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Bradley JM, Bunsick M, Ly G, Aquino B, Wang FZ, Holbrook-Smith D, Suginoo S, Bradizza D, Kato N, As'sadiq O, Marsh N, Osada H, Boyer FD, McErlean CSP, Tsuchiya Y, Subramaniam R, Bonetta D, McCourt P, Lumba S. Modulation of fungal phosphate homeostasis by the plant hormone strigolactone. Mol Cell 2024:S1097-2765(24)00737-8. [PMID: 39357514 DOI: 10.1016/j.molcel.2024.09.004] [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: 10/02/2023] [Revised: 07/12/2024] [Accepted: 09/05/2024] [Indexed: 10/04/2024]
Abstract
Inter-kingdom communication through small molecules is essential to the coexistence of organisms in an ecosystem. In soil communities, the plant root is a nexus of interactions for a remarkable number of fungi and is a source of small-molecule plant hormones that shape fungal compositions. Although hormone signaling pathways are established in plants, how fungi perceive and respond to molecules is unclear because many plant-associated fungi are recalcitrant to experimentation. Here, we develop an approach using the model fungus, Saccharomyces cerevisiae, to elucidate mechanisms of fungal response to plant hormones. Two plant hormones, strigolactone and methyl jasmonate, produce unique transcript profiles in yeast, affecting phosphate and sugar metabolism, respectively. Genetic analysis in combination with structural studies suggests that SLs require the high-affinity transporter Pho84 to modulate phosphate homeostasis. The ability to study small-molecule plant hormones in a tractable genetic system should have utility in understanding fungal-plant interactions.
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Affiliation(s)
- James M Bradley
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Michael Bunsick
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - George Ly
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Bruno Aquino
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Flora Zhiqi Wang
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | | | - Shingo Suginoo
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Dylan Bradizza
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Naoki Kato
- RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Omar As'sadiq
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Nina Marsh
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - François-Didier Boyer
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | | | - Yuichiro Tsuchiya
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | | | - Dario Bonetta
- Ontario Tech University, 2000 Simcoe St. N, Oshawa, ON L1G 0C5, Canada
| | - Peter McCourt
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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2
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Bachleitner S, Severinsen MM, Lutz G, Mattanovich D. Overexpression of the transcriptional activators Mxr1 and Mit1 enhances lactic acid production on methanol in Komagataellaphaffii. Metab Eng 2024; 85:133-144. [PMID: 39067842 DOI: 10.1016/j.ymben.2024.07.013] [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: 04/24/2024] [Revised: 07/07/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
A bio-based production of chemical building blocks from renewable, sustainable and non-food substrates is one key element to fight climate crisis. Lactic acid, one such chemical building block is currently produced from first generation feedstocks such as glucose and sucrose, both requiring land and water resources. In this study we aimed for lactic acid production from methanol by utilizing Komagataella phaffii as a production platform. Methanol, a single carbon source has potential as a sustainable substrate as technology allows (electro)chemical hydrogenation of CO2 for methanol production. Here we show that expression of the Lactiplantibacillus plantarum derived lactate dehydrogenase leads to L-lactic acid production in Komagataella phaffii, however, production resulted in low titers and cells subsequently consumed lactic acid again. Gene expression analysis of the methanol-utilizing genes AOX1, FDH1 and DAS2 showed that the presence of lactic acid downregulates transcription of the aforementioned genes, thereby repressing the methanol-utilizing pathway. For activation of the methanol-utilizing pathway in the presence of lactic acid, we constructed strains deficient in transcriptional repressors Nrg1, Mig1-1, and Mig1-2 as well as strains with overrepresentation of transcriptional activators Mxr1 and Mit1. While loss of transcriptional repressors had no significant impact on lactic acid production, overexpression of both transcriptional activators, MXR1 and MIT1, increased lactic acid titers from 4 g L-1 to 17 g L-1 in bioreactor cultivations.
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Affiliation(s)
- Simone Bachleitner
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Manja Mølgaard Severinsen
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Gregor Lutz
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Diethard Mattanovich
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria.
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3
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Yu MC, Sun YS. A Droplet-Based Microfluidic Platform for High-Throughput Culturing of Yeast Cells in Various Conditions. MICROMACHINES 2024; 15:1034. [PMID: 39203685 PMCID: PMC11356446 DOI: 10.3390/mi15081034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024]
Abstract
Yeast plays a significant role in a variety of fields. In particular, it is extensively used as a model organism in genetics and cellular biology studies, and is employed in the production of vaccines, pharmaceuticals, and biofuels. Traditional "bulk"-based studies on yeast growth often overlook cellular variability, emphasizing the need for single-cell analysis. Micro-droplets, tiny liquid droplets with high surface-area-to-volume ratios, offer a promising platform for investigating single or a small number of cells, allowing precise control and monitoring of individual cell behaviors. Microfluidic devices, which facilitate the generation of micro-droplets, are advantageous due to their reduced volume requirements and ability to mimic in vivo micro-environments. This study introduces a custom-designed microfluidic device to encapsulate yeasts in micro-droplets under various conditions in a parallel manner. The results reveal that optimal glucose concentrations promoted yeast growth while cycloheximide and Cu2+ ions inhibited it. This platform enhances yeast cultivation strategies and holds potential for high-throughput single-cell investigations in more complex organisms.
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Affiliation(s)
| | - Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City 24205, Taiwan;
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4
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de Holanda Paranhos L, Magalhães RSS, de Araújo Brasil A, Neto JRM, Ribeiro GD, Queiroz DD, Dos Santos VM, Eleutherio ECA. The familial amyotrophic lateral sclerosis-associated A4V SOD1 mutant is not able to regulate aerobic glycolysis. Biochim Biophys Acta Gen Subj 2024; 1868:130634. [PMID: 38788983 DOI: 10.1016/j.bbagen.2024.130634] [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: 02/08/2024] [Revised: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Under certain stress conditions, astrocytes operate in aerobic glycolysis, a process controlled by pyruvate dehydrogenase (PDH) inhibition through its E1 α subunit (Pda1) phosphorylation. This supplies lactate to neurons, which save glucose to obtain NADPH to, among other roles, counteract reactive oxygen species. A failure in this metabolic cooperation causes severe damage to neurons. In this work, using humanized Saccharomyces cerevisiae cells in which its endogenous Cu/Zn Superoxide Dismutase (SOD1) was replaced by human ortholog, we investigated the role of human SOD1 (hSOD1) in aerobic glycolysis regulation and its implications to amyotrophic lateral sclerosis (ALS), a neurodegenerative disease. Yeast cells ferment glucose even in the presence of oxygen and switch to respiratory metabolism after glucose exhaustion. However, like cells of SOD1-knockout strain, cells expressing A4V mutant of hSOD1 growing on glucose showed a respiratory phenotype, i.e., low glucose and high oxygen consumptions and low intracellular oxidation levels in response to peroxide stress, contrary to cells expressing wild-type (WT) SOD1 (yeast or human). The A4V mutation in hSOD1 is linked to ALS. In contrast to WT SOD1 strains, PDH activity of both sod1Δ and A4V hSOD1 cells did not change in response to a metabolic shift toward oxidative metabolism, which was associated to lower Pda1 phosphorylation levels under growth on glucose. Taken together, our results suggest that A4V mutant cannot regulate aerobic glycolysis via Pda1 phosphorylation the same way WT hSOD1, which might be linked to problems observed in the motor neurons of ALS patients with the SOD1 A4V mutation.
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Affiliation(s)
- Luan de Holanda Paranhos
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
| | | | - Aline de Araújo Brasil
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
| | | | - Gabriela Delaqua Ribeiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - Daniela Dias Queiroz
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - Vanessa Mattos Dos Santos
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
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Hernández-Vásquez CI, García-García JH, Pérez-Ortega ER, Martínez-Segundo AG, Damas-Buenrostro LC, Pereyra-Alférez B. Expression patterns of Mal genes and association with differential maltose and maltotriose transport rate of two Saccharomyces pastorianus yeasts. Appl Environ Microbiol 2024; 90:e0039724. [PMID: 38975758 PMCID: PMC11267901 DOI: 10.1128/aem.00397-24] [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: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Beer brewing is a well-known process that still faces great challenges, such as the total consumption of sugars present in the fermentation media. Lager-style beer, a major worldwide beer type, is elaborated by Saccharomyces pastorianus (Sp) yeast, which must ferment high maltotriose content worts, but its consumption represents a notable problem, especially among Sp strains belonging to group I. Factors, such as fermentation conditions, presence of maltotriose transporters, transporter copy number variation, and genetic regulation variations contribute to this issue. We assess the factors affecting fermentation in two Sp yeast strains: SpIB1, with limited maltotriose uptake, and SpIB2, known for efficient maltotriose transport. Here, SpIB2 transported significantly more maltose (28%) and maltotriose (32%) compared with SpIB1. Furthermore, SpIB2 expressed all MAL transporters (ScMALx1, SeMALx1, ScAGT1, SeAGT1, MTT1, and MPHx) on the first day of fermentation, whereas SpIB1 only exhibited ScMalx1, ScAGT1, and MPH2/3 genes. Some SpIB2 transporters had polymorphic transmembrane domains (TMD) resembling MTT1, accompanied by higher expression of these transporters and its positive regulator genes, such as MAL63. These findings suggest that, in addition to the factors mentioned above, positive regulators of Mal transporters contribute significantly to phenotypic diversity in maltose and maltotriose consumption among the studied lager yeast strains.IMPORTANCEBeer, the third most popular beverage globally with a 90% market share in the alcoholic beverage industry, relies on Saccharomyces pastorianus (Sp) strains for lager beer production. These strains exhibit phenotypic diversity in maltotriose consumption, a crucial process for the acceptable organoleptic profile in lager beer. This diversity ranges from Sp group II strains with a notable maltotriose-consuming ability to Sp group I strains with limited capacity. Our study highlights that differential gene expression of maltose and maltotriose transporters and its upstream trans-elements, such as MAL gene-positive regulators, adds complexity to this variation. This insight can contribute to a more comprehensive analysis needed to the development of controlled and efficient biotechnological processes in the beer brewing industry.
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Affiliation(s)
- César I. Hernández-Vásquez
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
| | - Jorge H. García-García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
| | | | | | | | - Benito Pereyra-Alférez
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
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6
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Ma Q, Yi J, Tang Y, Geng Z, Zhang C, Sun W, Liu Z, Xiong W, Wu H, Xie X. Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals. Biotechnol Adv 2024; 73:108380. [PMID: 38759845 DOI: 10.1016/j.biotechadv.2024.108380] [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: 01/07/2024] [Revised: 04/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Carbon source is crucial for the cell growth and metabolism in microorganisms, and its utilization significantly affects the synthesis efficiency of target products in microbial cell factories. Compared with a single carbon source, co-utilizing carbon sources provide an alternative approach to optimize the utilization of different carbon sources for efficient biosynthesis of many chemicals with higher titer/yield/productivity. However, the efficiency of bioproduction is significantly limited by the sequential utilization of a preferred carbon source and secondary carbon sources, attributed to carbon catabolite repression (CCR). This review aimed to introduce the mechanisms of CCR and further focus on the summary of the strategies for co-utilization of carbon sources, including alleviation of CCR, engineering of the transport and metabolism of secondary carbon sources, compulsive co-utilization in single culture, co-utilization of carbon sources via co-culture, and evolutionary approaches. The findings of representative studies with a significant improvement in the bioproduction of chemicals via the co-utilization of carbon sources were discussed in this review. It suggested that by combining rational metabolic engineering and irrational evolutionary approaches, co-utilizing carbon sources can significantly contribute to the bioproduction of chemicals.
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Affiliation(s)
- Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinhang Yi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yulin Tang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zihao Geng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chunyue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenchao Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengkai Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenwen Xiong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China.
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7
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Nguyen V, Li Y, Lu T. Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1442-1453. [PMID: 38657170 PMCID: PMC11103795 DOI: 10.1021/acssynbio.3c00542] [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] [Indexed: 04/26/2024]
Abstract
Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. This study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.
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Affiliation(s)
- Viviana Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yifei Li
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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8
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Rahmat E, Yu JS, Lee BS, Lee J, Ban Y, Yim NH, Park JH, Kang CH, Kim KH, Kang Y. Secondary metabolites and transcriptomic analysis of novel pulcherrimin producer Metschnikowia persimmonesis KIOM G15050: A potent and safe food biocontrol agent. Heliyon 2024; 10:e28464. [PMID: 38571591 PMCID: PMC10988027 DOI: 10.1016/j.heliyon.2024.e28464] [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: 11/09/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
Metschnikowia persimmonesis, a novel endophytic yeast strain isolated from Diospyros kaki calyx, possesses strong antimicrobial activity. We investigated its potential use as an environmentally safe food biocontrol agent through genomics, transcriptomics, and metabolomics. Secondary metabolites were isolated from M. persimmonesis, followed by chemical structure elucidation, PUL gene cluster identification, and RNA sequencing. Pulcherrimin was isolated using 2 M NaOH, its structure was confirmed, and the yield was quantified. Biocontrol efficacy of M. persimmonesis on persimmon fruits and calyx was evaluated by assessing lesion diameter and disease incidence. Following compounds were isolated from M. persimmonesis co-culture with Botrytis cinerea and Fusarium oxysporum: fusaric acid, benzoic acid, benzeneacetic acid, 4-hydroxybenzeneacetic acid, 4-(-2-hydoxyethyl)-benzoic acid, cyclo (Leu-Leu), benzenemethanol, 4-hydroxy-benzaldehide, 2-hydroxy-4-methoxy-benzoic acid, 4-hydroxy-benzoic acid, lumichrome, heptadecanoic acid, and nonadecanoic acid. Exposing M. persimmonesis to different growth media conditions (with or without sugar) resulted in the isolation of five compounds: Tyrosol, Cyclo (Pro-Val), cyclo(L-Pro-L-Tyr), cyclo(Leu-Leu), and cyclo(l-tyrosilylicine). Differentially expressed gene analysis revealed 3264 genes that were significantly expressed (fold change ≥2 and p-value ≤0.05) during M. persimmonesis growth in different media, of which only 270 (8.27%) showed altered expression in all sample combinations with Luria-Bertani Agar as control. Minimal media with ferric ions and tween-80 triggered the most gene expression changes, with the highest levels of PUL gene expression and pulcherrimin yield (262.166 mg/L) among all media treatments. M. persimmonesis also produced a higher amount of pulcherrimin (209.733 mg/L) than Metschnikowia pulcherrima (152.8 mg/L). M. persimmonesis inhibited the growth of Fusarium oxysporum in persimmon fruit and calyx. Toxicity evaluation of M. persimmonesis extracts showed no harmful effects on the liver and mitochondria of zebrafish, and no potential risk of cardiotoxicity in hERG-HEK293 cell lines. Thus, M. persimmonesis can be commercialized as a potent and safe biocontrol agent for preserving food products.
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Affiliation(s)
- Endang Rahmat
- Biotechnology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Jae Sik Yu
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, 05006, Republic of Korea
| | - Bum Soo Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jiyoung Lee
- University of Science & Technology (UST), KIOM Campus, Korean Convergence Medicine Major, Daejeon, 34054, Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Yeongjun Ban
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, 111 Geonjae-ro, Naju-si, Jeollanam-do, 58245, Republic of Korea
| | - Nam-Hui Yim
- Korean Medicine Application Center, Korea Institute of Oriental Medicine 70 Cheomdan-ro, Dong-gu, Daegu, 41062, Republic of Korea
| | - Jeong Hwan Park
- KM Data Division, Korea Institute of Oriental Medicine (KIOM), 1672 Yuseongdae-ro, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Youngmin Kang
- University of Science & Technology (UST), KIOM Campus, Korean Convergence Medicine Major, Daejeon, 34054, Republic of Korea
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, 111 Geonjae-ro, Naju-si, Jeollanam-do, 58245, Republic of Korea
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9
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Sjöberg G, Reķēna A, Fornstad M, Lahtvee PJ, van Maris AJA. Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae. Metab Eng 2024; 82:49-59. [PMID: 38309619 DOI: 10.1016/j.ymben.2024.01.007] [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: 08/21/2023] [Revised: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Enzyme-constrained genome-scale models (ecGEMs) have potential to predict phenotypes in a variety of conditions, such as growth rates or carbon sources. This study investigated if ecGEMs can guide metabolic engineering efforts to swap anaerobic redox-neutral ATP-providing pathways in yeast from alcoholic fermentation to equimolar co-production of 2,3-butanediol and glycerol. With proven pathways and low product toxicity, the ecGEM solution space aligned well with observed phenotypes. Since this catabolic pathway provides only one-third of the ATP of alcoholic fermentation (2/3 versus 2 ATP per glucose), the ecGEM predicted a growth decrease from 0.36 h-1 in the reference to 0.175 h-1 in the engineered strain. However, this <3-fold decrease would require the specific glucose consumption rate to increase. Surprisingly, after the pathway swap the engineered strain immediately grew at 0.15 h-1 with a glucose consumption rate of 29 mmol (g CDW)-1 h-1, which was indeed higher than reference (23 mmol (g CDW)-1 h-1) and one of the highest reported for S. cerevisiae. The accompanying 2,3-butanediol- (15.8 mmol (g CDW)-1 h-1) and glycerol (19.6 mmol (g CDW)-1 h-1) production rates were close to predicted values. Proteomics confirmed that this increased consumption rate was facilitated by enzyme reallocation from especially ribosomes (from 25.5 to 18.5 %) towards glycolysis (from 28.7 to 43.5 %). Subsequently, 200 generations of sequential transfer did not improve growth of the engineered strain, showing the use of ecGEMs in predicting opportunity space for laboratory evolution. The observations in this study illustrate both the current potential, as well as future improvements, of ecGEMs as a tool for both metabolic engineering and laboratory evolution.
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Affiliation(s)
- Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alīna Reķēna
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Matilda Fornstad
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petri-Jaan Lahtvee
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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10
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Watanabe D. Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation. Biosci Biotechnol Biochem 2024; 88:237-241. [PMID: 38006236 DOI: 10.1093/bbb/zbad167] [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: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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11
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Pontes A, Paraíso F, Liu YC, Limtong S, Jindamorakot S, Jespersen L, Gonçalves C, Rosa CA, Tsai IJ, Rokas A, Hittinger CT, Gonçalves P, Sampaio JP. Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. iScience 2024; 27:108987. [PMID: 38333711 PMCID: PMC10850751 DOI: 10.1016/j.isci.2024.108987] [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: 09/05/2023] [Revised: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Savitree Limtong
- Department of Microbiology Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
| | - Sasitorn Jindamorakot
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
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12
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Wang ZD, Wang BT, Jin L, Ruan HH, Jin FJ. Implications of carbon catabolite repression for Aspergillus-based cell factories: A review. Biotechnol J 2024; 19:e2300551. [PMID: 38403447 DOI: 10.1002/biot.202300551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 02/27/2024]
Abstract
Carbon catabolite repression (CCR) is a global regulatory mechanism that allows organisms to preferentially utilize a preferred carbon source (usually glucose) by suppressing the expression of genes associated with the utilization of nonpreferred carbon sources. Aspergillus is a large genus of filamentous fungi, some species of which have been used as microbial cell factories for the production of organic acids, industrial enzymes, pharmaceuticals, and other fermented products due to their safety, substrate convenience, and well-established post-translational modifications. Many recent studies have verified that CCR-related genetic alterations can boost the yield of various carbohydrate-active enzymes (CAZymes), even under CCR conditions. Based on these findings, we emphasize that appropriate regulation of the CCR pathway, especially the expression of the key transcription factor CreA gene, has great potential for further expanding the application of Aspergillus cell factories to develop strains for industrial CAZymes production. Further, the genetically modified CCR strains (chassis hosts) can also be used for the production of other useful natural products and recombinant proteins, among others. We here review the regulatory mechanisms of CCR in Aspergillus and its direct application in enzyme production, as well as its potential application in organic acid and pharmaceutical production to illustrate the effects of CCR on Aspergillus cell factories.
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Affiliation(s)
- Zhen-Dong Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Hua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
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13
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [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: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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14
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Navale AM. Glucose Transporter and Sensor Mechanisms in Fungal Pathogens as Potential Drug Targets. Curr Rev Clin Exp Pharmacol 2024; 19:250-258. [PMID: 37861001 DOI: 10.2174/0127724328263050230923154326] [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: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023]
Abstract
Fungal infections are emerging as major health challenges in recent years. The development of resistance against existing antifungal agents needs urgent attention and action. The limited classes of antifungal drugs available, their tendency to cause adverse effects, lack of effectiveness, etc., are the major limitations of current therapy. Thus, there is a pressing demand for new antifungal drug classes to cope with the present circumstances. Glucose is the key source of energy for all organisms, including fungi. Glucose plays a crucial role as a source of carbon and energy for processes like virulence, growth, invasion, biofilm formation, and resistance development. The glucose transport and sensing mechanisms are well developed in these organisms as an important strategy to sustain survival. Modulating these transport or sensor mechanisms may serve as an important strategy to inhibit fungal growth. Moreover, the structural difference between human and fungal glucose transporters makes them more appealing as drug targets. Limited literature is available for fungal glucose entry mechanisms. This review provides a comprehensive account of sugar transport mechanisms in common fungal pathogens.
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Affiliation(s)
- Archana Mohit Navale
- Department of Pharmacology, Parul Institute of Pharmacy, Parul University, Limda, India
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15
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Metur SP, Klionsky DJ. Nutrient-dependent signaling pathways that control autophagy in yeast. FEBS Lett 2024; 598:32-47. [PMID: 37758520 PMCID: PMC10841420 DOI: 10.1002/1873-3468.14741] [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: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Macroautophagy/autophagy is a highly conserved catabolic process vital for cellular stress responses and maintaining equilibrium within the cell. Malfunctioning autophagy has been implicated in the pathogenesis of various diseases, including certain neurodegenerative disorders, diabetes, metabolic diseases, and cancer. Cells face diverse metabolic challenges, such as limitations in nitrogen, carbon, and minerals such as phosphate and iron, necessitating the integration of complex metabolic information. Cells utilize a signal transduction network of sensors, transducers, and effectors to coordinate the execution of the autophagic response, concomitant with the severity of the nutrient-starvation condition. This review presents the current mechanistic understanding of how cells regulate the initiation of autophagy through various nutrient-dependent signaling pathways. Emphasizing findings from studies in yeast, we explore the emerging principles that underlie the nutrient-dependent regulation of autophagy, significantly shaping stress-induced autophagy responses under various metabolic stress conditions.
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Affiliation(s)
- Shree Padma Metur
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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16
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Feng Y, Chen Y, Wu X, Chen J, Zhou Q, Liu B, Zhang L, Yi C. Interplay of energy metabolism and autophagy. Autophagy 2024; 20:4-14. [PMID: 37594406 PMCID: PMC10761056 DOI: 10.1080/15548627.2023.2247300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Macroautophagy/autophagy, is widely recognized for its crucial role in enabling cell survival and maintaining cellular energy homeostasis during starvation or energy stress. Its regulation is intricately linked to cellular energy status. In this review, covering yeast, mammals, and plants, we aim to provide a comprehensive overview of the understanding of the roles and mechanisms of carbon- or glucose-deprivation related autophagy, showing how cells effectively respond to such challenges for survival. Further investigation is needed to determine the specific degraded substrates by autophagy during glucose or energy deprivation and the diverse roles and mechanisms during varying durations of energy starvation.Abbreviations: ADP: adenosine diphosphate; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATP: adenosine triphosphate; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD: glucose deprivation; GFP: green fluorescent protein; GTPases: guanosine triphosphatases; HK2: hexokinase 2; K phaffii: Komagataella phaffii; LD: lipid droplet; MAP1LC3/LC3: microtubule-associated protein1 light chain 3; MAPK: mitogen-activated protein kinase; Mec1: mitosis entry checkpoint 1; MTOR: mechanistic target of rapamycin kinase; NAD (+): nicotinamide adenine dinucleotide; OGD: oxygen and glucose deprivation; PAS: phagophore assembly site; PCD: programmed cell death; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; ROS: reactive oxygen species; S. cerevisiae: Saccharomyces cerevisiae; SIRT1: sirtuin 1; Snf1: sucrose non-fermenting 1; STK11/LKB1: serine/threonine kinase 11; TFEB: transcription factor EB; TORC1: target of rapamycin complex 1; ULK1: unc-51 like kinase 1; Vps27: vacuolar protein sorting 27; Vps4: vacuolar protein sorting 4.
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Affiliation(s)
- Yuyao Feng
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Ying Chen
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyong Wu
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junye Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Qingyan Zhou
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Cong Yi
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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17
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Watanabe D, Kumano M, Sugimoto Y, Takagi H. Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p in Saccharomyces cerevisiae. Int J Mol Sci 2023; 25:304. [PMID: 38203474 PMCID: PMC10778621 DOI: 10.3390/ijms25010304] [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: 12/03/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
A cell population characterized by the release of glucose repression and known as [GAR+] emerges spontaneously in the yeast Saccharomyces cerevisiae. This study revealed that the [GAR+] variants exhibit retarded alcoholic fermentation when glucose is the sole carbon source. To identify the key to the altered glucose response, the gene expression profile of [GAR+] cells was examined. Based on RNA-seq data, the [GAR+] status was linked to impaired function of the Cyc8p-Tup1p complex. Loss of Cyc8p led to a decrease in the initial rate of alcoholic fermentation under glucose-rich conditions via the inactivation of pyruvate decarboxylase, an enzyme unique to alcoholic fermentation. These results suggest that Cyc8p can become inactive to attenuate alcoholic fermentation. These findings may contribute to the elucidation of the mechanism of non-genetic heterogeneity in yeast alcoholic fermentation.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Maika Kumano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan
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18
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Chen Y, Xu J, Liu X, Guo L, Yi P, Cheng C. Potential therapies targeting nuclear metabolic regulation in cancer. MedComm (Beijing) 2023; 4:e421. [PMID: 38034101 PMCID: PMC10685089 DOI: 10.1002/mco2.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023] Open
Abstract
The interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism-genome transcriptional axis.
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Affiliation(s)
- Yanjie Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Jie Xu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Xiaoyi Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Linlin Guo
- Department of Microbiology and ImmunologyThe Indiana University School of MedicineIndianapolisIndianaUSA
| | - Ping Yi
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Chunming Cheng
- Department of Radiation OncologyJames Comprehensive Cancer Center and College of Medicine at The Ohio State UniversityColumbusOhioUSA
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19
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Bicev RN, de Souza Degenhardt MF, de Oliveira CLP, da Silva ER, Degrouard J, Tresset G, Ronsein GE, Demasi M, da Cunha FM. Glucose restriction in Saccharomyces cerevisiae modulates the phosphorylation pattern of the 20S proteasome and increases its activity. Sci Rep 2023; 13:19383. [PMID: 37938622 PMCID: PMC10632367 DOI: 10.1038/s41598-023-46614-x] [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: 04/17/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Caloric restriction is known to extend the lifespan and/or improve diverse physiological parameters in a vast array of organisms. In the yeast Saccharomyces cerevisiae, caloric restriction is performed by reducing the glucose concentration in the culture medium, a condition previously associated with increased chronological lifespan and 20S proteasome activity in cell extracts, which was not due to increased proteasome amounts in restricted cells. Herein, we sought to investigate the mechanisms through which glucose restriction improved proteasome activity and whether these activity changes were associated with modifications in the particle conformation. We show that glucose restriction increases the ability of 20S proteasomes, isolated from Saccharomyces cerevisiae cells, to degrade model substrates and whole proteins. In addition, threonine 55 and/or serine 56 of the α5-subunit, were/was consistently found to be phosphorylated in proteasomes isolated from glucose restricted cells, which may be involved in the increased proteolysis capacity of proteasomes from restricted cells. We were not able to observe changes in the gate opening nor in the spatial conformation in 20S proteasome particles isolated from glucose restricted cells, suggesting that the changes in activity were not accompanied by large conformational alterations in the 20S proteasome but involved allosteric activation of proteasome catalytic site.
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Affiliation(s)
- Renata Naporano Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | | | | | - Emerson Rodrigo da Silva
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405, Orsay, France
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405, Orsay, France
| | - Graziella Eliza Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Marilene Demasi
- Laboratório de Bioquímica, Instituto Butantan, São Paulo, SP, Brasil.
| | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil.
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20
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Harvey HJ, Hendry AC, Chirico M, Archer DB, Avery SV. Adaptation to sorbic acid in low sugar promotes resistance of yeast to the preservative. Heliyon 2023; 9:e22057. [PMID: 38034742 PMCID: PMC10682675 DOI: 10.1016/j.heliyon.2023.e22057] [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: 10/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
The weak acid sorbic acid is a common preservative used in soft drink beverages to control microbial spoilage. Consumers and industry are increasingly transitioning to low-sugar food formulations, but potential impacts of reduced sugar on sorbic acid efficacy are barely characterised. In this study, we report enhanced sorbic acid resistance of yeast in low-glucose conditions. We had anticipated that low glucose would induce respiratory metabolism, which was shown previously to be targeted by sorbic acid. However, a shift from respiratory to fermentative metabolism upon sorbic acid exposure of Saccharomyces cerevisiae was correlated with relative resistance to sorbic acid in low glucose. Fermentation-negative yeast species did not show the low-glucose resistance phenotype. Phenotypes observed for certain yeast deletion strains suggested roles for glucose signalling and repression pathways in the sorbic acid resistance at low glucose. This low-glucose induced sorbic acid resistance was reversed by supplementing yeast cultures with succinic acid, a metabolic intermediate of respiratory metabolism (and a food-safe additive) that promoted respiration. The results indicate that metabolic adaptation of yeast can promote sorbic acid resistance at low glucose, a consideration for the preservation of foodstuffs as both food producers and consumers move towards a reduced sugar landscape.
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Affiliation(s)
- Harry J. Harvey
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alex C. Hendry
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marcella Chirico
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David B. Archer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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21
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Liu H, Luo Z, Rao Y. Manipulation of fungal cell wall integrity to improve production of fungal natural products. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:49-78. [PMID: 38783724 DOI: 10.1016/bs.aambs.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Fungi, as an important industrial microorganism, play an essential role in the production of natural products (NPs) due to their advantages of utilizing cheap raw materials as substrates and strong protein secretion ability. Although many metabolic engineering strategies have been adopted to enhance the biosynthetic pathway of NPs in fungi, the fungal cell wall as a natural barrier tissue is the final and key step that affects the efficiency of NPs synthesis. To date, many important progresses have been achieved in improving the synthesis of NPs by regulating the cell wall structure of fungi. In this review, we systematically summarize and discuss various strategies for modifying the cell wall structure of fungi to improve the synthesis of NPs. At first, the cell wall structure of different types of fungi is systematically described. Then, strategies to disrupt cell wall integrity (CWI) by regulating the synthesis of cell wall polysaccharides and binding proteins are summarized, which have been applied to improve the synthesis of NPs. In addition, we also summarize the studies on the regulation of CWI-related signaling pathway and the addition of exogenous components for regulating CWI to improve the synthesis of NPs. Finally, we propose the current challenges and essential strategies to usher in an era of more extensive manipulation of fungal CWI to improve the production of fungal NPs.
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Affiliation(s)
- Huiling Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P.R. China
| | - Zhengshan Luo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P.R. China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P.R. China.
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22
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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Liu J, Yang J, Yuan L, Wu C, Jiang Y, Zhuang W, Ying H, Yang S. Modulated Arabinose Uptake and cAMP Signaling Synergistically Improve Glucose and Arabinose Consumption in Recombinant Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12797-12806. [PMID: 37592391 DOI: 10.1021/acs.jafc.3c04386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
During the production of ethanol from lignocellulose-derived sugars, recombinant yeasts tend to utilize xylose and arabinose after glucose exhaustion. So far, many glucose-insensitive pentose transporters have been reported to counteract this phenomenon, but few studies have described intracellular factors. In this study, the combination of adaptive evolution, comparative genomics, and genetic complementation revealed that the hexokinase-deficient (Hxk0) arabinose-fermenting Saccharomyces cerevisiae requires the arabinose transporter variant Gal2-N376T and the mutations of guanine nucleotide exchange factor Cdc25 to overcome glucose restriction during arabinose assimilation. The results showed that the Hxk0 recombinant yeasts could lower the metabolic/physiological threshold of cell proliferation by downregulating the intracellular cAMP levels, resulting in smaller cells and increased arabinose assimilation under glucose restriction. In the medium containing 80 g/L glucose and 20 g/L arabinose, the evolved strain restoring the hexokinase activity completed fermentation at 22 h, compared to 24 h for the parental strain. Overall, the experimental results provide new insights into glucose repression of biorefinery yeasts.
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Affiliation(s)
- Jinle Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Junjie Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lihua Yuan
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chunhua Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng Yang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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Wang L, Wang A, Wang D, Hong J. The novel properties of Kluyveromyces marxianus glucose sensor/receptor repressor pathway and the construction of glucose repression-released strains. Microb Cell Fact 2023; 22:123. [PMID: 37430283 DOI: 10.1186/s12934-023-02138-7] [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: 03/14/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Glucose repression in yeast leads to the sequential or diauxic utilization of mixed sugars and reduces the co-utilization of glucose and xylose from lignocellulosic biomasses. Study of the glucose sensing pathway helps to construct glucose repression-released yeast strains and enhance the utilization of lignocellulosic biomasses. RESULTS Herein, the glucose sensor/receptor repressor (SRR) pathway of Kluyveromyces marxianus which mainly consisted of KmSnf3, KmGrr1, KmMth1, and KmRgt1 was studied. The disruption of KmSNF3 led to a release of glucose repression, enhanced xylose consumption and did not result in deficient glucose utilization. Over-expression of glucose transporter gene restored the mild decrease of glucose utilization ability of Kmsnf3 strain to a similar level of the wildtype strain but did not restore glucose repression. Therefore, the repression on glucose transporter is parallel to glucose repression to xylose and other alternative carbon utilization. KmGRR1 disruption also released glucose repression and kept glucose utilization ability, although its xylose utilization ability was very weak with xylose as sole carbon source. The stable mutant of KmMth1-ΔT enabled the release of glucose repression irrespective that the genetic background was Kmsnf3, Kmmth1, or wildtype. Disruption of KmSNF1 in the Kmsnf3 strain or KmMTH1-ΔT overexpression in Kmsnf1 strain kept constitutive glucose repression, indicating that KmSNF1 was necessary to release the glucose repression in both SRR and Mig1-Hxk2 pathway. Finally, overexpression of KmMTH1-ΔT released the glucose repression to xylose utilization in S. cerevisiae. CONCLUSION The glucose repression-released K. marxianus strains constructed via a modified glucose SRR pathway did not lead to a deficiency in the utilization ability of sugar. The obtained thermotolerant, glucose repression-released, and xylose utilization-enhanced strains are good platforms for the construction of efficient lignocellulosic biomass utilization yeast strains.
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Affiliation(s)
- Lingya Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Anran Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, 230026, P. R. China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
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Vazquez‐Calvo C, Kohler V, Höög JL, Büttner S, Ott M. Newly imported proteins in mitochondria are particularly sensitive to aggregation. Acta Physiol (Oxf) 2023; 238:e13985. [PMID: 37171464 PMCID: PMC10909475 DOI: 10.1111/apha.13985] [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: 02/28/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
AIM A functional proteome is essential for life and maintained by protein quality control (PQC) systems in the cytosol and organelles. Protein aggregation is an indicator of a decline of PQC linked to aging and disease. Mitochondrial PQC is critical to maintain mitochondrial function and thus cellular fitness. How mitochondria handle aggregated proteins is not well understood. Here we tested how the metabolic status impacts on formation and clearance of aggregates within yeast mitochondria and assessed which proteins are particularly sensitive to denaturation. METHODS Confocal microscopy, electron microscopy, immunoblotting and genetics were applied to assess mitochondrial aggregate handling in response to heat shock and ethanol using the mitochondrial disaggregase Hsp78 as a marker for protein aggregates. RESULTS We show that aggregates formed upon heat or ethanol stress with different dynamics depending on the metabolic state. While fermenting cells displayed numerous small aggregates that coalesced into one large foci that was resistant to clearance, respiring cells showed less aggregates and cleared these aggregates more efficiently. Acute inhibition of mitochondrial translation had no effect, while preventing protein import into mitochondria by inhibition of cytosolic translation prevented aggregate formation. CONCLUSION Collectively, our data show that the metabolic state of the cells impacts the dynamics of aggregate formation and clearance, and that mainly newly imported and not yet assembled proteins are prone to form aggregates. Because mitochondrial functionality is crucial for cellular metabolism, these results highlight the importance of efficient protein biogenesis to maintain the mitochondrial proteome operational during metabolic adaptations and cellular stress.
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Affiliation(s)
- Carmela Vazquez‐Calvo
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Johanna L. Höög
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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26
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Nijland JG, Zhang X, Driessen AJM. D-xylose accelerated death of pentose metabolizing Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:67. [PMID: 37069654 PMCID: PMC10111712 DOI: 10.1186/s13068-023-02320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/10/2023] [Indexed: 04/19/2023]
Abstract
Rapid and effective consumption of D-xylose by Saccharomyces cerevisiae is essential for cost-efficient cellulosic bioethanol production. Hence, heterologous D-xylose metabolic pathways have been introduced into S. cerevisiae. An effective solution is based on a xylose isomerase in combination with the overexpression of the xylulose kinase (Xks1) and all genes of the non-oxidative branch of the pentose phosphate pathway. Although this strain is capable of consuming D-xylose, growth inhibition occurs at higher D-xylose concentrations, even abolishing growth completely at 8% D-xylose. The decreased growth rates are accompanied by significantly decreased ATP levels. A key ATP-utilizing step in D-xylose metabolism is the phosphorylation of D-xylulose by Xks1. Replacement of the constitutive promoter of XKS1 by the galactose tunable promoter Pgal10 allowed the controlled expression of this gene over a broad range. By decreasing the expression levels of XKS1, growth at high D-xylose concentrations could be restored concomitantly with increased ATP levels and high rates of xylose metabolism. These data show that in fermentations with high D-xylose concentrations, too high levels of Xks1 cause a major drain on the cellular ATP levels thereby reducing the growth rate, ultimately causing substrate accelerated death. Hence, expression levels of XKS1 in S. cerevisiae needs to be tailored for the specific growth conditions and robust D-xylose metabolism.
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Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Xiaohuan Zhang
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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Zhang Y, Su M, Chen Y, Wang Z, Nielsen J, Liu Z. Engineering yeast mitochondrial metabolism for 3-hydroxypropionate production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:64. [PMID: 37031180 PMCID: PMC10082987 DOI: 10.1186/s13068-023-02309-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND With unique physiochemical environments in subcellular organelles, there has been growing interest in harnessing yeast organelles for bioproduct synthesis. Among these organelles, the yeast mitochondrion has been found to be an attractive compartment for production of terpenoids and branched-chain alcohols, which could be credited to the abundant supply of acetyl-CoA, ATP and cofactors. In this study we explored the mitochondrial potential for production of 3-hydroxypropionate (3-HP) and performed the cofactor engineering and flux control at the acetyl-CoA node to maximize 3-HP synthesis. RESULTS Metabolic modeling suggested that the mitochondrion serves as a more suitable compartment for 3-HP synthesis via the malonyl-CoA pathway than the cytosol, due to the opportunity to obtain a higher maximum yield and a lower oxygen consumption. With the malonyl-CoA reductase (MCR) targeted into the mitochondria, the 3-HP production increased to 0.27 g/L compared with 0.09 g/L with MCR expressed in the cytosol. With enhanced expression of dissected MCR enzymes, the titer reached to 4.42 g/L, comparable to the highest titer achieved in the cytosol so far. Then, the mitochondrial NADPH supply was optimized by overexpressing POS5 and IDP1, which resulted in an increase in the 3-HP titer to 5.11 g/L. Furthermore, with induced expression of an ACC1 mutant in the mitochondria, the final 3-HP production reached 6.16 g/L in shake flask fermentations. The constructed strain was then evaluated in fed-batch fermentations, and produced 71.09 g/L 3-HP with a productivity of 0.71 g/L/h and a yield on glucose of 0.23 g/g. CONCLUSIONS In this study, the yeast mitochondrion is reported as an attractive compartment for 3-HP production. The final 3-HP titer of 71.09 g/L with a productivity of 0.71 g/L/h was achieved in fed-batch fermentations, representing the highest titer reported for Saccharomyces cerevisiae so far, that demonstrated the potential of recruiting the yeast mitochondria for further development of cell factories.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mo Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Zheng Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Zhang K, Zhang W, Qin M, Li Y, Wang H. Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis. Int J Mol Sci 2023; 24:ijms24065888. [PMID: 36982961 PMCID: PMC10055971 DOI: 10.3390/ijms24065888] [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: 02/03/2023] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for the commercial production of desirable bioproducts. Sugar transporters are responsible for the import of substrate sugars and the conversion of ethanol and other products. Glucose-facilitated diffusion protein Glf is responsible for facilitating the diffusion of glucose uptake in Z. mobilis. However, another sugar transporter-encoded gene, ZMO0293, is poorly characterized. We employed gene deletion and heterologous expression mediated by the CRISPR/Cas method to investigate the role of ZMO0293. The results showed that deletion of the ZMO0293 gene slowed growth and reduced ethanol production and the activities of key enzymes involved in glucose metabolism in the presence of high concentrations of glucose. Moreover, ZMO0293 deletion caused different transcriptional changes in some genes of the Entner Doudoroff (ED) pathway in the ZM4-ΔZM0293 strain but not in ZM4 cells. The integrated expression of ZMO0293 restored the growth of the glucose uptake-defective strain Escherichia coli BL21(DE3)-ΔptsG. This study reveals the function of the ZMO0293 gene in Z. mobilis in response to high concentrations of glucose and provides a new biological part for synthetic biology.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wenwen Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Mengxing Qin
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yi Li
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Leite AC, Barbedo M, Costa V, Pereira C. The APC/C Activator Cdh1p Plays a Role in Mitochondrial Metabolic Remodelling in Yeast. Int J Mol Sci 2023; 24:ijms24044111. [PMID: 36835555 PMCID: PMC9967508 DOI: 10.3390/ijms24044111] [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: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Cdh1p is one of the two substrate adaptor proteins of the anaphase promoting complex/cyclosome (APC/C), a ubiquitin ligase that regulates proteolysis during cell cycle. In this work, using a proteomic approach, we found 135 mitochondrial proteins whose abundance was significantly altered in the cdh1Δ mutant, with 43 up-regulated proteins and 92 down-regulated proteins. The group of significantly up-regulated proteins included subunits of the mitochondrial respiratory chain, enzymes from the tricarboxylic acid cycle and regulators of mitochondrial organization, suggesting a metabolic remodelling towards an increase in mitochondrial respiration. In accordance, mitochondrial oxygen consumption and Cytochrome c oxidase activity increased in Cdh1p-deficient cells. These effects seem to be mediated by the transcriptional activator Yap1p, a major regulator of the yeast oxidative stress response. YAP1 deletion suppressed the increased Cyc1p levels and mitochondrial respiration in cdh1Δ cells. In agreement, Yap1p is transcriptionally more active in cdh1Δ cells and responsible for the higher oxidative stress tolerance of cdh1Δ mutant cells. Overall, our results unveil a new role for APC/C-Cdh1p in the regulation of the mitochondrial metabolic remodelling through Yap1p activity.
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Affiliation(s)
- Ana Cláudia Leite
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Maria Barbedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Clara Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-220408800
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Identification of traits to improve co-assimilation of glucose and xylose by adaptive evolution of Spathaspora passalidarum and Scheffersomyces stipitis yeasts. Appl Microbiol Biotechnol 2023; 107:1143-1157. [PMID: 36625916 DOI: 10.1007/s00253-023-12362-1] [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: 08/26/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
Lignocellulosic biomass is a renewable raw material for producing several high-value-added chemicals and fuels. In general, xylose and glucose are the major sugars in biomass hydrolysates, and their efficient utilization by microorganisms is critical for an economical production process. Yeasts capable of co-consuming mixed sugars might lead to higher yields and productivities in industrial fermentation processes. Herein, we performed adaptive evolution assays with two xylose-fermenting yeasts, Spathaspora passalidarum and Scheffersomyces stipitis, to obtain derived clones with improved capabilities of glucose and xylose co-consumption. Adapted strains were obtained after successive growth selection using xylose and the non-metabolized glucose analog 2-deoxy-D-glucose as a selective pressure. The co-fermentation capacity of evolved and parental strains was evaluated on xylose-glucose mixtures. Our results revealed an improved co-assimilation capability by the evolved strains; however, xylose and glucose consumption were observed at slower rates than the parental yeasts. Genome resequencing of the evolved strains revealed genes affected by non-synonymous variants that might be involved with the co-consumption phenotype, including the HXT2.4 gene that encodes a putative glucose transporter in Sp. passalidarum. Expression of this mutant HXT2.4 in Saccharomyces cerevisiae improved the cells' co-assimilation of glucose and xylose. Therefore, our results demonstrated the successful improvement of co-fermentation through evolutionary engineering and the identification of potential targets for further genetic engineering of different yeast strains. KEY POINTS: • Laboratory evolution assay was used to obtain improved sugar co-consumption of non-Saccharomyces strains. • Evolved Sp. passalidarum and Sc. stipitis were able to more efficiently co-ferment glucose and xylose. • A mutant Hxt2.4 permease, which co-transports xylose and glucose, was identified.
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Yamada Y, Shiroma A, Hirai S, Iwasaki J. Zuo1, a ribosome-associated J protein, is involved in glucose repression in Saccharomyces cerevisiae. FEMS Yeast Res 2023; 23:foad038. [PMID: 37550218 DOI: 10.1093/femsyr/foad038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
In Saccharomyces cerevisiae, the J-protein Zuo1 and the nonconventional Hsp70 homologue Ssz1 stimulate the ATPase activity of the chaperone proteins Ssb1 and Ssb2 (Ssb1/2), which are associated with the ribosomes. The dephosphorylation of sucrose nonfermenting 1 (Snf1) on Thr210 is required for glucose repression. The Ssb1/2 and 14-3-3 proteins Bmh1 and Bmh2 appear to be responsible for the dephosphorylation of Snf1 on Thr210 and glucose repression. Here, we investigated the role of Zuo1 in glucose repression. The zuo1∆ strain as well as the ssb1∆ssb2∆ strain exhibited a glucose-specific growth defect during logarithmic growth on glucose. Many of the respiratory chain genes examined were statistically significantly upregulated, but less than 2-fold, in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain on glucose. In addition, excessive phosphorylation of Snf1 on Thr210 was observed in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain in the presence of glucose. The mRNA levels of SSB1/2 and BMH1 were statistically significantly reduced by approximately 0.5- to 0.8-fold relative to the wild-type level in the zuo1∆ strain on glucose. These results suggest that Zuo1 is responsible for glucose repression, possibly by increasing the mRNA levels of SSB1/2 and BMH1 during growth on glucose.
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Affiliation(s)
- Yoichi Yamada
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Atsuki Shiroma
- School of Biological Science and Technology, College of Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Suguru Hirai
- School of Biological Science and Technology, College of Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Jun Iwasaki
- School of Biological Science and Technology, College of Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan
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Natural Variation in Diauxic Shift between Patagonian Saccharomyces eubayanus Strains. mSystems 2022; 7:e0064022. [PMID: 36468850 PMCID: PMC9765239 DOI: 10.1128/msystems.00640-22] [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] [Indexed: 12/12/2022] Open
Abstract
The study of natural variation can untap novel alleles with immense value for biotechnological applications. Saccharomyces eubayanus Patagonian isolates exhibit differences in the diauxic shift between glucose and maltose, representing a suitable model to study their natural genetic variation for novel strains for brewing. However, little is known about the genetic variants and chromatin regulators responsible for these differences. Here, we show how genome-wide chromatin accessibility and gene expression differences underlie distinct diauxic shift profiles in S. eubayanus. We identified two strains with a rapid diauxic shift between glucose and maltose (CL467.1 and CBS12357) and one strain with a remarkably low fermentation efficiency and longer lag phase during diauxic shift (QC18). This is associated in the QC18 strain with lower transcriptional activity and chromatin accessibility of specific genes of maltose metabolism and higher expression levels of glucose transporters. These differences are governed by the HAP complex, which differentially regulates gene expression depending on the genetic background. We found in the QC18 strain a contrasting phenotype to those phenotypes described in S. cerevisiae, where hap4Δ, hap5Δ, and cin5Δ knockouts significantly improved the QC18 growth rate in the glucose-maltose shift. The most profound effects were found between CIN5 allelic variants, suggesting that Cin5p could strongly activate a repressor of the diauxic shift in the QC18 strain but not necessarily in the other strains. The differences between strains could originate from the tree host from which the strains were obtained, which might determine the sugar source preference and the brewing potential of the strain. IMPORTANCE The diauxic shift has been studied in budding yeast under laboratory conditions; however, few studies have addressed the diauxic shift between carbon sources under fermentative conditions. Here, we study the transcriptional and chromatin structure differences that explain the natural variation in fermentative capacity and efficiency during diauxic shift of natural isolates of S. eubayanus. Our results show how natural genetic variants in transcription factors impact sugar consumption preferences between strains. These variants have different effects depending on the genetic background, with a contrasting phenotype to those phenotypes previously described in S. cerevisiae. Our study shows how relatively simple genetic/molecular modifications/editing in the lab can facilitate the study of natural variations of microorganisms for the brewing industry.
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Rewiring regulation on respiro-fermentative metabolism relieved Crabtree effects in Saccharomyces cerevisiae. Synth Syst Biotechnol 2022; 7:1034-1043. [PMID: 35801089 PMCID: PMC9241035 DOI: 10.1016/j.synbio.2022.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 11/20/2022] Open
Abstract
The respiro-fermentative metabolism in the yeast Saccharomyces cerevisiae, also called the Crabtree effect, results in lower energy efficiency and biomass yield which can impact yields of chemicals to be produced using this cell factory. Although it can be engineered to become Crabtree negative, the slow growth and glucose consumption rate limit its industrial application. Here the Crabtree effect in yeast can be alleviated by engineering the transcription factor Mth1 involved in glucose signaling and a subunit of the RNA polymerase II mediator complex Med2. It was found that the mutant with the MTH1A81D&MED2*432Y allele could grow in glucose rich medium with a specific growth rate of 0.30 h−1, an ethanol yield of 0.10 g g−1, and a biomass yield of 0.21 g g−1, compared with a specific growth rate of 0.40 h−1, an ethanol yield of 0.46 g g−1, and a biomass yield of 0.11 g g−1 in the wild-type strain CEN.PK 113-5D. Transcriptome analysis revealed significant downregulation of the glycolytic process, as well as the upregulation of the TCA cycle and the electron transfer chain. Significant expression changes of several reporter transcription factors were also identified, which might explain the higher energy efficiencies in the engineered strain. We further demonstrated the potential of the engineered strain with the production of 3-hydroxypropionic acid at a titer of 2.04 g L−1, i.e., 5.4-fold higher than that of a reference strain, indicating that the alleviated glucose repression could enhance the supply of mitochondrial acetyl-CoA. These results suggested that the engineered strain could be used as an efficient cell factory for mitochondrial production of acetyl-CoA derived chemicals.
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Li J, Zeng Y, Wang WB, Wan QQ, Liu CG, den Haan R, van Zyl WH, Zhao XQ. Increasing extracellular cellulase activity of the recombinant Saccharomyces cerevisiae by engineering cell wall-related proteins for improved consolidated processing of carbon neutral lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 365:128132. [PMID: 36252752 DOI: 10.1016/j.biortech.2022.128132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Sustainable bioproduction usingcarbon neutral feedstocks, especially lignocellulosic biomass, has attracted increasing attention due to concern over climate change and carbon reduction. Consolidated bioprocessing (CBP) of lignocellulosic biomass using recombinantyeast of Saccharomyces cerevisiaeis a promising strategy forlignocellulosic biorefinery. However, the economic viability is restricted by low enzyme secretion levels.For more efficient CBP, MIG1spsc01isolated from the industrial yeast which encodes the glucose repression regulator derivative was overexpressed. Increased extracellular cellobiohydrolase (CBH) activity was observed with unexpectedly decreased cell wall integrity. Further studies revealed that disruption ofCWP2, YGP1, andUTH1,which are functionally related toMIG1spsc01, also enhanced CBH secretion. Subsequently, improved cellulase production was achieved by simultaneous disruption ofYGP1and overexpression ofSED5, which remarkably increased extracellular CBH activity of 2.2-fold over the control strain. These results provide a novel strategy to improve the CBP yeast for bioconversion of carbon neutral biomass.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zeng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing-Qing Wan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Willem H van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch 7600, South Africa
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Tadioto V, Deoti JR, Müller C, de Souza BR, Fogolari O, Purificação M, Giehl A, Deoti L, Lucaroni AC, Matsushika A, Treichel H, Stambuk BU, Alves Junior SL. Prospecting and engineering yeasts for ethanol production under inhibitory conditions: an experimental design analysis. Bioprocess Biosyst Eng 2022:10.1007/s00449-022-02812-x. [DOI: 10.1007/s00449-022-02812-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
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Shen D, He X, Weng P, Liu Y, Wu Z. A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation. FEMS Yeast Res 2022; 22:6775076. [PMID: 36288242 DOI: 10.1093/femsyr/foac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/21/2022] [Accepted: 10/22/2022] [Indexed: 01/07/2023] Open
Abstract
Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.
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Affiliation(s)
- Dongxu Shen
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Xiaoli He
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Peifang Weng
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
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Schubert OT, Bloom JS, Sadhu MJ, Kruglyak L. Genome-wide base editor screen identifies regulators of protein abundance in yeast. eLife 2022; 11:e79525. [PMID: 36326816 PMCID: PMC9633064 DOI: 10.7554/elife.79525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Proteins are key molecular players in a cell, and their abundance is extensively regulated not just at the level of gene expression but also post-transcriptionally. Here, we describe a genetic screen in yeast that enables systematic characterization of how protein abundance regulation is encoded in the genome. The screen combines a CRISPR/Cas9 base editor to introduce point mutations with fluorescent tagging of endogenous proteins to facilitate a flow-cytometric readout. We first benchmarked base editor performance in yeast with individual gRNAs as well as in positive and negative selection screens. We then examined the effects of 16,452 genetic perturbations on the abundance of eleven proteins representing a variety of cellular functions. We uncovered hundreds of regulatory relationships, including a novel link between the GAPDH isoenzymes Tdh1/2/3 and the Ras/PKA pathway. Many of the identified regulators are specific to one of the eleven proteins, but we also found genes that, upon perturbation, affected the abundance of most of the tested proteins. While the more specific regulators usually act transcriptionally, broad regulators often have roles in protein translation. Overall, our novel screening approach provides unprecedented insights into the components, scale and connectedness of the protein regulatory network.
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Affiliation(s)
- Olga T Schubert
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH)ZürichSwitzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Meru J Sadhu
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Institute for Quantitative and Computational Biology, University of California, Los AngelesLos AngelesUnited States
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Metabolic recycling of storage lipids promotes squalene biosynthesis in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:108. [PMID: 36224649 PMCID: PMC9555684 DOI: 10.1186/s13068-022-02208-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Metabolic rewiring in microbes is an economical and sustainable strategy for synthesizing valuable natural terpenes. Terpenes are the largest class of nature-derived specialized metabolites, and many have valuable pharmaceutical or biological activity. Squalene, a medicinal terpene, is used as a vaccine adjuvant to improve the efficacy of vaccines, including pandemic coronavirus disease 2019 (COVID-19) vaccines, and plays diverse biological roles as an antioxidant and anticancer agent. However, metabolic rewiring interferes with inherent metabolic pathways, often in a way that impairs the cellular growth and fitness of the microbial host. In particular, as the key starting molecule for producing various compounds including squalene, acetyl-CoA is involved in numerous biological processes with tight regulation to maintain metabolic homeostasis, which limits redirection of metabolic fluxes toward desired products. RESULTS In this study, focusing on the recycling of surplus metabolic energy stored in lipid droplets, we show that the metabolic recycling of the surplus energy to acetyl-CoA can increase squalene production in yeast, concomitant with minimizing the metabolic interferences in inherent pathways. Moreover, by integrating multiple copies of the rate-limiting enzyme and implementing N-degron-dependent protein degradation to downregulate the competing pathway, we systematically rewired the metabolic flux toward squalene, enabling remarkable squalene production (1024.88 mg/L in a shake flask). Ultimately, further optimization of the fed-batch fermentation process enabled remarkable squalene production of 6.53 g/L. CONCLUSIONS Our demonstration of squalene production via engineered yeast suggests that plant- or animal-based supplies of medicinal squalene can potentially be complemented or replaced by industrial fermentation. This approach will also provide a universal strategy for the more stable and sustainable production of high-value terpenes.
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Kwak S, Crook N, Yoneda A, Ahn N, Ning J, Cheng J, Dantas G. Functional mining of novel terpene synthases from metagenomes. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:104. [PMID: 36209178 PMCID: PMC9548185 DOI: 10.1186/s13068-022-02189-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/29/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the genomes of uncultivated organisms living in the soil, indicating a vast array of putative terpenoids waiting to be discovered. RESULTS We aimed to develop a high-throughput functional metagenomic screening system for identifying novel terpene synthases from bacterial metagenomes by relieving the toxicity of terpene biosynthesis precursors to the Escherichia coli host. The precursor toxicity was achieved using an inducible operon encoding the prenyl pyrophosphate synthetic pathway and supplementation of the mevalonate precursor. Host strain and screening procedures were finely optimized to minimize false positives arising from spontaneous mutations, which avoid the precursor toxicity. Our functional metagenomic screening of human fecal metagenomes yielded a novel β-farnesene synthase, which does not show amino acid sequence similarity to known β-farnesene synthases. Engineered S. cerevisiae expressing the screened β-farnesene synthase produced 120 mg/L β-farnesene from glucose (2.86 mg/g glucose) with a productivity of 0.721 g/L∙h. CONCLUSIONS A unique functional metagenomic screening procedure was established for screening terpene synthases from metagenomic libraries. This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats.
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Affiliation(s)
- Suryang Kwak
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
| | - Nathan Crook
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Aki Yoneda
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
| | - Naomi Ahn
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
| | - Jie Ning
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
| | - Jiye Cheng
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, 4515 McKinley Avenue, Room 5121, Campus Box 8510, Saint Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110 USA
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Waite KA, Roelofs J. Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling. J Cell Sci 2022; 135:jcs259778. [PMID: 35975718 PMCID: PMC9482347 DOI: 10.1242/jcs.259778] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, proteasomes are enriched in cell nuclei, in which they execute important cellular functions. Nutrient stress can change this localization, indicating that proteasomes respond to the metabolic state of the cell. However, the signals that connect these processes remain poorly understood. Carbon starvation triggers a reversible translocation of proteasomes to cytosolic condensates known as proteasome storage granules. Surprisingly, we observed strongly reduced levels of proteasome granules when cells had active cellular respiration prior to starvation. This suggests that the mitochondrial activity of cells is a determining factor in the response of proteasomes to carbon starvation. Consistent with this, upon inhibition of mitochondrial function, we observed that proteasomes relocalize to granules. These links between proteasomes and metabolism involve specific signaling pathways, as we identified a mitogen-activated protein kinase (MAPK) cascade that is critical to the formation of proteasome granules after respiratory growth but not following glycolytic growth. Furthermore, the yeast homolog of AMP kinase, Snf1, is important for proteasome granule formation induced by mitochondrial inhibitors, but it is dispensable for granule formation following carbon starvation. We propose a model in which mitochondrial activity promotes nuclear localization of the proteasome. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., HLSIC 1077, Kansas City, KS 66160-7421, USA
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Xie D, Sun Y, Lei Y. Effect of glucose levels on carbon flow rate, antioxidant status, and enzyme activity of yeast during fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5333-5347. [PMID: 35318660 DOI: 10.1002/jsfa.11887] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The physiological metabolism of yeast has a significant impact on the quality of fermentation products. The present study aimed to investigate yeast metabolism in response to a changing glucose content environment, especially in fermentation products, as well as the change of carbon flow rate, antioxidant status, and yeast enzyme activity. RESULTS Yeast in a 0 g L-1 glucose level was subjected to carbon starvation stress, cell growth retardation and cell proliferation was significantly inadequate; in the logarithmic growth stage of yeast, at a 30 g L-1 glucose level, the carbon source mainly flowed to tricarboxylic acid cycle and pentose phosphate metabolism, cell division, proliferation, and increased cell growth. In later logarithmic growth period and stable period, carbon flowed into glycerol and trehalose metabolism, to cope with the environmental stress; yeast in 60 and 150 g L-1 glucose levels faced high glucose stress at the beginning, the content of reactive oxygen increased, malondialdehyde content increased, cell damage was reduced through the regulation of superoxide dismutase and catalase enzyme activities, and most of the carbon flowed into the metabolic pathway of ethanol, glycerol, and trehalose to cope with high glucose stress, the pentose phosphate pathway showed a large late influx, and NADPH also started to increase rapidly after 24 h. CONCLUSION Yeast was stressed in a high-sugar environment and ensured the activity of yeast by preferentially increasing the metabolic intensity of trehalose, glycerol, and glycolytic metabolism, weakening tricarboxylic acid metabolism, and first weakening and then increasing pentose phosphate metabolism. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Xie
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yingqi Sun
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yanan Lei
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
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Role of ROX1, SKN7, and YAP6 Stress Transcription Factors in the Production of Secondary Metabolites in Xanthophyllomyces dendrorhous. Int J Mol Sci 2022; 23:ijms23169282. [PMID: 36012547 PMCID: PMC9409151 DOI: 10.3390/ijms23169282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Xanthophyllomyces dendrorhous is a natural source of astaxanthin and mycosporines. This yeast has been isolated from high and cold mountainous regions around the world, and the production of these secondary metabolites may be a survival strategy against the stress conditions present in its environment. Biosynthesis of astaxanthin is regulated by catabolic repression through the interaction between MIG1 and corepressor CYC8–TUP1. To evaluate the role of the stress-associated transcription factors SKN7, ROX1, and YAP6, we employed an omic and phenotypic approach. Null mutants were constructed and grown in two fermentable carbon sources. The yeast proteome and transcriptome were quantified by iTRAQ and RNA-seq, respectively. The total carotenoid, sterol, and mycosporine contents were determined and compared to the wild-type strain. Each mutant strain showed significant metabolic changes compared to the wild type that were correlated to its phenotype. In a metabolic context, the principal pathways affected were glycolysis/gluconeogenesis, the pentose phosphate (PP) pathway, and the citrate (TCA) cycle. Additionally, fatty acid synthesis was affected. The absence of ROX1 generated a significant decline in carotenoid production. In contrast, a rise in mycosporine and sterol synthesis was shown in the absence of the transcription factors SKN7 and YAP6, respectively.
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2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity. PLoS Genet 2022; 18:e1010169. [PMID: 35951639 PMCID: PMC9398028 DOI: 10.1371/journal.pgen.1010169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/23/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export—thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.
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Supasil R, Suttisansanee U, Santivarangkna C, Tangsuphoom N, Khemthong C, Chupeerach C, On-nom N. Improvement of Sourdough and Bread Qualities by Fermented Water of Asian Pears and Assam Tea Leaves with Co-Cultures of Lactiplantibacillus plantarum and Saccharomyces cerevisiae. Foods 2022; 11:foods11142071. [PMID: 35885314 PMCID: PMC9318377 DOI: 10.3390/foods11142071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
Qualities of sourdough and sourdough bread using fermented water from Asian pears and Assam tea leaves with Lactiplantibacillus plantarum 299v and Saccharomyces cerevisiae TISTR 5059 as starter cultures were evaluated. Changes in the growth of lactic acid bacteria and yeast, pH, sourdough height, total phenolic contents (TPCs) and antioxidant activities detected by ORAC, FRAP and DPPH radical scavenging assays were monitored during sourdough production. Mature sourdough was achieved within 4 h after 18 h retard fermentation and used for bread production. The bread was then analyzed to determine chemical and physical properties, nutritional compositions, TPCs, antioxidant activities and sensory properties as well as shelf-life stability. Results showed that fermented water significantly promoted the growth of yeast and increased TPCs and antioxidant activities of sourdough. Compared to common sourdough bread, fermented water sourdough bread resulted in 10% lower sugar and 12% higher dietary fiber with improved consumer acceptability; TPCs and antioxidant activities also increased by 2–3 times. The fermented water sourdough bread maintained microbial quality within the standard range, with adequate TPCs after storage at room temperature for 7 days. Fermented water from Asian pears and Assam tea leaves with L. plantarum 299v and S. cerevisiae TISTR 5059 as starter cultures improved dough fermentation and bread quality.
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
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Wadler CS, Wolters JF, Fortney NW, Throckmorton KO, Zhang Y, Miller CR, Schneider RM, Wendt-Pienkowski E, Currie CR, Donohue TJ, Noguera DR, Hittinger CT, Thomas MG. Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:70. [PMID: 35751080 PMCID: PMC9233362 DOI: 10.1186/s13068-022-02168-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.
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Affiliation(s)
- Caryn S Wadler
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - John F Wolters
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Nathaniel W Fortney
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Kurt O Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Yaoping Zhang
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Caroline R Miller
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Rachel M Schneider
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Evelyn Wendt-Pienkowski
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Daniel R Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Chris Todd Hittinger
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA.
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47
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Garza NM, Zulkifli M, Gohil VM. Elesclomol elevates cellular and mitochondrial iron levels by delivering copper to the iron import machinery. J Biol Chem 2022; 298:102139. [PMID: 35714767 PMCID: PMC9270252 DOI: 10.1016/j.jbc.2022.102139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 01/16/2023] Open
Abstract
Copper (Cu) and iron (Fe) are redox-active metals that serve as cofactors for many essential cellular enzymes. Disruption in the intracellular homeostasis of these metals results in debilitating and frequently fatal human disorders, such as Menkes disease and Friedreich's ataxia. Recently, we reported that an investigational anticancer drug, elesclomol (ES), can deliver Cu to critical mitochondrial cuproenzymes and has the potential to be repurposed for treatment of Cu deficiency disorders. Here, we sought to determine the specificity of ES and the ES-Cu complex in delivering Cu to cuproenzymes in different intracellular compartments. Using a combination of yeast genetics, subcellular fractionation, and inductively coupled plasma-mass spectrometry-based metal measurements, we showed that ES and ES-Cu treatment results in an increase in cellular and mitochondrial Fe content, along with the expected increase in Cu. Utilizing yeast mutants of Cu and Fe transporters, we demonstrate that ES-based elevation in cellular Fe levels is independent of the major cellular Cu importer, but is dependent on the Fe importer Ftr1 and its partner Fet3, a multicopper-oxidase. As Fet3 is metallated in the Golgi lumen, we sought to uncover the mechanism by which Fet3 receives Cu from ES. Using yeast knockouts of genes involved in Cu delivery to Fet3, we determined that ES can bypass Atx1, a metallochaperone involved in Cu delivery to the Golgi membrane Cu pump, Ccc2, but not Ccc2 itself. Taken together, our study provides a mechanism by which ES distributes Cu in cells and impacts cellular and mitochondrial Fe homeostasis.
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Affiliation(s)
- Natalie M Garza
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA.
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Genome-edited Saccharomyces cerevisiae strains for improving quality, safety, and flavor of fermented foods. Food Microbiol 2022; 104:103971. [DOI: 10.1016/j.fm.2021.103971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/02/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
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49
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Sahin B, Hosoglu MI, Guneser O, Karagul-Yuceer Y. Fermented Spirulina products with Saccharomyces and non- Saccharomyces yeasts: Special reference to their microbial, physico-chemical and sensory characterizations. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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50
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Beimers W, Braun M, Schwinefus K, Pearson K, Wilbanks B, Maher LJ. A suppressor of dioxygenase inhibition in a yeast model of SDH deficiency. Endocr Relat Cancer 2022; 29:345-358. [PMID: 35315791 PMCID: PMC9175558 DOI: 10.1530/erc-21-0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022]
Abstract
A fascinating class of familial paraganglioma (PGL) neuroendocrine tumors is driven by the loss of the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) resulting in succinate accumulation as an oncometabolite and other metabolic derangements. Here, we exploit a Saccharomyces cerevisiae yeast model of SDH loss where accumulating succinate, and possibly reactive oxygen species, poison a dioxygenase enzyme required for sulfur scavenging. Using this model, we performed a chemical suppression screen for compounds that relieve dioxygenase inhibition. After testing 1280 pharmaceutically active compounds, we identified meclofenoxate HCl and its hydrolysis product, dimethylaminoethanol (DMAE), as suppressors of dioxygenase intoxication in SDH-loss yeast cells. We show that DMAE acts to alter metabolism so as to normalize the succinate:2-ketoglutarate ratio, improving dioxygenase function. This study raises the possibility that oncometabolite effects might be therapeutically suppressed by drugs that rewire metabolism to reduce the flux of carbon into pathological metabolic pathways.
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Affiliation(s)
- William Beimers
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Megan Braun
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Kaleb Schwinefus
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Keenan Pearson
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Brandon Wilbanks
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
- Correspondence should be addressed to L J Maher:
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