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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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Muñoz-Miranda LA, Zepeda-Peña AC, Casas-Godoy L, Pereira-Santana A, Méndez-Zamora A, Barrera-Martínez I, Rodríguez-Zapata L, Gschaedler-Mathis AC, Figueroa-Yáñez LJ. CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3. World J Microbiol Biotechnol 2024; 40:121. [PMID: 38441729 DOI: 10.1007/s11274-023-03811-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/18/2023] [Indexed: 03/07/2024]
Abstract
Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.
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Affiliation(s)
- Luis A Muñoz-Miranda
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Andrea Catalina Zepeda-Peña
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Leticia Casas-Godoy
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Alejandro Pereira-Santana
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. Subsede Sureste, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Andrés Méndez-Zamora
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Iliana Barrera-Martínez
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Luis Rodríguez-Zapata
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, México
| | - Anne Christine Gschaedler-Mathis
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
| | - Luis J Figueroa-Yáñez
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
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3
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Liu N, Qin L, Zeng H, Wen A, Miao S. Integrative proteomic-transcriptomic analysis revealed the lifestyles of Lactobacillus paracasei H4-11 and Kluyveromyces marxianus L1-1 under co-cultivation conditions. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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4
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Hoffmann A, Franz A, Walther T, Löser C. Utilization of delactosed whey permeate for the synthesis of ethyl acetate with Kluyveromyces marxianus. Appl Microbiol Biotechnol 2023; 107:1635-1648. [PMID: 36786916 PMCID: PMC10006051 DOI: 10.1007/s00253-023-12419-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
Ethyl acetate is an important organic solvent and currently produced from fossil carbon resources. Microbial synthesis of this ester from sugar-rich waste could be an interesting alternative. Therefore, synthesis of ethyl acetate by Kluyveromyces marxinanus DSM 5422 from delactosed whey permeate (DWP) was studied in an aerated stirred bioreactor at 40 °C. DWP is mainly composed of residual lactose and minerals. The minerals inhibited yeast growth, as witnessed by an increased lag period, a reduced growth rate, and an extended process duration. All experiments were therefore carried out with diluted DWP. In a series of batch experiments, the pH of iron-deficient DWP medium varied between 4.8 and 5.9. The pH of the cultivation medium significantly influenced cell growth and product syntheses, with the highest ethyl acetate yield of 0.347 g g-1 and lowest by-product formation achieved at pH 5.1. It is likely that this effect is due to pH-dependent iron chelation, which affects the iron bioavailability and the intracellular iron content, thus affecting growth and metabolite synthesis. The viability of yeast cells was always high despite the harsh conditions in DWP medium, which enabled extended usage of the biomass in repeated-batch and fed-batch cultivations. These two culture techniques increased the volume of DWP processed per time by 32 and 84% for the repeated-batch and the fed-batch cultivation, respectively, without a drop of the ester yield. KEY POINTS: • Delactosed whey permeate was converted to ethyl acetate with a high rate and yield. • The formation of ethyl acetate in DWP medium at iron limitation is pH-dependent. • Highly active yeasts from batch processes enabled extension as fed and repeated batch.
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Affiliation(s)
- Andreas Hoffmann
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Alexander Franz
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
- Biophysical Chemistry, Institute of Biochemistry, University of Leipzig, 04103, Leipzig, Germany
| | - Thomas Walther
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christian Löser
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany.
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5
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Nyhan L, Sahin AW, Arendt EK. Co-fermentation of non- Saccharomyces yeasts with Lactiplantibacillus plantarum FST 1.7 for the production of non-alcoholic beer. Eur Food Res Technol 2023; 249:167-181. [PMID: 36466321 PMCID: PMC9702684 DOI: 10.1007/s00217-022-04142-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/11/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022]
Abstract
The non-alcoholic beer (NAB) sector has experienced steady growth in recent years, with breweries continuously seeking new ways to fulfil consumer demands. NAB can be produced by limited fermentation of non-Saccharomyces yeasts; however, beer produced in this manner is often critiqued for its sweet taste and wort-like off-flavours due to high levels of residual sugars and lack of flavour metabolites. The use of Lactobacillus in limited co-fermentation with non-Saccharomyces yeasts is a novel approach to produce NABs with varying flavour and aroma characteristics. In this study, lab-scale fermentations of Lachancea fermentati KBI 12.1 and Cyberlindnera subsufficiens C6.1 with Lactiplantibacillus plantarum FST 1.7 were performed and compared to a brewer's yeast, Saccharomyces cerevisiae WLP001. Fermentations were monitored for pH, TTA, extract reduction, alcohol production, and microbial cell count. The final beers were analysed for sugar and organic acid concentration, free amino nitrogen content (FAN), glycerol, and levels of volatile metabolites. The inability of the non-Saccharomyces yeasts to utilise maltotriose as an energy source resulted in extended fermentation times compared to S. cerevisiae WLP001. Co-fermentation of yeasts with lactic acid bacteria (LAB) resulted in a decreased pH, higher TTA and increased levels of lactic acid in the final beers. The overall acceptability of the NABs produced by co-fermentation was higher than or similar to that of the beers fermented with the yeasts alone, indicating that LAB fermentation did not negatively impact the sensory attributes of the beer. C. subsufficiens C6.1 and L. plantarum FST 1.7 NAB was characterised as fruity tasting with the significantly higher ester concentrations masking the wort-like flavours resulting from limited fermentation. NAB produced with L. fermentati KBI12.1 and L. plantarum FST1.7 had decreased levels of the undesirable volatile compound diacetyl and was described as 'fruity' and 'acidic', with the increased sourness masking the sweet, wort-like characteristics of the NAB. Moreover, this NAB was ranked as the most highly acceptable in the sensory evaluation. In conclusion, the limited co-fermentation of non-Saccharomyces yeasts with LAB is a promising strategy for the production of NAB.
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Affiliation(s)
- Laura Nyhan
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Aylin W. Sahin
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Elke K. Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland ,APC Microbiome Ireland, University College Cork, Cork, Ireland
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6
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Liu N, Qin L, Hu L, Miao S. Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Bohnenkamp AC, Wijffels RH, Kengen SWM, Weusthuis RA. Co-production of hydrogen and ethyl acetate in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:192. [PMID: 34598726 PMCID: PMC8487115 DOI: 10.1186/s13068-021-02036-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Ethyl acetate (C4H8O2) and hydrogen (H2) are industrially relevant compounds that preferably are produced via sustainable, non-petrochemical production processes. Both compounds are volatile and can be produced by Escherichia coli before. However, relatively low yields for hydrogen are obtained and a mix of by-products renders the sole production of hydrogen by micro-organisms unfeasible. High yields for ethyl acetate have been achieved, but accumulation of formate remained an undesired but inevitable obstacle. Coupling ethyl acetate production to the conversion of formate into H2 may offer an interesting solution to both drawbacks. Ethyl acetate production requires equimolar amounts of ethanol and acetyl-CoA, which enables a redox neutral fermentation, without the need for production of by-products, other than hydrogen and CO2. RESULTS We engineered Escherichia coli towards improved conversion of formate into H2 and CO2 by inactivating the formate hydrogen lyase repressor (hycA), both uptake hydrogenases (hyaAB, hybBC) and/or overexpressing the hydrogen formate lyase activator (fhlA), in an acetate kinase (ackA) and lactate dehydrogenase (ldhA)-deficient background strain. Initially 10 strains, with increasing number of modifications were evaluated in anaerobic serum bottles with respect to growth. Four reference strains ΔldhAΔackA, ΔldhAΔackA p3-fhlA, ΔldhAΔackAΔhycAΔhyaABΔhybBC and ΔldhAΔackAΔhycAΔhyaABΔhybBC p3-fhlA were further equipped with a plasmid carrying the heterologous ethanol acyltransferase (Eat1) from Wickerhamomyces anomalus and analyzed with respect to their ethyl acetate and hydrogen co-production capacity. Anaerobic co-production of hydrogen and ethyl acetate via Eat1 was achieved in 1.5-L pH-controlled bioreactors. The cultivation was performed at 30 °C in modified M9 medium with glucose as the sole carbon source. Anaerobic conditions and gas stripping were established by supplying N2 gas. CONCLUSIONS We showed that the engineered strains co-produced ethyl acetate and hydrogen to yields exceeding 70% of the pathway maximum for ethyl acetate and hydrogen, and propose in situ product removal via gas stripping as efficient technique to isolate the products of interest.
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Affiliation(s)
- Anna C Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - René H Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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8
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Feng J, Zhang J, Ma Y, Feng Y, Wang S, Guo N, Wang H, Wang P, Jiménez-Bonilla P, Gu Y, Zhou J, Zhang ZT, Cao M, Jiang D, Wang S, Liu XW, Shao Z, Borovok I, Huang H, Wang Y. Renewable fatty acid ester production in Clostridium. Nat Commun 2021; 12:4368. [PMID: 34272383 PMCID: PMC8285483 DOI: 10.1038/s41467-021-24038-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Bioproduction of renewable chemicals is considered as an urgent solution for fossil energy crisis. However, despite tremendous efforts, it is still challenging to generate microbial strains that can produce target biochemical to high levels. Here, we report an example of biosynthesis of high-value and easy-recoverable derivatives built upon natural microbial pathways, leading to improvement in bioproduction efficiency. By leveraging pathways in solventogenic clostridia for co-producing acyl-CoAs, acids and alcohols as precursors, through rational screening for host strains and enzymes, systematic metabolic engineering-including elimination of putative prophages, we develop strains that can produce 20.3 g/L butyl acetate and 1.6 g/L butyl butyrate. Techno-economic analysis results suggest the economic competitiveness of our developed bioprocess. Our principles of selecting the most appropriate host for specific bioproduction and engineering microbial chassis to produce high-value and easy-separable end products may be applicable to other bioprocesses. Esters can be used as fuels and specialty chemicals for food flavoring, cosmetic and pharmaceutical industries. Here, the authors systematically engineer clostridia, including discovery and deletion of prophages to increase strain stability, for the production of butyl acetate and butyl butyrate from corn stover at low cost.
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Affiliation(s)
- Jun Feng
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Jie Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Yuechao Ma
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Yiming Feng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
| | - Shangjun Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Na Guo
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Haijiao Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Pixiang Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Pablo Jiménez-Bonilla
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA.,School of Chemistry, National University (UNA), Heredia, Costa Rica
| | - Yanyan Gu
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Junping Zhou
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Zhong-Tian Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA.,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Di Jiang
- Department of Applied Chemistry, University of Science and Technology of China, Hefei, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xian-Wei Liu
- Department of Applied Chemistry, University of Science and Technology of China, Hefei, China
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Haibo Huang
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA.
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, USA. .,Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA.
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9
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Leonel LV, Arruda PV, Chandel AK, Felipe MGA, Sene L. Kluyveromyces marxianus: a potential biocatalyst of renewable chemicals and lignocellulosic ethanol production. Crit Rev Biotechnol 2021; 41:1131-1152. [PMID: 33938342 DOI: 10.1080/07388551.2021.1917505] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Kluyveromyces marxianus is an ascomycetous yeast which has shown promising results in cellulosic ethanol and renewable chemicals production. It can survive on a variety of carbon sources under industrially favorable conditions due to its fast growth rate, thermotolerance, and acid tolerance. K. marxianus, is generally regarded as a safe (GRAS) microorganism, is widely recognized as a powerhouse for the production of heterologous proteins and is accepted by the US Food and Drug Administration (USFDA) for its pharmaceutical and food applications. Since lignocellulosic hydrolysates are comprised of diverse monomeric sugars, oligosaccharides and potential metabolism inhibiting compounds, this microorganism can play a pivotal role as it can grow on lignocellulosic hydrolysates coping with vegetal cell wall derived inhibitors. Furthermore, advancements in synthetic biology, for example CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, will enable development of an engineered yeast for the production of biochemicals and biopharmaceuticals having a myriad of industrial applications. Genetic engineering companies such as Cargill, Ginkgo Bioworks, DuPont, Global Yeast, Genomatica, and several others are actively working to develop designer yeasts. Given the important traits and properties of K. marxianus, these companies may find it to be a suitable biocatalyst for renewable chemicals and fuel production on the large scale. This paper reviews the recent progress made with K. marxianus biotechnology for sustainable production of ethanol, and other products utilizing lignocellulosic sugars.
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Affiliation(s)
- L V Leonel
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
| | - P V Arruda
- Department of Bioprocess Engineering and Biotechnology - COEBB/TD, Federal University of Technology - Paraná (UTFPR), Toledo, Brazil
| | - A K Chandel
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - M G A Felipe
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - L Sene
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
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10
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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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11
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Hoffmann A, Kupsch C, Walther T, Löser C. Synthesis of ethyl acetate from glucose by Kluyveromyces marxianus, Cyberlindnera jadinii and Wickerhamomyces anomalus depending on the induction mode. Eng Life Sci 2021; 21:154-168. [PMID: 33716614 PMCID: PMC7923572 DOI: 10.1002/elsc.202000048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/28/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
Ethyl acetate is currently produced from fossil carbon resources. This ester could also be microbially synthesized from sugar-rich wastes of the food industry. Wild-type strains with GRAS status are preferred for such applications. Production of ethyl acetate by wild-type yeasts has been repeatedly reported, but comparative studies with several strains at various induction modes are largely missing. Here, synthesis of ethyl acetate by three yeasts with GRAS status, Kluyveromyces marxianus DSM 5422, Cyberlindnera jadinii DSM 2361 and Wickerhamomyces anomalus DSM 6766, was studied under identical and well-defined conditions in an aerated bioreactor, by inducing the ester synthesis via iron or oxygen limitation. Balancing the ester synthesis was based on measured concentrations of ethyl acetate in the exhaust gas, delivering masses of synthesized ester and synthesis rates in a high temporal resolution. All tested yeasts synthesized ethyl acetate under these conditions, but the intensity varied with the strain and induction mode. The highest yields were achieved under iron limitation with K. marxianus (0.182 g g-1) and under oxygen limitation with W. anomalus (0.053 g g-1). Iron limitation proved to be the better inducer for ester synthesis while oxygen limitation favored ethanol formation. K. marxianus DSM 5422 was the most potent producer of ethyl acetate exhibiting the highest biomass-specific synthesis rate of 0.5 g g-1h-1 under moderate iron limitation.
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Affiliation(s)
- Andreas Hoffmann
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Kupsch
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Thomas Walther
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Löser
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
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12
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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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13
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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14
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Patinios C, Lanza L, Corino I, Franssen MCR, Van der Oost J, Weusthuis RA, Kengen SWM. Eat1-Like Alcohol Acyl Transferases From Yeasts Have High Alcoholysis and Thiolysis Activity. Front Microbiol 2020; 11:579844. [PMID: 33193208 PMCID: PMC7658179 DOI: 10.3389/fmicb.2020.579844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/09/2020] [Indexed: 11/13/2022] Open
Abstract
Esters are important flavor and fragrance compounds that are present in many food and beverage products. Many of these esters are produced by yeasts and bacteria during fermentation. While ester production in yeasts through the alcohol acyl transferase reaction has been thoroughly investigated, ester production through alcoholysis has been completely neglected. Here, we further analyze the catalytic capacity of the yeast Eat1 enzyme and demonstrate that it also has alcoholysis and thiolysis activities. Eat1 can perform alcoholysis in an aqueous environment in vitro, accepting a wide range of alcohols (C2-C10) but only a small range of acyl donors (C2-C4). We show that alcoholysis occurs in vivo in several Crabtree negative yeast species but also in engineered Saccharomyces cerevisiae strains that overexpress Eat1 homologs. The alcoholysis activity of Eat1 was also used to upgrade ethyl esters to butyl esters in vivo by overexpressing Eat1 in Clostridium beijerinckii. Approximately 17 mM of butyl acetate and 0.3 mM of butyl butyrate could be produced following our approach. Remarkably, the in vitro alcoholysis activity is 445 times higher than the previously described alcohol acyl transferase activity. Thus, alcoholysis is likely to affect the ester generation, both quantitatively and qualitatively, in food and beverage production processes. Moreover, mastering the alcoholysis activity of Eat1 may give rise to the production of novel food and beverage products.
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Affiliation(s)
- Constantinos Patinios
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Bioprocess Engineering, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Lucrezia Lanza
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Inge Corino
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Maurice C. R. Franssen
- Laboratory of Organic Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - John Van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Ruud A. Weusthuis
- Laboratory of Bioprocess Engineering, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands
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15
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Karim A, Gerliani N, Aïder M. Kluyveromyces marxianus: An emerging yeast cell factory for applications in food and biotechnology. Int J Food Microbiol 2020; 333:108818. [PMID: 32805574 DOI: 10.1016/j.ijfoodmicro.2020.108818] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022]
Abstract
Several yeasts, which are eukaryotic microorganisms, have long been used in different industries due to their potential applications, both for fermentation and for the production of specific metabolites. Kluyveromyces marxianus is one of the most auspicious nonconventional yeasts, generally isolated from wide-ranging natural habitats such as fermented traditional dairy products, kefir grain, sewage from sugar industries, sisal leaves, and plants. This is a food-grade yeast with various beneficial traits, such as rapid growth rate and thermotolerance that make it appealing for different industrial food and biotechnological applications. K. marxianus is a respiro-fermentative yeast likely to produce energy by either respiration or fermentation pathways. It generates a wide-ranging specific metabolites and could contribute to a variety of different food and biotechnological industries. Although Saccharomyces cerevisiae is the most widely used dominant representative in all aspects, many applications of K. marxianus in biotechnology, food and environment have only started to emerge nowadays; some of the most promising applications are reviewed here. The general physiology of K. marxianus is outlined, and then the different applications are discussed: first, the applications of K. marxianus in biotechnology, and then the recent advances and possible applications in food, feed and environmental industries. Finally, this review provides a discussion of the main challenges and some perspectives for targeted applications of K. marxianus in the modern food technology and applied biotechnology in order to exploit the full potential of this yeast which can be used as a cell factory with great efficiency.
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Affiliation(s)
- Ahasanul Karim
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada
| | - Natela Gerliani
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada
| | - Mohammed Aïder
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada.
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16
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Valdez Castillo M, Laxman Pachapur V, Brar SK, Naghdi M, Arriaga S, Ávalos Ramirez A. Yeast-driven whey biorefining to produce value-added aroma, flavor, and antioxidant compounds: technologies, challenges, and alternatives. Crit Rev Biotechnol 2020; 40:930-950. [PMID: 32693642 DOI: 10.1080/07388551.2020.1792407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Whey is a liquid residue generated during the production of cheese and yogurt. It has a pH between 3.9 and 5.6, and a high chemical oxygen demand (COD), from 60 to 80 g/L. Whey contains lactose, proteins, and minerals. Globally, approximately 50% of the whey generated is untreated and is released directly into the environment, which represents an environmental risk. To overcome whey management problems, conventional thermo-physical valorization treatments have been explored, which are complex, costly and energy-intensive. As an alternative, whey fermentation processes employing bacteria, fungi and yeast are economical and promising methods. Among them, yeast fermentation creates value-added products such as antimicrobials, biofuels, aromas, flavors, and antioxidants with no need for previous conditioning of the whey, such as hydrolysis of the lactose, prior to whey biorefining. The biorefining concept applied to whey is discussed using chemical and biological transformation pathways, showing their pluses and minuses, such as technical drawbacks. The main challenges and solutions for the production of fusel alcohols, specifically for 2-phenylethanol, are also discussed in this review.
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Affiliation(s)
- Mariana Valdez Castillo
- Centre-Eau Terre Environnement, Institut national de la recherche scientifique, Québec, Canada
| | - Vinayak Laxman Pachapur
- Centre-Eau Terre Environnement, Institut national de la recherche scientifique, Québec, Canada
| | - Satinder Kaur Brar
- Centre-Eau Terre Environnement, Institut national de la recherche scientifique, Québec, Canada.,Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Canada
| | - Mitra Naghdi
- Centre-Eau Terre Environnement, Institut national de la recherche scientifique, Québec, Canada
| | - Sonia Arriaga
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), San Luis Potosí, México
| | - Antonio Ávalos Ramirez
- Centre-Eau Terre Environnement, Institut national de la recherche scientifique, Québec, Canada.,Centre National en Électrochimie et en Technologies Environnementales Inc, Shawinigan, Canada
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17
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Zhang S, Guo F, Yan W, Dong W, Zhou J, Zhang W, Xin F, Jiang M. Perspectives for the microbial production of ethyl acetate. Appl Microbiol Biotechnol 2020; 104:7239-7245. [PMID: 32656615 DOI: 10.1007/s00253-020-10756-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/13/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022]
Abstract
Ethyl acetate is one of the short-chain esters and widely used in the food, beverage, and solvent areas. The ethyl acetate production currently proceeds through unsustainable and energy intensive processes, which are based on natural gas and crude oil. Microbial conversion of biomass-derived sugars into ethyl acetate may provide a sustainable alternative. In this review, the perspectives of bio-catalyzing ethanol and acetic acid to ethyl acetate using lipases in vitro was introduced. Besides, the crucial elements for high yield of ethyl acetate in fermentation was expounded. Also, metabolic engineering in yeasts to product ethyl acetate in vivo using alcohol acyl transferases (AAT) was discussed. KEY POINTS: •The accumulation of acetyl-CoA is crucial for synthesizing ethyl acetate in vivo; AAT-mediated metabolic engineering could efficiently improve ethyl acetate production.
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Affiliation(s)
- Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wei Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
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18
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Control of Specific Growth Rate in Fed-Batch Bioprocesses: Novel Controller Design for Improved Noise Management. Processes (Basel) 2020. [DOI: 10.3390/pr8060679] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Accurate control of the specific growth rate (µ) of microorganisms is dependent on the ability to quantify the evolution of biomass reliably in real time. Biomass concentration can be monitored online using various tools and methods, but the obtained signal is often very noisy and unstable, leading to inaccuracies in the estimation of μ. Furthermore, controlling the growth rate is challenging as the process evolves nonlinearly and is subject to unpredictable disturbances originating from the culture’s metabolism. In this work, a novel feedforward-feedback controller logic is presented to counter the problem of noise and oscillations in the control variable and to address the exponential growth dynamics more effectively. The controller was tested on fed-batch cultures of Kluyveromyces marxianus, during which μ was estimated in real time from online biomass concentration measurements obtained with dielectric spectroscopy. It is shown that the specific growth rate can be maintained at different setpoint values with an average root mean square control error of 23 ± 6%.
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19
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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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20
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Bohnenkamp AC, Kruis AJ, Mars AE, Wijffels RH, van der Oost J, Kengen SWM, Weusthuis RA. Multilevel optimisation of anaerobic ethyl acetate production in engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:65. [PMID: 32280373 PMCID: PMC7137189 DOI: 10.1186/s13068-020-01703-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/25/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ethyl acetate is a widely used industrial solvent that is currently produced by chemical conversions from fossil resources. Several yeast species are able to convert sugars to ethyl acetate under aerobic conditions. However, performing ethyl acetate synthesis anaerobically may result in enhanced production efficiency, making the process economically more viable. RESULTS We engineered an E. coli strain that is able to convert glucose to ethyl acetate as the main fermentation product under anaerobic conditions. The key enzyme of the pathway is an alcohol acetyltransferase (AAT) that catalyses the formation of ethyl acetate from acetyl-CoA and ethanol. To select a suitable AAT, the ethyl acetate-forming capacities of Atf1 from Saccharomyces cerevisiae, Eat1 from Kluyveromyces marxianus and Eat1 from Wickerhamomyces anomalus were compared. Heterologous expression of the AAT-encoding genes under control of the inducible LacI/T7 and XylS/Pm promoters allowed optimisation of their expression levels. CONCLUSION Engineering efforts on protein and fermentation level resulted in an E. coli strain that anaerobically produced 42.8 mM (3.8 g/L) ethyl acetate from glucose with an unprecedented efficiency, i.e. 0.48 C-mol/C-mol or 72% of the maximum pathway yield.
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Affiliation(s)
- Anna C. Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Aleksander J. Kruis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Astrid E. Mars
- Biobased Products, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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21
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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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22
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Lai YT, Cheng KC, Lai CN, Lai YJ. Isolation and identification of aroma producing strain with esterification capacity from yellow water. PLoS One 2019; 14:e0211356. [PMID: 30763353 PMCID: PMC6375555 DOI: 10.1371/journal.pone.0211356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/13/2019] [Indexed: 11/18/2022] Open
Abstract
Kaoliang is a refreshing fragranced type of Chinese spirits with slight apple fragrance that comes from ethyl acetate (EA). Special aromas are produced by esterification microorganisms, which affect the taste and quality of the wine. In this study, new yeast strains were isolated from yellow water, a by-product during fermentation process. Meanwhile, the optimal culture condition was determined for its growth and EA production. Three new strains, Kazachstaniaexigua, Candida humilis and Saccharomyces cerevisiae were identified from yellow water. Among these strains, S. cerevisiae S5 was the new and dominant strain. Results from response surface methodology showed that S. cerevisiae S5 produced 161.88 ppm of EA, in the medium with 4.91% yeast extract, 9.82% peptone, and 20.91% glucose after 96 hours of cultivation at 27.53°C. GC analysis showed that aroma compounds, such as EA, isoamyl acetate and 2-phenylethanol increased from the sample of optimal condition when compared to the one from initial fermentation condition.
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Affiliation(s)
- Yen-Tso Lai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Kuan-Chen Cheng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Food Science Technology, National Taiwan University, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chia-Nuan Lai
- Graduate Institute of Food Science Technology, National Taiwan University, Taipei, Taiwan
| | - Ying-Jang Lai
- Department of Food Science, National Quemoy University, Kinmen, Taiwan
- * E-mail:
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23
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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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Alcohol Acetyltransferase Eat1 Is Located in Yeast Mitochondria. Appl Environ Microbiol 2018; 84:AEM.01640-18. [PMID: 30054364 DOI: 10.1128/aem.01640-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/24/2018] [Indexed: 11/20/2022] Open
Abstract
Eat1 is a recently discovered alcohol acetyltransferase responsible for bulk ethyl acetate production in yeasts such as Wickerhamomyces anomalus and Kluyveromyces lactis These yeasts have the potential to become efficient bio-based ethyl acetate producers. However, some fundamental features of Eat1 are still not understood, which hampers the rational engineering of efficient production strains. The cellular location of Eat1 in yeast is one of these features. To reveal its location, Eat1 was fused with yeast-enhanced green fluorescent protein (yEGFP) to allow intracellular tracking. Despite the current assumption that bulk ethyl acetate production occurs in the yeast cytosol, most of Eat1 localized to the mitochondria of Kluyveromyces lactis CBS 2359 Δku80 We then compared five bulk ethyl acetate-producing yeasts in iron-limited chemostats with glucose as the carbon source. All yeasts produced ethyl acetate under these conditions. This strongly suggests that the mechanism and location of bulk ethyl acetate synthesis are similar in these yeast strains. Furthermore, an in silico analysis showed that Eat1 proteins from various yeasts were mostly predicted as mitochondrial. Altogether, it is concluded that Eat1-catalyzed ethyl acetate production occurs in yeast mitochondria. This study has added new insights into bulk ethyl acetate synthesis in yeast, which is relevant for developing efficient production strains.IMPORTANCE Ethyl acetate is a common bulk chemical that is currently produced from petrochemical sources. Several Eat1-containing yeast strains naturally produce large amounts of ethyl acetate and are potential cell factories for the production of bio-based ethyl acetate. Rational design of the underlying metabolic pathways may result in improved production strains, but it requires fundamental knowledge on the function of Eat1. A key feature is the location of Eat1 in the yeast cell. The precursors for ethyl acetate synthesis can be produced in multiple cellular compartments through different metabolic pathways. The location of Eat1 determines the relevance of each pathway, which will provide future targets for the metabolic engineering of bulk ethyl acetate production in yeast.
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Löser C, Haas C, Liu W, Grahl S, Bley T. Uptake of iron by Kluyveromyces marxianus DSM 5422 cultivated in a whey-based medium. Eng Life Sci 2018; 18:459-474. [PMID: 32624927 DOI: 10.1002/elsc.201700195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Abstract
The ability of Kluyveromyces marxianus for converting lactose into ethyl acetate offers a chance for the economical reuse of whey. Iron plays a significant role in this process as ester synthesis requires a low intracellular iron content, xFe . The iron content in turn is decreased by growth due to cell expansion and increased by iron uptake. Thus, the iron-uptake rate, ψ, is important for the considered process. Iron uptake by K. marxianus DSM 5422 was studied in aerobic cultivation on a whey-borne medium with varied initial iron content, in part combined with a feed of iron under intensive growth conditions. A possible precipitation of iron that would pretend iron uptake was verified not to have occurred. Regularly measured dissolved iron concentrations, CFe,L , allowed the xFe and ψ parameters to be obtained by model-based iron balancing. The achieved data were used for establishing a ψ(CFe,L , xFe ) model. Mathematical simulations based on this iron-uptake model reproduced the performed cultivation processes. The created iron-uptake model allows for a future predictive system to be developed for the optimization of biotechnological ester production.
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Affiliation(s)
- Christian Löser
- Chair of Bioprocess Engineering Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Christiane Haas
- Chair of Bioprocess Engineering Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Wanqiong Liu
- Chair of Bioprocess Engineering Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Sebastian Grahl
- Chair of Bioprocess Engineering Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Thomas Bley
- Chair of Bioprocess Engineering Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
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26
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Yeast diversity in relation to the production of fuels and chemicals. Sci Rep 2017; 7:14259. [PMID: 29079838 PMCID: PMC5660169 DOI: 10.1038/s41598-017-14641-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/09/2017] [Indexed: 12/27/2022] Open
Abstract
In addition to ethanol, yeasts have the potential to produce many other industrially-relevant chemicals from numerous different carbon sources. However there remains a paucity of information about overall capability across the yeast family tree. Here, 11 diverse species of yeasts with genetic backgrounds representative of different branches of the family tree were investigated. They were compared for their abilities to grow on a range of sugar carbon sources, to produce potential platform chemicals from such substrates and to ferment hydrothermally pretreated rice straw under simultaneous saccharification and fermentation conditions. The yeasts differed considerably in their metabolic capabilities and production of ethanol. A number could produce significant amounts of ethyl acetate, arabinitol, glycerol and acetate in addition to ethanol, including from hitherto unreported carbon sources. They also demonstrated widely differing efficiencies in the fermentation of sugars derived from pre-treated rice straw biomass and differential sensitivities to fermentation inhibitors. A new catabolic property of Rhodotorula mucilaginosa (NCYC 65) was discovered in which sugar substrate is cleaved but the products are not metabolised. We propose that engineering this and some of the other properties discovered in this study and transferring such properties to conventional industrial yeast strains could greatly expand their biotechnological utility.
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27
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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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28
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Ahtesh FB, Apostolopoulos V, Stojanovska L, Shah NP, Mishra VK. Effects of fermented skim milk drink by Kluyveromyces marxianus
LAF4 co-cultured with lactic acid bacteria to release angiotensin-converting enzyme inhibitory activities. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fatah B Ahtesh
- Center for Chronic Disease; College of Health and Biomedicine; Victoria University; Werribee Campus P.O. Box 14428 Melbourne Vic. 8001 Australia
| | - Vasso Apostolopoulos
- Center for Chronic Disease; College of Health and Biomedicine; Victoria University; Werribee Campus P.O. Box 14428 Melbourne Vic. 8001 Australia
| | - Lily Stojanovska
- Center for Chronic Disease; College of Health and Biomedicine; Victoria University; Werribee Campus P.O. Box 14428 Melbourne Vic. 8001 Australia
| | - Nagendra P Shah
- Food and Nutritional Science; School of Biological Sciences 6N08; Kadoorie Biological Sciences Building; The University of Hong Kong Hong Kong
| | - Vijay Kumar Mishra
- Center for Chronic Disease; College of Health and Biomedicine; Victoria University; Werribee Campus P.O. Box 14428 Melbourne Vic. 8001 Australia
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Pentjuss A, Stalidzans E, Liepins J, Kokina A, Martynova J, Zikmanis P, Mozga I, Scherbaka R, Hartman H, Poolman MG, Fell DA, Vigants A. Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. J Ind Microbiol Biotechnol 2017; 44:1177-1190. [PMID: 28444480 DOI: 10.1007/s10295-017-1946-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/16/2017] [Indexed: 12/11/2022]
Abstract
The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism's potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.
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Affiliation(s)
- A Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - E Stalidzans
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia.
| | - J Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - A Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - J Martynova
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - P Zikmanis
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - I Mozga
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - R Scherbaka
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - H Hartman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - M G Poolman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - D A Fell
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - A Vigants
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
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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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Löbs A, Lin J, Cook M, Wheeldon I. High throughput, colorimetric screening of microbial ester biosynthesis reveals high ethyl acetate production from
Kluyveromyces marxianus
on C5, C6, and C12 carbon sources. Biotechnol J 2016; 11:1274-1281. [DOI: 10.1002/biot.201600060] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Ann‐Kathrin Löbs
- Department of Chemical and Environmental Engineering UC Riverside Riverside California USA
| | - Jyun‐Liang Lin
- Department of Chemical and Environmental Engineering UC Riverside Riverside California USA
| | - Megan Cook
- Department of Chemical and Environmental Engineering UC Riverside Riverside California USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering UC Riverside Riverside California USA
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32
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Martynova J, Kokina A, Kibilds J, Liepins J, Scerbaka R, Vigants A. Effects of acetate on Kluyveromyces marxianus DSM 5422 growth and metabolism. Appl Microbiol Biotechnol 2016; 100:4585-94. [DOI: 10.1007/s00253-016-7392-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
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Celińska E, Borkowska M, Białas W. Evaluation of a recombinant insect-derived amylase performance in simultaneous saccharification and fermentation process with industrial yeasts. Appl Microbiol Biotechnol 2015; 100:2693-707. [PMID: 26545757 PMCID: PMC4761610 DOI: 10.1007/s00253-015-7098-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/11/2015] [Accepted: 10/13/2015] [Indexed: 12/18/2022]
Abstract
Starch is the dominant feedstock consumed for the bioethanol production, accounting for 60 % of its global production. Considering the significant contribution of bioethanol to the global fuel market, any improvement in its major operating technologies is economically very attractive. It was estimated that up to 40 % of the final ethanol unit price is derived from the energy input required for the substrate pre-treatment. Application of raw starch hydrolyzing enzymes (RSHE), combined with operation of the process according to a simultaneous saccharification and fermentation (SSF) strategy, constitutes the most promising solutions to the current technologies limitations. In this study, we expressed the novel RSHE derived from an insect in Saccharomyces cerevisiae strain dedicated for the protein overexpression. Afterwards, the enzyme performance was assessed in SSF process conducted by industrial ethanologenic or thermotolerant yeast species. Comparison of the insect-derived RSHE preparation with commercially available amylolytic RSH preparation was conducted. Our results demonstrate that the recombinant alpha-amylase from rice weevil can be efficiently expressed and secreted with its native signal peptide in S. cerevisiae INVSc-pYES2-Amy1 expression system (accounting for nearly 72 % of the strain’s secretome). Application of the recombinant enzyme-based preparation in SSF process secured sufficient amylolytic activity for the yeast cell propagation and ethanol formation from raw starch. (Oligo)saccharide profiles generated by the compared preparations differed with respect to homogeneity of the sugar mixtures. Concomitantly, as demonstrated by a kinetic model developed in this study, the kinetic parameters describing activity of the compared preparations were different.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
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