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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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Fu Y, Xu R, Yang B, Wu Y, Xia L, Tawfik A, Meng F. Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal. Appl Environ Microbiol 2023; 89:e0070923. [PMID: 37404187 PMCID: PMC10370321 DOI: 10.1128/aem.00709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.
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Affiliation(s)
- Yue Fu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Boyi Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Yingxin Wu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Lichao Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, Dokki, Cairo, Egypt
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
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Hu ZY, Lin YP, Wang QT, Zhang YX, Tang J, Hong SD, Dai K, Wang S, Lu YZ, van Loosdrecht MCM, Wu J, Zeng RJ, Zhang F. Identification and degradation of structural extracellular polymeric substances in waste activated sludge via a polygalacturonate-degrading consortium. WATER RESEARCH 2023; 233:119800. [PMID: 36868117 DOI: 10.1016/j.watres.2023.119800] [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: 12/05/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
By maintaining the cell integrity of waste activated sludge (WAS), structural extracellular polymeric substances (St-EPS) resist WAS anaerobic fermentation. This study investigates the occurrence of polygalacturonate in WAS St-EPS by combining chemical and metagenomic analyses that identify ∼22% of the bacteria, including Ferruginibacter and Zoogloea, that are associated with polygalacturonate production using the key enzyme EC 5.1.3.6. A highly active polygalacturonate-degrading consortium (GDC) was enriched and the potential of this GDC for degrading St-EPS and promoting methane production from WAS was investigated. The percentage of St-EPS degradation increased from 47.6% to 85.2% after inoculation with the GDC. Methane production was also increased by up to 2.3 times over a control group, with WAS destruction increasing from 11.5% to 28.4%. Zeta potential and rheological behavior confirmed the positive effect which GDC has on WAS fermentation. The major genus in the GDC was identified as Clostridium (17.1%). Extracellular pectate lyases (EC 4.2.2.2 and 4.2.2.9), excluding polygalacturonase (EC 3.2.1.15), were observed in the metagenome of the GDC and most likely play a core role in St-EPS hydrolysis. Dosing with GDC provides a good biological method for St-EPS degradation and thereby enhances the conversion of WAS to methane.
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Affiliation(s)
- Zhi-Yi Hu
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Peng Lin
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qing-Ting Wang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Xin Zhang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Tang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Si-Di Hong
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kun Dai
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuai Wang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Ze Lu
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, the Netherlands
| | - Jianrong Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Raymond Jianxiong Zeng
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Fang Zhang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Mastella L, Senatore V, Beltrani T, Branduardi P. Scheffersomyces stipitis ability to valorize different residual biomasses for vitamin B 9 production. Microb Biotechnol 2022; 16:392-403. [PMID: 36527241 PMCID: PMC9871510 DOI: 10.1111/1751-7915.14177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
Sugar beet pulp (SBP), sugar beet molasses (SBM) and unfermented grape marcs (UGM) represent important waste in the agro-food sector. If suitably pre-treated, hexose and pentose sugars can be released in high quantities and can subsequently be used by appropriate cell factories as growth media and for the production of (complex) biomolecules, accomplishing the growing demand for products obtained from sustainable resources. One example is vitamin B9 or folate, a B-complex vitamin currently produced by chemical synthesis, almost exclusively in the oxidized form of folic acid (FA). It is therefore desirable to develop novel competitive strategies for replacing its current fossil-based production with a sustainable bio-based process. In this study, we assessed the production of natural folate by the yeast Scheffersomyces stipitis, investigating SBM, SBP and UGM as potential growth media. Pre-treatment of SBM and SBP had previously been optimized in our laboratory; thus, here we focused only on UGM pre-treatment and hydrolysis strategies for the release of fermentable sugars. Then, we optimized the growth of S. stipitis on the three media formulated from those biomasses, working on inoculum pre-adaptation, oxygen availability and supplementation of necessary nutrients to support the microorganism. Folate production, measured with a microbiological assay, reached 188.2 ± 24.86 μg/L on SBM, 130.6 ± 1.34 μg/L on SBP and 101.9 ± 6.62 μg/L on UGM. Here, we demonstrate the flexibility of S. stipitis in utilizing different residual biomasses as growth media. Moreover, we assessed the production of folate from waste, and to the best of our knowledge, we obtained the highest production of folate from residual biomasses ever reported, providing the first indications for the future development of this microbial production process.
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Affiliation(s)
- Luca Mastella
- Department of Biotechnology and BiosciencesUniversity of Milano BicoccaMilanItaly
| | - Vittorio Senatore
- Department of Biotechnology and BiosciencesUniversity of Milano BicoccaMilanItaly
| | - Tiziana Beltrani
- Laboratory for Resources Valorization (RISE), Department for SustainabilityENEA‐ Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRomeItaly
| | - Paola Branduardi
- Department of Biotechnology and BiosciencesUniversity of Milano BicoccaMilanItaly
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Peltonen KE, Richard P. Identification of a D-galacturonate reductase efficiently using NADH as a cofactor. BIOTECHNOLOGY REPORTS 2022; 35:e00744. [PMID: 35711324 PMCID: PMC9192788 DOI: 10.1016/j.btre.2022.e00744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
D-galacturonate reductase EC 1.1.1.365 uses NADH efficiently. Identification of the D-galacturonate reductase gene in Euglena gracilis. A useful tool for the engineering of a pathway for efficient fermentation of D-galacturonic acid.
D-galacturonate reductases are catalysing the reversible reduction of D-galacturonate to L-galactonate using NAD(P)H as a cofactor. The enzymes are part of two different pathways. One pathway is the fungal pathway for the catabolism of the main compound of pectin, D-galacturonate. The other pathway is a a pathway in plants for L-ascorbic acid synthesis. The previously described naturally occurring enzymes preferably use NADPH as a cofactor. Although certain D-galacturonate reductases, such as the reductases from Aspergillus niger or Euglena gracilis also accept NADH, their activity is significantly higher with NADPH. We identified in E. gracilis a gene, called gaa1, coding for a D-galacturonate reductase with similar activities with NADH and NADPH. It is potentially useful for the metabolic engineering of microbes to make use of pectin rich biomass.
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Yang P, Jiang S, Jiang S, Lu S, Zheng Z, Chen J, Wu W, Jiang S. CRISPR-Cas9 Approach Constructed Engineered Saccharomyces cerevisiae with the Deletion of GPD2, FPS1, and ADH2 to Enhance the Production of Ethanol. J Fungi (Basel) 2022; 8:jof8070703. [PMID: 35887459 PMCID: PMC9316504 DOI: 10.3390/jof8070703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023] Open
Abstract
Bioethanol plays an important value in renewable liquid fuel. The excessive accumulation of glycerol and organic acids caused the decrease of ethanol content in the process of industrial ethanol production. In this study, the CRISPR-Cas9 approach was used to construct S. cerevisiae engineering strains by the deletion of GPD2, FPS1, and ADH2 for the improvement of ethanol production. RNA sequencing and transcriptome analysis were used to investigate the effect of gene deletion on gene expression. The results indicated that engineered S. cerevisiae SCGFA by the simultaneous deletion of GPD2, FPS1, and ADH2 produced 23.1 g/L ethanol, which increased by 0.18% in comparison with the wild-type strain with 50 g/L of glucose as substrate. SCGFA strain exhibited the ethanol conversion rate of 0.462 g per g of glucose. In addition, the contents of glycerol, lactic acid, acetic acid, and succinic acid in SCGFA decreased by 22.7, 12.7, 8.1, 19.9, and 20.7% compared with the wild-type strain, respectively. The up-regulated gene enrichment showed glycolysis, fatty acid, and carbon metabolism could affect the ethanol production of SCGFA according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Therefore, the engineering strain SCGFA had great potential in the production of bioethanol.
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Affiliation(s)
- Peizhou Yang
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
- Correspondence: ; Tel.: +86-15155197790
| | - Shuying Jiang
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
| | - Suwei Jiang
- Department of Biological, Food and Environment Engineering, Hefei University, Hefei 230601, China;
| | - Shuhua Lu
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
| | - Zhi Zheng
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
| | - Jianchao Chen
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
| | - Wenjing Wu
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
| | - Shaotong Jiang
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, College of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China; (S.J.); (S.L.); (Z.Z.); (J.C.); (W.W.); (S.J.)
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:jof8070687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Correspondence:
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Identification of the Aldo-Keto Reductase Responsible for d-Galacturonic Acid Conversion to l-Galactonate in Saccharomyces cerevisiae. J Fungi (Basel) 2021; 7:jof7110914. [PMID: 34829203 PMCID: PMC8622349 DOI: 10.3390/jof7110914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/03/2022] Open
Abstract
d-galacturonic acid (d-GalUA) is the main constituent of pectin, a complex polysaccharide abundant in several agro-industrial by-products such as sugar beet pulp or citrus peel. During several attempts to valorise d-GalUA by engineering the popular cell factory Saccharomyces cerevisiae, it became obvious that d-GalUA is, to a certain degree, converted to l-galactonate (l-GalA) by an endogenous enzymatic activity. The goal of the current work was to clarify the identity of the responsible enzyme(s). A protein homology search identified three NADPH-dependent unspecific aldo-keto reductases in baker’s yeast (encoded by GCY1, YPR1 and GRE3) that show sequence similarities to known d-GalUA reductases from filamentous fungi. Characterization of the respective deletion mutants and an in vitro enzyme assay with a Gcy1 overproducing strain verified that Gcy1 is mainly responsible for the detectable reduction of d-GalUA to l-GalA.
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