summarizes the recent findings in physiological, genetic and biochemical traits related to the application of Brettanomyces species for brewing.
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Affiliation(s)
- Marc Serra Colomer
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Birgitte Funch
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Jochen Forster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
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Feng Y, Bruton R, Park A, Zhang A. Identification of attractive blend for spotted wing drosophila, Drosophila suzukii, from apple juice. JOURNAL OF PEST SCIENCE 2018; 91:1251-1267. [PMID: 30100831 PMCID: PMC6063330 DOI: 10.1007/s10340-018-1006-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/29/2018] [Accepted: 06/16/2018] [Indexed: 06/08/2023]
Abstract
Drosophila suzukii, commonly known as the spotted wing drosophila (SWD), is an exotic fruit fly from Southeast Asia that was introduced to the temperate regions of North America and Europe in 2008. It attacks a wide variety of fruits and has become a devastating pest of soft-skinned fruit crops. Due to the rapid spread of SWD across the newly invaded continents, fresh fruit markets have a zero-tolerance policy regarding D. suzukii infestation. Specific and efficient D. suzukii detection tools are urgently needed so that farmers can deliver timely management interventions to meet market demands. Since SWD is known to be attracted to damaged and rotting fruits, headspace volatiles from fresh and fermented apple juices were collected and analyzed by gas chromatography-mass spectrometry. Special attention was given to the compounds produced and/or enriched during the fermentation process. After performing a series of laboataory and field tests, we identified a quinary blend, which is more efficient and selective for D. suzukii than the currently standard apple cider vinegar and commercially available SWD lure under field conditions. Identification of SWD attractant will help growers accurately detect D. suzukii adult infestations in orchards, thereby allowing for timely pest management interventions while reducing conventional insecticidal usage to protect our crops, environment, and ecosystem.
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Affiliation(s)
- Yan Feng
- Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, Bldg. 007, Rm. 312, BARC-W, Beltsville, MD 20705 USA
| | - Robert Bruton
- Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, Bldg. 007, Rm. 312, BARC-W, Beltsville, MD 20705 USA
| | - Alexis Park
- Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, Bldg. 007, Rm. 312, BARC-W, Beltsville, MD 20705 USA
| | - Aijun Zhang
- Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, Bldg. 007, Rm. 312, BARC-W, Beltsville, MD 20705 USA
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22
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Lee SR, Lee J, Cho SH, Kim J, Oh JI, Tsang DCW, Jeong KH, Kwon EE. Quantification of volatile fatty acids from cattle manure via non-catalytic esterification for odour indication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:992-996. [PMID: 28838036 DOI: 10.1016/j.scitotenv.2017.08.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/10/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
This report proposes a new approach to evaluate the odour nuisance of cattle manure samples from three different cattle breeds (i.e., native cattle, beef cattle, and milk cow) by means of quantification and speciation of volatile fatty acids (VFAs). To this end, non-catalytic esterification thermally induced in the presence of a porous material (silica) was undertaken, and the optimal operational parameters such as the derivatizing temperature (330°C) for the maximum yield (≥99±0.4%) of volatile fatty acid methyl esters (VFAMEs) were established. Among the VFA species in cattle manure based on quantification of VFAs, the major species were acetic, butyric and valeric acid. Considering the odour threshold of each VFA, our experimental results suggested that the major contributors to odour nuisance were C4-5 VFA species (i.e., butyric and valeric acid). Hydrothermal treatment was performed at 150°C for 0-40min to correlate the formation of VFAs with different types of cattle feed formulations. Our experimental data demonstrated that the formation of total VFAs is linearly proportional to the hydrothermal treatment duration and the total content of VFAs in native cattle, beef cattle, and milk cow manure samples reached up to ~1000, ~3200, and ~2800ppm, respectively. Thus, this study demonstrated that the degree of VFA formation is highly dependent on cattle feed formulations, which rely significantly on the protein content. Furthermore, the hydrothermal treatment provides a favourable condition for generating more VFAs. In this context, producing cattle manure into refused derived fuel (RDF) via a hydrothermal treatment is not a viable option to control odour.
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Affiliation(s)
- Sang-Ryong Lee
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea; Department of Animal Biotechnology and Environment, National Institute of Animal Science, Jeollabuk-do 55365, Republic of Korea
| | - Jechan Lee
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Seong-Heon Cho
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Jieun Kim
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Jeong-Ik Oh
- Advanced Technology Development, Land & Housing Institute, Daejeon 34047, Republic of Korea
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwang-Hwa Jeong
- Department of Animal Biotechnology and Environment, National Institute of Animal Science, Jeollabuk-do 55365, Republic of Korea
| | - Eilhann E Kwon
- Department of Environment and Energy, Sejong University, Seoul 05006, Republic of Korea.
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Löbs AK, Schwartz C, Wheeldon I. Genome and metabolic engineering in non-conventional yeasts: Current advances and applications. Synth Syst Biotechnol 2017; 2:198-207. [PMID: 29318200 PMCID: PMC5655347 DOI: 10.1016/j.synbio.2017.08.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 12/26/2022] Open
Abstract
Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.
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Affiliation(s)
- Ann-Kathrin Löbs
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
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Lin JL, Zhu J, Wheeldon I. Synthetic Protein Scaffolds for Biosynthetic Pathway Colocalization on Lipid Droplet Membranes. ACS Synth Biol 2017; 6:1534-1544. [PMID: 28497697 DOI: 10.1021/acssynbio.7b00041] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Eukaryotic biochemistry is organized throughout the cell in and on membrane-bound organelles. When engineering metabolic pathways this organization is often lost, resulting in flux imbalance and a loss of kinetic advantages from enzyme colocalization and substrate channeling. Here, we develop a protein-based scaffold for colocalizing multienzyme pathways on the membranes of intracellular lipid droplets. Scaffolds based on the plant lipid droplet protein oleosin and cohesin-dockerin interaction pairs recruited upstream enzymes in yeast ester biosynthesis to the native localization of the terminal reaction step, alcohol-O-acetyltransferase (Atf1). The native localization is necessary for high activity and pathway assembly in close proximity to Atf1 increased pathway flux. Screening a library of scaffold variants further showed that pathway structure can alter catalysis and revealed an optimized scaffold and pathway expression levels that produced ethyl acetate at a rate nearly 2-fold greater than unstructured pathways. This strategy should prove useful in spatially organizing other metabolic pathways with key lipid droplet-localized and membrane-bound reaction steps.
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Affiliation(s)
- Jyun-Liang Lin
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jie Zhu
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Ian Wheeldon
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
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25
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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Löbs AK, Engel R, Schwartz C, Flores A, Wheeldon I. CRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:164. [PMID: 28652865 PMCID: PMC5483312 DOI: 10.1186/s13068-017-0854-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/16/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND The thermotolerant yeast Kluyveromyces marxianus shows promise as an industrial host for the biochemical production of fuels and chemicals. Wild-type strains are known to ferment high titers of ethanol and can effectively convert a wide range of C5, C6, and C12 sugars into the volatile short-chain ester ethyl acetate. Strain engineering, however, has been limited due to a lack of advanced genome-editing tools and an incomplete understanding of ester and ethanol biosynthesis. RESULTS Enabled by the design of hybrid RNA polymerase III promoters, this work adapts the CRISPR-Cas9 system from Streptococcus pyogenes for use in K. marxianus. The system was used to rapidly create functional disruptions to alcohol dehydrogenase (ADH) and alcohol-O-acetyltransferase (ATF) genes with putative function in ethyl acetate and ethanol biosynthesis. Screening of the KmATF disrupted strain revealed that Atf activity contributes to ethyl acetate biosynthesis, but the knockout reduced ethyl acetate titers by only ~15%. Overexpression experiments revealed that KmAdh7 can catalyze the oxidation of hemiacetal to ethyl acetate. Finally, analysis of the KmADH2 disrupted strain showed that the knockout almost completely eliminated ethanol production and resulted in the accumulation of acetaldehyde. CONCLUSIONS Newly designed RNA polymerase III promoters for sgRNA expression in K. marxianus enable a CRISPR-Cas9 genome-editing system for the thermotolerant yeast. This system was used to disrupt genes involved in ethyl acetate biosynthesis, specifically KmADH1-7 and KmATF. KmAdh2 was found to be critical for aerobic and anaerobic ethanol production. Aerobically produced ethanol supplies the biosynthesis of ethyl acetate catalyzed by KmAtf. KmAdh7 was found to exhibit activity toward the oxidation of hemiacetal, a possible alternative route for the synthesis of ethyl acetate.
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Affiliation(s)
- Ann-Kathrin Löbs
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ronja Engel
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
- Mannheim University of Applied Sciences, Mannheim, Germany
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Andrew Flores
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
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