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Chiarelli DP, Sharma BD, Hon S, Bergamo LW, Lynd LR, Olson DG. Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metab Eng Commun 2024; 19:e00243. [PMID: 39040142 PMCID: PMC11260334 DOI: 10.1016/j.mec.2024.e00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.
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Affiliation(s)
- Daniela Prates Chiarelli
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bishal Dev Sharma
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Luana Walravens Bergamo
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lee R. Lynd
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G. Olson
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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O'Connor SE. Reduction hits the sweet spot: A revised biosynthesis of dolichol. Cell 2024; 187:3502-3503. [PMID: 38996484 DOI: 10.1016/j.cell.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 07/14/2024]
Abstract
Dolichol is a lipid that is involved in protein glycosylation, a process that is essential for all eukaryotic life. In this issue of Cell, Wilson and coworkers1 report how a rare human genetic disorder led to the discovery of dolichol biosynthesis.
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Affiliation(s)
- Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
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3
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Poopanitpan N, Piampratom S, Viriyathanit P, Lertvatasilp T, Horiuchi H, Fukuda R, Kiatwuthinon P. SNF1 plays a crucial role in the utilization of n-alkane and transcriptional regulation of the genes involved in it in the yeast Yarrowia lipolytica. Heliyon 2024; 10:e32886. [PMID: 38975102 PMCID: PMC11226914 DOI: 10.1016/j.heliyon.2024.e32886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Yarrowia lipolytica is an ascomycetous yeast that can assimilate hydrophobic carbon sources including oil and n-alkane. The sucrose non-fermenting 1/AMP-activated protein kinase (Snf1/AMPK) complex is involved in the assimilation of non-fermentable carbon sources in various yeasts. However, the role of the Snf1/AMPK complex in n-alkane assimilation in Y. lipolytica has not yet been elucidated. This study aimed to clarify the role of Y. lipolytica SNF1 (YlSNF1) in the utilization of n-alkane. The deletion mutant of YlSNF1 (ΔYlsnf1) exhibited substantial growth defects on n-alkanes of various lengths (C10, C12, C14, and C16), and its growth was restored through the introduction of YlSNF1. Microscopic observations revealed that YlSnf1 tagged with enhanced green fluorescence protein showed dot-like distribution patterns in some cells cultured in the medium containing n-decane, which were not observed in cells cultured in the medium containing glucose or glycerol. The RNA sequencing analysis of ΔYlsnf1 cultured in the medium containing n-decane exhibited 302 downregulated and 131 upregulated genes compared with the wild-type strain cultured in the same medium. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that a significant fraction of the downregulated genes functioned in peroxisomes or were involved in the metabolism of n-alkane and fatty acids. Quantitative real-time PCR analysis confirmed the downregulation of 12 genes involved in the metabolism of n-alkane and fatty acid, ALK1-ALK3, ALK5, ADH7, PAT1, POT1, POX2, PEX3, PEX11, YAS1, and HFD3. Furthermore, ΔYlsnf1 exhibited growth defects on the medium containing the metabolites of n-alkane (fatty alcohol and fatty aldehyde). These findings suggest that YlSNF1 plays a crucial role in the utilization of n-alkane in Y. lipolytica. This study provides important insights into the advanced biotechnological applications of this yeast, including the bioconversion of n-alkane to useful chemicals and the bioremediation of petroleum-contaminated environments.
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Affiliation(s)
- Napapol Poopanitpan
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sorawit Piampratom
- Interdisciplinary Program in Genetic Engineering, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Patthanant Viriyathanit
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Threesara Lertvatasilp
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Pichamon Kiatwuthinon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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4
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Wang Z, Zhang Q, Zhang H, Lu Y. Roles of alcohol dehydrogenase 1 in the biological activities of Candida albicans. Crit Rev Microbiol 2024:1-15. [PMID: 38916139 DOI: 10.1080/1040841x.2024.2371510] [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: 11/17/2023] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
Candida albicans stands as the foremost prevalent human commensal pathogen and a significant contributor to nosocomial fungal infections. In the metabolism of C. albicans, alcohol dehydrogenase 1 (Adh1) is one of the important enzymes that converts acetaldehyde produced by pyruvate decarboxylation into ethanol at the end of glycolysis. Leveraging the foundational processes of alcoholic fermentation, Adh1 plays an active role in multiple biological phenomena, including biofilm formation, interactions between different species, the development of drug resistance, and the potential initiation of gastrointestinal cancer. Additionally, Adh1 within C. albicans has demonstrated associations with regulating the cell cycle, stress responses, and various intracellular states. Furthermore, Adh1 is extracellularly localized on the cell wall surface, where it plays roles in processes such as tissue invasion and host immune responses. Drawing from an analysis of ADH1 gene structure, expression patterns, and fundamental functions, this review elucidates the intricate connections between Adh1 and various biological processes within C. albicans, underscoring its potential implications for the prevention, diagnosis, and treatment of candidiasis.
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Affiliation(s)
- Ziqi Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qi Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Haoying Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Lu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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Pontes A, Paraíso F, Silva M, Lagoas C, Aires A, Brito PH, Rosa CA, Lachance MA, Sampaio JP, Gonçalves C, Gonçalves P. Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage. BMC Biol 2024; 22:128. [PMID: 38816863 PMCID: PMC11140947 DOI: 10.1186/s12915-024-01929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT). RESULTS Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway. CONCLUSIONS These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catarina Lagoas
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Andreia Aires
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- PYCC - Portuguese Yeast Culture Collection, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Patrícia H Brito
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- PYCC - Portuguese Yeast Culture Collection, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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Zhu H, He Y. Transcriptome Sequencing and Analysis of Trichoderma polysporum Infection in Avena fatua L. Leaves before and after Infection. J Fungi (Basel) 2024; 10:346. [PMID: 38786701 PMCID: PMC11121786 DOI: 10.3390/jof10050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Biological control is a scientific management method used in modern agricultural production, and microbially derived biopesticides are one effective method with which to control weeds in agricultural fields. In order to determine the key genes for weed control by Trichoderma polysporum, transcriptome sequencing was carried out by high-throughput sequencing technology, and the strains of T. polysporum HZ-31 infesting Avena fatua L. at 24, 48, and 72 h were used as the experimental group, with 0 h as the control group. A total of 690,713,176 clean reads were obtained, and the sequencing results for each experimental group and the control group (0 h) were analyzed. In total, 3464 differentially expressed genes were found after 24 h of infection with the pathogen, including 1283 down-regulated genes and 2181 up-regulated genes. After 48 h of infection, the number of differentially expressed genes was 3885, of which 2242 were up-regulated and 1643 were down-regulated. The number of differentially expressed genes after 72 h of infection was the highest among all the groups, with 4594 differentially expressed genes, of which 2648 were up-regulated and 1946 were down-regulated. The up-regulated genes were analyzed by GO and KEGG, and the results showed that the up-regulated differentially expressed genes were mainly enriched in the biosynthesis of phenylalanine, tyrosine, and tryptophan; the degradation of aromatic compounds; methane metabolism; and other pathways. Among them, the PHA2, GDH, ADH2, and AROF genes were significantly enriched in the above-mentioned pathways, so they were hypothesized to play an important role in the synthesis of the herbicidally active substances of T. polysporum HZ-31. The results of this study can provide a theoretical basis for further studies on the pathogenicity of T. polysporum to A. fatua L., and accelerate the development and utilization of new and efficient bioherbicides.
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Affiliation(s)
- Haixia Zhu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China;
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Agricultural Integrated Pest Management of Qinghai Province, Xining 810016, China
| | - Yushan He
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China;
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Agricultural Integrated Pest Management of Qinghai Province, Xining 810016, China
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7
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Muyanlı EB, Yılmaz R. RT-qPCR based quantitative analysis of ARO and ADH genes in Saccharomyces cerevisiae and Metschnikowia pulcherrima strains growth white grape juice. Mol Biol Rep 2024; 51:547. [PMID: 38642187 DOI: 10.1007/s11033-024-09444-2] [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: 02/09/2024] [Accepted: 03/13/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Yeast biosynthesizes fusel alcohols in fermentation through amino acid catabolism via the Ehrlich pathway. ARO8 and ARO9 genes are involved in the first step of the Ehrlich pathway, while ADH2 and ADH5 genes are involved in the last step. In this study, we describe RT-qPCR methods to determine the gene expression level of genes (ARO8, ARO9, ADH2, ADH5) found in Saccharomyces cerevisiae (Sc) and Metschnikowia pulcherrima (Mp) strains growth pasteurized white grape juice. METHODS AND RESULTS We used RNA extraction and cDNA synthesis protocols. The RT-qPCR efficiency of primer pairs was evaluated by generating a standard curve through serial dilution of yeast-derived cDNA. Method performance criteria were determined for each RT-qPCR assay. Then, we evaluated the gene expression levels of the four genes in all samples. RNA extraction and cDNA synthesis from yeast samples demonstrated the method's capability to generate high-yield, high-purity nucleic acids, supporting further RT-qPCR analysis. The highest normalized gene expression levels of ARO8 and ARO9 were observed in SC1, SC4, and SC5 samples. No significant difference in ADH2 gene expression among Mp strains was observed during the examination of ADH2 and ADH5 genes (p < 0.05). We observed no expression of the ADH5 gene in Mp strains except MP6 strain. The expression of ADH2 and ADH5 genes was higher in Sc strains compared to Mp strains. CONCLUSIONS The results suggest that the proposed RT-qPCR methods can measure gene expression of ARO8, ARO9, ADH2, and ADH5 in Sc and Mp strains growing in pasteurized white grape juice.
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Affiliation(s)
- Elif Bircan Muyanlı
- FoodOmics Laboratory, Department of Food Engineering, Hacettepe University, Beytepe Campus, 06800, Ankara, Turkey
| | - Remziye Yılmaz
- FoodOmics Laboratory, Department of Food Engineering, Hacettepe University, Beytepe Campus, 06800, Ankara, Turkey.
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8
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Zhu Z, Chen R, Zhang L. Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production. Nat Prod Rep 2024; 41:6-24. [PMID: 37807808 DOI: 10.1039/d3np00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
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Affiliation(s)
- Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China
- Innovative Drug R&D Centre, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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Geng K, Lin Y, Zheng X, Li C, Chen S, Ling H, Yang J, Zhu X, Liang S. Enhanced Expression of Alcohol Dehydrogenase I in Pichia pastoris Reduces the Content of Acetaldehyde in Wines. Microorganisms 2023; 12:38. [PMID: 38257867 PMCID: PMC10820543 DOI: 10.3390/microorganisms12010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Acetaldehyde is an important carbonyl compound commonly detected in wines. A high concentration of acetaldehyde can affect the flavor of wines and result in adverse effects on human health. Alcohol dehydrogenase I (ADH1) in Saccharomyces cerevisiae catalyzes the reduction reaction of acetaldehyde into ethanol in the presence of cofactors, showing the potential to reduce the content of acetaldehyde in wines. In this study, ADH1 was successfully expressed in Pichia pastoris GS115 based on codon optimization. Then, the expression level of ADH1 was enhanced by replacing its promoter with optimized promoters and increasing the copy number of the expression cassette, with ADH1 being purified using nickel column affinity chromatography. The enzymatic activity of purified ADH1 reached 605.44 ± 44.30 U/mg. The results of the effect of ADH1 on the content of acetaldehyde in wine revealed that the acetaldehyde content of wine samples was reduced from 168.05 ± 0.55 to 113.17 ± 6.08 mg/L with the addition of 5 mM NADH and the catalysis of ADH1, and from 135.53 ± 4.08 to 52.89 ± 2.20 mg/L through cofactor regeneration. Our study provides a novel approach to reducing the content of acetaldehyde in wines through enzymatic catalysis.
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Affiliation(s)
- Kun Geng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xueyun Zheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
- Key Laboratory of Fermentation Engineering of Ministry of Education, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shuting Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - He Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jun Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiangyu Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
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10
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van Aalst ACA, van der Meulen IS, Jansen MLA, Mans R, Pronk JT. Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield. Metab Eng 2023; 80:151-162. [PMID: 37751790 DOI: 10.1016/j.ymben.2023.09.010] [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: 06/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]
Abstract
Glycerol is the major organic byproduct of industrial ethanol production with the yeast Saccharomyces cerevisiae. Improved ethanol yields have been achieved with engineered S. cerevisiae strains in which heterologous pathways replace glycerol formation as the predominant mechanism for anaerobic re-oxidation of surplus NADH generated in biosynthetic reactions. Functional expression of heterologous phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes enables yeast cells to couple a net oxidation of NADH to the conversion of glucose to ethanol. In another strategy, NADH-dependent reduction of exogenous acetate to ethanol is enabled by introduction of a heterologous acetylating acetaldehyde dehydrogenase (A-ALD). This study explores potential advantages of co-cultivating engineered PRK-RuBisCO-based and A-ALD-based strains in anaerobic bioreactor batch cultures. Co-cultivation of these strains, which in monocultures showed reduced glycerol yields and improved ethanol yields, strongly reduced the formation of acetaldehyde and acetate, two byproducts that were formed in anaerobic monocultures of a PRK-RuBisCO-based strain. In addition, co-cultures on medium with low acetate-to-glucose ratios that mimicked those in industrial feedstocks completely removed acetate from the medium. Kinetics of co-cultivation processes and glycerol production could be optimized by tuning the relative inoculum sizes of the two strains. Co-cultivation of a PRK-RuBisCO strain with a Δgpd1 Δgpd2 A-ALD strain, which was unable to grow in the absence of acetate and evolved for faster anaerobic growth in acetate-supplemented batch cultures, further reduced glycerol formation but led to extended fermentation times. These results demonstrate the potential of using defined consortia of engineered S. cerevisiae strains for high-yield, minimal-waste ethanol production.
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Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Igor S van der Meulen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX, Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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11
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Willetts A. Bicyclo[3.2.0]carbocyclic Molecules and Redox Biotransformations: The Evolution of Closed-Loop Artificial Linear Biocatalytic Cascades and Related Redox-Neutral Systems. Molecules 2023; 28:7249. [PMID: 37959669 PMCID: PMC10649493 DOI: 10.3390/molecules28217249] [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: 08/22/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
The role of cofactor recycling in determining the efficiency of artificial biocatalytic cascades has become paramount in recent years. Closed-loop cofactor recycling, which initially emerged in the 1990s, has made a valuable contribution to the development of this aspect of biotechnology. However, the evolution of redox-neutral closed-loop cofactor recycling has a longer history that has been integrally linked to the enzymology of oxy-functionalised bicyclo[3.2.0]carbocyclic molecule metabolism throughout. This review traces that relevant history from the mid-1960s to current times.
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Affiliation(s)
- Andrew Willetts
- Curnow Consultancies Ltd., Trewithen House, Helston TR13 9PQ, Cornwall, UK
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12
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Khamwachirapithak P, Sae-Tang K, Mhuantong W, Tanapongpipat S, Zhao XQ, Liu CG, Wei DQ, Champreda V, Runguphan W. Optimizing Ethanol Production in Saccharomyces cerevisiae at Ambient and Elevated Temperatures through Machine Learning-Guided Combinatorial Promoter Modifications. ACS Synth Biol 2023; 12:2897-2908. [PMID: 37681736 PMCID: PMC10594650 DOI: 10.1021/acssynbio.3c00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 09/09/2023]
Abstract
Bioethanol has gained popularity in recent decades as an ecofriendly alternative to fossil fuels due to increasing concerns about global climate change. However, economically viable ethanol fermentation remains a challenge. High-temperature fermentation can reduce production costs, but Saccharomyces cerevisiae yeast strains normally ferment poorly under high temperatures. In this study, we present a machine learning (ML) approach to optimize bioethanol production in S. cerevisiae by fine-tuning the promoter activities of three endogenous genes. We created 216 combinatorial strains of S. cerevisiae by replacing native promoters with five promoters of varying strengths to regulate ethanol production. Promoter replacement resulted in a 63% improvement in ethanol production at 30 °C. We created an ML-guided workflow by utilizing XGBoost to train high-performance models based on promoter strengths and cellular metabolite concentrations obtained from ethanol production of 216 combinatorial strains at 30 °C. This strategy was then applied to optimize ethanol production at 40 °C, where we selected 31 strains for experimental fermentation. This reduced experimental load led to a 7.4% increase in ethanol production in the second round of the ML-guided workflow. Our study offers a comprehensive library of promoter strength modifications for key ethanol production enzymes, showcasing how machine learning can guide yeast strain optimization and make bioethanol production more cost-effective and efficient. Furthermore, we demonstrate that metabolic engineering processes can be accelerated and optimized through this approach.
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Affiliation(s)
- Peerapat Khamwachirapithak
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kittapong Sae-Tang
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sutipa Tanapongpipat
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - 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, People’s
Republic of China
| | - Chen-Guang Liu
- 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, People’s
Republic of China
| | - Dong-Qing Wei
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Verawat Champreda
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Weerawat Runguphan
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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13
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Rudzka A, Zdun B, Antos N, Montero LM, Reiter T, Kroutil W, Borowiecki P. Biocatalytic characterization of an alcohol dehydrogenase variant deduced from Lactobacillus kefir in asymmetric hydrogen transfer. Commun Chem 2023; 6:217. [PMID: 37828252 PMCID: PMC10570314 DOI: 10.1038/s42004-023-01013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Hydrogen transfer biocatalysts to prepare optically pure alcohols are in need, especially when it comes to sterically demanding ketones, whereof the bioreduced products are either essential precursors of pharmaceutically relevant compounds or constitute APIs themselves. In this study, we report on the biocatalytic potential of an anti-Prelog (R)-specific Lactobacillus kefir ADH variant (Lk-ADH-E145F-F147L-Y190C, named Lk-ADH Prince) employed as E. coli/ADH whole-cell biocatalyst and its characterization for stereoselective reduction of prochiral carbonyl substrates. Key enzymatic reaction parameters, including the reaction medium, evaluation of cofactor-dependency, organic co-solvent tolerance, and substrate loading, were determined employing the drug pentoxifylline as a model prochiral ketone. Furthermore, to tap the substrate scope of Lk-ADH Prince in hydrogen transfer reactions, a broad range of 34 carbonylic derivatives was screened. Our data demonstrate that E. coli/Lk-ADH Prince exhibits activity toward a variety of structurally different ketones, furnishing optically active alcohol products at the high conversion of 65-99.9% and in moderate-to-high isolated yields (38-91%) with excellent anti-Prelog (R)-stereoselectivity (up to >99% ee) at substrate concentrations up to 100 mM.
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Affiliation(s)
- Aleksandra Rudzka
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Beata Zdun
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Natalia Antos
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland
| | - Lia Martínez Montero
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Tamara Reiter
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstrasse 28, 8010, Graz, Austria
| | - Paweł Borowiecki
- Laboratory of Biocatalysis and Biotransformation, Department of Drugs Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-662, Warsaw, Poland.
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14
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Gutiérrez-Corona JF, González-Hernández GA, Padilla-Guerrero IE, Olmedo-Monfil V, Martínez-Rocha AL, Patiño-Medina JA, Meza-Carmen V, Torres-Guzmán JC. Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential. Cells 2023; 12:2239. [PMID: 37759461 PMCID: PMC10526403 DOI: 10.3390/cells12182239] [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: 06/30/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Fungal alcohol dehydrogenases (ADHs) participate in growth under aerobic or anaerobic conditions, morphogenetic processes, and pathogenesis of diverse fungal genera. These processes are associated with metabolic operation routes related to alcohol, aldehyde, and acid production. The number of ADH enzymes, their metabolic roles, and their functions vary within fungal species. The most studied ADHs are associated with ethanol metabolism, either as fermentative enzymes involved in the production of this alcohol or as oxidative enzymes necessary for the use of ethanol as a carbon source; other enzymes participate in survival under microaerobic conditions. The fast generation of data using genome sequencing provides an excellent opportunity to determine a correlation between the number of ADHs and fungal lifestyle. Therefore, this review aims to summarize the latest knowledge about the importance of ADH enzymes in the physiology and metabolism of fungal cells, as well as their structure, regulation, evolutionary relationships, and biotechnological potential.
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Affiliation(s)
- J. Félix Gutiérrez-Corona
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Gloria Angélica González-Hernández
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Israel Enrique Padilla-Guerrero
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Ana Lilia Martínez-Rocha
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - J. Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Víctor Meza-Carmen
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Juan Carlos Torres-Guzmán
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
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15
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van Aalst ACA, Jansen MLA, Mans R, Pronk JT. Quantification and mitigation of byproduct formation by low-glycerol-producing Saccharomyces cerevisiae strains containing Calvin-cycle enzymes. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:81. [PMID: 37173767 PMCID: PMC10176687 DOI: 10.1186/s13068-023-02329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Anaerobic Saccharomyces cerevisiae cultures require glycerol formation to re-oxidize NADH formed in biosynthetic processes. Introduction of the Calvin-cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been shown to couple re-oxidation of biosynthetic NADH to ethanol production and improve ethanol yield on sugar in fast-growing batch cultures. Since growth rates in industrial ethanol production processes are not constant, performance of engineered strains was studied in slow-growing cultures. RESULTS In slow-growing anaerobic chemostat cultures (D = 0.05 h-1), an engineered PRK/RuBisCO strain produced 80-fold more acetaldehyde and 30-fold more acetate than a reference strain. This observation suggested an imbalance between in vivo activities of PRK/RuBisCO and formation of NADH in biosynthesis. Lowering the copy number of the RuBisCO-encoding cbbm expression cassette from 15 to 2 reduced acetaldehyde and acetate production by 67% and 29%, respectively. Additional C-terminal fusion of a 19-amino-acid tag to PRK reduced its protein level by 13-fold while acetaldehyde and acetate production decreased by 94% and 61%, respectively, relative to the 15 × cbbm strain. These modifications did not affect glycerol production at 0.05 h-1 but caused a 4.6 fold higher glycerol production per amount of biomass in fast-growing (0.29 h-1) anaerobic batch cultures than observed for the 15 × cbbm strain. In another strategy, the promoter of ANB1, whose transcript level positively correlated with growth rate, was used to control PRK synthesis in a 2 × cbbm strain. At 0.05 h-1, this strategy reduced acetaldehyde and acetate production by 79% and 40%, respectively, relative to the 15 × cbbm strain, without affecting glycerol production. The maximum growth rate of the resulting strain equalled that of the reference strain, while its glycerol production was 72% lower. CONCLUSIONS Acetaldehyde and acetate formation by slow-growing cultures of engineered S. cerevisiae strains carrying a PRK/RuBisCO bypass of yeast glycolysis was attributed to an in vivo overcapacity of PRK and RuBisCO. Reducing the capacity of PRK and/or RuBisCO was shown to mitigate this undesirable byproduct formation. Use of a growth rate-dependent promoter for PRK expression highlighted the potential of modulating gene expression in engineered strains to respond to growth-rate dynamics in industrial batch processes.
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Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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16
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Ghaddar A, Mony VK, Mishra S, Berhanu S, Johnson JC, Enriquez-Hesles E, Harrison E, Patel A, Horak MK, Smith JS, O'Rourke EJ. Increased alcohol dehydrogenase 1 activity promotes longevity. Curr Biol 2023; 33:1036-1046.e6. [PMID: 36805847 PMCID: PMC10236445 DOI: 10.1016/j.cub.2023.01.059] [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: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023]
Abstract
Several molecules can extend healthspan and lifespan across organisms. However, most are upstream signaling hubs or transcription factors orchestrating complex anti-aging programs. Therefore, these molecules point to but do not reveal the fundamental mechanisms driving longevity. Instead, downstream effectors that are necessary and sufficient to promote longevity across conditions or organisms may reveal the fundamental anti-aging drivers. Toward this goal, we searched for effectors acting downstream of the transcription factor EB (TFEB), known as HLH-30 in C. elegans, because TFEB/HLH-30 is necessary across anti-aging interventions and its overexpression is sufficient to extend C. elegans lifespan and reduce biomarkers of aging in mammals including humans. As a result, we present an alcohol-dehydrogenase-mediated anti-aging response (AMAR) that is essential for C. elegans longevity driven by HLH-30 overexpression, caloric restriction, mTOR inhibition, and insulin-signaling deficiency. The sole overexpression of ADH-1 is sufficient to activate AMAR, which extends healthspan and lifespan by reducing the levels of glycerol-an age-associated and aging-promoting alcohol. Adh1 overexpression is also sufficient to promote longevity in yeast, and adh-1 orthologs are induced in calorically restricted mice and humans, hinting at ADH-1 acting as an anti-aging effector across phyla.
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Affiliation(s)
- Abbas Ghaddar
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Vinod K Mony
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Swarup Mishra
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Samuel Berhanu
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - James C Johnson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Emma Harrison
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Aaroh Patel
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Mary Kate Horak
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Eyleen J O'Rourke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; Robert M. Berne Cardiovascular Research Center, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA.
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17
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Yukawa T, Bamba T, Matsuda M, Yoshida T, Inokuma K, Kim J, Won Lee J, Jin YS, Kondo A, Hasunuma T. Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnol Bioeng 2023; 120:511-523. [PMID: 36321324 DOI: 10.1002/bit.28278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
To realize lignocellulose-based bioeconomy, efficient conversion of xylose into valuable chemicals by microbes is necessary. Xylose oxidative pathways that oxidize xylose into xylonate can be more advantageous than conventional xylose assimilation pathways because of fewer reaction steps without loss of carbon and ATP. Moreover, commodity chemicals like 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone can be produced from the intermediates of xylose oxidative pathway. However, successful implementations of xylose oxidative pathway in yeast have been hindered because of the secretion and accumulation of xylonate which is a key intermediate of the pathway, leading to low yield of target product. Here, high-yield production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. Specifically, 3,4-dihydroxybutyrate biosynthetic pathway was established in yeast through deletion of ADH6 and overexpression of yneI. Also, inspired by the mismatch of pH between host strain and key enzyme of XylD, alkaline fermentations (pH ≥ 7.0) were performed to minimize xylonate accumulation. Under the alkaline conditions, xylonate was re-assimilated by engineered yeast and combined product yields of 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone resulted in 0.791 mol/mol-xylose, which is highest compared with previous study. These results shed light on the utility of the xylose oxidative pathway in yeast.
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Affiliation(s)
- Takahiro Yukawa
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Jungyeon Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jae Won Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
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18
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Muratovska N, Carlquist M. Recombinant yeast for production of the pain receptor modulator nonivamide from vanillin. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2022.1097215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We report on the development of a method based on recombinant yeast Saccharomyces cerevisiae to produce nonivamide, a capsaicinoid and potent agonist of the pain receptor TRPV1. Nonivamide was produced in a two-step batch process where yeast was i) grown aerobically on glucose and ii) used to produce nonivamide from vanillin and non-anoic acid by bioconversion. The yeast was engineered to express multiple copies of an amine transaminase from Chromobacterium violaceum (CvTA), along with an NADH-dependent alanine dehydrogenase from Bacillus subtilis (BsAlaDH) to enable efficient reductive amination of vanillin. Oxygen-limited conditions and the use of ethanol as a co-substrate to regenerate NADH were identified to favour amination over the formation of the by-products vanillic alcohol and vanillic acid. The native alcohol dehydrogenase ADH6 was deleted to further reduce the formation of vanillic alcohol. A two-enzyme system consisting of an N-acyltransferase from Capsicum annuum (CaAT), and a CoA ligase from Sphingomonas sp. Ibu-2 (IpfF) was co-expressed to produce the amide. This study provides proof of concept for yeast-based production of non-ivamide by combined transamination and amidation of vanillin.
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19
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He S, Zhang Z, Lu W. Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2023; 50:6986260. [PMID: 36633543 PMCID: PMC9936215 DOI: 10.1093/jimb/kuac029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.
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Affiliation(s)
| | - Zhanwei Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wenyu Lu
- Correspondence should be addressed to: W. Y. Lu, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China. Phone: +86-22-853-56523. Fax: +86-22-274-00973. E-mail:
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20
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Kwolek-Mirek M, Bednarska S, Dubicka-Lisowska A, Maslanka R, Zadrag-Tecza R, Kaszycki P. Unbalance between Pyridine Nucleotide Cofactors in The SOD1 Deficient Yeast Saccharomyces cerevisiae Causes Hypersensitivity to Alcohols and Aldehydes. Int J Mol Sci 2022; 24:ijms24010659. [PMID: 36614102 PMCID: PMC9820918 DOI: 10.3390/ijms24010659] [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: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
Alcohol and aldehyde dehydrogenases are especially relevant enzymes involved in metabolic and detoxification reactions that occur in living cells. The comparison between the gene expression, protein content, and enzymatic activities of cytosolic alcohol and aldehyde dehydrogenases of the wild-type strain and the Δsod1 mutant lacking superoxide dismutase 1, which is hypersensitive to alcohols and aldehydes, shows that the activity of these enzymes is significantly higher in the Δsod1 mutant, but this is not a mere consequence of differences in the enzymatic protein content nor in the expression levels of genes. The analysis of the NAD(H) and NADP(H) content showed that the higher activity of alcohol and aldehyde dehydrogenases in the Δsod1 mutant could be a result of the increased availability of pyridine nucleotide cofactors. The higher level of NAD+ in the Δsod1 mutant is not related to the higher level of tryptophan; in turn, a higher generation of NADPH is associated with the upregulation of the pentose phosphate pathway. It is concluded that the increased sensitivity of the Δsod1 mutant to alcohols and aldehydes is not only a result of the disorder of redox homeostasis caused by the induction of oxidative stress but also a consequence of the unbalance between pyridine nucleotide cofactors.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Sabina Bednarska
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Aleksandra Dubicka-Lisowska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
| | - Roman Maslanka
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Pawel Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
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21
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DafaAlla TEIM, Abdalla M, El-Arabey AA, Eltayb WA, Mohapatra RK. Botrytis cinerea alcohol dehydrogenase mediates fungal development, environmental adaptation and pathogenicity. J Biomol Struct Dyn 2022; 40:12426-12438. [PMID: 34472419 DOI: 10.1080/07391102.2021.1971112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Botrytis cinerea is an economically critical necrotrophic fungus that infecting many types of plants species. Although the lifestyle adaptations and genetic foundations of several enzymes and metabolites involved in B. cinerea virulence during host plant infection are well studied, the role of B. cinerea alcohol dehydrogenase (ADH) enzymes in these processes is poorly understood. Herein, we identified a significant up-regulation of the transcriptional levels of the BcADH1 gene during the tomato - B. cinerea strain B0510 interaction and at the early stage of infection. Substantially, we used a recent approach for replacement of gene by utilizing homologous recombination to generate knock-out mutants (Δbcadh1) and their effective complementary strains (Δbcadh1/C). A strong difference in the morphology of Δbcadh1 mutants from the wild type (WT) was detected, with respect to the conidiospore, conidial germination, and formation of branches, sporulation and sclerotia. In addition, the Δbcadh1 mutants showed significant differences in their virulence on tomato leaves relative to the WT. Moreover, the Δbcadh1 mutants appeared to have higher sensitivity to oxygen limitation (hypoxia) and reactive oxygen species, and had lost their ability of alcoholic fermentation compared with the WT and complementary strains. These results provide strong evidence for the requirement of the ADH1 gene for fungal development, environmental adaptation and its ability for full pathogenicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tayb Elassma I M DafaAlla
- College of Plant Sciences, Jilin University, Changchun, China.,College of Natural Resources and Environmental Studies, Sinnar University, Sinnar, Sudan
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Amr Ahmed El-Arabey
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Wafa Ali Eltayb
- Department biotechnology, Faculty of Science and Technology, Shendi University, Shendi, Sudan
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Keonjhar, India
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22
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Utilizing Alcohol for Alkane Biosynthesis by Introducing a Fatty Alcohol Dehydrogenase. Appl Environ Microbiol 2022; 88:e0126422. [PMID: 36416567 PMCID: PMC9746291 DOI: 10.1128/aem.01264-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alkanes produced by microorganisms are expected to be an alternative to fossil fuels as an energy source. Microbial synthesis of alkanes involves the formation of fatty aldehydes via fatty acyl coenzyme A (acyl-CoA) intermediates derived from fatty acid metabolism, followed by aldehyde decarbonylation to generate alkanes. Advancements in metabolic engineering have enabled the construction of such pathways in various microorganisms, including Escherichia coli. However, endogenous aldehyde reductases in the host microorganisms are highly active in converting fatty aldehydes to fatty alcohols, limiting the substrate pool for alkane production. To reuse the alcohol by-product, a screening of fatty alcohol-assimilating microorganisms was conducted, and a bacterial strain, Pantoea sp. strain 7-4, was found to convert 1-tetradecanol to tetradecanal. From this strain, an alcohol dehydrogenase, PsADH, was purified and found to be involved in 1-tetradecanol-oxidizing reaction. Subsequent heterologous expression of the PsADH gene in E. coli was conducted, and recombinant PsADH was purified for a series of biochemical characterizations, including cofactors, optimal reaction conditions, and kinetic parameters. Furthermore, direct alkane production from alcohol was achieved in E. coli by coexpressing PsADH with a cyanobacterial aldehyde-deformylating oxygenase and a reducing system, including ferredoxin and ferredoxin reductase, from Nostoc punctiforme PCC73102. The alcohol-aldehyde-alkane synthetic route established in this study will provide a new approach to utilizing fatty alcohols for the production of alkane biofuel. IMPORTANCE Alcohol dehydrogenases are a group of enzymes found in many organisms. Unfortunately, studies on these enzymes mainly focus on their activities toward short-chain alcohols. In this study, we discovered an alcohol dehydrogenase, PsADH, from the bacterium Pantoea sp. 7-4, which can oxidize 1-tetradecanol to tetradecanal. The medium-chain aldehyde products generated by this enzyme can serve as the substrate of aldehyde-deformylating oxygenase to produce alkanes. The enzyme found in this study can be applied to the biosynthetic pathway involving the formation of medium-chain aldehydes to produce alkanes and other valuable compounds.
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23
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Acetate-rich Cellulosic Hydrolysates and Their Bioconversion Using Yeasts. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0217-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Saccharomyces cerevisiae cis-acting DNA sequences curation pipeline (Sc-cADSs-CP): Master transcription factors prediction in yeasts. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Ribeiro-Filho N, Linforth R, Bora N, Powell CD, Fisk ID. The role of inorganic-phosphate, potassium and magnesium in yeast-flavour formation. Food Res Int 2022; 162:112044. [DOI: 10.1016/j.foodres.2022.112044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
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26
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Quenching of Protein Fluorescence by Fullerenol C 60(OH) 36 Nanoparticles. Int J Mol Sci 2022; 23:ijms232012382. [PMID: 36293241 PMCID: PMC9603995 DOI: 10.3390/ijms232012382] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
The effect of the interaction between fullerenol C60(OH)36 (FUL) and alcohol dehydrogenase (ADH) from Saccharomyces cerevisiae and human serum albumin (HSA) was studied by absorption spectroscopy, fluorescence spectroscopy, and time-resolved fluorescence spectroscopy. As shown in the study, the fluorescence intensities of ADH and HSA at excitation wavelengths λex = 280 nm (Trp, Tyr) and λex = 295 nm (Trp) are decreased with the increase in the FUL concentration. The results of time-resolved measurements indicate that both quenching mechanisms, dynamic and static, are present. The binding constant Kb and the number of binding sites were obtained for HSA and ADH. Thus, the results indicated the formation of FUL complexes and proteins. However, the binding of FUL to HSA is much stronger than that of ADH. The transfer of energy from the protein to FUL was also proved.
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27
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Shah AM, Mohamed H, Fazili ABA, Yang W, Song Y. Investigating the Effect of Alcohol Dehydrogenase Gene Knockout on Lipid Accumulation in Mucor circinelloides WJ11. J Fungi (Basel) 2022; 8:jof8090917. [PMID: 36135642 PMCID: PMC9503276 DOI: 10.3390/jof8090917] [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: 07/31/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Mucor circinelloides is an oleaginous, dimorphic zygomycete fungus species that produces appreciable levels of ethanol when grown under aerobic conditions in the presence of high glucose, indicating the fungus is a Crabtree-positive microorganism. Engineering efforts to redirect carbon flux from ethanol to lipid biosynthesis may shed light on the critical role of ethanol biosynthesis during aerobic fermentation in M. circinelloides. Therefore, in this study, the alcohol dehydrogenase gene (ADH1) of M. circinelloides WJ11 was deleted, and its effects on growth, lipid production, and fatty acid content were analyzed. Our results showed that knocking out of adh1∆ reduced the ethanol concentration by 85–90% in fermented broth, indicating that this gene is the major source of ethanol production. Parallel to these findings, the lipid and fatty acid content of the mutant was decreased, while less change in the growth of WJ11 was observed. Furthermore, a fermentation study showed the lipid and fatty acid content was restored in the mutant strain when the fermentation media was supplemented with 0.5% external ethanol, indicating the importance of alcohol dehydrogenase and its product on growth and lipid biosynthesis in M. circinelloides. To our knowledge, this is the first study to show a link between alcohol dehydrogenase and lipid production in M. circinelloides.
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Affiliation(s)
- Aabid Manzoor Shah
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Hassan Mohamed
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Abu Bakr Ahmad Fazili
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Wu Yang
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Yuanda Song
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
- Correspondence:
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28
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Fermentation performance of a Mexican native Clavispora lusitaniae strain for xylitol and ethanol production from xylose, glucose and cellobiose. Enzyme Microb Technol 2022; 160:110094. [PMID: 35810624 DOI: 10.1016/j.enzmictec.2022.110094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022]
Abstract
Lignocellulose hydrolysates are rich in fermentable sugars such as xylose, cellobiose and glucose, with high potential in the biotechnology industry to obtain bioproducts of higher economic value. Thus, it is important to search for and study new yeast strains that co-consume these sugars to achieve better yields and productivity in the processes. The yeast Clavispora lusitaniae CDBB-L-2031, a native strain isolated from mezcal must, was studied under various culture conditions to potentially produce ethanol and xylitol due to its ability to assimilate xylose, cellobiose and glucose. This yeast produced ethanol under microaerobic conditions with yields of 0.451 gethanol/gglucose and 0.344 gethanol/gcellobiose, when grown on 1% glucose or cellobiose, respectively. In mixtures (0.5% each) of glucose:xylose and glucose:xylose:cellobiose the yields were 0.367 gethanol/gGX and 0. 380 gethanol/gGXC, respectively. Likewise, in identical conditions, C. lusitaniae produced xylitol from xylose with a yield of 0.421 gxylitol/gxylose. In 5% glucose or xylose, this yeast had better ethanol and xylitol titers and yields, respectively. However, glucose negatively affected xylitol production in the mixture of both sugars (3% each), producing only ethanol. Xylose reductase (XR) and xylitol dehydrogenase (XDH) activities were evaluated in cultures growing on xylose or glucose, obtaining the highest values in cultures on xylose at 8 h (25.9 and 6.22 mU/mg, respectively). While in glucose cultures, XR and XDH activities were detected once this substrate was consumed (4.06 and 3.32 mU/mg, respectively). Finally, the XYL1 and XYL2 genes encoding xylose reductase and xylitol dehydrogenase, respectively, were up-regulated by xylose, whereas glucose down-regulated their expression.
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29
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Muratovska N, Silva P, Pozdniakova T, Pereira H, Grey C, Johansson B, Carlquist M. Towards engineered yeast as production platform for capsaicinoids. Biotechnol Adv 2022; 59:107989. [PMID: 35623491 DOI: 10.1016/j.biotechadv.2022.107989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/23/2022]
Abstract
Capsaicinoids are bioactive alkaloids produced by the chili pepper fruit and are known to be the most potent agonists of the human pain receptor TRPV1 (Transient Receptor Potential Cation Channel Subfamily V Member 1). They are currently produced by extraction from chili pepper fruit or by chemical synthesis. Transfer of the biosynthetic route to a microbial host could enable more efficient capsaicinoid production by fermentation and may also enable the use of synthetic biology to create a diversity of new compounds with potentially improved properties. This review summarises the current state of the art on the biosynthesis of capsaicinoid precursors in baker's yeast, Saccharomyces cerevisiae, and discusses bioengineering strategies for achieving total synthesis from sugar.
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Affiliation(s)
- Nina Muratovska
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden
| | - Paulo Silva
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Tatiana Pozdniakova
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Humberto Pereira
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Carl Grey
- Division of Biotechnology, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00 Lund, Sweden.
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30
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Kim HS, Choi JA, Kim BY, Ferrer L, Choi JM, Wendisch VF, Lee JH. Engineered Corynebacterium glutamicum as the Platform for the Production of Aromatic Aldehydes. Front Bioeng Biotechnol 2022; 10:880277. [PMID: 35646884 PMCID: PMC9133326 DOI: 10.3389/fbioe.2022.880277] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
Aromatic aldehydes, including 4-hydroxybenzaldehyde (4-HB aldehyde), protocatechuic (PC) aldehyde, and vanillin, are used as important flavors, fragrances, and pharmaceutical precursors and have several biological and therapeutic effects. Production of aromatic aldehydes in microbial hosts poses a challenge due to its rapid and endogenous reduction to alcohols. To address this hurdle, prospecting of the genome of Corynebacterium glutamicum yielded 27 candidate proteins that were used in comprehensive screening with a 4-hydroxybenzyl (4-HB) alcohol–producing strain. We identified that NCgl0324 has aromatic aldehyde reductase activity and contributed to 4-HB aldehyde reduction in vivo since the NCgl0324 deletion strain HB-Δ0324 produced 1.36 g/L of 4-HB aldehyde, that is, about 188% more than its parental strain. To demonstrate that NCgl0324 knockout can also improve production of PC aldehyde and vanillin, first, a basal MA303 strain that produces protocatechuate was engineered from 4-hydroxybenzoate-synthesizing C. glutamicum APS963, followed by deletion of NCgl0324 to generate PV-Δ0324. The PC aldehyde/alcohol or vanillin/vanillyl alcohol biosynthetic pathways, respectively, were able to be expanded from protocatechuate upon introduction of carboxylic acid reductase (CAR) and catechol O-methyltransferase encoded by a mutated comtm gene. In shake flask culture, the resulting NCgl0324 deletion strains PV-IΔ0324 and PV-IYΔ0324 were shown to produce 1.18 g/L PC aldehyde and 0.31 g/L vanillin, respectively. Thus, modulation of the identified NCgl0324 gene was shown to have the potential to boost production of valuable aromatic aldehydes and alcohols.
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Affiliation(s)
- Hyun-Song Kim
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Jung-A Choi
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Bu-Yeon Kim
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Lenny Ferrer
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jung-Min Choi
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Department of Food Science and Biotechnology, Kyungsung University, Busan, South Korea
- *Correspondence: Jin-Ho Lee,
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31
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van Aalst AC, de Valk SC, van Gulik WM, Jansen ML, Pronk JT, Mans R. Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production. Synth Syst Biotechnol 2022; 7:554-566. [PMID: 35128088 PMCID: PMC8792080 DOI: 10.1016/j.synbio.2021.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth and glycerol formation. Particular attention is paid to strategies aimed at altering energy coupling of alcoholic fermentation and to strategies for altering redox-cofactor coupling in carbon and nitrogen metabolism that aim to reduce or eliminate the role of glycerol formation in anaerobic redox metabolism. In addition to providing an overview of scientific advances we discuss context dependency, theoretical impact and potential for industrial application of different proposed and developed strategies.
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Affiliation(s)
- Aafke C.A. van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Sophie C. de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Walter M. van Gulik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Mickel L.A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX Delft, the Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
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32
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Godillot J, Sanchez I, Perez M, Picou C, Galeote V, Sablayrolles JM, Farines V, Mouret JR. The Timing of Nitrogen Addition Impacts Yeast Genes Expression and the Production of Aroma Compounds During Wine Fermentation. Front Microbiol 2022; 13:829786. [PMID: 35273585 PMCID: PMC8902367 DOI: 10.3389/fmicb.2022.829786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/23/2022] Open
Abstract
Among the different compounds present in the must, nitrogen is an essential nutrient for the management of fermentation kinetics but also plays an important role in the synthesis of fermentative aromas. To address the problems related to nitrogen deficiencies, nitrogen additions during alcoholic fermentation have been implemented. The consequences of such additions on the main reaction are well known. However, their impact on aromas synthesis is still poorly understood. So, the main objective of this study was to determine the impact of nitrogen addition during the stationary phase on both the fermentation kinetics and aroma synthesis. To reach this goal, we used a transdisciplinary approach combining statistical modeling (Box-Behnken design and response surface modeling) and gene expression study (transcriptomic analysis). Our results indicated that nitrogen metabolism, central carbon metabolism (CCM), fermentation kinetics and aroma production were significantly impacted by nitrogen addition. The most remarkable point was the different regulation of the bioconversion of higher alcohols into acetate esters on one hand and of fatty acids into ethyl esters on the other hand. We highlighted that the conversion of higher alcohols into acetate esters was maximum when nitrogen was added at the beginning of the stationary phase. Conversely, the highest conversion of acids into ethyl esters was reached when nitrogen was added close to the end of the stationary phase. Moreover, even if the key element in the production of these two ester families appeared to be the enzymatic activity responsible for their production, rather than the availability of the corresponding precursors, these enzymatic activities were differently regulated. For acetate esters, the regulation occurred at gene level: the ATF2 gene was overexpressed following nitrogen addition during the stationary phase. On the opposite, no induction of gene expression was noted for ethyl esters; it seemed that there was an allosteric regulation.
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Affiliation(s)
- Joséphine Godillot
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
| | | | - Marc Perez
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
| | - Christian Picou
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
| | - Virginie Galeote
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
| | | | - Vincent Farines
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
| | - Jean-Roch Mouret
- SPO, INRAE, L’Institut Agro Montpellier, Université de Montpellier, Montpellier, France
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33
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Cho HY, Nam MS, Hong HJ, Song WS, Yoon SI. Structural and Biochemical Analysis of the Furan Aldehyde Reductase YugJ from Bacillus subtilis. Int J Mol Sci 2022; 23:ijms23031882. [PMID: 35163804 PMCID: PMC8836905 DOI: 10.3390/ijms23031882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023] Open
Abstract
NAD(H)/NADP(H)-dependent aldehyde/alcohol oxidoreductase (AAOR) participates in a wide range of physiologically important cellular processes by reducing aldehydes or oxidizing alcohols. Among AAOR substrates, furan aldehyde is highly toxic to microorganisms. To counteract the toxic effect of furan aldehyde, some bacteria have evolved AAOR that converts furan aldehyde into a less toxic alcohol. Based on biochemical and structural analyses, we identified Bacillus subtilis YugJ as an atypical AAOR that reduces furan aldehyde. YugJ displayed high substrate specificity toward 5-hydroxymethylfurfural (HMF), a furan aldehyde, in an NADPH- and Ni2+-dependent manner. YugJ folds into a two-domain structure consisting of a Rossmann-like domain and an α-helical domain. YugJ interacts with NADP and Ni2+ using the interdomain cleft of YugJ. A comparative analysis of three YugJ structures indicated that NADP(H) binding plays a key role in modulating the interdomain dynamics of YugJ. Noticeably, a nitrate ion was found in proximity to the nicotinamide ring of NADP in the YugJ structure, and the HMF-reducing activity of YugJ was inhibited by nitrate, providing insights into the substrate-binding mode of YugJ. These findings contribute to the characterization of the YugJ-mediated furan aldehyde reduction mechanism and to the rational design of improved furan aldehyde reductases for the biofuel industry.
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Affiliation(s)
- Hye Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Mi Sun Nam
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Ho Jeong Hong
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (W.S.S.); (S.-i.Y.)
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (H.Y.C.); (M.S.N.); (H.J.H.)
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (W.S.S.); (S.-i.Y.)
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34
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Ji J, Damschroder D, Bessert D, Lazcano P, Wessells R, Reynolds CA, Greenberg ML. NAD supplementation improves mitochondrial performance of cardiolipin mutants. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159094. [PMID: 35051613 PMCID: PMC8883178 DOI: 10.1016/j.bbalip.2021.159094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 12/01/2022]
Abstract
Cardiolipin (CL) deficiency causes mitochondrial dysfunction and aberrant metabolism that are associated in humans with the severe disease Barth syndrome (BTHS). Several metabolic abnormalities are observed in BTHS patients and model systems, including decreased oxidative phosphorylation, reduced tricarboxylic acid (TCA) cycle flux, and accumulated lactate and D-β-hydroxybutyrate, which strongly suggests that nicotinamide adenine dinucleotide (NAD) redox metabolism may be altered in CL-deficient cells. In this study, we identified abnormal NAD+ metabolism in multiple BTHS model systems and demonstrate that supplementation of NAD+ precursors such as nicotinamide mononucleotide (NMN) improves mitochondrial function. Improved mitochondrial function in the Drosophila model was associated with restored exercise endurance, which suggests a potential therapeutic benefit of NAD+ precursor supplementation in the management of BTHS patients.
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Affiliation(s)
- Jiajia Ji
- Department of Biological Sciences, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, United States of America
| | - Deena Damschroder
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Denise Bessert
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Pablo Lazcano
- Department of Biological Sciences, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, United States of America
| | - Robert Wessells
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Christian A Reynolds
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, United States of America.
| | - Miriam L Greenberg
- Department of Biological Sciences, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI, United States of America.
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Erden-Karaoğlan F, Karaoğlan M, Yılmaz G, Yılmaz S, İnan M. Deletion analysis of Pichia pastoris alcohol dehydrogenase 2 (ADH2) promoter and development of synthetic promoters. Biotechnol J 2021; 17:e2100332. [PMID: 34870891 DOI: 10.1002/biot.202100332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 01/02/2023]
Abstract
Pichia pastoris (Komagataella phaffii) is a non-conventional Crabtree-negative yeast with the capability of reaching very high cell densities in a fed-batch fermentation process. The alcohol dehydrogenase (ADH) genes of P. pastoris involved in ethanol metabolism were identified and were previously characterized. This work aimed to extend current knowledge of the regulation of the ADH2 promoter. To this end, we first determined the upstream activator (UAS) and repressor (URS) sequences of the promoter by deletion assays. Two upstream activator sites have been identified, positioned between -900 and -801 bp, and -284 and -108 bp upstream of the ADH2 transcription start site. The sequences positioned between -361 and -262 bp had a negative effect on the promoter activity and designated a repressor sequence (URS). We then demonstrated that Mxr1 (methanol expression regulator 1) transcription factor activates the ADH2 promoter through the direct interaction with UAS regions in response to ethanol. Furthermore, five different synthetic promoters were constructed by adding or deleting the regulatory sites. These synthetic promoters were tested for extracellular xylanase production at shake flask level by inducing with ethanol. These promoter variants improved the xylanase production ranging between 165% and 200% of the native promoter. The synthetic promoter 5 (SNT5) that displayed the highest activity was further evaluated at the fermenter scale. The modification in the promoter features might have several implications for industrial processes where decoupling the cell growth and product formation is advantageous.
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Affiliation(s)
- Fidan Erden-Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Turkey.,Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Turkey.,Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Gürkan Yılmaz
- Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | | | - Mehmet İnan
- Department of Food Engineering, Akdeniz University, Antalya, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey
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36
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Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Wang Y, Lin W, Yan H, Neng J, Zheng Y, Yang K, Xing F, Sun P. iTRAQ proteome analysis of the antifungal mechanism of citral on mycelial growth and OTA production in Aspergillus ochraceus. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:4969-4979. [PMID: 33543481 DOI: 10.1002/jsfa.11140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/28/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Aspergillus ochraceus causes food spoilage and produces mycotoxin ochratoxin A (OTA) during storage of agricultural commodities. In this study, citral was used to inhibit A. ochraceus growth and OTA accumulation, proteomic analysis was employed to verify the mechanism of citral. RESULTS Citral was found to significantly inhibit fungal growth and mycotoxin production in A. ochraceus. Specifically, 75, 125, 150 and 200 μL L-1 citral suppressed mycelial growth by 33%, 46%, 50% and 100%, respectively. Additionally, 75 μL L-1 citral inhibited OTA accumulation by 25%. Proteomic analysis was performed to elucidate the inhibitory mechanism of citral on mycelial growth and OTA production at subinhibitory concentrations (75 μL L-1 ). Proteomics analysis identified 2646 proteins in A. ochraceus fc-1, of which 218 were differentially expressed between control and 75 μL L-1 citral treatment samples. Differentially expressed proteins were identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of biological process, cellular component and molecular function terms. Potential factors affecting mycelial growth and OTA production were analysed, and OTA production was revealed to be a complex process involving many associated factors related to various processes including nutrient intake, sterol biosynthesis, ribosome biogenesis, energy metabolism, oxidative stress and amino acid metabolism. In addition, citral at 75 μL L-1 down-regulated OTA biosynthetic genes including pks and nrps, but slightly up-regulated the global regulatory factors veA, velB and laeA. CONCLUSION The findings further demonstrate the potential of citral for the preservation of grains and other agricultural products, and provide new insight into its antifungal mechanisms at subinhibitory concentrations. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Yan Wang
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
| | - Wei Lin
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
| | - Hao Yan
- Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou, China
| | - Jing Neng
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
| | - Yong Zheng
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
| | - Kai Yang
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
| | - Fuguo Xing
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Peilong Sun
- College of Food Science and Technology, Zhejiang University of Technology/Key Laboratory of Food Macromolecular Resources Processing Technology Research (Zhejiang University of Technology), China National Light Industry, Hangzhou, China
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38
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Wu L, Wen Y, Chen W, Yan T, Tian X, Zhou S. Simultaneously deleting ADH2 and THI3 genes of Saccharomyces cerevisiae for reducing the yield of acetaldehyde and fusel alcohols. FEMS Microbiol Lett 2021; 368:6354780. [PMID: 34410369 DOI: 10.1093/femsle/fnab094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
The reduced yields of acetaldehyde and fusel alcohols through fermentation by Saccharomyces cerevisiae is of significance for the improvement of the flavor and health of alcoholic beverages. In this study, the ADH2 (encode alcohol dehydrogenase) and THI3 (encode decarboxylase) genes of the industrial diploid strain S. cerevisiae XF1 were deleted. Results showed that single-gene-deletion mutants by separate gene deletion of ADH2 or THI3 led to a reduced production of the acetaldehyde or fusel alcohols, respectively. In the meantime, the double-gene-deletion mutant S. cerevisiae XF1-AT was constructed by deleting the ADH2 and THI3 simultaneously. An equivalent level of the ethanol production by the S. cerevisiae XF1-AT could be achieved but with the yields of acetaldehyde, isoamyl alcohol and iso-butanol reduced by 42.09%, 15.65% and 20.16%, respectively. In addition, there was no interaction between the ADH2 deletion and THI3 deletion in reducing the production of acetaldehyde and fusel alcohols. The engineered S. cerevisiae XF1-AT provided a new strategy to alcoholic beverages brewing industry for reducing the production of acetaldehyde as well as the fusel alcohols.
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Affiliation(s)
- Liang Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yongdi Wen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Wenying Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Tongshuai Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaofei Tian
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.,Guangxi Key Laboratory of Clean Pulp and Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning, Guangxi 530004, China
| | - Shishui Zhou
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
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Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Front Bioeng Biotechnol 2021; 9:701120. [PMID: 34409021 PMCID: PMC8366029 DOI: 10.3389/fbioe.2021.701120] [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: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Large enzyme families such as the groups of zinc-dependent alcohol dehydrogenases (ADHs), long chain alcohol oxidases (AOxs) or amine dehydrogenases (AmDHs) with, sometimes, more than one million sequences in the non-redundant protein database and hundreds of experimentally characterized enzymes are excellent cases for protein engineering efforts aimed at refining and modifying substrate specificity. Yet, the backside of this wealth of information is that it becomes technically difficult to rationally select optimal sequence targets as well as sequence positions for mutagenesis studies. In all three cases, we approach the problem by starting with a group of experimentally well studied family members (including those with available 3D structures) and creating a structure-guided multiple sequence alignment and a modified phylogenetic tree (aka binding site tree) based just on a selection of potential substrate binding residue positions derived from experimental information (not from the full-length sequence alignment). Hereupon, the remaining, mostly uncharacterized enzyme sequences can be mapped; as a trend, sequence grouping in the tree branches follows substrate specificity. We show that this information can be used in the target selection for protein engineering work to narrow down to single suitable sequences and just a few relevant candidate positions for directed evolution towards activity for desired organic compound substrates. We also demonstrate how to find the closest thermophile example in the dataset if the engineering is aimed at achieving most robust enzymes.
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Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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40
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Agarwal G, Gitaitis RD, Dutta B. Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer. Microorganisms 2021; 9:1761. [PMID: 34442840 PMCID: PMC8399035 DOI: 10.3390/microorganisms9081761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
| | | | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
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41
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Kang NK, Lee JW, Ort DR, Jin YS. L-malic acid production from xylose by engineered Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2000431. [PMID: 34390209 DOI: 10.1002/biot.202000431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/07/2022]
Abstract
L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titers of malic acid from xylose than glucose. Interestingly, the engineered strain had higher malic acid yield from lower concentrations (10 g/L) of xylose, with no ethanol production, than from higher xylose concentrations (20 g/L and 40 g/L). As such, a fed-batch culture maintaining xylose concentrations at low levels was conducted and 61.2 g/L of malic acid was produced, with a productivity of 0.32 g/L∙h. These results represent successful engineering of S. cerevisiae for the production of malic acid from xylose, confirming that that xylose offers the efficient production of various biofuels and chemicals by engineered S. cerevisiae. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nam Kyu Kang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jae Won Lee
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Departments of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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42
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Lee JW, Lee YG, Jin YS, Rao CV. Metabolic engineering of non-pathogenic microorganisms for 2,3-butanediol production. Appl Microbiol Biotechnol 2021; 105:5751-5767. [PMID: 34287658 DOI: 10.1007/s00253-021-11436-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
2,3-Butanediol (2,3-BDO) is a promising commodity chemical with various industrial applications. While petroleum-based chemical processes currently dominate the industrial production of 2,3-BDO, fermentation-based production of 2,3-BDO provides an attractive alternative to chemical-based processes with regards to economic and environmental sustainability. The achievement of high 2,3-BDO titer, yield, and productivity in microbial fermentation is a prerequisite for the production of 2,3-BDO at large scales. Also, enantiopure production of 2,3-BDO production is desirable because 2,3-BDO stereoisomers have unique physicochemical properties. Pursuant to these goals, many metabolic engineering strategies to improve 2,3-BDO production from inexpensive sugars by Klebsiella oxytoca, Bacillus species, and Saccharomyces cerevisiae have been developed. This review summarizes the recent advances in metabolic engineering of non-pathogenic microorganisms to enable efficient and enantiopure production of 2,3-BDO. KEY POINTS: • K. oxytoca, Bacillus species, and S. cerevisiae have been engineered to achieve efficient 2,3-BDO production. • Metabolic engineering of non-pathogenic microorganisms enabled enantiopure production of 2,3-BDO. • Cost-effective 2,3-BDO production can be feasible by using renewable biomass.
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Affiliation(s)
- Jae Won Lee
- 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
| | - Ye-Gi Lee
- 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
| | - Christopher V Rao
- 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. .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Expression, purification and X-ray crystal diffraction analysis of alcohol dehydrogenase 1 from Artemisia annua L. Protein Expr Purif 2021; 187:105943. [PMID: 34273542 DOI: 10.1016/j.pep.2021.105943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022]
Abstract
Alcohol dehydrogenase 1 identified from Artemisia annua (AaADH1) is a 40 kDa protein that predominately expressed in young leaves and buds, and catalyzes dehydrogenation of artemisinic alcohol to artemisinic aldehyde in artemisinin biosynthetic pathway. In this study, AaADH1 encoding gene was subcloned into vector pET-21a(+) and expressed in Escherichia coli. BL21(DE3), and purified by Co2+ affinity chromatography. Anion exchange chromatography was performed until the protein purity reached more than 90%. Crystallization of AaADH1 was conducted for further investigation of the molecular mechanism of catalysis, and hanging-drop vapour diffusion method was used in experiments. The results showed that the apo AaADH1 crystal diffracted to 2.95 Å resolution, and belongs to space group P1, with unit-cell parameters, a = 77.53 Å, b = 78.49 Å, c = 102.44 Å, α = 71.88°, β = 74.02°, γ = 59.97°. The crystallization condition consists of 0.1 M Bis-Tris pH 6.0, 13% (w/v) PEG 8000 and 5% (v/v) glycerol.
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Ribeaucourt D, Bissaro B, Lambert F, Lafond M, Berrin JG. Biocatalytic oxidation of fatty alcohols into aldehydes for the flavors and fragrances industry. Biotechnol Adv 2021; 56:107787. [PMID: 34147589 DOI: 10.1016/j.biotechadv.2021.107787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023]
Abstract
From Egyptian mummies to the Chanel n°5 perfume, fatty aldehydes have long been used and keep impacting our senses in a wide range of foods, beverages and perfumes. Natural sources of fatty aldehydes are threatened by qualitative and quantitative variability while traditional chemical routes are insufficient to answer the society shift toward more sustainable and natural products. The production of fatty aldehydes using biotechnologies is therefore the most promising alternative for the flavors and fragrances industry. In this review, after drawing the portrait of the origin and characteristics of fragrant fatty aldehydes, we present the three main classes of enzymes that catalyze the reaction of fatty alcohols oxidation into aldehydes, namely alcohol dehydrogenases, flavin-dependent alcohol oxidases and copper radical alcohol oxidases. The constraints, challenges and opportunities to implement these oxidative enzymes in the flavors and fragrances industry are then discussed. By setting the scene on the biocatalytic production of fatty aldehydes, and providing a critical assessment of its potential, we expect this review to contribute to the development of biotechnology-based solutions in the flavors and fragrances industry.
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Affiliation(s)
- David Ribeaucourt
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France; V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France; Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Fanny Lambert
- V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France
| | - Mickael Lafond
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France.
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Tailor-made novel electrospun polystyrene/poly(d,l-lactide-co-glycolide) for oxidoreductases immobilization: Improvement of catalytic properties under extreme reaction conditions. Bioorg Chem 2021; 114:105036. [PMID: 34120021 DOI: 10.1016/j.bioorg.2021.105036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/15/2021] [Accepted: 05/28/2021] [Indexed: 11/24/2022]
Abstract
Immobilized enzymes find applications in many areas such as pharmacy, medicine, food production and environmental protection. However, protecting these biocatalysts against harsh reaction conditions and retaining their enzymatic activity even after several biocatalytic cycles are major challenges. Properly selected supports and type of surface modifier therefore seem to be crucial for achieving high retention of catalytic activity of immobilized biomolecules. Here we propose production of novel composite electrospun fibers from polystyrene/poly(d,l-lactide-co-glycolide) (PS/PDLG) and its application as a support for immobilization of oxidoreductases such as alcohol dehydrogenase (ADH) and laccase (LAC). Two strategies of covalent binding, (i) (3-aminopropyl)triethoxysilane (APTES) with glutaraldehyde (GA) and (ii) polydopamine (PDA), were applied to attach oxidoreductases to PS/PDLG. The average fiber diameter was shown to increase from 1.252 µm to even 3.367 µm after enzyme immobilization. Effective production of PS/PDLG fibers and biomolecule attachment were confirmed by Fourier transform infrared spectroscopy analysis. The highest substrate conversion efficiency was observed at pH 6.5 and 5 for ADH and LAC, respectively, and at 25 °C for enzymes attached using the APTES + GA approach. Improvement of enzyme stabilization at high temperatures was confirmed in that relative activities of enzymes immobilized onto PS/PDLG fibers were over 20% higher than those of the free biomolecules, and enzyme leaching from the support using acetate and MES buffers was below 10 mg/g.
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46
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Hayashi S, Kuramata M, Abe T, Yamaguchi N, Takagi H, Tanikawa H, Iino M, Sugimoto K, Ishikawa S. Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters. PLANT PHYSIOLOGY 2021; 186:611-623. [PMID: 33620496 PMCID: PMC8154085 DOI: 10.1093/plphys/kiab086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 05/14/2023]
Abstract
Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.
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Affiliation(s)
- Shimpei Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Hiroki Takagi
- Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Manaka Iino
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8604, Japan
- Author for communication:
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Ohashi Y, Huang S, Maeda I. Biosyntheses of geranic acid and citronellic acid from monoterpene alcohols by Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2021; 85:1530-1535. [PMID: 33713103 DOI: 10.1093/bbb/zbab039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/08/2021] [Indexed: 11/12/2022]
Abstract
Geraniol is one of the important aromatic ingredients in alcoholic beverages. Bioconversions of geraniol to other terpenoids and genes involved in the oxidation of geraniol were investigated. Geranic acid and citronellic acid were detected in yeast culture, where geraniol or nerol was added. Addition of citral, a mixture of geranial and neral, resulted in the production of geranic acid and citronellic acid, whereas the addition of citral or citronellal resulted in the production of citronellic acid, suggesting that citronellic acid might be produced through the conversion of citral to citronellal followed by the oxidation of citronellal. Consumption of geraniol and production of geranic acid, citronellic acid, and citronellol were affected in adh1Δ, adh3Δ, adh4Δ, and sfa1Δ yeast strains, which possess single deletion of a gene encoding alcohol dehydrogenase. This is the first report of the bioconversion of monoterpene alcohols, geraniol and nerol, to geranic acid and citronellic acid in yeast culture.
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Affiliation(s)
- Yuka Ohashi
- Department of Applied Biological Chemistry, School of Agriculture, Utsunomiya University, Tochigi, Japan
| | - Shuai Huang
- Department of Applied Biological Chemistry, School of Agriculture, Utsunomiya University, Tochigi, Japan
| | - Isamu Maeda
- Department of Applied Biological Chemistry, School of Agriculture, Utsunomiya University, Tochigi, Japan
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Dank A, van Mastrigt O, Yang Z, Dinesh VM, Lillevang SK, Weij C, Smid EJ. The cross-over fermentation concept and its application in a novel food product: The dairy miso case study. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Watcharawipas A, Sae-Tang K, Sansatchanon K, Sudying P, Boonchoo K, Tanapongpipat S, Kocharin K, Runguphan W. Systematic engineering of Saccharomyces cerevisiae for D-lactic acid production with near theoretical yield. FEMS Yeast Res 2021; 21:6226681. [PMID: 33856451 DOI: 10.1093/femsyr/foab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
D-lactic acid is a chiral three-carbon organic acid that can improve the thermostability of polylactic acid. Here, we systematically engineered Saccharomyces cerevisiae to produce D-lactic acid from glucose, a renewable carbon source, at near theoretical yield. Specifically, we screened D-lactate dehydrogenase (DLDH) variants from lactic acid bacteria in three different genera and identified the Leuconostoc pseudomesenteroides variant (LpDLDH) as having the highest activity in yeast. We then screened single-gene deletions to minimize the production of the side products ethanol and glycerol as well as prevent the conversion of D-lactic acid back to pyruvate. Based on the results of the DLDH screening and the single-gene deletions, we created a strain called ASc-d789M which overexpresses LpDLDH and contains deletions in glycerol pathway genes GPD1 and GPD2 and lactate dehydrogenase gene DLD1, as well as downregulation of ethanol pathway gene ADH1 using the L-methionine repressible promoter to minimize impact on growth. ASc-d789M produces D-lactic acid at a titer of 17.09 g/L in shake-flasks (yield of 0.89 g/g glucose consumed or 89% of the theoretical yield). Fed-batch fermentation resulted in D-lactic acid titer of 40.03 g/L (yield of 0.81 g/g glucose consumed). Altogether, our work represents progress towards efficient microbial production of D-lactic acid.
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Affiliation(s)
- Akaraphol Watcharawipas
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittapong Sae-Tang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kitisak Sansatchanon
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Pipat Sudying
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kriengsak Boonchoo
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kanokarn Kocharin
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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Romero-Frasca E, Velasquez-Orta SB, Escobar-Sánchez V, Tinoco-Valencia R, Orta Ledesma MT. Bioprospecting of wild type ethanologenic yeast for ethanol fuel production from wastewater-grown microalgae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:93. [PMID: 33836818 PMCID: PMC8035739 DOI: 10.1186/s13068-021-01925-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/07/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Wild-type yeasts have been successfully used to obtain food products, yet their full potential as fermenting microorganisms for large-scale ethanol fuel production has to be determined. In this study, wild-type ethanologenic yeasts isolated from a secondary effluent were assessed for their capability to ferment saccharified microalgae sugars. RESULTS Yeast species in wastewater were identified sequencing the Internal Transcribed Spacers 1 and 2 regions of the ribosomal cluster. Concurrently, microalgae biomass sugars were saccharified via acid hydrolysis, producing 5.0 ± 0.3 g L-1 of fermentable sugars. Glucose consumption and ethanol production of yeasts in hydrolyzed-microalgae liquor were tested at different initial sugar concentrations and fermentation time. The predominant ethanologenic yeast species was identified as Candida sp., and glucose consumption for this strain and S. cerevisiae achieved 75% and 87% of the initial concentration at optimal conditions, respectively. Relatively similar ethanol yields were determined for both species, achieving 0.45 ± 0.05 (S. cerevisiae) and 0.46 ± 0.05 g ethanol per g glucose (Candida sp.). CONCLUSION Overall, the results provide a first insight of the fermentation capacities of specific wild-type Candida species, and their potential role in ethanol industries seeking to improve their cost-efficiency.
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Affiliation(s)
- Enrique Romero-Frasca
- Instituto de Ingeniería, Coordinación de Ingeniería Ambiental, Universidad Nacional Autónoma de México, Apartado Postal 70-472, Coyoacán, 04510, Ciudad de México, México
| | | | - Viviana Escobar-Sánchez
- Laboratorio de Biología Molecular Y Genómica, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Raunel Tinoco-Valencia
- Instituto de Biotecnología, Unidad de Escalamiento Y Planta Piloto, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - María Teresa Orta Ledesma
- Instituto de Ingeniería, Coordinación de Ingeniería Ambiental, Universidad Nacional Autónoma de México, Apartado Postal 70-472, Coyoacán, 04510, Ciudad de México, México
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