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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] [MESH Headings] [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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Mining transcriptomic data to identify Saccharomyces cerevisiae signatures related to improved and repressed ethanol production under fermentation. PLoS One 2022; 17:e0259476. [PMID: 35881609 PMCID: PMC9321456 DOI: 10.1371/journal.pone.0259476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/12/2022] [Indexed: 11/19/2022] Open
Abstract
Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Underlying the dynamics of gene expression in S. cerevisiae in response to fermentation could provide informative results, required for the establishment of any ethanol production improvement program. Thus, representing a new approach, this study was conducted to identify the discriminative genes between improved and repressed ethanol production as well as clarifying the molecular responses to this process through mining the transcriptomic data. The significant differential expression probe sets were extracted from available microarray datasets related to yeast fermentation performance. To identify the most effective probe sets contributing to discriminate ethanol content, 11 machine learning algorithms from RapidMiner were employed. Further analysis including pathway enrichment and regulatory analysis were performed on discriminative probe sets. Besides, the decision tree models were constructed, the performance of each model was evaluated and the roots were identified. Based on the results, 171 probe sets were identified by at least 5 attribute weighting algorithms (AWAs) and 17 roots were recognized with 100% performance Some of the top ranked presets were found to be involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering validated the top-ranked selective probe sets. In addition, the top-ranked genes were validated based on GSE78759 and GSE5185 dataset. From all discriminative probe sets, OLI1 and CYC3 were identified as the roots with the best performance, demonstrated by the most weighting algorithms and linked to top two significant enriched pathways including porphyrin biosynthesis and oxidative phosphorylation. ADH5 and PDA1 were also recognized as differential top-ranked genes that contribute to ethanol production. According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes CYC3 and ADH5 genes. This study provides a basic understanding of the S. cerevisiae cell molecular mechanism and responses to two different medium conditions (Mg2+ and Cu2+) during the fermentation process.
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Wang Z, Ji X, Wang S, Wu Q, Xu Y. Sugar profile regulates the microbial metabolic diversity in Chinese Baijiu fermentation. Int J Food Microbiol 2021; 359:109426. [PMID: 34627066 DOI: 10.1016/j.ijfoodmicro.2021.109426] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
Cereals are widely used as raw material for food fermentation, and they can provide a variety of sugars in the fermentation via saccharification. However, the effect of sugar profile on microbial metabolism in spontaneous food fermentation is still unclear. Here, this work studied the regulation of sugar profile on the diversity of microbiota and their metabolism in Chinese Baijiu fermentation using sorghum as raw material. Six sugars were detected during Baijiu fermentation with 6 different cultivars of sorghum. The diversity of microbiota (ANOSIM: bacteria: P = 0.001, R = 0.77; fungi: P = 0.009, R = 0.33) and metabolites (ANOSIM: P = 0.001, R = 0.50) had different profiles during Baijiu fermentation. Among these sugars, glucose, fructose, and arabinose were identified as key sugars driving both the microbial and the metabolic diversity during Chinese Baijiu fermentation, and the metabolic diversity was positively correlated with the microbial diversity (P < 0.05). Hence, response surface methodology was used to establish a predictive model for regulating the metabolic diversity with the combination of three key sugars. The metabolic diversity significantly increased to 0.42 with the optimized levels of glucose (31.82 g/L), fructose (4.81 g/L), and arabinose (0.20 g/L), compared with unoptimized low-level average metabolic diversity (0.29). This work would provide a strategy to control microbial metabolism in spontaneous food fermentation, hence to improve the quality of fermented foods.
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Affiliation(s)
- Zheng Wang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xueao Ji
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shilei Wang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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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: 1.0] [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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Martins LC, Palma M, Angelov A, Nevoigt E, Liebl W, Sá-Correia I. Complete Utilization of the Major Carbon Sources Present in Sugar Beet Pulp Hydrolysates by the Oleaginous Red Yeasts Rhodotorula toruloides and R. mucilaginosa. J Fungi (Basel) 2021; 7:jof7030215. [PMID: 33802726 PMCID: PMC8002571 DOI: 10.3390/jof7030215] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Agro-industrial residues are low-cost carbon sources (C-sources) for microbial growth and production of value-added bioproducts. Among the agro-industrial residues available, those rich in pectin are generated in high amounts worldwide from the sugar industry or the industrial processing of fruits and vegetables. Sugar beet pulp (SBP) hydrolysates contain predominantly the neutral sugars d-glucose, l-arabinose and d-galactose, and the acidic sugar d-galacturonic acid. Acetic acid is also present at significant concentrations since the d-galacturonic acid residues are acetylated. In this study, we have examined and optimized the performance of a Rhodotorula mucilaginosa strain, isolated from SBP and identified at the molecular level during this work. This study was extended to another oleaginous red yeast species, R. toruloides, envisaging the full utilization of the C-sources from SBP hydrolysate (at pH 5.0). The dual role of acetic acid as a carbon and energy source and as a growth and metabolism inhibitor was examined. Acetic acid prevented the catabolism of d-galacturonic acid and l-arabinose after the complete use of the other C-sources. However, d-glucose and acetic acid were simultaneously and efficiently metabolized, followed by d-galactose. SBP hydrolysate supplementation with amino acids was crucial to allow d-galacturonic acid and l-arabinose catabolism. SBP valorization through the production of lipids and carotenoids by Rhodotorula strains, supported by complete catabolism of the major C-sources present, looks promising for industrial implementation.
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Affiliation(s)
- Luís C. Martins
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Margarida Palma
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Angel Angelov
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (A.A.); (W.L.)
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany;
| | - Wolfgang Liebl
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (A.A.); (W.L.)
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Correspondence:
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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Martins LC, Monteiro CC, Semedo PM, Sá-Correia I. Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges. Appl Microbiol Biotechnol 2020; 104:6527-6547. [PMID: 32474799 PMCID: PMC7347521 DOI: 10.1007/s00253-020-10697-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/19/2020] [Indexed: 01/29/2023]
Abstract
Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.
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Affiliation(s)
- Luís C Martins
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina C Monteiro
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Paula M Semedo
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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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: 4.0] [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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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: 0.2] [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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