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Andrade Silva CAD, Oka ML, da Silva PGP, Honma JM, Leite RSR, Fonseca GG. Physiological evaluation of yeast strains under anaerobic conditions using glucose, fructose, or sucrose as the carbon source. J Biosci Bioeng 2024; 137:420-428. [PMID: 38493064 DOI: 10.1016/j.jbiosc.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 03/18/2024]
Abstract
The aim of this study was to evaluate the physiology of 13 yeast strains by assessing their kinetic parameters under anaerobic conditions. They included Saccharomyces cerevisiae CAT-1 and 12 isolated yeasts from different regions in Brazil. The study aimed to enhance understanding of the metabolism of these strains for more effective applications. Measurements included quantification of sugars, ethanol, glycerol, and organic acids. Various kinetic parameters were analyzed, such as specific substrate utilization rate (qS), maximum specific growth rate (μmax), doubling time, biomass yield, product yield, maximum cell concentration, ethanol productivity (PEth), biomass productivity, and CO2 concentration. S. cerevisiae CAT-1 exhibited the highest values in glucose for μmax (0.35 h-1), qS (3.06 h-1), and PEth (0.69 gEth L-1 h-1). Candida parapsilosis Recol 37 did not fully consume the substrate. In fructose, S. cerevisiae CAT-1 stood out with higher values for μmax (0.25 h-1), qS (2.24 h-1), and PEth (0.60 gEth L-1 h-1). Meyerozyma guilliermondii Recol 09 and C. parapsilosis Recol 37 had prolonged fermentation times and residual substrate. In sucrose, only S. cerevisiae CAT-1, S. cerevisiae BB9, and Pichia kudriavzevii Recol 39 consumed all the substrate, displaying higher PEth (0.72, 0.51, and 0.44 gEth L-1 h-1, respectively) compared to other carbon sources.
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Affiliation(s)
- Cinthia Aparecida de Andrade Silva
- Center for Studies in Natural Resources, State University of Mato Grosso do Sul, Dourados, MS, Brazil; Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Marta Ligia Oka
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Pedro Garcia Pereira da Silva
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Janaina Mayumi Honma
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Rodrigo Simões Ribeiro Leite
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Health, Business and Science, University of Akureyri, Akureyri, Iceland.
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Bassett S, Da Silva NA. Engineering a carbon source-responsive promoter for improved biosynthesis in the non-conventional yeast Kluyveromyces marxianus. Metab Eng Commun 2024; 18:e00238. [PMID: 38845682 PMCID: PMC11153928 DOI: 10.1016/j.mec.2024.e00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Many desired biobased chemicals exhibit a range of toxicity to microbial cell factories, making industry-level biomanufacturing more challenging. Separating microbial growth and production phases is known to be beneficial for improving production of toxic products. Here, we developed a novel synthetic carbon-responsive promoter for use in the rapidly growing, stress-tolerant yeast Kluyveromyces marxianus, by fusing carbon-source responsive elements of the native ICL1 promoter to the strong S. cerevisiae TDH3 or native NC1 promoter cores. Two hybrids, P IT350 and P IN450 , were validated via EGFP fluorescence and demonstrated exceptional strength, partial repression during growth, and late phase activation in glucose- and lactose-based medium, respectively. Expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for synthesis of the polyketide triacetic acid lactone (TAL) under the control of P IN450 increased TAL more than 50% relative to the native NC1 promoter, and additional promoter engineering further increased TAL titer to 1.39 g/L in tube culture. Expression of the Penicillium griseofulvum 6-methylsalicylic acid synthase (6-MSAS) under the control of P IN450 resulted in a 6.6-fold increase in 6-MSA titer to 1.09 g/L and a simultaneous 1.5-fold increase in cell growth. Finally, we used P IN450 to express the Pseudomonas savastanoi IaaM and IaaH proteins and the Salvia pomifera sabinene synthase protein to improve production of the auxin hormone indole-3-acetic acid and the monoterpene sabinene, respectively, both extremely toxic to yeast. The development of carbon-responsive promoters adds to the synthetic biology toolbox and available metabolic engineering strategies for K. marxianus, allowing greater control over heterologous protein expression and improved production of toxic metabolites.
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Affiliation(s)
- Shane Bassett
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
| | - Nancy A. Da Silva
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
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3
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Zeng DW, Yang YQ, Wang Q, Zhang FL, Zhang MD, Liao S, Liu ZQ, Fan YC, Liu CG, Zhang L, Zhao XQ. Transcriptome analysis of Kluyveromyces marxianus under succinic acid stress and development of robust strains. Appl Microbiol Biotechnol 2024; 108:293. [PMID: 38592508 PMCID: PMC11003901 DOI: 10.1007/s00253-024-13097-3] [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: 10/17/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
Kluyveromyces marxianus has become an attractive non-conventional yeast cell factory due to its advantageous properties such as high thermal tolerance and rapid growth. Succinic acid (SA) is an important platform molecule that has been applied in various industries such as food, material, cosmetics, and pharmaceuticals. SA bioproduction may be compromised by its toxicity. Besides, metabolite-responsive promoters are known to be important for dynamic control of gene transcription. Therefore, studies on global gene transcription under various SA concentrations are of great importance. Here, comparative transcriptome changes of K. marxianus exposed to various concentrations of SA were analyzed. Enrichment and analysis of gene clusters revealed repression of the tricarboxylic acid cycle and glyoxylate cycle, also activation of the glycolysis pathway and genes related to ergosterol synthesis. Based on the analyses, potential SA-responsive promoters were investigated, among which the promoter strength of IMTCP2 and KLMA_50231 increased 43.4% and 154.7% in response to 15 g/L SA. In addition, overexpression of the transcription factors Gcr1, Upc2, and Ndt80 significantly increased growth under SA stress. Our results benefit understanding SA toxicity mechanisms and the development of robust yeast for organic acid production. KEY POINTS: • Global gene transcription of K. marxianus is changed by succinic acid (SA) • Promoter activities of IMTCP2 and KLMA_50123 are regulated by SA • Overexpression of Gcr1, Upc2, and Ndt80 enhanced SA tolerance.
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Affiliation(s)
- Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong-Qiang Yang
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Qi Wang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mao-Dong Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Zhi-Qiang Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Ya-Chao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Chen-Guang Liu
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China.
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Wu P, Mo W, Tian T, Song K, Lyu Y, Ren H, Zhou J, Yu Y, Lu H. Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus. MLIFE 2024; 3:129-142. [PMID: 38827505 PMCID: PMC11139206 DOI: 10.1002/mlf2.12115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/08/2023] [Accepted: 12/23/2023] [Indexed: 06/04/2024]
Abstract
Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins. Improving the yield in K. marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering. To address these issues, linear and circular yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K. marxianus. These modules contained up to seven genes with a maximum size of 15 kb. KmYACs carried telomeres either from K. marxianus or Tetrahymena. KmYACs were transferred successfully into K. marxianus and stably propagated without affecting the normal growth of the host, regardless of the type of telomeres and configurations of KmYACs. KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins. In high-density fermentation, the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l, the highest reported level to date in K. marxianus. Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis, enhanced flux entering the tricarboxylic acid cycle, and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins. Consistently, supplementing lysine or arginine further improved the yield. Therefore, KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research. Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins, and this strategy may be applied to optimize other microbial cell factories.
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Affiliation(s)
- Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Wenjuan Mo
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Tian Tian
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Kunfeng Song
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Yilin Lyu
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Haiyan Ren
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghaiChina
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5
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Qiu Y, Lei P, Wang R, Sun L, Luo Z, Li S, Xu H. Kluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications. Biotechnol Adv 2023; 64:108125. [PMID: 36870581 DOI: 10.1016/j.biotechadv.2023.108125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.
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Affiliation(s)
- Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Zhengshan Luo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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6
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Dupuis JH, Cheung LKY, Newman L, Dee DR, Yada RY. Precision cellular agriculture: The future role of recombinantly expressed protein as food. Compr Rev Food Sci Food Saf 2023; 22:882-912. [PMID: 36546356 DOI: 10.1111/1541-4337.13094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Cellular agriculture is a rapidly emerging field, within which cultured meat has attracted the majority of media attention in recent years. An equally promising area of cellular agriculture, and one that has produced far more actual food ingredients that have been incorporated into commercially available products, is the use of cellular hosts to produce soluble proteins, herein referred to as precision cellular agriculture (PCAg). In PCAg, specific animal- or plant-sourced proteins are expressed recombinantly in unicellular hosts-the majority of which are yeast-and harvested for food use. The numerous advantages of PCAg over traditional agriculture, including a smaller carbon footprint and more consistent products, have led to extensive research on its utility. This review is the first to survey proteins currently being expressed using PCAg for food purposes. A growing number of viable expression hosts and recent advances for increased protein yields and process optimization have led to its application for producing milk, egg, and muscle proteins; plant hemoglobin; sweet-tasting plant proteins; and ice-binding proteins. Current knowledge gaps present research opportunities for optimizing expression hosts, tailoring posttranslational modifications, and expanding the scope of proteins produced. Considerations for the expansion of PCAg and its implications on food regulation, society, ethics, and the environment are also discussed. Considering the current trajectory of PCAg, food proteins from any biological source can likely be expressed recombinantly and used as purified food ingredients to create novel and tailored food products.
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Affiliation(s)
- John H Dupuis
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lennie K Y Cheung
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lenore Newman
- Food and Agriculture Institute, University of the Fraser Valley, Abbotsford, British Columbia, Canada
| | - Derek R Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rickey Y Yada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
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7
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Prospects of thermotolerant Kluyveromyces marxianus for high solids ethanol fermentation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:134. [PMID: 36474296 PMCID: PMC9724321 DOI: 10.1186/s13068-022-02232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
Simultaneous saccharification and fermentation (SSF) is effective for minimizing sugar inhibition during high solids fermentation of biomass solids to ethanol. However, fungal enzymes used during SSF are optimal between 50 and 60 °C, whereas most fermentative yeast, such as Saccharomyces cerevisiae, do not tolerate temperatures above 37 °C. Kluyveromyces marxianus variant CBS 6556 is a thermotolerant eukaryote that thrives at 43 °C, thus potentially serving as a promising new host for SSF operation in biorefineries. Here, we attempt to leverage the thermotolerance of the strain to demonstrate the application of CBS 6556 in a high solids (up to 20 wt% insoluble solid loading) SSF configuration to understand its capabilities and limitations as compared to a proven SSF strain, S. cerevisiae D5A. For this study, we first pretreated hardwood poplar chips using Co-Solvent Enhanced Lignocellulosic Fractionation (CELF) to remove lignin and hemicellulose and to produce cellulose-enriched pretreated solids for SSF. Our results demonstrate that although CBS 6556 could not directly outperform D5A, it demonstrated similar tolerance to high gravity sugar solutions, superior growth rates at higher temperatures and higher early stage ethanol productivity. We discovered that CBS 6556's membrane was particularly sensitive to higher ethanol concentrations causing it to suffer earlier fermentation arrest than D5A. Cross-examination of metabolite data between CBS 6556 and D5A and cell surface imaging suggests that the combined stresses of high ethanol concentrations and temperature to CBS 6556's cell membrane was a primary factor limiting its ethanol productivity. Hence, we believe K. marxianus to be an excellent host for future genetic engineering efforts to improve membrane robustness especially at high temperatures in order to achieve higher ethanol productivity and titers, serving as a viable alternative to D5A.
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8
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Fonseca GG. Metabolic engineering of Kluyveromyces marxianus for biomass-based applications. 3 Biotech 2022; 12:259. [PMID: 36068842 PMCID: PMC9440961 DOI: 10.1007/s13205-022-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/22/2022] [Indexed: 11/01/2022] Open
Abstract
Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03324-x.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Business and Science, University of Akureyri, Borgir v. Nordurslod, 600 Akureyri, Iceland
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9
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Bever D, Wheeldon I, Da Silva N. RNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of Kluyveromyces marxianus. Metab Eng Commun 2022; 15:e00208. [PMID: 36249306 PMCID: PMC9558044 DOI: 10.1016/j.mec.2022.e00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus, there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K. marxianus strains. The use of a strong RNA polymerase II promoter allows efficient expression of gRNAs flanked by the self-cleaving RNA structures, tRNA and HDV ribozyme, from a single plasmid co-expressing a codon optimized Cas9. Implementing this system resulted in nearly 100% efficiency of gene disruptions in both NHEJ-functional and NHEJ-deficient K. marxianus strains, with donor integration efficiencies reaching 50% and 100% in the two strains, respectively. The high gRNA targeting performance also proved instrumental for selection of engineered strains with lower growth rate but improved polyketide biosynthesis by avoiding an extended outgrowth period, a common method used to enrich for edited cells but that fails to recover advantageous mutants with even slightly impaired fitness. Finally, we provide the first demonstration of simultaneous, markerless integrations at multiple loci in K. marxianus using a 2.6 kb and a 7.6 kb donor, achieving a dual integration efficiency of 25.5% in a NHEJ-deficient strain. These results highlight both the ease of use and general robustness of this system for rapid and flexible metabolic engineering in this non-conventional yeast. RNAP II-driven tRNA-gRNA-HDV ribozyme cassette built for K. marxianus genome editing. Gene integrations up to 7.6 kb were achieved with only 40 bp homology sequences. Recovery of growth-biased modifications achievable as extended outgrowth not required. Application (ZWF1 and GPD1 knockouts) increased polyketide specific titers. Expressing two unique gRNAs from one cassette enabled integrations at separate loci.
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10
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Sahin B, Hosoglu MI, Guneser O, Karagul-Yuceer Y. Fermented Spirulina products with Saccharomyces and non- Saccharomyces yeasts: Special reference to their microbial, physico-chemical and sensory characterizations. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Wu P, Zhou J, Yu Y, Lu H. Characterization of essential elements for improved episomal expressions in
Kluyveromyces marxianus. Biotechnol J 2022; 17:e2100382. [DOI: 10.1002/biot.202100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Pingping Wu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
- National Technology Innovation Center of Synthetic Biology Tianjin China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology Shanghai China
- National Technology Innovation Center of Synthetic Biology Tianjin China
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12
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Malina C, Yu R, Björkeroth J, Kerkhoven EJ, Nielsen J. Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast. Proc Natl Acad Sci U S A 2021; 118:e2112836118. [PMID: 34903663 PMCID: PMC8713813 DOI: 10.1073/pnas.2112836118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose availability. Not all yeasts exhibit the Crabtree effect, and it is not known why Crabtree-negative yeasts can grow at rates comparable to Crabtree-positive yeasts. Here, we quantitatively compared two Crabtree-positive yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two Crabtree-negative yeasts, Kluyveromyces marxianus and Scheffersomyces stipitis, cultivated under glucose excess conditions. Combining physiological and proteome quantification with genome-scale metabolic modeling, we found that the two groups differ in energy metabolism and translation efficiency. In Crabtree-positive yeasts, the central carbon metabolism flux and proteome allocation favor a glucose utilization strategy minimizing proteome cost as proteins translation parameters, including ribosomal content and/or efficiency, are lower. Crabtree-negative yeasts, however, use a strategy of maximizing ATP yield, accompanied by higher protein translation parameters. Our analyses provide insight into the underlying reasons for the Crabtree effect, demonstrating a coupling to adaptations in both metabolism and protein translation.
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Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Wallenberg Center for Protein Research, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Rosemary Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Johan Björkeroth
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden;
- Wallenberg Center for Protein Research, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
- BioInnovation Institute, DK-2200, Copenhagen N, Denmark
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13
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Liu B, Wu P, Zhou J, Yin A, Yu Y, Lu H. Characterization and optimization of the LAC4 upstream region for low-leakage expression in Kluyveromyces marxianus. Yeast 2021; 39:283-296. [PMID: 34791694 DOI: 10.1002/yea.3682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/07/2022] Open
Abstract
Kluyveromyces marxianus is a promising host for the production of heterologous proteins, chemicals, and bioethanol. One superior feature of this species is its capacity to assimilate lactose, which is rendered by the LAC12-LAC4 gene pair encoding a lactose permease and a β-galactosidase enzyme. Little is known about the regulation of LAC4 in K. marxianus. In this study, we showed the presence of weak glucose repression in the regulation of LAC4 and that might contribute to the leaky expression of LAC4 in the glucose medium. In a mutagenesis screen of 1000-bp LAC4 upstream region, one mutant region, named H1, drove low-leakage expression of a URA3 reporter gene in glucose medium. Two mutations inside a polyadenosine stretch (poly(A)) of 5' UTR were major contributors to the low-leakage phenotype of H1. H1 directed low-leakage expression of GFP on a plasmid and that of LAC4 in situ in the glucose medium, which was not due to the reduction of mRNA levels. Meanwhile, H1 did not affect the induction of GFP or LAC4 by lactose. Cre recombinase expressed by H1 caused lower toxicity in the repressive condition and achieved higher yield after induction, compared with that expressed by a wild-type LAC4 upstream region or a strong INU1 promoter. Our study suggested that poly(A) inside 5' UTR played a role in regulating the expression of LAC4 in the repressive condition. Meanwhile, H1 provided a base for the development of a strict inducible system for expressing industrial proteins, especially toxic proteins.
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Affiliation(s)
- Benxin Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Anqi Yin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, Shanghai, China
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14
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Nieland S, Barig S, Salzmann J, Gehrau F, Zamani AI, Richter A, Ibrahim J, Gräser Y, Ng CL, Stahmann K. Aspergillus fumigatus AR04 obeys Arrhenius' rule in cultivation temperature shifts from 30 to 40°C. Microb Biotechnol 2021; 14:1422-1432. [PMID: 33421319 PMCID: PMC8313250 DOI: 10.1111/1751-7915.13739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023] Open
Abstract
To set a benchmark in fungal growth rate, a differential analysis of prototrophic Aspergillus fumigatus AR04 with three ascomycetes applied in > 103 t year-1 scale was performed, i.e. Ashbya gosspyii (riboflavin), Aspergillus niger (citric acid) and Aspergillus oryzae (food-processing). While radial colony growth decreased 0.5-fold when A. gossypii was cultivated at 40°C instead of 28°C, A. fumigatus AR04 responded with 1.7-fold faster hyphal growth. A. niger and A. oryzae formed colonies at 40°C, but not at 43°C. Moreover, all A. fumigatus strains tested grew even at 49°C. In chemostat experiments, A. fumigatus AR04 reached steady state at a dilution rate of 0.7 h-1 at 40°C, 120% more than reported for A. gossypii at 28°C. To study mycelial growth rates under unlimited conditions, carbon dioxide increase rates were calculated from concentrations detected online in the exhaust of batch fermentations for 3 h only. All rates calculated suggest that A. fumigatus AR04 approximates Arrhenius' rule when comparing short cultivations at 30°C with those at 40°C. Linearization of the exponential phase and comparison of the slopes revealed an increase to 192% by the 10°C up-shift.
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Affiliation(s)
- Susanne Nieland
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Susann Barig
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Julian Salzmann
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Frauke Gehrau
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Arief Izzairy Zamani
- Institute of Systems BiologyUniversiti Kebangsaan MalaysiaBangiSelangor43600 UKMMalaysia
| | - Annabell Richter
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
| | - Julia Ibrahim
- Sime Darby Technology CentreUPM‐MTDC Technology Centre IIILebuh Silikon1st Floor Block BUPM 43400SerdangSelangorMalaysia
| | - Yvonne Gräser
- Institute of Microbiology and ImmunologyCharité ‐ Universitätsmedizin BerlinCorporate Member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlinGermany
- Berlin Institute of HealthHindenburgdamm 30BerlinD‐12203Germany
| | - Chyan Leong Ng
- Institute of Systems BiologyUniversiti Kebangsaan MalaysiaBangiSelangor43600 UKMMalaysia
| | - Klaus‐Peter Stahmann
- Institute of BiotechnologyBrandenburg University of Technology Cottbus ‐ SenftenbergUniversitätsplatz 1SenftenbergD‐01958Germany
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15
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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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16
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Ha-Tran DM, Lai RY, Nguyen TTM, Huang E, Lo SC, Huang CC. Construction of engineered RuBisCO Kluyveromyces marxianus for a dual microbial bioethanol production system. PLoS One 2021; 16:e0247135. [PMID: 33661900 PMCID: PMC7932148 DOI: 10.1371/journal.pone.0247135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/02/2021] [Indexed: 11/28/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes play important roles in CO2 fixation and redox balancing in photosynthetic bacteria. In the present study, the kefir yeast Kluyveromyces marxianus 4G5 was used as host for the transformation of form I and form II RubisCO genes derived from the nonsulfur purple bacterium Rhodopseudomonas palustris using the Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO) method. Hungateiclostridium thermocellum ATCC 27405, a well-known bacterium for its efficient solubilization of recalcitrant lignocellulosic biomass, was used to degrade Napier grass and rice straw to generate soluble fermentable sugars. The resultant Napier grass and rice straw broths were used as growth media for the engineered K. marxianus. In the dual microbial system, H. thermocellum degraded the biomass feedstock to produce both C5 and C6 sugars. As the bacterium only used hexose sugars, the remaining pentose sugars could be metabolized by K. marxianus to produce ethanol. The transformant RubisCO K. marxianus strains grew well in hydrolyzed Napier grass and rice straw broths and produced bioethanol more efficiently than the wild type. Therefore, these engineered K. marxianus strains could be used with H. thermocellum in a bacterium-yeast coculture system for ethanol production directly from biomass feedstocks.
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Affiliation(s)
- Dung Minh Ha-Tran
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Rou-Yin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Trinh Thi My Nguyen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Eugene Huang
- College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Shou-Chen Lo
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (SCL); (CCH)
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (SCL); (CCH)
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17
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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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18
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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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19
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The identification of novel promoters and terminators for protein expression and metabolic engineering applications in Kluyveromyces marxianus. Metab Eng Commun 2021; 12:e00160. [PMID: 33489753 PMCID: PMC7808952 DOI: 10.1016/j.mec.2020.e00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 11/29/2022] Open
Abstract
The K. marxianus has emerged as a potential yeast strain for various biotechnological applications. However, the limited number of available genetic tools has hindered the widespread usage of this yeast. In the current study we have expanded the molecular tool box by identifying novel sets of promoters and terminators for increased recombinant protein expression in K. marxianus. The previously available transcriptomic data were analyzed to identify top 10 promoters of highest gene expression activity. We further characterized and compared strength of these identified promoters using eGFP as a reporter protein, at different temperatures and carbon sources. To examine the regulatory region driving protein expression, serially truncated shorter versions of two selected strong promoters were designed, and examined for their ability to drive eGFP protein expression. The activities of these two promoters were further enhanced using different combinations of native transcription terminators of K. marxianus. We further utilized the identified DNA cassette encoding strong promoter in metabolic engineering of K. marxianus for enhanced β-galactosidase activity. The present study thus provides novel sets of promoters and terminators as well as engineered K. marxianus strain for its wider utility in applications requiring lactose degradation such as in cheese whey and milk. Novel promoters and terminators for constitutive gene expression in K. marxianus. The promoters show constitutive expression at varying temperature and carbon source. K. marxianus strain with improved production of β-galactosidase.
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20
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Evaluating crude whey for bioethanol production using non-Saccharomyces yeast, Kluyveromyces marxianus. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-020-03996-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
AbstractEthanol production from non-food substrate is strongly recommended to avoid competition with food production. Whey, which is rich in nutrients, is one of the non-food substrate for ethanol production by Kluyveromyces spp. The purpose of this study was to optimize ethanol from different crude (non-deproteinized, non-pH adjusted, and non-diluted) whey using K. marxianus ETP87 which was isolated from traditional yoghurt. The sterilized and non-sterilized whey were employed for K. marxianus ETP87 substrate to evaluate the yeast competition potential with lactic acid and other microflora in whey. The effect of pH and temperature on ethanol productivity from whey was also investigated. Peptone, yeast extract, ammonium sulfate ((NH4)2SO4), and urea were supplemented to whey in order to investigate the requirement of additional nutrient for ethanol optimization. The ethanol obtained from non-sterilized whey was slightly and statistically lower than sterilized whey. The whey storage at 4 °C didn’t guarantee the constant lactose presence at longer preservation time. Significantly high amount of ethanol was attained from whey without pH adjustment (3.9) even if it was lower than pH controlled (5.0) whey. The thermophilic yeast, K. marxianus ETP87, yielded high ethanol between 30 and 35 °C, and the yeast was able to produce high ethanol until 45 °C, and significantly lower ethanol was recorded at 50 °C. The ammonium sulfate and peptone enhanced ethanol productivity, whereas yeast extract and urea depressed the yeast ethanol fermentation capability. The K. marxianus ETP87, the yeast isolated from traditional yoghurt, is capable of producing ethanol from non-sterilized and non-deproteinized substrates.
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21
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Leonarski E, Cesca K, Zanella E, Stambuk BU, de Oliveira D, Poletto P. Production of kombucha-like beverage and bacterial cellulose by acerola byproduct as raw material. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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22
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Nascimento VM, Antoniolli GTU, Leite RSR, Fonseca GG. Effects of the carbon source on the physiology and invertase activity of the yeast Saccharomyces cerevisiae FT858. 3 Biotech 2020; 10:348. [PMID: 32728515 DOI: 10.1007/s13205-020-02335-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/12/2020] [Indexed: 11/25/2022] Open
Abstract
Saccharomyces cerevisiae FT858 is an industrial yeast strain with high fermentative efficiency, but marginally studied so far. The aim of this work was to evaluate the biotechnological potential of S. cerevisiae FT858 through kinetic growth parameters, and the influence of the concentration of the substrate on the synthesis of the invertase enzyme. Invertases have a high biotechnological potential and their production through yeast is strongly influenced by the sugars in the medium. S. cerevisiae FT858 has an excellent biotechnological potential compared to the industrial yeast reference S. cerevisiae CAT-1, as it presented a low glycerol yield on the substrate (Y GLY/S) and a 10% increase in ethanol yield on sucrose in cultures with sucrose at 37 °C. The substrate concentration directly interfered in invertase production and the enzymatic expression underwent strong regulation through glucose concentration in the culture medium and S. cerevisiae CAT-1 presented constitutive behavior for the invertase enzyme.
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Affiliation(s)
- Valkirea Matos Nascimento
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, CEP 79.804-970 Brazil
| | - Gabriela Totino Ulian Antoniolli
- Laboratory of Enzymology and Fermentative Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, CEP 79.804-970 Brazil
| | - Rodrigo Simões Ribeiro Leite
- Laboratory of Enzymology and Fermentative Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, CEP 79.804-970 Brazil
| | - Gustavo Graciano Fonseca
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, CEP 79.804-970 Brazil
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23
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Evaluation of the Fermentative Capacity of Saccharomyces cerevisiae CAT-1 and BB9 Strains and Pichia kudriavzevii BB2 at Simulated Industrial Conditions. Indian J Microbiol 2020; 60:494-504. [PMID: 33087999 DOI: 10.1007/s12088-020-00891-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023] Open
Abstract
The search for promising yeasts that surpass the fermentative capacity of commercial strains, such as Saccharomyces cerevisiae CAT-1, is of great importance for industrial ethanol processes in the world. Two yeasts, Pichia kudriavzevii BB2 and Saccharomyces cerevisiae BB9, were evaluated in comparison to the industrial yeast S. cerevisiae CAT-1. The objective was to evaluate the performance profile of the three studied strains in terms of growth, substrate consumption, and metabolite formation, aiming to determine their behaviour in different media and pH conditions. The results showed that under cultivation conditions simulating the medium used in the industrial process (must at 22° Brix at pH 3.0) the highest ethanol productivity was 0.41 g L-1 h-1 for S. cerevisiae CAT-1, compared to 0.11 g L-1 h-1 and 0.16 g L-1 h-1 for P. kudriavzevii and S. cerevisiae BB2, respectively. S. cerevisiae CAT-1 produced three times more ethanol in must at pH 3.0 (28.30 g L-1) and in mineral medium at pH 3.0 (29.17 g L-1) and 5.0 (30.70 g L-1) when compared to the value obtained in sugarcane must pH 3.0 (9.89 g L-1). It was concluded that S. cerevisiae CAT-1 was not limited by the variation in pH in the mineral medium due to its nutritional composition, guaranteeing better performance of the yeast even in the presence of stressors. Only S. cerevisiae CAT-1 expressed he constitutive invertase enzyme, which is responsible for hydrolysing the sucrose contained in the must.
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da Silva AA, Fonseca GG. Influence of luminosity, carbon source and concentration of salts in the physiology of Chlorella sorokiniana. ENVIRONMENTAL TECHNOLOGY 2020; 41:719-729. [PMID: 30092717 DOI: 10.1080/09593330.2018.1509889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Growth studies are important to increase the knowledge about the physiology of microalgae. The development of suitable culture media allows optimum growth to each species. The genus Chlorella has the ability to adapt to various environmental and nutritional conditions. Thus, the aim of this work was to evaluate the physiology of Chlorella sorokiniana CTT 7727 at different growth conditions with Basal Bold (BB) medium. For that, heterotrophic, autotrophic and mixotrophic cultures were carried out. The maximum specific growth rates (µmax), the maximum biomass concentrations (Xmax) and cell productivities (PX) were calculated for each experiment. Among all the treatments evaluated, that with 24 h light, 3x BB (g L-1) and CO2 presented a higher µmax (0.40 day-1) and maximum cell concentration due the increased concentration of nutrients. Replacement of dark to light has increased Xmax from 2.3 × 105 to 9.3 × 106 cells mL-1 in regular BB medium and 3.6 × 105 to 2.1 × 107 cells mL-1 in 3x BB medium in autotrophic cultivations. The PX increased from 2.4 × 104 cells mL-1 h-1 (1x BB (g L-1)) to 3.6 × 104 cells mL-1 h-1 (3x BB (g L-1)), in the presence of 24 light and CO2. However, the same behaviour was not observed when BB concentration was increased 6, 8 or 10 times the initial concentration of BB medium. Experiments with pulses of concentrated nutrients showed that declining cells can resume their growth after nutrient depletion, but the viability is decreased after successive pulses.
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Affiliation(s)
- Alisson Alves da Silva
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, Brazil
| | - Gustavo Graciano Fonseca
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, Brazil
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25
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Nascimento VM, Fonseca GG. Effects of the carbon source and the interaction between carbon sources on the physiology of the industrial Saccharomyces cerevisiae CAT-1. Prep Biochem Biotechnol 2019; 50:349-356. [PMID: 31847699 DOI: 10.1080/10826068.2019.1703192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
During industrial fermentation, wild isolates are able to persist and even predominate in the bioreactors. Saccharomyces cerevisiae CAT-1 was one of these isolates and now is one of the yeasts mostly used in industrial ethanol processes in Brazil due to its efficient fermentation capacity. Despite it, the strain's physiology has been marginally studied so far. Since strains of the same species may have different responses to a specific cultivation condition, this work aimed to evaluate the physiology of S. cerevisiae CAT-1 in batch cultures using different carbon sources (glucose, fructose, sucrose, maltose, and galactose) as a sole carbon source and in binary mixtures, at 30 and 37 °C. The results showed that the fructose, sucrose, and maltose were the sugars that presented the highest ethanol yields on the substrate (0.40 gethanol gsubstrate-1) at both temperatures. Galactose was the sugar that the yeast had the lowest affinity given the lowest maximum specific growth rate (0.28 h-1). Despite the influence of a variety of mechanisms for sugar transport, the cells consume first substrates with fewer metabolic steps to catabolism and are susceptible to adaptive evolution depending on the availability of substrate.
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Affiliation(s)
- Valkirea Matos Nascimento
- Faculty of Biological and Environmental Sciences, Laboratory of Bioengineering, Federal University of Grande Dourados, Dourados, Brazil
| | - Gustavo Graciano Fonseca
- Faculty of Biological and Environmental Sciences, Laboratory of Bioengineering, Federal University of Grande Dourados, Dourados, Brazil
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Lehnen M, Ebert BE, Blank LM. Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts. BMC Microbiol 2019; 19:100. [PMID: 31101012 PMCID: PMC6525440 DOI: 10.1186/s12866-019-1453-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses. RESULTS To elaborate on the metabolic network response to increased fermentation temperatures of up to 49 °C, comprehensive physiological datasets of several Kluyveromyces and Ogataea strains were generated and used for 13C-metabolic flux analyses. While the maximum growth temperature was very similar in all investigated strains, the metabolic network response to elevated temperatures was not conserved among the different species. In fact, metabolic flux distributions were remarkably irresponsive to increasing temperatures in O. polymorpha, while the K. marxianus strains exhibited extensive flux rerouting at elevated temperatures. CONCLUSIONS While a clear mechanism of thermotolerance is not deducible from the fluxome level alone, the generated data can be valued as a knowledge repository for using temperature to modulate the metabolic activity towards engineering goals.
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Affiliation(s)
- Mathias Lehnen
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Birgitta E. Ebert
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Lars M. Blank
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
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de Andrade Silva CA, Oka ML, Fonseca GG. Physiology of yeast strains isolated from Brazilian biomes in a minimal medium using fructose as the sole carbon source reveals potential biotechnological applications. 3 Biotech 2019; 9:191. [PMID: 31065491 DOI: 10.1007/s13205-019-1721-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to evaluate the kinetic parameters and the production of metabolites of 13 novel yeasts isolated from a distillery and fruits, and Saccharomyces cerevisiae CAT-1, cultivated in fructose-based medium. The yeasts with the highest µ max were obtained from must, Pichia kudriavzevii BB2, P. kudriavzevii BB1, and S. cerevisiae BB9 (0.47-0.49 h-1). S. cerevisiae CAT-1 (3.02 g gDCM-1 h-1), S. cerevisiae BB9 (3.01 g gDCM-1 h-1), and Candida glabrata Recol 41 (2.52 g gDCM-1 h-1) stood out in terms of µ S. C. parapsilosis Recol 29, and Rhodotorula mucilaginosa Recol 03 strains showed the highest Y X/S (0.30 and 0.28 gDCM g-1, respectively). C. glabrata Recol 10 and S. cerevisiae BB9 strains stood out for their higher substrate conversion rates into ethanol (0.44 and 0.41 gEth gS-1, respectively). R. mucilaginosa Recol 03 presented the poorest performance in substrate consumption (0.87 g gDCM-1 h-1), while the strains isolated from must and C. glabrata Recol 10 showed the highest ethanol production and the C. parapsilosis Recol 29 showed the highest biomass conversion.
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McTaggart TL, Bever D, Bassett S, Da Silva NA. Synthesis of polyketides from low cost substrates by the thermotolerant yeast
Kluyveromyces marxianus. Biotechnol Bioeng 2019; 116:1721-1730. [DOI: 10.1002/bit.26976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/07/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Tami L. McTaggart
- Department of Chemical and Biomolecular Engineering University of California Irvine California
| | - Danielle Bever
- Department of Chemical and Biomolecular Engineering University of California Irvine California
| | - Shane Bassett
- Department of Chemical and Biomolecular Engineering University of California Irvine California
| | - Nancy A. Da Silva
- Department of Chemical and Biomolecular Engineering University of California Irvine California
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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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Converting Galactose into the Rare Sugar Talose with Cellobiose 2-Epimerase as Biocatalyst. Molecules 2018; 23:molecules23102519. [PMID: 30275414 PMCID: PMC6222537 DOI: 10.3390/molecules23102519] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 09/26/2018] [Accepted: 09/29/2018] [Indexed: 11/17/2022] Open
Abstract
Cellobiose 2-epimerase from Rhodothermus marinus (RmCE) reversibly converts a glucose residue to a mannose residue at the reducing end of β-1,4-linked oligosaccharides. In this study, the monosaccharide specificity of RmCE has been mapped and the synthesis of d-talose from d-galactose was discovered, a reaction not yet known to occur in nature. Moreover, the conversion is industrially relevant, as talose and its derivatives have been reported to possess important antimicrobial and anti-inflammatory properties. As the enzyme also catalyzes the keto-aldo isomerization of galactose to tagatose as a minor side reaction, the purity of talose was found to decrease over time. After process optimization, 23 g/L of talose could be obtained with a product purity of 86% and a yield of 8.5% (starting from 4 g (24 mmol) of galactose). However, higher purities and concentrations can be reached by decreasing and increasing the reaction time, respectively. In addition, two engineering attempts have also been performed. First, a mutant library of RmCE was created to try and increase the activity on monosaccharide substrates. Next, two residues from RmCE were introduced in the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) (S99M/Q371F), increasing the kcat twofold.
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Camargo JZ, Nascimento VM, Stefanello I, Andrade Silva CAD, Gonçalves FA, Perdomo IC, Vilela DM, Simionatto S, Pereira RM, da Paz MF, Leite RSR, Lafayette Neves Gelinski JM, Fonseca GG. Biochemical evaluation, molecular characterization and identification of novel yeast strains isolated from Brazilian savannah fruits, chicken litter and a sugar and alcohol mill with biotechnological potential for biofuel and food industries. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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da Silveira FA, Diniz RHS, Sampaio GMS, Brandão RL, da Silveira WB, Castro IM. Sugar transport systems in Kluyveromyces marxianus CCT 7735. Antonie van Leeuwenhoek 2018; 112:211-223. [DOI: 10.1007/s10482-018-1143-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/11/2018] [Indexed: 11/30/2022]
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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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34
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Varela JA, Montini N, Scully D, Van der Ploeg R, Oreb M, Boles E, Hirota J, Akada R, Hoshida H, Morrissey JP. Polymorphisms in the LAC12 gene explain lactose utilisation variability in Kluyveromyces marxianus strains. FEMS Yeast Res 2018; 17:3739724. [PMID: 28444380 DOI: 10.1093/femsyr/fox021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/16/2017] [Indexed: 01/29/2023] Open
Abstract
Kluyveromyces marxianus is a safe yeast used in the food and biotechnology sectors. One of the important traits that sets it apart from the familiar yeasts, Saccharomyces cerevisiae, is its capacity to grow using lactose as a carbon source. Like in its close relative, Kluyveromyces lactis, this requires lactose transport via a permease and intracellular hydrolysis of the disaccharide. Given the importance of the trait, it was intriguing that most, but not all, strains of K. marxianus are reported to consume lactose efficiently. In this study, primarily through heterologous expression in S. cerevisiae and K. marxianus, it was established that a single gene, LAC12, is responsible for lactose uptake in K. marxianus. Strains that failed to transport lactose showed variation in 13 amino acids in the Lac12p protein, rendering the protein non-functional for lactose transport. Genome analysis showed that the LAC12 gene is present in four copies in the subtelomeric regions of three different chromosomes but only the ancestral LAC12 gene encodes a functional lactose transporter. Other copies of LAC12 may be non-functional or have alternative substrates. The analysis raises some interesting questions regarding the evolution of sugar transporters in K. marxianus.
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Affiliation(s)
- Javier A Varela
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | - Noemi Montini
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | - Damhan Scully
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | | | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Junya Hirota
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan
| | - Rinji Akada
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan.,Biomedical Engineering Center, Yamaguchi University, Ube 755-8611, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan.,Biomedical Engineering Center, Yamaguchi University, Ube 755-8611, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan
| | - John P Morrissey
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
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Ortiz-Merino RA, Varela JA, Coughlan AY, Hoshida H, da Silveira WB, Wilde C, Kuijpers NGA, Geertman JM, Wolfe KH, Morrissey JP. Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates. Front Genet 2018; 9:94. [PMID: 29619042 PMCID: PMC5871668 DOI: 10.3389/fgene.2018.00094] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/05/2018] [Indexed: 11/20/2022] Open
Abstract
Kluyveromyces marxianus is traditionally associated with fermented dairy products, but can also be isolated from diverse non-dairy environments. Because of thermotolerance, rapid growth and other traits, many different strains are being developed for food and industrial applications but there is, as yet, little understanding of the genetic diversity or population genetics of this species. K. marxianus shows a high level of phenotypic variation but the only phenotype that has been clearly linked to a genetic polymorphism is lactose utilisation, which is controlled by variation in the LAC12 gene. The genomes of several strains have been sequenced in recent years and, in this study, we sequenced a further nine strains from different origins. Analysis of the Single Nucleotide Polymorphisms (SNPs) in 14 strains was carried out to examine genome structure and genetic diversity. SNP diversity in K. marxianus is relatively high, with up to 3% DNA sequence divergence between alleles. It was found that the isolates include haploid, diploid, and triploid strains, as shown by both SNP analysis and flow cytometry. Diploids and triploids contain long genomic tracts showing loss of heterozygosity (LOH). All six isolates from dairy environments were diploid or triploid, whereas 6 out 7 isolates from non-dairy environment were haploid. This also correlated with the presence of functional LAC12 alleles only in dairy haplotypes. The diploids were hybrids between a non-dairy and a dairy haplotype, whereas triploids included three copies of a dairy haplotype.
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Affiliation(s)
- Raúl A Ortiz-Merino
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Aisling Y Coughlan
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | | | | | | | | | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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Kluyveromyces marxianus, an Attractive Yeast for Ethanolic Fermentation in the Presence of Imidazolium Ionic Liquids. Int J Mol Sci 2018; 19:ijms19030887. [PMID: 29547579 PMCID: PMC5877748 DOI: 10.3390/ijms19030887] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/11/2018] [Accepted: 03/14/2018] [Indexed: 11/25/2022] Open
Abstract
Imidazolium ionic liquids (ILs) are promising solvents for lignocellulosic biomass (LCB) pretreatment and allow the achievement of higher ethanolic yields after enzymatic hydrolysis and ethanolic fermentation. However, residual ILs entrapped in pretreated biomass are often toxic for fermentative microorganisms, but interaction mechanisms between ILs and cells are still unknown. Here we studied the effects of 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO2] on Kluyveromyces marxianus, a thermotolerant ethanologenic yeast. Morphological impacts induced by ILs on K. marxianus were characterized by Scanning Electron Microscopy analysis and showed wrinkled, softened, and holed shapes. In Yeast-Malt-Dextrose (YMD) medium, K. marxianus tolerated IL additions up to 2% for [Emim][OAc] and 6% for [Emim][MeO(H)PO2]. Below these thresholds, some IL concentrations enhanced ethanolic yields up to +34% by switching the metabolic status from respiratory to fermentative. Finally, K. marxianus fermentation was applied on several substrates pretreated with [Emim][OAc] or [Emim][MeO(H)PO2] and enzymatically hydrolyzed: a model long fiber cellulose and two industrial LCBs, softwood (spruce) and hardwood (oak) sawdusts. The maximum ethanolic yields obtained were 1.8 to 3.9 times higher when substrates were pretreated with imidazolium ILs. Therefore K. marxianus is an interesting fermentative yeast in a second-generation bioethanol process implying IL pretreatment.
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İşleten Hoşoğlu M. STUDY OF INCREASING THE PRODUCTION OF VOLATILE FLAVOR COMPOUNDS BY THE YEAST Kluyveromyces marxianus THROUGH OPTIMIZATION OF CARBON AND NITROGEN SOURCES. ACTA ACUST UNITED AC 2018. [DOI: 10.3153/fh18011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Xylose transport in yeast for lignocellulosic ethanol production: Current status. J Biosci Bioeng 2017; 125:259-267. [PMID: 29196106 DOI: 10.1016/j.jbiosc.2017.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/07/2017] [Accepted: 10/10/2017] [Indexed: 01/07/2023]
Abstract
Lignocellulosic ethanol has been considered as an alternative transportation fuel. Utilization of hemicellulosic fraction in lignocelluloses is crucial in economical production of lignocellulosic ethanol. However, this fraction has not efficiently been utilized by traditional yeast Saccharomyces cerevisiae. Genetically modified S. cerevisiae, which can utilize xylose, has several limitations including low ethanol yield, redox imbalance, and undesired metabolite formation similar to native xylose utilizing yeasts. Besides, xylose uptake is a major issue, where sugar transport system plays an important role. These genetically modified and wild-type yeast strains have further been engineered for improved xylose uptake. Various techniques have been employed to facilitate the xylose transportation in these strains. The present review is focused on the sugar transport machineries, mechanisms of xylose transport, limitations and how to deal with xylose transport for xylose assimilation in yeast cells. The recent advances in different techniques to facilitate the xylose transportation have also been discussed.
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Evolutionary adaptation of Kluyveromyces marxianus strain for efficient conversion of whey lactose to bioethanol. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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40
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Beniwal A, Saini P, Kokkiligadda A, Vij S. Physiological growth and galactose utilization by dairy yeast Kluyveromyces marxianus in mixed sugars and whey during fermentation. 3 Biotech 2017; 7:349. [PMID: 28955646 DOI: 10.1007/s13205-017-0985-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/18/2017] [Indexed: 11/25/2022] Open
Abstract
The dairy yeast Kluyveromyces marxianus represents a promising industrial strain useful for the production of bioethanol from cheese whey. Physiology of the five K. marxianus strains on galactose was examined during batch cultivation under controlled aerobic conditions on minimal media and one of the strains designated K. marxianus strain 6C17 which presented the highest specific galactose consumption rate. A maximum specific growth rate of 0.34 and 0.37 h-1, respectively, was achieved using batch cultivation in a minimal medium and a complex medium amended with galactose (50 g/L) at 37 °C. The sugar was metabolized for the production of ethanol as the chief metabolite with a maximum ethanol yield of 0.39 g/g of galactose. Different growth behaviors were observed when galactose was used with other sugar such as glucose, lactose and fructose. The growth rates on hydrolyzed cheese whey were also measured, and a maximum specific growth rate of 0.39 and 0.32 h-1 was observed with glucose and galactose, respectively, with the maximum flux diverted toward ethanol production. This approach of studying the physiology of thermotolerant K. marxianus on hydrolyzed whey during fermentation would be helpful in achieving higher yields of ethanol.
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Affiliation(s)
- Arun Beniwal
- Dairy Microbiology Division, National Dairy Research Institute, Karnal, 132001 India
| | - Priyanka Saini
- Dairy Microbiology Division, National Dairy Research Institute, Karnal, 132001 India
| | - Anusha Kokkiligadda
- Dairy Microbiology Division, National Dairy Research Institute, Karnal, 132001 India
| | - Shilpa Vij
- Dairy Microbiology Division, National Dairy Research Institute, Karnal, 132001 India
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41
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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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Gombert AK, Madeira JV, Cerdán ME, González-Siso MI. Kluyveromyces marxianus as a host for heterologous protein synthesis. Appl Microbiol Biotechnol 2016; 100:6193-6208. [PMID: 27260286 DOI: 10.1007/s00253-016-7645-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/22/2016] [Accepted: 05/25/2016] [Indexed: 01/08/2023]
Abstract
The preferentially respiring and thermotolerant yeast Kluyveromyces marxianus is an emerging host for heterologous protein synthesis, surpassing the traditional preferentially fermenting yeast Saccharomyces cerevisiae in some important aspects: K . marxianus can grow at temperatures 10 °C higher than S. cerevisiae, which may result in decreased costs for cooling bioreactors and reduced contamination risk; has ability to metabolize a wider variety of sugars, such as lactose and xylose; is the fastest growing eukaryote described so far; and does not require special cultivation techniques (such as fed-batch) to avoid fermentative metabolism. All these advantages exist together with a high secretory capacity, performance of eukaryotic post-translational modifications, and with a generally regarded as safe (GRAS) status. In the last years, replication origins from several Kluyveromyces spp. have been used for the construction of episomal vectors, and also integrative strategies have been developed based on the tendency for non-homologous recombination displayed by K. marxianus. The recessive URA3 auxotrophic marker and the dominant Kan(R) are mostly used for selection of transformed cells, but other markers have been made available. Homologous and heterologous promoters and secretion signals have been characterized, with the K. marxianus INU1 expression and secretion system being of remarkable functionality. The efficient synthesis of roughly 50 heterologous proteins has been demonstrated, including one thermophilic enzyme. In this mini-review, we summarize the physiological characteristics of K. marxianus relevant for its use in the efficient synthesis of heterologous proteins, the efforts performed hitherto in the development of a molecular toolbox for this purpose, and some successful examples.
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Affiliation(s)
- Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, Campinas, SP, 13083-862, Brazil
| | - José Valdo Madeira
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, Campinas, SP, 13083-862, Brazil
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain.
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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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Gao J, Yuan W, Li Y, Xiang R, Hou S, Zhong S, Bai F. Transcriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:115. [PMID: 26273319 PMCID: PMC4535673 DOI: 10.1186/s13068-015-0295-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/24/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Ethanol production from non-crop materials, such as Jerusalem artichokes, would make a great contribution to the energy industry. The non-conventional yeast, Kluyveromyces marxianus, is able to carry out ethanol fermentation of sugar molecules obtained from inulin-containing materials by consolidated bioprocessing. Lower inulin concentrations and micro-aeration can lead to a relatively fast and ideal fermentation process; however, it is unclear what causes the inhibition of higher concentrations of inulin and the promotion effect of aeration. RESULTS Next-generation sequencing technology was used to study the global transcriptional response of K. marxianus Y179 under three fermentation conditions, including 120 g/L inulin without aeration (120-N), 230 g/L inulin without aeration (230-N), 230 g/L inulin with aeration by ORP controlling at -130 mV (230-130mV). A total of 35.55 million clean reads were generated from three samples, of which 4,820 predicted that open reading frames were annotated. For differential expression analysis, 950 and 1,452 differentially expressed genes were discovered under the conditions of 230-130mV and 120-N, respectively, and the sample 230-N was used as the control. These genes are mainly associated with the pathways of central carbon metabolism and ethanol formation. Increased expression of inulinase and the low activity of the autophagy-related gene, ATG8, ensured fast and ideal fermentation processes. CONCLUSIONS Despite being reported as the "crabtree-negative" species, K. marxianus Y179 could achieve favorable ethanol fermentation profiles under micro-aeration and high inulin concentrations. K. marxianus Y179 cells responded to inulin concentrations and micro-aeration that is involved in the whole ethanol metabolism network. These results will serve as an important foundation for further exploration of the regulatory mechanisms involved in ethanol fermentation from inulin by consolidated bioprocessing and also provide a valuable reference for future studies on optimization and reconstruction of the metabolism network in K. marxianus.
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Affiliation(s)
- Jiaoqi Gao
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Wenjie Yuan
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Yimin Li
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ruijuan Xiang
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Shengbo Hou
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Shijun Zhong
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Fengwu Bai
- />School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
- />School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
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Arbulu M, Sampedro MC, Gómez-Caballero A, Goicolea MA, Barrio RJ. Untargeted metabolomic analysis using liquid chromatography quadrupole time-of-flight mass spectrometry for non-volatile profiling of wines. Anal Chim Acta 2014; 858:32-41. [PMID: 25597799 DOI: 10.1016/j.aca.2014.12.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
Abstract
The current study presents a method for comprehensive untargeted metabolomic fingerprinting of the non-volatile profile of the Graciano Vitis vinifera wine variety, using liquid chromatography/electrospray ionization time of flight mass spectrometry (LC-ESI-QTOF). Pre-treatment of samples, chromatographic columns, mobile phases, elution gradients and ionization sources, were evaluated for the extraction of the maximum number of metabolites in red wine. Putative compounds were extracted from the raw data using the extraction algorithm, molecular feature extractor (MFE). For the metabolite identification the WinMet database was designed based on electronic databases and literature research and includes only the putative metabolites reported to be present in oenological matrices. The results from WinMet were compared with those in the METLIN database to evaluate how much the databases overlap for performing identifications. The reproducibility of the analysis was assessed using manual processing following replicate injections of Vitis vinifera cv. Graciano wine spiked with external standards. In the present work, 411 different metabolites in Graciano Vitis vinifera red wine were identified, including primary wine metabolites such as sugars (4%), amino acids (23%), biogenic amines (4%), fatty acids (2%), and organic acids (32%) and secondary metabolites such as phenols (27%) and esters (8%). Significant differences between varieties Tempranillo and Graciano were related to the presence of fifteen specific compounds.
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Affiliation(s)
- M Arbulu
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - M C Sampedro
- Central Service of Analysis, SGIker, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - A Gómez-Caballero
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - M A Goicolea
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - R J Barrio
- Department of Analytical Chemistry, Faculty of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain.
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Albuquerque TLD, da Silva IJ, de Macedo GR, Rocha MVP. Biotechnological production of xylitol from lignocellulosic wastes: A review. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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50
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Camargo D, Gomes SD, Sene L. Ethanol production from sunflower meal biomass by simultaneous saccharification and fermentation (SSF) with Kluyveromyces marxianus ATCC 36907. Bioprocess Biosyst Eng 2014; 37:2235-42. [PMID: 24794173 DOI: 10.1007/s00449-014-1201-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/15/2014] [Indexed: 10/25/2022]
Abstract
The lignocellulosic materials are considered promising renewable resources for ethanol production, but improvements in the processes should be studied to reduce operating costs. Thus, the appropriate enzyme loading for cellulose saccharification is critical for process economics. This study aimed at evaluating the concentration of cellulase and β-glucosidase in the production of bioethanol by simultaneous saccharification and fermentation (SSF) of sunflower meal biomass. The sunflower biomass was pretreated with 6% H2SO4 (w/v), at 121 °C, for 20 min, for hemicellulose removal and delignificated with 1% NaOH. SSF was performed with Kluyveromyces marxianus ATCC 36907, at 38 °C, 150 rpm, for 72 h, with different enzyme concentrations (Cellulase Complex NS22086-10, 15 and 20 FPU/gsubstrate and β-Glucosidase NS22118, with a cellulase to β-glucosidase ratio of 1.5:1; 2:1 and 3:1). The best condition for ethanol production was cellulase 20 FPU/gsubstrate and β-glucosidase 13.3 CBU/gsubstrate, resulting in 27.88 g/L ethanol, yield of 0.47 g/g and productivity of 0.38 g/L h. Under this condition the highest enzymatic conversion of cellulose to glucose was attained (87.06%).
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Affiliation(s)
- Danielle Camargo
- Post-Graduate Program in Agricultural Engineering, PGEAGRI, Center of Exact and Technological Sciences, Western Paraná State University, Rua Universitária, 2069, Cascavel-PR, Cascavel, Paraná, CEP 85819-110, Brazil,
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