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Choi B, Tafur Rangel A, Kerkhoven EJ, Nygård Y. Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass. Metab Eng 2024; 84:23-33. [PMID: 38788894 DOI: 10.1016/j.ymben.2024.05.003] [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: 02/16/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Metabolic engineering for high productivity and increased robustness is needed to enable sustainable biomanufacturing of lactic acid from lignocellulosic biomass. Lactic acid is an important commodity chemical used for instance as a monomer for production of polylactic acid, a biodegradable polymer. Here, rational and model-based optimization was used to engineer a diploid, xylose fermenting Saccharomyces cerevisiae strain to produce L-lactic acid. The metabolic flux was steered towards lactic acid through the introduction of multiple lactate dehydrogenase encoding genes while deleting ERF2, GPD1, and CYB2. A production of 93 g/L of lactic acid with a yield of 0.84 g/g was achieved using xylose as the carbon source. To increase xylose utilization and reduce acetic acid synthesis, PHO13 and ALD6 were also deleted from the strain. Finally, CDC19 encoding a pyruvate kinase was overexpressed, resulting in a yield of 0.75 g lactic acid/g sugars consumed, when the substrate used was a synthetic lignocellulosic hydrolysate medium, containing hexoses, pentoses and inhibitors such as acetate and furfural. Notably, modeling also provided leads for understanding the influence of oxygen in lactic acid production. High lactic acid production from xylose, at oxygen-limitation could be explained by a reduced flux through the oxidative phosphorylation pathway. On the contrast, higher oxygen levels were beneficial for lactic acid production with the synthetic hydrolysate medium, likely as higher ATP concentrations are needed for tolerating the inhibitors therein. The work highlights the potential of S. cerevisiae for industrial production of lactic acid from lignocellulosic biomass.
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Affiliation(s)
- Bohyun Choi
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Albert Tafur Rangel
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Eduard J Kerkhoven
- Department of Life Sciences, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
| | - Yvonne Nygård
- Department of Life Sciences, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden; VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
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2
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Jeong D, Park S, Evelina G, Kim S, Park H, Lee JM, Kim SK, Kim IJ, Oh EJ, Kim SR. Bioconversion of citrus waste into mucic acid by xylose-fermenting Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2024; 393:130158. [PMID: 38070579 DOI: 10.1016/j.biortech.2023.130158] [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: 09/22/2023] [Revised: 12/03/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024]
Abstract
Mucic acid holds promise as a platform chemical for bio-based nylon synthesis; however, its biological production encounters challenges including low yield and productivity. In this study, an efficient and high-yield method for mucic acid production was developed by employing genetically engineered Saccharomyces cerevisiae expressing the NAD+-dependent uronate dehydrogenase (udh) gene. To overcome the NAD+ dependency for the conversion of pectin to mucic acid, xylose was utilized as a co-substrate. Through optimization of the udh expression system, the engineered strain achieved a notable output, producing 20 g/L mucic acid with a highest reported productivity of 0.83 g/L-h and a theoretical yield of 0.18 g/g when processing pectin-containing citrus peel waste. These results suggest promising industrial applications for the biological production of mucic acid. Additionally, there is potential to establish a viable bioprocess by harnessing pectin-rich fruit waste alongside xylose-rich cellulosic biomass as raw materials.
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Affiliation(s)
- Deokyeol Jeong
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United State
| | - Sujeong Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Grace Evelina
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Suhyeung Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Heeyoung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
| | - In Jung Kim
- Department of Food Science & Technology, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United State.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea; Research Institute of Tailored Food Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
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3
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Hector RE, Mertens JA, Nichols NN. Metabolic engineering of a stable haploid strain derived from lignocellulosic inhibitor tolerant Saccharomyces cerevisiae natural isolate YB-2625. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:190. [PMID: 38057826 DOI: 10.1186/s13068-023-02442-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Significant genetic diversity exists across Saccharomyces strains. Natural isolates and domesticated brewery and industrial strains are typically more robust than laboratory strains when challenged with inhibitory lignocellulosic hydrolysates. These strains also contain genes that are not present in lab strains and likely contribute to their superior inhibitor tolerance. However, many of these strains have poor sporulation efficiencies and low spore viability making subsequent gene analysis, further metabolic engineering, and genomic analyses of the strains challenging. This work aimed to develop an inhibitor tolerant haploid with stable mating type from S. cerevisiae YB-2625, which was originally isolated from bagasse. RESULTS Haploid spores isolated from four tetrads from strain YB-2625 were tested for tolerance to furfural and HMF. Due to natural mutations present in the HO-endonuclease, all haploid strains maintained a stable mating type. One of the haploids, YRH1946, did not flocculate and showed enhanced tolerance to furfural and HMF. The tolerant haploid strain was further engineered for xylose fermentation by integration of the genes for xylose metabolism at two separate genomic locations (ho∆ and pho13∆). In fermentations supplemented with inhibitors from acid hydrolyzed corn stover, the engineered haploid strain derived from YB-2625 was able to ferment all of the glucose and 19% of the xylose, whereas the engineered lab strains performed poorly in fermentations. CONCLUSIONS Understanding the molecular mechanisms of inhibitor tolerance will aid in developing strains with improved growth and fermentation performance using biomass-derived sugars. The inhibitor tolerant, xylose fermenting, haploid strain described in this work has potential to serve as a platform strain for identifying pathways required for inhibitor tolerance, and for metabolic engineering to produce fuels and chemicals from undiluted lignocellulosic hydrolysates.
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Affiliation(s)
- Ronald E Hector
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA.
| | - Jeffrey A Mertens
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA
| | - Nancy N Nichols
- Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL, 61604, USA
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Vargas BDO, dos Santos JR, Pereira GAG, de Mello FDSB. An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae. PeerJ 2023; 11:e16340. [PMID: 38047029 PMCID: PMC10691383 DOI: 10.7717/peerj.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 12/05/2023] Open
Abstract
Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
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Affiliation(s)
- Beatriz de Oliveira Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jade Ribeiro dos Santos
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
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Liu L, Helal SE, Peng N. CRISPR-Cas-Based Engineering of Probiotics. BIODESIGN RESEARCH 2023; 5:0017. [PMID: 37849462 PMCID: PMC10541000 DOI: 10.34133/bdr.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Probiotics are the treasure of the microbiology fields. They have been widely used in the food industry, clinical treatment, and other fields. The equivocal health-promoting effects and the unknown action mechanism were the largest obstacles for further probiotic's developed applications. In recent years, various genome editing techniques have been developed and applied to explore the mechanisms and functional modifications of probiotics. As important genome editing tools, CRISPR-Cas systems that have opened new improvements in genome editing dedicated to probiotics. The high efficiency, flexibility, and specificity are the advantages of using CRISPR-Cas systems. Here, we summarize the classification and distribution of CRISPR-Cas systems in probiotics, as well as the editing tools developed on the basis of them. Then, we discuss the genome editing of probiotics based on CRISPR-Cas systems and the applications of the engineered probiotics through CRISPR-Cas systems. Finally, we proposed a design route for CRISPR systems that related to the genetically engineered probiotics.
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Affiliation(s)
- Ling Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, China
| | - Shimaa Elsayed Helal
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Kim SR, Cha M, Kim T, Song S, Kang HJ, Jung Y, Cho JY, Moh SH, Kim SJ. Sustainable Production of Shinorine from Lignocellulosic Biomass by Metabolically Engineered Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15848-15858. [PMID: 36475725 DOI: 10.1021/acs.jafc.2c07218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mycosporine-like amino acids (MAAs) have been used in cosmetics and pharmaceuticals. The purpose of this work was to develop yeast strains for sustainable and economical production of MAAs, especially shinorine. First, genes involved in MAA biosynthetic pathway from Actinosynnema mirum were introduced into Saccharomyces cerevisiae for heterologous shinorine production. Second, combinatorial expression of wild and mutant xylose reductase was adopted in the engineered S. cerevisiae to facilitate xylose utilization in the pentose phosphate pathway. Finally, the accumulation of sedoheptulose 7-phosphate (S7P) was attempted by deleting transaldolase-encoding TAL1 in the pentose phosphate pathway to increase carbon flux toward shinorine production. In fed-batch fermentation, the engineered strain (DXdT-M) produced 751 mg/L shinorine in 71 h. Ultimately, 54 mg/L MAAs was produced by DXdT-M from rice straw hydrolysate. The results suggest that shinorine production by S. cerevisiae might be a promising process for sustainable production and industrial applications.
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Affiliation(s)
- So-Rim Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Minseok Cha
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Taeok Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sihoon Song
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hye Jee Kang
- School of Food Science and Biotechnology and Institute of Fermentation Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Younghoon Jung
- School of Food Science and Biotechnology and Institute of Fermentation Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Yong Cho
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Food Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang Hyun Moh
- Bio-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Food Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
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7
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Identification of Mutations Responsible for Improved Xylose Utilization in an Adapted Xylose Isomerase Expressing Saccharomyces cerevisiae Strain. FERMENTATION 2022. [DOI: 10.3390/fermentation8120669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Economic conversion of biomass to biofuels and chemicals requires efficient and complete utilization of xylose. Saccharomyces cerevisiae strains engineered for xylose utilization are still considerably limited in their overall ability to metabolize xylose. In this study, we identified causative mutations resulting in improved xylose fermentation of an adapted S. cerevisiae strain expressing codon-optimized xylose isomerase and xylulokinase genes from the rumen bacterium Prevotella ruminicola. Genome sequencing identified single-nucleotide polymorphisms in seven open reading frames. Tetrad analysis showed that mutations in both PBS2 and PHO13 genes were required for increased xylose utilization. Single deletion of either PBS2 or PHO13 did not improve xylose utilization in strains expressing the xylose isomerase pathway. Saccharomyces can also be engineered for xylose metabolism using the xylose reductase/xylitol dehydrogenase genes from Scheffersomyces stipitis. In strains expressing the xylose reductase pathway, single deletion of PHO13 did show a significant increase xylose utilization, and further improvement in growth and fermentation was seen when PBS2 was also deleted. These findings will extend the understanding of metabolic limitations for xylose utilization in S. cerevisiae as well as understanding of how they differ among strains engineered with two different xylose utilization pathways.
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8
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Jin C, Kim S, Moon S, Jin H, Hahn JS. Efficient production of shinorine, a natural sunscreen material, from glucose and xylose by deleting HXK2 encoding hexokinase in Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6382129. [PMID: 34612490 DOI: 10.1093/femsyr/foab053] [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: 07/15/2021] [Accepted: 10/01/2021] [Indexed: 11/14/2022] Open
Abstract
Mycosporine-like amino acids (MAAs), microbial secondary metabolites with ultraviolet (UV) absorption properties, are promising natural sunscreen materials. Due to the low efficiency of extracting MAAs from natural producers, production in heterologous hosts has recently received attention. Shinorine is a well characterized MAA with strong UV-A absorption property. Previous, we developed Saccharomyces cerevisiae strain producing shinorine by introducing four shinorine biosynthetic genes from cyanobacterium Nostoc punctiforme. Shinorine is produced from sedoheptulose 7-phosphate (S7P), an intermediate in the pentose phosphate pathway. Shinorine production was greatly improved by using xylose as a co-substrate, which can increase the S7P pool. However, due to a limited xylose-utilizing capacity of the engineered strain, glucose was used as a co-substrate to support cell growth. In this study, we further improved shinorine production by attenuating glucose catabolism via glycolysis, which can redirect the carbon flux from glucose to the pentose phosphate pathway favoring shinorine production. Of the strategies we examined to reduce glycolytic flux, deletion of HXK2, encoding hexokinase, was most effective in increasing shinorine production. Furthermore, by additional expression of Ava3858 from Anabaena variabilis, encoding a rate-limiting enzyme 2-demethyl 4-deoxygadusol synthase, 68.4 mg/L of shinorine was produced in an optimized medium containing 14 g/L glucose and 6 g/L xylose, achieving a 2.2-fold increase compared with the previous strain.
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Affiliation(s)
- Chaeyeon Jin
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sojeong Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seokjun Moon
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyunbin Jin
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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9
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Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
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10
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Shin M, Park H, Kim S, Oh EJ, Jeong D, Florencia C, Kim KH, Jin YS, Kim SR. Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2021; 9:654177. [PMID: 33842449 PMCID: PMC8027353 DOI: 10.3389/fbioe.2021.654177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.
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Affiliation(s)
- Minhye Shin
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Heeyoung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Sooah Kim
- Department of Environment Science and Biotechnology, Jeonju University, Jeonju, South Korea
| | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN, United States
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Clarissa Florencia
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, South Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea
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11
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Sun L, Jin YS. Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae. Biotechnol J 2020; 16:e2000142. [PMID: 33135317 DOI: 10.1002/biot.202000142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/15/2020] [Indexed: 11/09/2022]
Abstract
Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.
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Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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12
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Enhanced 2′-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate. Metab Eng 2020; 62:322-329. [DOI: 10.1016/j.ymben.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
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13
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Shin M, Kim SR. Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae. Microorganisms 2020; 8:E1499. [PMID: 33003408 PMCID: PMC7599485 DOI: 10.3390/microorganisms8101499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/19/2022] Open
Abstract
Glucose repression has been extensively studied in Saccharomyces cerevisiae, including the regulatory systems responsible for efficient catabolism of glucose, the preferred carbon source. However, how these regulatory systems would alter central metabolism if new foreign pathways are introduced is unknown, and the regulatory networks between glycolysis and the pentose phosphate pathway, the two major pathways in central carbon metabolism, have not been systematically investigated. Here we disrupted gcr2, a key transcriptional regulator, in S. cerevisiae strain SR7 engineered to heterologously express the xylose-assimilating pathway, activating genes involved in glycolysis, and evaluated the global metabolic changes. gcr2 deletion reduced cellular growth in glucose but significantly increased growth when xylose was the sole carbon source. Global metabolite profiling revealed differential regulation of yeast metabolism in SR7-gcr2Δ, especially carbohydrate and nucleotide metabolism, depending on the carbon source. In glucose, the SR7-gcr2Δ mutant showed overall decreased abundance of metabolites, such as pyruvate and sedoheptulose-7-phosphate, associated with central carbon metabolism including glycolysis and the pentose phosphate pathway. However, SR7-gcr2Δ showed an increase in metabolites abundance (ribulose-5-phosphate, sedoheptulose-7-phosphate, and erythrose-4-phosphate) notably from the pentose phosphate pathway, as well as alteration in global metabolism when compared to SR7. These results provide insights into how the regulatory system GCR2 coordinates the transcription of glycolytic genes and associated metabolic pathways.
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Affiliation(s)
- Minhye Shin
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea;
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea
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14
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Sharma S, Arora A. Tracking strategic developments for conferring xylose utilization/fermentation by Saccharomyces cerevisiae. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01590-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Efficient ethanol production through lignocellulosic biomass hydrolysates could solve energy crisis as it is economically sustainable and ecofriendly. Saccharomyces cerevisiae is the work horse for lignocellulosic bioethanol production at industrial level. But its inability to ferment and utilize xylose limits the overall efficacy of the process.
Method
Data for the review was selected using different sources, such as Biofuels digest, Statista, International energy agency (IEA). Google scholar was used as a search engine to search literature for yeast metabolic engineering approaches. Keywords used were metabolic engineering of yeast for bioethanol production from lignocellulosic biomass.
Result
Through these approaches, interconnected pathways can be targeted randomly. Moreover, the improved strains genetic makeup can help us understand the mechanisms involved for this purpose.
Conclusion
This review discusses all possible approaches for metabolic engineering of yeast. These approaches may reveal unknown hidden mechanisms and construct ways for the researchers to produce novel and modified strains.
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15
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Jeong D, Oh EJ, Ko JK, Nam JO, Park HS, Jin YS, Lee EJ, Kim SR. Metabolic engineering considerations for the heterologous expression of xylose-catabolic pathways in Saccharomyces cerevisiae. PLoS One 2020; 15:e0236294. [PMID: 32716960 PMCID: PMC7384654 DOI: 10.1371/journal.pone.0236294] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Xylose, the second most abundant sugar in lignocellulosic biomass hydrolysates, can be fermented by Saccharomyces cerevisiae expressing one of two heterologous xylose pathways: a xylose oxidoreductase pathway and a xylose isomerase pathway. Depending on the type of the pathway, its optimization strategies and the fermentation efficiencies vary significantly. In the present study, we constructed two isogenic strains expressing either the oxidoreductase pathway (XYL123) or the isomerase pathway (XI-XYL3), and delved into simple and reproducible ways to improve the resulting strains. First, the strains were subjected to the deletion of PHO13, overexpression of TAL1, and adaptive evolution, but those individual approaches were only effective in the XYL123 strain but not in the XI-XYL3 strain. Among other optimization strategies of the XI-XYL3 strain, we found that increasing the copy number of the xylose isomerase gene (xylA) is the most promising but yet preliminary strategy for the improvement. These results suggest that the oxidoreductase pathway might provide a simpler metabolic engineering strategy than the isomerase pathway for the development of efficient xylose-fermenting strains under the conditions tested in the present study.
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Affiliation(s)
- Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Ju-Ock Nam
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical Engineering, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
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16
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Combining Xylose Reductase from Spathaspora arborariae with Xylitol Dehydrogenase from Spathaspora passalidarum to Promote Xylose Consumption and Fermentation into Xylitol by Saccharomyces cerevisiae. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6030072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In recent years, many novel xylose-fermenting yeasts belonging to the new genus Spathaspora have been isolated from the gut of wood-feeding insects and/or wood-decaying substrates. We have cloned and expressed, in Saccharomyces cerevisiae, a Spathaspora arborariae xylose reductase gene (SaXYL1) that accepts both NADH and NADPH as co-substrates, as well as a Spathaspora passalidarum NADPH-dependent xylose reductase (SpXYL1.1 gene) and the SpXYL2.2 gene encoding for a NAD+-dependent xylitol dehydrogenase. These enzymes were co-expressed in a S. cerevisiae strain over-expressing the native XKS1 gene encoding xylulokinase, as well as being deleted in the alkaline phosphatase encoded by the PHO13 gene. The S. cerevisiae strains expressing the Spathaspora enzymes consumed xylose, and xylitol was the major fermentation product. Higher specific growth rates, xylose consumption and xylitol volumetric productivities were obtained by the co-expression of the SaXYL1 and SpXYL2.2 genes, when compared with the co-expression of the NADPH-dependent SpXYL1.1 xylose reductase. During glucose-xylose co-fermentation by the strain with co-expression of the SaXYL1 and SpXYL2.2 genes, both ethanol and xylitol were produced efficiently. Our results open up the possibility of using the advantageous Saccharomyces yeasts for xylitol production, a commodity with wide commercial applications in pharmaceuticals, nutraceuticals, food and beverage industries.
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17
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Jeong D, Ye S, Park H, Kim SR. Data for simultaneous fermentation of galacturonic acid and five-carbon sugars by engineered Saccharomyces cerevisiae. Data Brief 2020; 29:105359. [PMID: 32195298 PMCID: PMC7078300 DOI: 10.1016/j.dib.2020.105359] [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: 01/15/2020] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces cerevisiae expressing heterologous pathways for xylose, arabinose, and galacturonic acid metabolism has been constructed by a Cas9-based genome editing technology [1]. The fermentation performance of the final strain (YE9) was tested under various substrate conditions, and the fermentation parameters were calculated. The dataset can be used for designing bioprocesses for pectin-rich biomass.
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Affiliation(s)
- Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, South Korea
| | - Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, South Korea
| | - Heeyoung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, South Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, South Korea
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18
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Sukwong P, Sunwoo IY, Jeong DY, Kim SR, Jeong GT, Kim SK. Improvement of bioethanol production by Saccharomyces cerevisiae through the deletion of GLK1, MIG1 and MIG2 and overexpression of PGM2 using the red seaweed Gracilaria verrucosa. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Jeong D, Ye S, Park H, Kim SR. Simultaneous fermentation of galacturonic acid and five-carbon sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2020; 295:122259. [PMID: 31639627 DOI: 10.1016/j.biortech.2019.122259] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Pectin-rich biomass has garnered attention as an alternative biomass source. However, some monomers derived from pectin-rich biomass, namely d-galacturonic acid, l-arabinose, and d-xylose, are not fermentable by industrial microorganisms such as Saccharomyces cerevisiae. The purpose of this study is to develop a S. cerevisiae strain capable of fermenting the pectin monomers. Expressions of eight heterologous genes and deletion of two endogenous genes, all of which were successfully completed by Cas9-based in vivo assembly and integration strategy, allowed the consumption of pectin monomers as sole carbon sources. To facilitate the consumption of galacturonic acid, which had the most limitations, the use of a co-substrate was tested using various sugars. As a result, we found that arabinose and xylose allowed simultaneous consumption of galacturonic acid. Based on intracellular metabolite profiling, it was concluded that the five-carbon sugars partially resolve the metabolic bottleneck of galacturonic acid.
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Affiliation(s)
- Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, South Korea
| | - Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, South Korea
| | - Heeyoung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, South Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, South Korea.
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20
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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21
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Ye S, Jeong D, Shon JC, Liu KH, Kim KH, Shin M, Kim SR. Deletion of PHO13 improves aerobic L-arabinose fermentation in engineered Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:1725-1731. [PMID: 31501960 DOI: 10.1007/s10295-019-02233-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/31/2019] [Indexed: 10/26/2022]
Abstract
Pentose sugars are increasingly being used in industrial applications of Saccharomyces cerevisiae. Although L-arabinose is a highlighted pentose that has been identified as next-generation biomass, arabinose fermentation has not yet undergone extensive development for industrial utilization. In this study, we integrated a heterologous fungal arabinose pathway with a deletion of PHO13 phosphatase gene. PHO13 deletion increased arabinose consumption rate and specific ethanol productivity under aerobic conditions and consequently depleted sedoheptulose by activation of the TAL1 gene. Global metabolite profiling indicated upregulation of the pentose phosphate pathway and downstream effects such as trehalose accumulation and downregulation of the TCA cycle. Our results suggest that engineering of PHO13 has ample potential for arabinose conversion to ethanol as an industrial source for biofuels.
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Affiliation(s)
- Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Jong Cheol Shon
- Department of Environmental Toxicology Research Center, Korea Institute of Toxicology, Jinju, Republic of Korea.,College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kwang-Hyeon Liu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea.
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22
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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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23
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Turner TL, Lane S, Jayakody LN, Zhang GC, Kim H, Cho W, Jin YS. Deletion of JEN1 and ADY2 reduces lactic acid yield from an engineered Saccharomyces cerevisiae, in xylose medium, expressing a heterologous lactate dehydrogenase. FEMS Yeast Res 2019; 19:5556531. [DOI: 10.1093/femsyr/foz050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/27/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Microorganisms have evolved to produce specific end products for many reasons, including maintaining redox balance between NAD+ and NADH. The yeast Saccharomyces cerevisiae, for example, produces ethanol as a primary end product from glucose for the regeneration of NAD+. Engineered S. cerevisiae strains have been developed to ferment lignocellulosic sugars, such as xylose, to produce lactic acid by expression of a heterologous lactate dehydrogenase (ldhA from Rhizopus oryzae) without genetic perturbation to the native ethanol pathway. Surprisingly, the engineered yeast strains predominantly produce ethanol from glucose, but produce lactic acid as the major product from xylose. Here, we provide initial evidence that the shift in product formation from ethanol to lactic acid during xylose fermentation is at least partially dependent on the presence of functioning monocarboxylate transporter genes/proteins, including JEN1 and ADY2, which are downregulated and unstable in the presence of glucose, but upregulated/stable on xylose. Future yeast metabolic engineering studies may find the feedstock/carbon selection, such as xylose, an important step toward improving the yield of target end products.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Lane
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lahiru N Jayakody
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Whiyeon Cho
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, 260 Bevier Hall, 905 South Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Metabolite Repair Enzymes Control Metabolic Damage in Glycolysis. Trends Biochem Sci 2019; 45:228-243. [PMID: 31473074 DOI: 10.1016/j.tibs.2019.07.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/19/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022]
Abstract
Hundreds of metabolic enzymes work together smoothly in a cell. These enzymes are highly specific. Nevertheless, under physiological conditions, many perform side-reactions at low rates, producing potentially toxic side-products. An increasing number of metabolite repair enzymes are being discovered that serve to eliminate these noncanonical metabolites. Some of these enzymes are extraordinarily conserved, and their deficiency can lead to diseases in humans or embryonic lethality in mice, indicating their central role in cellular metabolism. We discuss how metabolite repair enzymes eliminate glycolytic side-products and prevent negative interference within and beyond this core metabolic pathway. Extrapolating from the number of metabolite repair enzymes involved in glycolysis, hundreds more likely remain to be discovered that protect a wide range of metabolic pathways.
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25
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Frasse PM, Odom John AR. Haloacid Dehalogenase Proteins: Novel Mediators of Metabolic Plasticity in Plasmodium falciparum. Microbiol Insights 2019; 12:1178636119848435. [PMID: 31205418 PMCID: PMC6537242 DOI: 10.1177/1178636119848435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/09/2019] [Indexed: 11/17/2022] Open
Abstract
Widespread antimalarial drug resistance has prompted the need for new therapeutics and greater understanding of malaria parasite biology. To this end, the isoprenoid biosynthesis inhibitor fosmidomycin has been used to probe the metabolic regulation in the malaria parasite, Plasmodium falciparum. Genetic changes in the haloacid dehalogenase (HAD) superfamily member HAD2 conferred resistance to fosmidomycin, at the cost of decreased fitness. In the absence of fosmidomycin, parasites gained mutations to phosphofructokinase that restored growth and fosmidomycin sensitivity, thus revealing an intriguing example of plasticity in a core glycolytic process. Moreover, this study marks a second report of a HAD superfamily protein-modulating metabolic homeostasis in P falciparum parasites. Haloacid dehalogenase enzymes are distributed across all domains of life and have increasingly been found to influence central carbon metabolism and drug sensitivity in P falciparum. Investigating the mechanisms by which HAD superfamily members modulate metabolism may shed light on how metabolic networks are connected in apicomplexan parasites and other organisms and may guide future therapeutic endeavors.
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Affiliation(s)
- Philip M Frasse
- Department of Pediatrics,
Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey R Odom John
- Department of Pediatrics,
Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular
Microbiology, Washington University School of Medicine, St. Louis, MO,
USA
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26
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Sukwong P, Sunwoo IY, Jeong DY, Kim SR, Jeong GT, Kim SK. Enhancement of bioethanol production from Gracilaria verrucosa by Saccharomyces cerevisiae through the overexpression of SNR84 and PGM2. Bioprocess Biosyst Eng 2019; 42:1421-1433. [PMID: 31055665 DOI: 10.1007/s00449-019-02139-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 04/26/2019] [Indexed: 12/13/2022]
Abstract
A total monosaccharide concentration of 47.0 g/L from 12% (w/v) Gracilaria verrucosa was obtained by hyper thermal acid hydrolysis with 0.2 M HCl at 140°C for 15 min and enzymatic saccharification with CTec2. To improve galactose utilization, we overexpressed two genes, SNR84 and PGM2, in a Saccharomyces cerevisiae CEN-PK2 using CRISPR/Cas-9. The overexpression of both SNR84 and PGM2 improved galactose utilization and ethanol production compared to the overexpression of each gene alone. The overexpression of both SNR84 and PGM2 and of PGM2 and SNR84 singly in S. cerevisiae CEN-PK2 Cas9 produced 20.0, 18.5, and 16.5 g/L ethanol with ethanol yield (YEtOH) values of 0.43, 0.39, and 0.35, respectively. However, S. cerevisiae CEN-PK2 adapted to high concentration of galactose consumed galactose completely and produced 22.0 g/L ethanol at a YEtOH value of 0.47. The overexpression of both SNR84 and PGM2 increased the transcriptional levels of GAL and regulatory genes; however, the transcriptional levels of these genes were lower than those in S. cerevisiae adapted to high galactose concentrations.
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Affiliation(s)
- Pailin Sukwong
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - In Yung Sunwoo
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Deok Yeol Jeong
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu, 37224, South Korea
| | - Soo Rin Kim
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu, 37224, South Korea
| | - Gwi-Taek Jeong
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Sung-Koo Kim
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea.
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27
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Sunwoo IY, Sukwong P, Jeong DY, Kim SR, Jeong GT, Kim SK. Enhancement of galactose consumption rate in Saccharomyces cerevisiae CEN.PK2-1 by CRISPR Cas9 and adaptive evolution for fermentation of Kappaphycus alvarezii hydrolysate. J Biotechnol 2019; 297:78-84. [DOI: 10.1016/j.jbiotec.2019.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 10/27/2022]
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28
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Shin M, Kim JW, Ye S, Kim S, Jeong D, Lee DY, Kim JN, Jin YS, Kim KH, Kim SR. Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis. Appl Microbiol Biotechnol 2019; 103:5435-5446. [PMID: 31001747 DOI: 10.1007/s00253-019-09829-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/18/2019] [Accepted: 04/04/2019] [Indexed: 01/22/2023]
Abstract
Bioconversion of lignocellulosic biomass into ethanol requires efficient xylose fermentation. Previously, we developed an engineered Saccharomyces cerevisiae strain, named SR8, through rational and inverse metabolic engineering strategies, thereby improving its xylose fermentation and ethanol production. However, its fermentation characteristics have not yet been fully evaluated. In this study, we investigated the xylose fermentation and metabolic profiles for ethanol production in the SR8 strain compared with native Scheffersomyces stipitis. The SR8 strain showed a higher maximum ethanol titer and xylose consumption rate when cultured with a high concentration of xylose, mixed sugars, and under anaerobic conditions than Sch. stipitis. However, its ethanol productivity was less on 40 g/L xylose as the sole carbon source, mainly due to the formation of xylitol and glycerol. Global metabolite profiling indicated different intracellular production rates of xylulose and glycerol-3-phosphate in the two strains. In addition, compared with Sch. stipitis, SR8 had increased abundances of metabolites from sugar metabolism and decreased abundances of metabolites from energy metabolism and free fatty acids. These results provide insights into how to control and balance redox cofactors for the production of fuels and chemicals from xylose by the engineered S. cerevisiae.
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Affiliation(s)
- Minhye Shin
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Jeong-Won Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Suji Ye
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea
| | - Do Yup Lee
- Department of Bio and Fermentation Convergence Technology, BK21 PLUS Program, Kookmin University, Seoul, Korea
| | - Jong Nam Kim
- Department of Food Science and Nutrition, Dongseo University, Busan, Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, the University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Korea.
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29
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Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLoS Genet 2019; 15:e1008037. [PMID: 30856163 PMCID: PMC6428351 DOI: 10.1371/journal.pgen.1008037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/21/2019] [Accepted: 02/20/2019] [Indexed: 01/08/2023] Open
Abstract
Microbes can be metabolically engineered to produce biofuels and biochemicals, but rerouting metabolic flux toward products is a major hurdle without a systems-level understanding of how cellular flux is controlled. To understand flux rerouting, we investigated a panel of Saccharomyces cerevisiae strains with progressive improvements in anaerobic fermentation of xylose, a sugar abundant in sustainable plant biomass used for biofuel production. We combined comparative transcriptomics, proteomics, and phosphoproteomics with network analysis to understand the physiology of improved anaerobic xylose fermentation. Our results show that upstream regulatory changes produce a suite of physiological effects that collectively impact the phenotype. Evolved strains show an unusual co-activation of Protein Kinase A (PKA) and Snf1, thus combining responses seen during feast on glucose and famine on non-preferred sugars. Surprisingly, these regulatory changes were required to mount the hypoxic response when cells were grown on xylose, revealing a previously unknown connection between sugar source and anaerobic response. Network analysis identified several downstream transcription factors that play a significant, but on their own minor, role in anaerobic xylose fermentation, consistent with the combinatorial effects of small-impact changes. We also discovered that different routes of PKA activation produce distinct phenotypes: deletion of the RAS/PKA inhibitor IRA2 promotes xylose growth and metabolism, whereas deletion of PKA inhibitor BCY1 decouples growth from metabolism to enable robust fermentation without division. Comparing phosphoproteomic changes across ira2Δ and bcy1Δ strains implicated regulatory changes linked to xylose-dependent growth versus metabolism. Together, our results present a picture of the metabolic logic behind anaerobic xylose flux and suggest that widespread cellular remodeling, rather than individual metabolic changes, is an important goal for metabolic engineering.
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Affiliation(s)
- Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nicholas M. Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trey K. Sato
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Justin Heilberger
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Audrey P. Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, United States of America
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30
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Zhang MM, Xiong L, Tang YJ, Mehmood MA, Zhao ZK, Bai FW, Zhao XQ. Enhanced acetic acid stress tolerance and ethanol production in Saccharomyces cerevisiae by modulating expression of the de novo purine biosynthesis genes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:116. [PMID: 31168321 PMCID: PMC6509782 DOI: 10.1186/s13068-019-1456-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/02/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Yeast strains that are tolerant to multiple environmental stresses are highly desired for various industrial applications. Despite great efforts in identifying key genes involved in stress tolerance of budding yeast Saccharomyces cerevisiae, the effects of de novo purine biosynthesis genes on yeast stress tolerance are still not well explored. Our previous studies showed that zinc sulfate addition improved yeast acetic acid tolerance, and key genes involved in yeast stress tolerance were further investigated in this study. RESULTS Three genes involved in de novo purine biosynthesis, namely, ADE1, ADE13, and ADE17, showed significantly increased transcription levels by zinc sulfate supplementation under acetic acid stress, and overexpression of these genes in S. cerevisiae BY4741 enhanced cell growth under various stress conditions. Meanwhile, ethanol productivity was also improved by overexpression of the three ADE genes under stress conditions, among which the highest improvement attained 158.39% by ADE17 overexpression in the presence of inhibitor mixtures derived from lignocellulosic biomass. Elevated levels of adenine-nucleotide pool "AXP" ([ATP] + [ADP] + [AMP]) and ATP content were observed by overexpression of ADE17, both under control condition and under acetic acid stress, and is consistent with the better growth of the recombinant yeast strain. The global intracellular amino acid profiles were also changed by overexpression of the ADE genes. Among the changed amino acids, significant increase of the stress protectant γ-aminobutyric acid (GABA) was revealed by overexpression of the ADE genes under acetic acid stress, suggesting that overexpression of the ADE genes exerts control on both purine biosynthesis and amino acid biosynthesis to protect yeast cells against the stress. CONCLUSION We proved that the de novo purine biosynthesis genes are useful targets for metabolic engineering of yeast stress tolerance. The engineered strains developed in this study with improved tolerance against multiple inhibitors can be employed for efficient lignocellulosic biorefinery to produce biofuels and biochemicals.
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Affiliation(s)
- Ming-Ming Zhang
- State 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
| | - Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Muhammad Aamer Mehmood
- State 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
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, 38000 Pakistan
| | - Zongbao Kent Zhao
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Feng-Wu Bai
- State 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
| | - Xin-Qing Zhao
- State 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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31
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Cunha JT, Romaní A, Costa CE, Sá-Correia I, Domingues L. Molecular and physiological basis of Saccharomyces cerevisiae tolerance to adverse lignocellulose-based process conditions. Appl Microbiol Biotechnol 2018; 103:159-175. [PMID: 30397768 DOI: 10.1007/s00253-018-9478-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/27/2022]
Abstract
Lignocellulose-based biorefineries have been gaining increasing attention to substitute current petroleum-based refineries. Biomass processing requires a pretreatment step to break lignocellulosic biomass recalcitrant structure, which results in the release of a broad range of microbial inhibitors, mainly weak acids, furans, and phenolic compounds. Saccharomyces cerevisiae is the most commonly used organism for ethanol production; however, it can be severely distressed by these lignocellulose-derived inhibitors, in addition to other challenging conditions, such as pentose sugar utilization and the high temperatures required for an efficient simultaneous saccharification and fermentation step. Therefore, a better understanding of the yeast response and adaptation towards the presence of these multiple stresses is of crucial importance to design strategies to improve yeast robustness and bioconversion capacity from lignocellulosic biomass. This review includes an overview of the main inhibitors derived from diverse raw material resultants from different biomass pretreatments, and describes the main mechanisms of yeast response to their presence, as well as to the presence of stresses imposed by xylose utilization and high-temperature conditions, with a special emphasis on the synergistic effect of multiple inhibitors/stressors. Furthermore, successful cases of tolerance improvement of S. cerevisiae are highlighted, in particular those associated with other process-related physiologically relevant conditions. Decoding the overall yeast response mechanisms will pave the way for the integrated development of sustainable yeast cell-based biorefineries.
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Affiliation(s)
- Joana T Cunha
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Aloia Romaní
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Carlos E Costa
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), University of Minho, 4710-057, Braga, Portugal.
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32
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Kobayashi Y, Sahara T, Ohgiya S, Kamagata Y, Fujimori KE. Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae. AMB Express 2018; 8:139. [PMID: 30151682 PMCID: PMC6111014 DOI: 10.1186/s13568-018-0670-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/22/2018] [Indexed: 01/31/2023] Open
Abstract
The pentose phosphate pathway (PPP) plays an important role in the synthesis of ribonucleotides and aromatic amino acids. During bioethanol production from cellulosic biomass composed mainly of d-glucose and d-xylose, the PPP is also involved in xylose metabolism by engineered Saccharomyces cerevisiae. Although the activities and thermostabilities of the four PPP enzymes (transaldolase: TAL1, transketolase: TKL1, ribose-5-phosphate ketol-isomerase: RKI1 and d-ribulose-5-phosphate 3-epimerase: RPE1) can affect the efficiency of cellulosic ethanol production at high temperatures, little is known about the suitable expression levels of these PPP genes. Here, we overexpressed PPP genes from S. cerevisiae and the thermotolerant yeast Kluyveromyces marxianus either singly or in combination in recombinant yeast strains harboring a mutant of xylose isomerase (XI) and evaluated xylose consumption and ethanol production of these yeast transformants in glucose/xylose mixed media at 36 °C. Among the PPP genes examined, we found that: (1) strains that overexpressed S. cerevisiae TKL1 exhibited the highest rate of xylose consumption relative to strains that overexpressed other PPP genes alone; (2) overexpression of RKI1 and TAL1 derived from K. marxianus with S. cerevisiae TKL1 increased the xylose consumption rate by 1.87-fold at 24 h relative to the control strain (from 0.55 to 1.03 g/L/h); (3) the strains with XI showed higher ethanol yield than strains with xylose reductase and xylitol dehydrogenase and (4) PHO13 disruption did not improve xylose assimilation under the experimental conditions. Together these results indicated that optimization of PPP activity improves xylose metabolism in genetically engineered yeast strains, which could be useful for commercial production of ethanol from cellulosic material.
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33
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Kim H, Oh EJ, Lane ST, Lee WH, Cate JH, Jin YS. Enhanced cellobiose fermentation by engineered Saccharomyces cerevisiae expressing a mutant cellodextrin facilitator and cellobiose phosphorylase. J Biotechnol 2018; 275:53-59. [DOI: 10.1016/j.jbiotec.2018.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/28/2017] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
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34
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Lane S, Xu H, Oh EJ, Kim H, Lesmana A, Jeong D, Zhang G, Tsai CS, Jin YS, Kim SR. Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Sci Rep 2018; 8:2613. [PMID: 29422502 PMCID: PMC5805702 DOI: 10.1038/s41598-018-20804-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023] Open
Abstract
Microorganisms commonly exhibit preferential glucose consumption and diauxic growth when cultured in mixtures of glucose and other sugars. Although various genetic perturbations have alleviated the effects of glucose repression on consumption of specific sugars, a broadly applicable mechanism remains unknown. Here, we report that a reduction in the rate of glucose phosphorylation alleviates the effects of glucose repression in Saccharomyces cerevisiae. Through adaptive evolution under a mixture of xylose and the glucose analog 2-deoxyglucose, we isolated a mutant strain capable of simultaneously consuming glucose and xylose. Genome sequencing of the evolved mutant followed by CRISPR/Cas9-based reverse engineering revealed that mutations in the glucose phosphorylating enzymes (Hxk1, Hxk2, Glk1) were sufficient to confer simultaneous glucose and xylose utilization. We then found that varying hexokinase expression with an inducible promoter led to the simultaneous utilization of glucose and xylose. Interestingly, no mutations in sugar transporters occurred during the evolution, and no specific transporter played an indispensable role in simultaneous sugar utilization. Additionally, we demonstrated that slowing glucose consumption also enabled simultaneous utilization of glucose and galactose. These results suggest that the rate of intracellular glucose phosphorylation is a decisive factor for metabolic regulations of mixed sugars.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haiqing Xu
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eun Joong Oh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anastashia Lesmana
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Guochang Zhang
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ching-Sung Tsai
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea. .,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea.
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35
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Yun EJ, Oh EJ, Liu JJ, Yu S, Kim DH, Kwak S, Kim KH, Jin YS. Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:140. [PMID: 29785207 PMCID: PMC5950193 DOI: 10.1186/s13068-018-1135-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/28/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae. Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites. RESULTS Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively. CONCLUSIONS The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.
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Affiliation(s)
- Eun Ju Yun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Eun Joong Oh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Sora Yu
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Dong Hyun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Suryang Kwak
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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36
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Mert MJ, Rose SH, la Grange DC, Bamba T, Hasunuma T, Kondo A, van Zyl WH. Quantitative metabolomics of a xylose-utilizing Saccharomyces cerevisiae strain expressing the Bacteroides thetaiotaomicron xylose isomerase on glucose and xylose. J Ind Microbiol Biotechnol 2017; 44:1459-1470. [PMID: 28744577 DOI: 10.1007/s10295-017-1969-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/18/2017] [Indexed: 11/26/2022]
Abstract
The yeast Saccharomyces cerevisiae cannot utilize xylose, but the introduction of a xylose isomerase that functions well in yeast will help overcome the limitations of the fungal oxido-reductive pathway. In this study, a diploid S. cerevisiae S288c[2n YMX12] strain was constructed expressing the Bacteroides thetaiotaomicron xylA (XI) and the Scheffersomyces stipitis xyl3 (XK) and the changes in the metabolite pools monitored over time. Cultivation on xylose generally resulted in gradual changes in metabolite pool size over time, whereas more dramatic fluctuations were observed with cultivation on glucose due to the diauxic growth pattern. The low G6P and F1,6P levels observed with cultivation on xylose resulted in the incomplete activation of the Crabtree effect, whereas the high PEP levels is indicative of carbon starvation. The high UDP-D-glucose levels with cultivation on xylose indicated that the carbon was channeled toward biomass production. The adenylate and guanylate energy charges were tightly regulated by the cultures, while the catabolic and anabolic reduction charges fluctuated between metabolic states. This study helped elucidate the metabolite distribution that takes place under Crabtree-positive and Crabtree-negative conditions when cultivating S. cerevisiae on glucose and xylose, respectively.
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Affiliation(s)
- M J Mert
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - S H Rose
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - D C la Grange
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - T Bamba
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - T Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - A Kondo
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - W H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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37
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Suástegui M, Yu Ng C, Chowdhury A, Sun W, Cao M, House E, Maranas CD, Shao Z. Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Hou J, Qiu C, Shen Y, Li H, Bao X. Engineering of Saccharomyces cerevisiae for the efficient co-utilization of glucose and xylose. FEMS Yeast Res 2017; 17:3861258. [DOI: 10.1093/femsyr/fox034] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jin Hou
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Chenxi Qiu
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Hongxing Li
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, China
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39
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Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. ACTA ACUST UNITED AC 2017; 44:879-891. [DOI: 10.1007/s10295-017-1912-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
Abstract
Abstract
The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S. cerevisiae) at 30 °C and over-expression of all PPP genes at 36 °C resulted in the highest ethanol productivities. Furthermore, combinatorial over-expression of PPP genes derived from S. cerevisiae and a thermostable yeast Kluyveromyces marxianus allowed the strain to ferment xylose with ethanol productivity of 0.51 g/L/h, even at 38 °C. These results clearly demonstrate that xylose metabolism can be improved by the utilization of appropriate combinations of thermostable PPP genes in high-temperature production of ethanol.
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40
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Kwak S, Jin YS. Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 2017; 16:82. [PMID: 28494761 PMCID: PMC5425999 DOI: 10.1186/s12934-017-0694-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD+-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.
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Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol. Metab Eng 2017; 40:176-185. [DOI: 10.1016/j.ymben.2017.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 12/25/2022]
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Xia PF, Zhang GC, Walker B, Seo SO, Kwak S, Liu JJ, Kim H, Ort DR, Wang SG, Jin YS. Recycling Carbon Dioxide during Xylose Fermentation by Engineered Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:276-283. [PMID: 27744692 DOI: 10.1021/acssynbio.6b00167] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Global climate change caused by the emission of anthropogenic greenhouse gases (GHGs) is a grand challenge to humanity. To alleviate the trend, the consumption of fossil fuels needs to be largely reduced and alternative energy technologies capable of controlling GHG emissions are anticipated. In this study, we introduced a synthetic reductive pentose phosphate pathway (rPPP) into a xylose-fermenting Saccharomyces cerevisiae strain SR8 to achieve simultaneous lignocellulosic bioethanol production and carbon dioxide recycling. Specifically, ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and phosphoribulokinase from Spinacia oleracea were introduced into the SR8 strain. The resulting strain with the synthetic rPPP was able to exhibit a higher yield of ethanol and lower yields of byproducts (xylitol and glycerol) than a control strain. In addition, the reduced release of carbon dioxide by the engineered strain was observed during xylose fermentation, suggesting that the carbon dioxide generated by pyruvate decarboxylase was partially reassimilated through the synthetic rPPP. These results demonstrated that recycling of carbon dioxide from the ethanol fermentation pathway in yeast can be achieved during lignocellulosic bioethanol production through a synthetic carbon conservative metabolic pathway. This strategy has a great potential to alleviate GHG emissions during the production of second-generation ethanol.
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Affiliation(s)
- Peng-Fei Xia
- School
of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan 250100, People’s Republic of China
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Guo-Chang Zhang
- Department
of Food Science and Human Nutrition, University of Illinois at Urbana−Champaign, 905 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Berkley Walker
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Photosynthetic
Research Unit, United States Department of Agriculture, Urbana Illinois 61801, United States
| | - Seung-Oh Seo
- Department
of Food Science and Human Nutrition, University of Illinois at Urbana−Champaign, 905 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Suryang Kwak
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department
of Food Science and Human Nutrition, University of Illinois at Urbana−Champaign, 905 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Jing-Jing Liu
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Heejin Kim
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department
of Food Science and Human Nutrition, University of Illinois at Urbana−Champaign, 905 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Donald R. Ort
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Photosynthetic
Research Unit, United States Department of Agriculture, Urbana Illinois 61801, United States
- Department
of Plant Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shu-Guang Wang
- School
of Environmental Science and Engineering, Shandong University, 27 Shanda Nanlu, Jinan 250100, People’s Republic of China
| | - Yong-Su Jin
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department
of Food Science and Human Nutrition, University of Illinois at Urbana−Champaign, 905 South Goodwin Avenue, Urbana, Illinois 61801, United States
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Bommer GT, Baldin F, Van Schaftingen E. Accumulation of metabolic side products might favor the production of ethanol in Pho13 knockout strains. MICROBIAL CELL 2016; 3:495-499. [PMID: 28357317 PMCID: PMC5348983 DOI: 10.15698/mic2016.10.532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Guido T Bommer
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Laboratory of Physiological Chemistry, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Francesca Baldin
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Laboratory of Physiological Chemistry, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Emilie Van Schaftingen
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Laboratory of Physiological Chemistry, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
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45
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Suástegui M, Guo W, Feng X, Shao Z. Investigating strain dependency in the production of aromatic compounds in
Saccharomyces cerevisiae. Biotechnol Bioeng 2016; 113:2676-2685. [DOI: 10.1002/bit.26037] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/16/2016] [Accepted: 06/13/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Miguel Suástegui
- Department of Chemical and Biological EngineeringIowa State UniversityAmesIowa
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC)AmesIowa
| | - Weihua Guo
- Department of Biological Systems EngineeringVirginia Polytechnic Institute and State UniversityBlacksburgVirginia
| | - Xueyang Feng
- Department of Biological Systems EngineeringVirginia Polytechnic Institute and State UniversityBlacksburgVirginia
| | - Zengyi Shao
- Department of Chemical and Biological EngineeringIowa State UniversityAmesIowa
- NSF Engineering Research Center for Biorenewable Chemicals (CBiRC)AmesIowa
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46
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A conserved phosphatase destroys toxic glycolytic side products in mammals and yeast. Nat Chem Biol 2016; 12:601-7. [PMID: 27294321 DOI: 10.1038/nchembio.2104] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 03/28/2016] [Indexed: 11/08/2022]
Abstract
Metabolic enzymes are very specific. However, most of them show weak side activities toward compounds that are structurally related to their physiological substrates, thereby producing side products that may be toxic. In some cases, 'metabolite repair enzymes' eliminating side products have been identified. We show that mammalian glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase, two core glycolytic enzymes, produce 4-phosphoerythronate and 2-phospho-L-lactate, respectively. 4-Phosphoerythronate strongly inhibits an enzyme of the pentose phosphate pathway, whereas 2-phospho-L-lactate inhibits the enzyme producing the glycolytic activator fructose 2,6-bisphosphate. We discovered that a single, widely conserved enzyme, known as phosphoglycolate phosphatase (PGP) in mammals, dephosphorylates both 4-phosphoerythronate and 2-phospho-L-lactate, thereby preventing a block in the pentose phosphate pathway and glycolysis. Its yeast ortholog, Pho13, similarly dephosphorylates 4-phosphoerythronate and 2-phosphoglycolate, a side product of pyruvate kinase. Our work illustrates how metabolite repair enzymes can make up for the limited specificity of metabolic enzymes and permit high flux in central metabolic pathways.
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Xu H, Kim S, Sorek H, Lee Y, Jeong D, Kim J, Oh EJ, Yun EJ, Wemmer DE, Kim KH, Kim SR, Jin YS. PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metab Eng 2016; 34:88-96. [DOI: 10.1016/j.ymben.2015.12.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/30/2015] [Accepted: 12/17/2015] [Indexed: 11/28/2022]
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48
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Bamba T, Hasunuma T, Kondo A. Disruption of PHO13 improves ethanol production via the xylose isomerase pathway. AMB Express 2016; 6:4. [PMID: 26769491 PMCID: PMC4713403 DOI: 10.1186/s13568-015-0175-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/11/2015] [Indexed: 01/08/2023] Open
Abstract
Xylose is the second most abundant sugar in lignocellulosic materials and can be converted to ethanol by recombinant Saccharomyces cerevisiae yeast strains expressing heterologous genes involved in xylose assimilation pathways. Recent research demonstrated that disruption of the alkaline phosphatase gene, PHO13, enhances ethanol production from xylose by a strain expressing the xylose reductase (XR) and xylitol dehydrogenase (XDH) genes; however, the yield of ethanol is poor. In this study, PHO13 was disrupted in a recombinant strain harboring multiple copies of the xylose isomerase (XI) gene derived from Orpinomyces sp., coupled with overexpression of the endogenous xylulokinase (XK) gene and disruption of GRE3, which encodes aldose reductase. The resulting YΔGP/XK/XI strain consumed 2.08 g/L/h of xylose and produced 0.88 g/L/h of volumetric ethanol, for an 86.8 % theoretical ethanol yield, and only YΔGP/XK/XI demonstrated increase in cell concentration. Transcriptome analysis indicated that expression of genes involved in the pentose phosphate pathway (GND1, SOL3, TAL1, RKI1, and TKL1) and TCA cycle and respiratory chain (NDE1, ACO1, ACO2, SDH2, IDH1, IDH2, ATP7, ATP19, SDH4, SDH3, CMC2, and ATP15) was upregulated in the YΔGP/XK/XI strain. And the expression levels of 125 cell cycle genes were changed by deletion of PHO13.
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Comparison of xylose fermentation by two high-performance engineered strains of Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2016; 9:53-56. [PMID: 28352592 PMCID: PMC5360988 DOI: 10.1016/j.btre.2016.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/04/2016] [Accepted: 01/20/2016] [Indexed: 12/21/2022]
Abstract
Economical biofuel production from plant biomass requires the conversion of both cellulose and hemicellulose in the plant cell wall. The best industrial fermentation organism, the yeast Saccharomyces cerevisiae, has been developed to utilize xylose by heterologously expressing either a xylose reductase/xylitol dehydrogenase (XR/XDH) pathway or a xylose isomerase (XI) pathway. Although it has been proposed that the optimal means for fermenting xylose into biofuels would use XI instead of the XR/XDH pathway, no clear comparison of the best publicly-available yeast strains engineered to use XR/XDH or XI has been published. We therefore compared two of the best-performing engineered yeast strains in the public domain-one using the XR/XDH pathway and another using XI-in anaerobic xylose fermentations. We find that, regardless of conditions, the strain using XR/XDH has substantially higher productivity compared to the XI strain. By contrast, the XI strain has better yields in nearly all conditions tested.
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50
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Tsai CS, Kong II, Lesmana A, Million G, Zhang GC, Kim SR, Jin YS. Rapid and marker-free refactoring of xylose-fermenting yeast strains with Cas9/CRISPR. Biotechnol Bioeng 2015; 112:2406-11. [DOI: 10.1002/bit.25632] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/24/2015] [Accepted: 04/30/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Ching-Sung Tsai
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - In Iok Kong
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Anastashia Lesmana
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Gyver Million
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Guo-Chang Zhang
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Soo Rin Kim
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
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