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Duncan JD, Devillers H, Camarasa C, Setati ME, Divol B. Oxygen alters redox cofactor dynamics and induces metabolic shifts in Saccharomyces cerevisiae during alcoholic fermentation. Food Microbiol 2024; 124:104624. [PMID: 39244375 DOI: 10.1016/j.fm.2024.104624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/08/2024] [Accepted: 08/25/2024] [Indexed: 09/09/2024]
Abstract
Environmental conditions significantly impact the metabolism of Saccharomyces cerevisiae, a Crabtree-positive yeast that maintains a fermentative metabolism in high-sugar environments even in the presence of oxygen. Although the introduction of oxygen has been reported to induce alterations in yeast metabolism, knowledge of the mechanisms behind these metabolic adaptations in relation to redox cofactor metabolism and their implications in the context of wine fermentation remains limited. This study aimed to compare the intracellular redox cofactor levels, the cofactor ratios, and primary metabolite production in S. cerevisiae under aerobic and anaerobic conditions in synthetic grape juice. The molecular mechanisms underlying these metabolic differences were explored using a transcriptomic approach. Aerobic conditions resulted in an enhanced fermentation rate and biomass yield. Total NADP(H) levels were threefold higher during aerobiosis, while a decline in the total levels of NAD(H) was observed. However, there were stark differences in the ratio of NAD+/NADH between the treatments. Despite few changes in the differential expression of genes involved in redox cofactor metabolism, anaerobiosis resulted in an increased expression of genes involved in lipid biosynthesis pathways, while the presence of oxygen increased the expression of genes associated with thiamine, methionine, and sulfur metabolism. The production of fermentation by-products was linked with differences in the redox metabolism in each treatment. This study provides valuable insights that may help steer the production of metabolites of industrial interest during alcoholic fermentation (including winemaking) by using oxygen as a lever of redox metabolism.
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Affiliation(s)
- James D Duncan
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Hugo Devillers
- UMR SPO, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Carole Camarasa
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; UMR SPO, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Mathabatha E Setati
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Benoit Divol
- South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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2
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Bögel G, Sváb G, Murányi J, Szokol B, Kukor Z, Kardon T, Őrfi L, Tretter L, Hrabák A. The role of PI3K-Akt-mTOR axis in Warburg effect and its modification by specific protein kinase inhibitors in human and rat inflammatory macrophages. Int Immunopharmacol 2024; 141:112957. [PMID: 39197292 DOI: 10.1016/j.intimp.2024.112957] [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: 02/29/2024] [Revised: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024]
Abstract
The Warburg effect occurs both in cancer cells and in inflammatory macrophages. The aim of our work was to demonstrate the role of PI3K-Akt-mTOR axis in the Warburg effect in HL-60 derived, rat peritoneal and human blood macrophages and to investigate the potential of selected inhibitors of this pathway to antagonize it. M1 polarization in HL-60-derived and human blood monocyte-derived macrophages was supported by the increased expression of NOS2 and inflammatory cytokines. All M1 polarized and inflammatory macrophages investigated expressed higher levels of HIF-1α and NOS2, which were reduced by selected kinase inhibitors, supporting the role of PI3K-Akt-mTOR axis. Using Seahorse XF plates, we found that in HL-60-derived and human blood-derived macrophages, glucose loading reduced oxygen consumption (OCR) and increased glycolysis (ECAR) in M1 polarization, which was antagonized by selected kinase inhibitors and by dichloroacetate. In rat peritoneal macrophages, the changes in oxidative and glycolytic metabolism were less marked and the NOS2 inhibitor decreased OCR and increased ECAR. Non-mitochondrial oxygen consumption and ROS production were likely due to NADPH oxidase, expressed in each macrophage type, independently of PI3K-Akt-mTOR axis. Our results suggest that inflammation changed the metabolism in each macrophage model, but a clear relationship between polarization and Warburg effect was confirmed only after glucose loading in HL-60 and human blood derived macrophages. The effect of kinase inhibitors on Warburg effect was variable in different cell types, whereas dichloroacetate caused a shift toward oxidative metabolism. Our findings suggest that these originally anti-cancer inhibitors may also be candidates for anti-inflammatory therapy.
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Affiliation(s)
- Gábor Bögel
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - Gergely Sváb
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - József Murányi
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - Bálint Szokol
- Vichem Chemie Research Ltd., Veszprém, H-8200, Viola u. 2., Hungary
| | - Zoltán Kukor
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - Tamás Kardon
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - László Őrfi
- Vichem Chemie Research Ltd., Veszprém, H-8200, Viola u. 2., Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, H-1092 Hőgyes E. u. 9., Hungary
| | - László Tretter
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary
| | - András Hrabák
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, H-1094 Tűzoltó u. 37-47, Hungary.
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Ohsawa S, Schwaiger M, Iesmantavicius V, Hashimoto R, Moriyama H, Matoba H, Hirai G, Sodeoka M, Hashimoto A, Matsuyama A, Yoshida M, Yashiroda Y, Bühler M. Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast. EMBO J 2024; 43:4604-4624. [PMID: 39256560 DOI: 10.1038/s44318-024-00224-z] [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: 03/01/2024] [Revised: 08/08/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin nitrogen signaling factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program without any change in the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.
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Affiliation(s)
- Shin Ohsawa
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
- Swiss Institute of Bioinformatics, 4056, Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
| | - Rio Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
| | - Hiromitsu Moriyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
| | - Hiroaki Matoba
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi Higashi-ku, 812-8582, Fukuoka, Japan
| | - Go Hirai
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi Higashi-ku, 812-8582, Fukuoka, Japan
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Mikiko Sodeoka
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Atsushi Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Akihisa Matsuyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Office of University Professors, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Yoko Yashiroda
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan.
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan.
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland.
- University of Basel, Petersplatz 10, 4003, Basel, Switzerland.
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Pei M, Abubakar YS, Ali H, Lin L, Dou X, Lu G, Wang Z, Olsson S, Li Y. Whole genome regulatory effect of MoISW2 and consequences for the evolution of the rice plant pathogenic fungus Magnaporthe oryzae. mBio 2024:e0159024. [PMID: 39292005 DOI: 10.1128/mbio.01590-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 06/27/2024] [Indexed: 09/19/2024] Open
Abstract
Isw2 proteins, ubiquitous across eukaryotes, exhibit a propensity for DNA binding and exert dynamic influences on local chromosome condensation in an ATP-dependent fashion, thereby modulating the accessibility of neighboring genes to transcriptional machinery. Here, we report the deletion of a putative MoISW2 gene, yielding substantial ramifications on plant pathogenicity. Subsequent gene complementation and chromatin immunoprecipitation sequencing (ChIP-seq) analyses were conducted to delineate binding sites. RNA sequencing (RNA-seq) assays revealed discernible impacts on global gene regulation along chromosomes in both mutant and wild-type strains, with comparative analyses against 55 external RNA-seq data sets corroborating these findings. Notably, MoIsw2-mediated binding and activities delineate genomic loci characterized by pronounced gene expression variability proximal to MoIsw2 binding sites, juxtaposed with comparatively stable expression in surrounding regions. The contingent genes influenced by MoIsw2 activity predominantly encompass niche-determinant genes, including those encoding secreted proteins, secondary metabolites, and stress-responsive elements, alongside avirulence genes. Furthermore, our investigations unveil a spatial correlation between MoIsw2 binding motifs and known transposable elements (TEs), suggesting a potential interplay wherein TE transposition at these loci could modulate the transcriptional landscape of Magnaporthe oryzae in a strain-specific manner. Collectively, these findings position MoIsw2 as a plausible master regulator orchestrating the delicate equilibrium between genes vital for biomass proliferation, akin to housekeeping genes, and niche-specific determinants crucial for ecological adaptability. Stress-induced TE transposition, in conjunction with MoIsw2 activity, emerges as a putative mechanism fostering enhanced mutagenesis and accelerated evolution of niche-determinant genes relative to housekeeping counterparts.IMPORTANCEIsw2 proteins are conserved in plants, fungi, animals, and other eukaryotes. We show that a fungal Isw2 protein in the rice pathogen Magnaporthe oryzae binds to retrotransposon (RT) DNA motifs and affects the epigenetic gene expression landscape of the fungal genome. Mainly ecological niche determinant genes close to the binding motifs are affected. RT elements occur frequently in DNA between genes in most organisms. They move place and multiply in the genome, especially under physiological stress. We further discuss the Isw2 and RT combined activities as a possible sought-after mechanism that can cause biased mutation rates and faster evolution of genes necessary for reacting to abiotic and biotic challenges. The most important biotic challenges for plant pathogens are the ones from the host plants' innate immunity. The overall result of these combined activities will be an adaptation-directed evolution of niche-determinant genes.
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Affiliation(s)
- Mengtian Pei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakubu Saddeeq Abubakar
- Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Hina Ali
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianying Dou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Synthetic Biology Center, College of Future Technologies, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ya Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
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Monnin L, Nidelet T, Noble J, Galeote V. Insights into intraspecific diversity of central carbon metabolites in Saccharomyces cerevisiae during wine fermentation. Food Microbiol 2024; 121:104513. [PMID: 38637075 DOI: 10.1016/j.fm.2024.104513] [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: 10/27/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
Saccharomyces cerevisiae is a major actor in winemaking that converts sugars from the grape must into ethanol and CO2 with outstanding efficiency. Primary metabolites produced during fermentation have a great importance in wine. While ethanol content contributes to the overall profile, other metabolites like glycerol, succinate, acetate or lactate also have significant impacts, even when present in lower concentrations. S. cerevisiae is known for its great genetic diversity that is related to its natural or technological environment. However, the variation range of metabolic diversity which can be exploited to enhance wine quality depends on the pathway considered. Our experiment assessed the diversity of primary metabolites production in a set of 51 S. cerevisiae strains from various genetic backgrounds. Results pointed out great yield differences depending on the metabolite considered, with ethanol having the lowest variation. A negative correlation between ethanol and glycerol was observed, confirming glycerol synthesis as a suitable lever to reduce ethanol yield. Genetic groups were linked to specific yields, such as the wine group and high α-ketoglutarate and low acetate yields. This research highlights the potential of using natural yeast diversity in winemaking. It also provides a detailed data set on production of well known (ethanol, glycerol, acetate) or little-known (lactate) primary metabolites.
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Affiliation(s)
- Ludovic Monnin
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France; Lallemand Oenology, Blagnac, France
| | - Thibault Nidelet
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France.
| | | | - Virginie Galeote
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
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6
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Ewald J, He Z, Dimitriew W, Schuster S. Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells. NPJ Syst Biol Appl 2024; 10:77. [PMID: 39025861 PMCID: PMC11258256 DOI: 10.1038/s41540-024-00393-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: 11/13/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Energy metabolism is crucial for all living cells, especially during fast growth or stress scenarios. Many cancer and activated immune cells (Warburg effect) or yeasts (Crabtree effect) mostly rely on aerobic glucose fermentation leading to lactate or ethanol, respectively, to generate ATP. In recent years, several mathematical models have been proposed to explain the Warburg effect on theoretical grounds. Besides glucose, glutamine is a very important substrate for eukaryotic cells-not only for biosynthesis, but also for energy metabolism. Here, we present a minimal constraint-based stoichiometric model for explaining both the classical Warburg effect and the experimentally observed respirofermentation of glutamine (WarburQ effect). We consider glucose and glutamine respiration as well as the respective fermentation pathways. Our resource allocation model calculates the ATP production rate, taking into account enzyme masses and, therefore, pathway costs. While our calculation predicts glucose fermentation to be a superior energy-generating pathway in human cells, different enzyme characteristics in yeasts reduce this advantage, in some cases to such an extent that glucose respiration is preferred. The latter is observed for the fungal pathogen Candida albicans, which is a known Crabtree-negative yeast. Further, optimization results show that glutamine is a valuable energy source and important substrate under glucose limitation, in addition to its role as a carbon and nitrogen source of biomass in eukaryotic cells. In conclusion, our model provides insights that glutamine is an underestimated fuel for eukaryotic cells during fast growth and infection scenarios and explains well the observed parallel respirofermentation of glucose and glutamine in several cell types.
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Affiliation(s)
- Jan Ewald
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Humboldtstraße 25, 04105, Leipzig, Germany
| | - Ziyang He
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Wassili Dimitriew
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [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: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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Koukoumaki DI, Papanikolaou S, Ioannou Z, Mourtzinos I, Sarris D. Single-Cell Protein and Ethanol Production of a Newly Isolated Kluyveromyces marxianus Strain through Cheese Whey Valorization. Foods 2024; 13:1892. [PMID: 38928833 PMCID: PMC11203209 DOI: 10.3390/foods13121892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The present work examined the production of single-cell protein (SCP) by a newly isolated strain of Kluyveromyces marxianus EXF-5288 under increased lactose concentration of deproteinized cheese whey (DCW) and different temperatures (in °C: 20.0, 25.0, 30.0 and 35.0). To the best of the authors' knowledge, this is the first report examining the ability of Kluyveromyces marxianus species to produce SCP at T = 20.0 °C. Different culture temperatures led to significant differences in the strain's growth, while maximum biomass and SCP production (14.24 ± 0.70 and 6.14 ± 0.66 g/L, respectively) were observed in the cultivation of K. marxianus strain EXF-5288 in shake-flask cultures at T = 20.0 °C. Increased DCW lactose concentrations (35.0-100.0 g/L) led to increased ethanol production (Ethmax = 35.5 ± 0.2 g/L), suggesting that K. marxianus strain EXF-5288 is "Crabtree-positive". Batch-bioreactor trials shifted the strain's metabolism to alcoholic fermentation, favoring ethanol production. Surprisingly, K. marxianus strain EXF-5288 was able to catabolize the produced ethanol under limited carbon presence in the medium. The dominant amino acids in SCP were glutamate (15.5 mg/g), aspartic acid (12.0 mg/g) and valine (9.5 mg/g), representing a balanced nutritional profile.
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Affiliation(s)
- Danai Ioanna Koukoumaki
- Laboratory of Physico-Chemical and Biotechnological Valorization of Food By-Products, Department of Food Science & Nutrition, School of Environment, University of the Aegean, Leoforos Dimokratias 66, 81400 Myrina, Lemnos, Greece; (D.I.K.); (Z.I.)
| | - Seraphim Papanikolaou
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece;
| | - Zacharias Ioannou
- Laboratory of Physico-Chemical and Biotechnological Valorization of Food By-Products, Department of Food Science & Nutrition, School of Environment, University of the Aegean, Leoforos Dimokratias 66, 81400 Myrina, Lemnos, Greece; (D.I.K.); (Z.I.)
| | - Ioannis Mourtzinos
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Dimitris Sarris
- Laboratory of Physico-Chemical and Biotechnological Valorization of Food By-Products, Department of Food Science & Nutrition, School of Environment, University of the Aegean, Leoforos Dimokratias 66, 81400 Myrina, Lemnos, Greece; (D.I.K.); (Z.I.)
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9
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Koltai T, Fliegel L. Dichloroacetate for Cancer Treatment: Some Facts and Many Doubts. Pharmaceuticals (Basel) 2024; 17:744. [PMID: 38931411 PMCID: PMC11206832 DOI: 10.3390/ph17060744] [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: 03/28/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Rarely has a chemical elicited as much controversy as dichloroacetate (DCA). DCA was initially considered a dangerous toxic industrial waste product, then a potential treatment for lactic acidosis. However, the main controversies started in 2008 when DCA was found to have anti-cancer effects on experimental animals. These publications showed contradictory results in vivo and in vitro such that a thorough consideration of this compound's in cancer is merited. Despite 50 years of experimentation, DCA's future in therapeutics is uncertain. Without adequate clinical trials and health authorities' approval, DCA has been introduced in off-label cancer treatments in alternative medicine clinics in Canada, Germany, and other European countries. The lack of well-planned clinical trials and its use by people without medical training has discouraged consideration by the scientific community. There are few thorough clinical studies of DCA, and many publications are individual case reports. Case reports of DCA's benefits against cancer have been increasing recently. Furthermore, it has been shown that DCA synergizes with conventional treatments and other repurposable drugs. Beyond the classic DCA target, pyruvate dehydrogenase kinase, new target molecules have also been recently discovered. These findings have renewed interest in DCA. This paper explores whether existing evidence justifies further research on DCA for cancer treatment and it explores the role DCA may play in it.
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Affiliation(s)
- Tomas Koltai
- Hospital del Centro Gallego de Buenos Aires, Buenos Aires 2199, Argentina
| | - Larry Fliegel
- Department of Biochemistry, University Alberta, Edmonton, AB T6G 2H7, Canada;
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10
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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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11
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Pontes A, Paraíso F, Silva M, Lagoas C, Aires A, Brito PH, Rosa CA, Lachance MA, Sampaio JP, Gonçalves C, Gonçalves P. Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage. BMC Biol 2024; 22:128. [PMID: 38816863 PMCID: PMC11140947 DOI: 10.1186/s12915-024-01929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT). RESULTS Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway. CONCLUSIONS These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catarina Lagoas
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Andreia Aires
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- PYCC - Portuguese Yeast Culture Collection, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Patrícia H Brito
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- PYCC - Portuguese Yeast Culture Collection, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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12
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Gao X, Pang C, Fan Z, Wang Y, Duan Y, Zhan H. Regulation of newly identified lysine lactylation in cancer. Cancer Lett 2024; 587:216680. [PMID: 38346584 DOI: 10.1016/j.canlet.2024.216680] [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: 12/04/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024]
Abstract
Metabolic reprogramming is a typical hallmark of cancer. Enhanced glycolysis in tumor cells leads to the accumulation of lactate, which is traditionally considered metabolic waste. With the development of high-resolution liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), the lactate-derived, lysine lactylation(Kla), has been identified. Kla can alter the spatial configuration of chromatin and regulate the expression of corresponding genes. Metabolic reprogramming and epigenetic remodeling have been extensively linked. Accumulating studies have subsequently expanded the framework on the key roles of this protein translational modification (PTM) in tumors and have provided a new concept of cancer-specific regulation by Kla.
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Affiliation(s)
- Xin Gao
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Chaoyu Pang
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Zhiyao Fan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, 250012, China.
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13
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Whitaker-Lockwood JA, Scholten SK, Karim F, Luiten AN, Perrella C. Comb spectroscopy of CO 2 produced from microbial metabolism. BIOMEDICAL OPTICS EXPRESS 2024; 15:1553-1570. [PMID: 38495728 PMCID: PMC10942673 DOI: 10.1364/boe.515988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
We have developed a direct frequency comb spectroscopy instrument, which we have tested on Saccharomyces cerevisiae (baker's yeast) by measuring its CO2 output and production rate as we varied the environmental conditions, including the amount and type of feed sugar, the temperature, and the amount of yeast. By feeding isotopically-enhanced sugar to the yeast, we demonstrate the capability of our device to differentiate between two isotopologues of CO2, with a concentration measurement precision of 260 ppm for 12C16O2 and 175 ppm for 13C16O2. We also demonstrate the ability of our spectrometer to measure the proportion of carbon in the feed sugar converted to CO2, and estimate the amount incorporated into the yeast biomass.
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Affiliation(s)
- Joshua A Whitaker-Lockwood
- Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Sarah K Scholten
- Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS), University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Faisal Karim
- Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - André N Luiten
- Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS), University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Christopher Perrella
- Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- ARC Centre of Excellence in Optical Microcombs for Breakthrough Science (COMBS), University of Adelaide, Adelaide, South Australia, 5005, Australia
- Centre of Light for Life and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
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14
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Tamama K, Kruckenberg KM, DiMartini AF. Gut and bladder fermentation syndromes: a narrative review. BMC Med 2024; 22:26. [PMID: 38246992 PMCID: PMC10801939 DOI: 10.1186/s12916-023-03241-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
We recently reported the first clinical case of bladder fermentation syndrome (BFS) or urinary auto-brewery syndrome, which caused the patient to fail abstinence monitoring. In BFS, ethanol is generated by Crabtree-positive fermenting yeast Candida glabrata in a patient with poorly controlled diabetes. One crucial characteristic of BFS is the absence of alcoholic intoxication, as the bladder lumen contains transitional epithelium with low ethanol permeability. In contrast, patients with gut fermentation syndrome (GFS) or auto-brewery syndrome can spontaneously develop symptoms of ethanol intoxication even without any alcohol ingestion because of alcoholic fermentation in the gut lumen. In abstinence monitoring, a constellation of laboratory findings with positive urinary glucose and ethanol, negative ethanol metabolites, and the presence of yeast in urinalysis should raise suspicion for BFS, whereas endogenous ethanol production needs to be shown by a carbohydrate challenge test for GFS diagnosis. GFS patients will also likely fail abstinence monitoring because of the positive ethanol blood testing. BFS and GFS are treated by yeast eradication of fermenting microorganisms with antifungals (or antibiotics for bacterial GFS cases) and modification of underlying conditions (diabetes for BFS and gut dysbiosis for GFS). The under-recognition of these rare medical conditions has led to not only harm but also adverse legal consequences for patients, such as driving under the influence (DUI). GFS patients may be at risk of various alcohol-related diseases.
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Affiliation(s)
- Kenichi Tamama
- Clinical Laboratories, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, 3477 Euler Way, UPMC Presbyterian Clinical Laboratory Building, Pittsburgh, PA, 15213, USA.
| | - Katherine M Kruckenberg
- Department of Psychiatry, University of California San Diego School of Medicine, San Diego, CA, USA
- Departments of Psychiatry and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrea F DiMartini
- Departments of Psychiatry and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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15
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Porninta K, Khemacheewakul J, Techapun C, Phimolsiripol Y, Jantanasakulwong K, Sommanee S, Mahakuntha C, Feng J, Htike SL, Moukamnerd C, Zhuang X, Wang W, Qi W, Li FL, Liu T, Kumar A, Nunta R, Leksawasdi N. Pretreatment and enzymatic hydrolysis optimization of lignocellulosic biomass for ethanol, xylitol, and phenylacetylcarbinol co-production using Candida magnoliae. Front Bioeng Biotechnol 2024; 11:1332185. [PMID: 38304106 PMCID: PMC10830760 DOI: 10.3389/fbioe.2023.1332185] [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: 11/02/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Cellulosic bioethanol production generally has a higher operating cost due to relatively expensive pretreatment strategies and low efficiency of enzymatic hydrolysis. The production of other high-value chemicals such as xylitol and phenylacetylcarbinol (PAC) is, thus, necessary to offset the cost and promote economic viability. The optimal conditions of diluted sulfuric acid pretreatment under boiling water at 95°C and subsequent enzymatic hydrolysis steps for sugarcane bagasse (SCB), rice straw (RS), and corn cob (CC) were optimized using the response surface methodology via a central composite design to simplify the process on the large-scale production. The optimal pretreatment conditions (diluted sulfuric acid concentration (% w/v), treatment time (min)) for SCB (3.36, 113), RS (3.77, 109), and CC (3.89, 112) and the optimal enzymatic hydrolysis conditions (pretreated solid concentration (% w/v), hydrolysis time (h)) for SCB (12.1, 93), RS (10.9, 61), and CC (12.0, 90) were achieved. CC xylose-rich and CC glucose-rich hydrolysates obtained from the respective optimal condition of pretreatment and enzymatic hydrolysis steps were used for xylitol and ethanol production. The statistically significant highest (p ≤ 0.05) xylitol and ethanol yields were 65% ± 1% and 86% ± 2% using Candida magnoliae TISTR 5664. C. magnoliae could statistically significantly degrade (p ≤ 0.05) the inhibitors previously formed during the pretreatment step, including up to 97% w/w hydroxymethylfurfural, 76% w/w furfural, and completely degraded acetic acid during the xylitol production. This study was the first report using the mixed whole cells harvested from xylitol and ethanol production as a biocatalyst in PAC biotransformation under a two-phase emulsion system (vegetable oil/1 M phosphate (Pi) buffer). PAC concentration could be improved by 2-fold compared to a single-phase emulsion system using only 1 M Pi buffer.
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Affiliation(s)
- Kritsadaporn Porninta
- Program in Biotechnology, Multidisciplinary and Interdisciplinary School, Chiang Mai University, Chiang Mai, Thailand
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Julaluk Khemacheewakul
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Charin Techapun
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Yuthana Phimolsiripol
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Jantanasakulwong
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Sumeth Sommanee
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchadaporn Mahakuntha
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Juan Feng
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Su Lwin Htike
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | | | - Xinshu Zhuang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Wen Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Wei Qi
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Tianzhong Liu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Anbarasu Kumar
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Department of Biotechnology, Periyar Maniammai Institute of Science & Technology (Deemed to be University), Thanjavur, India
| | - Rojarej Nunta
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Division of Food Innovation and Business, Faculty of Agricultural Technology, Lampang Rajabhat University, Lampang, Thailand
| | - Noppol Leksawasdi
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
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16
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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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17
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Uysal Özdemir Ö, Krapp A, Mangeat B, Spaltenstein M, Simanis V. A role for the carbon source of the cell and protein kinase A in regulating the S. pombe septation initiation network. J Cell Sci 2024; 137:jcs261488. [PMID: 38197775 PMCID: PMC10906493 DOI: 10.1242/jcs.261488] [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: 07/13/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
The septation initiation network (SIN) is a conserved signal transduction network, which is important for cytokinesis in Schizosaccharomyces pombe. The SIN component Etd1p is required for association of some SIN proteins with the spindle pole body (SPB) during anaphase and for contractile ring formation. We show that tethering of Cdc7p or Sid1p to the SIN scaffold Cdc11p at the SPB, rescues etd1-Δ. Analysis of a suppressor of the mutant etd1-M9 revealed that SIN signalling is influenced by the carbon source of the cell. Growth on a non-fermentable carbon source glycerol reduces the requirement for SIN signalling but does not bypass it. The decreased need for SIN signalling is mediated largely by reduction of protein kinase A activity, and it is phenocopied by deletion of pka1 on glucose medium. We conclude that protein kinase A is an important regulator of the SIN, and that SIN signalling is regulated by the carbon source of the cell.
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Affiliation(s)
- Özge Uysal Özdemir
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, CH - 1015 Lausanne, Switzerland
| | - Andrea Krapp
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, CH - 1015 Lausanne, Switzerland
| | - Bastien Mangeat
- EPFL SV PTECH PTEG, SV 1535 (Bâtiment SV), Station 19, CH-1015 Lausanne, Switzerland
| | - Marc Spaltenstein
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, CH - 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, CH - 1015 Lausanne, Switzerland
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18
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Fitzgerald S, Holland L, Ahmed W, Piechulla B, Fowler SJ, Morrin A. Volatilomes of human infection. Anal Bioanal Chem 2024; 416:37-53. [PMID: 37843549 PMCID: PMC10758372 DOI: 10.1007/s00216-023-04986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
The human volatilome comprises a vast mixture of volatile emissions produced by the human body and its microbiomes. Following infection, the human volatilome undergoes significant shifts, and presents a unique medium for non-invasive biomarker discovery. In this review, we examine how the onset of infection impacts the production of volatile metabolites that reflects dysbiosis by pathogenic microbes. We describe key analytical workflows applied across both microbial and clinical volatilomics and emphasize the value in linking microbial studies to clinical investigations to robustly elucidate the metabolic species and pathways leading to the observed volatile signatures. We review the current state of the art across microbial and clinical volatilomics, outlining common objectives and successes of microbial-clinical volatilomic workflows. Finally, we propose key challenges, as well as our perspectives on emerging opportunities for developing clinically useful and targeted workflows that could significantly enhance and expedite current practices in infection diagnosis and monitoring.
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Affiliation(s)
- Shane Fitzgerald
- SFI Insight Centre for Data Analytics, School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | - Linda Holland
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Waqar Ahmed
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Birgit Piechulla
- Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Stephen J Fowler
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
- Respiratory Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Aoife Morrin
- SFI Insight Centre for Data Analytics, School of Chemical Sciences, National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
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19
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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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20
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Torello Pianale L, Caputo F, Olsson L. Four ways of implementing robustness quantification in strain characterisation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:195. [PMID: 38115067 PMCID: PMC10729505 DOI: 10.1186/s13068-023-02445-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors). RESULTS Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively. CONCLUSIONS Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.
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Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Fabio Caputo
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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21
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Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial genome diversity across the subphylum Saccharomycotina. Front Microbiol 2023; 14:1268944. [PMID: 38075892 PMCID: PMC10701893 DOI: 10.3389/fmicb.2023.1268944] [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: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 12/20/2023] Open
Abstract
Introduction Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. Methods By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Results Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. Discussion As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
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Affiliation(s)
- John F. Wolters
- 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, United States
| | - Abigail L. LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Dana A. Opulente
- 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, United States
- Biology Department, Villanova University, Villanova, PA, United States
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - 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, United States
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22
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Pettersen JP, Castillo S, Jouhten P, Almaas E. Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts. BMC Bioinformatics 2023; 24:438. [PMID: 37990145 PMCID: PMC10664357 DOI: 10.1186/s12859-023-05506-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce the final alcohol content. Given the metabolic differences between the yeast species, we wanted to account for some of the differences by using in silico models. RESULTS We created and studied genome-scale metabolic models of five different non-Saccharomyces species using an automated processes. These were: Metschnikowia pulcherrima, Lachancea thermotolerans, Hanseniaspora osmophila, Torulaspora delbrueckii and Kluyveromyces lactis. Using the models, we predicted that M. pulcherrima, when compared to the other species, conducts more respiration and thus produces less fermentation products, a finding which agrees with experimental data. Complex I of the electron transport chain was to be present in M. pulcherrima, but absent in the others. The predicted importance of Complex I was diminished when we incorporated constraints on the amount of enzymatic protein, as this shifts the metabolism towards fermentation. CONCLUSIONS Our results suggest that Complex I in the electron transport chain is a key differentiator between Metschnikowia pulcherrima and the other yeasts considered. Yet, more annotations and experimental data have the potential to improve model quality in order to increase fidelity and confidence in these results. Further experiments should be conducted to confirm the in vivo effect of Complex I in M. pulcherrima and its respiratory metabolism.
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Affiliation(s)
- Jakob P Pettersen
- Department of Biotechnology and Food Science, NTNU-Norwegian University of Science and Technology, Trondheim, Norway.
| | | | - Paula Jouhten
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU-Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Public Health and General Practice, K.G. Jebsen Center for Genetic Epidemiology, NTNU- Norwegian University of Science and Technology, Trondheim, Norway.
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23
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Alberghina L. The Warburg Effect Explained: Integration of Enhanced Glycolysis with Heterogeneous Mitochondria to Promote Cancer Cell Proliferation. Int J Mol Sci 2023; 24:15787. [PMID: 37958775 PMCID: PMC10648413 DOI: 10.3390/ijms242115787] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The Warburg effect is the long-standing riddle of cancer biology. How does aerobic glycolysis, inefficient in producing ATP, confer a growth advantage to cancer cells? A new evaluation of a large set of literature findings covering the Warburg effect and its yeast counterpart, the Crabtree effect, led to an innovative working hypothesis presented here. It holds that enhanced glycolysis partially inactivates oxidative phosphorylation to induce functional rewiring of a set of TCA cycle enzymes to generate new non-canonical metabolic pathways that sustain faster growth rates. The hypothesis has been structured by constructing two metabolic maps, one for cancer metabolism and the other for the yeast Crabtree effect. New lines of investigation, suggested by these maps, are discussed as instrumental in leading toward a better understanding of cancer biology in order to allow the development of more efficient metabolism-targeted anticancer drugs.
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Affiliation(s)
- Lilia Alberghina
- Centre of Systems Biology, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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24
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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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25
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Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial Genome Diversity across the Subphylum Saccharomycotina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551029. [PMID: 37577532 PMCID: PMC10418067 DOI: 10.1101/2023.07.28.551029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
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Affiliation(s)
- John F. Wolters
- 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
| | - Abigail L. LaBella
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC, 28223, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A. Opulente
- 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
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - 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
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26
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Rothman DL, Moore PB, Shulman RG. The impact of metabolism on the adaptation of organisms to environmental change. Front Cell Dev Biol 2023; 11:1197226. [PMID: 37377740 PMCID: PMC10291235 DOI: 10.3389/fcell.2023.1197226] [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: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Since Jacob and Monod's discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as "metabolic reprogramming." The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.
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Affiliation(s)
- Douglas L. Rothman
- Departments of Radiology, Yale University, New Haven, CT, United States
- Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Peter B. Moore
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Robert G. Shulman
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
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27
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Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S. Optimization of energy production and central carbon metabolism in a non-respiring eukaryote. Curr Biol 2023; 33:2175-2186.e5. [PMID: 37164017 PMCID: PMC7615655 DOI: 10.1016/j.cub.2023.04.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.
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Affiliation(s)
- Sara Alam
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Polina Reichert
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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28
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Adame-Soto PJ, Aréchiga-Carvajal ET, González-Herrera SM, Moreno-Jiménez MR, Rutiaga-Quiñones OM. Characterization of mating type on aroma production and metabolic properties wild Kluyveromyces marxianus yeasts. World J Microbiol Biotechnol 2023; 39:216. [PMID: 37269405 DOI: 10.1007/s11274-023-03659-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/22/2023] [Indexed: 06/05/2023]
Abstract
Kluyveromyces marxianus yeasts represent a valuable industry alternative due to their biotechnological potential to produce aromatic compounds. 2-phenylethanol and 2-phenylethylacetate are significant aromatic compounds widely used in food and cosmetics due to their pleasant odor. Natural obtention of these compounds increases their value, and because of this, bioprocesses such as de novo synthesis has become of great significance. However, the relationship between aromatic compound production and yeast's genetic diversity has yet to be studied. In the present study, the analysis of the genetic diversity in K. marxianus isolated from the natural fermentation of Agave duranguensis for Mezcal elaboration is presented. The results of strains in a haploid and diploid state added to the direct relationship between the mating type locus MAT with metabolic characteristics are studied. Growth rate, assimilate carbohydrates (glucose, lactose, and chicory inulin), and the production of aromatic compounds such as ethyl acetate, isoamyl acetate, isoamyl alcohol, 2-phenylethyl butyrate and phenylethyl propionate and the diversity in terms of the output of 2-phenylethanol and 2-phenylethylacetate by de novo synthesis were determinate, obtaining maximum concentrations of 51.30 and 60.39 mg/L by ITD0049 and ITD 0136 yeasts respectively.
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Affiliation(s)
- P J Adame-Soto
- Department of Chemical and Biochemical Engineering, National Technological Institute of Mexico, Technological Institute of Durango, Felipe Pescador 1803 Ote, Colonia Nueva Vizcaya, 34080, Durango, Dgo, Mexico
| | - E T Aréchiga-Carvajal
- Genetic Manipulation Unit of the Mycology and Phytopathology Laboratory, Department of Microbiology, and Immunology, Faculty of Biological Sciences, Unit C Ciudad Universitaria, Autonomous University of Nuevo León, 66451, San Nicolás de Los Garza, Nuevo León, Mexico
| | - S M González-Herrera
- Department of Chemical and Biochemical Engineering, National Technological Institute of Mexico, Technological Institute of Durango, Felipe Pescador 1803 Ote, Colonia Nueva Vizcaya, 34080, Durango, Dgo, Mexico
| | - M R Moreno-Jiménez
- Department of Chemical and Biochemical Engineering, National Technological Institute of Mexico, Technological Institute of Durango, Felipe Pescador 1803 Ote, Colonia Nueva Vizcaya, 34080, Durango, Dgo, Mexico
| | - O M Rutiaga-Quiñones
- Department of Chemical and Biochemical Engineering, National Technological Institute of Mexico, Technological Institute of Durango, Felipe Pescador 1803 Ote, Colonia Nueva Vizcaya, 34080, Durango, Dgo, Mexico.
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29
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Deng H, Du Z, Lu S, Wang Z, He X. Regulation of Cat8 in energy metabolic balance and glucose tolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12593-2. [PMID: 37249587 DOI: 10.1007/s00253-023-12593-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023]
Abstract
Cat8 is a C6 zinc cluster transcription activator in yeast. It is generally recognized that the transcription of CAT8 is inhibited and that Cat8 is inactive in the presence of high concentrations of glucose. However, our recent study found that constitutively overexpressed Cat8 played a regulatory role in Saccharomyces cerevisiae in the presence of 20 g/L glucose. To explore the regulatory network of Cat8 at high glucose concentrations, CAT8 was both overexpressed and deleted in this study. Cell growth and glucose consumption in different media were significantly accelerated by the deletion of CAT8, while the lag period was greatly shortened. RNA-seq and genetic modification showed that the deletion of CAT8 changed the type of energy metabolism in yeast cells. Many genes related to the mitochondrial respiratory chain were downregulated, resulting in a reduction in aerobic respiration and the tricarboxylic acid cycle. Meanwhile, both the energy supply of anaerobic ethanol fermentation and the Crabtree effect of S. cerevisiae were enhanced by the deletion of CAT8. CAT8 knockout cells show a higher sugar uptake rate, a higher cell growth rate, and higher tolerance to glucose than the wild-type strain YS58. This study expands the understanding of the regulatory network of Cat8 and provides guidance for modulating yeast cell growth. KEY POINTS: • The deletion of CAT8 promoted cell growth of S. cerevisiae. • Transcriptome analysis revealed the regulation network of Cat8 under 1% glucose condition. • CAT8 deletion increases the glucose tolerance of cells by enhancing the Crabtree effect.
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Affiliation(s)
- Hong Deng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Surui Lu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Tomazin R, Pliberšek T, Oštrbenk Valenčak A, Matos T. Different BD BACTEC ™ Blood Culture Bottle Types for the Detection of Fungi in Simulated Sterile Body Fluid Samples. Diagnostics (Basel) 2023; 13:diagnostics13101699. [PMID: 37238183 DOI: 10.3390/diagnostics13101699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Blood culture systems are a potential alternative to classical cultivation of fungi on mycological media, but there are limited data on the suitability of these systems for culturing other sample types (e.g., sterile body fluids). We conducted a prospective study to evaluate different types of blood culture (BC) bottles for the detection of different fungal species in non-blood samples. A total of 43 fungal isolates were tested for their ability to grow in BD BACTEC Mycosis-IC/F (Mycosis bottles), BD BACTEC Plus Aerobic/F (Aerobic bottles) and BD BACTEC Plus Anaerobic/F (Anaerobic bottles) (Becton Dickinson, East Rutherford, NJ, USA) BC bottles inoculated with spiked samples without the addition of blood or fastidious organism supplement. Time to detection (TTD) was determined for all BC types tested and compared between groups. In general, Mycosis and Aerobic bottles were similar (p > 0.05). The Anaerobic bottles failed to support growth in >86% of cases. The Mycosis bottles were superior in detecting Candida glabrata, Cryptococcus spp. and Aspergillus spp. (p < 0.05). The performance of Mycosis and Aerobic bottles was similar, but if cryptococcosis or aspergillosis is suspected, the use of Mycosis bottles is recommended. Anaerobic bottles are not recommended for fungal detection.
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Affiliation(s)
- Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
| | | | - Anja Oštrbenk Valenčak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
| | - Tadeja Matos
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
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31
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Bieringer E, García Vázquez U, Klein L, Moretó Bravo N, Tobler M, Weuster-Botz D. Bioproduction and applications of aldobionic acids with a focus on maltobionic and cellobionic acid. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02872-7. [PMID: 37058246 DOI: 10.1007/s00449-023-02872-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
Aldobionic acids are sugar acids which consist of a disaccharide with an anomeric acid group. The most famous is lactobionic acid (LBA). LBA is used in many applications such as food and beverages, pharmaceuticals and medicine, cosmetics or chemical processes. During the last decade, all these industries are observing a shift of consumer preferences towards plant-based options. Thus, the biotechnological industry is trying to replace the animal-derived LBA. Maltobionic acid (MBA) and cellobionic acid (CBA) are two stereoisomers of LBA which have emerged as vegan alternatives. However, MBA and CBA face different obstacles related to their industrial production. While traditionally used electrochemical or chemical catalysis often rely on cost intensive and/or hazardous catalysts, novel production methods with microorganisms are still poorly studied. In the first part, this paper discusses both alternatives in terms of their characteristics and applications. In the second part, it reviews the long-studied chemical production and the novel bioproduction methods, which are based on enzymatic and microbial systems. This review concludes with a discussion of future work needed to bring their production to the industrial scale.
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Affiliation(s)
- Emmeran Bieringer
- TUM School of Engineering and Design, Department of Energy and Process Engineering, Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Uxía García Vázquez
- TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Luisa Klein
- TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Núria Moretó Bravo
- TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Matthias Tobler
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Petersgasse 5, 94315, Straubing, Germany
| | - Dirk Weuster-Botz
- TUM School of Engineering and Design, Department of Energy and Process Engineering, Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
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Pérez-Díaz AJ, Vázquez-Marín B, Vicente-Soler J, Prieto-Ruiz F, Soto T, Franco A, Cansado J, Madrid M. cAMP-Protein kinase A and stress-activated MAP kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation. Autophagy 2023; 19:1311-1331. [PMID: 36107819 PMCID: PMC10012941 DOI: 10.1080/15548627.2022.2125204] [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: 03/31/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022] Open
Abstract
Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast Saccharomyces cerevisiae, little is known about how this coping response is regulated in the evolutionary distant fission yeast Schizosaccharomyces pombe. Here, we show that S. pombe autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to S. cerevisiae, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses S. pombe autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct in vivo phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in S. pombe and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
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Affiliation(s)
- Armando Jesús Pérez-Díaz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Beatriz Vázquez-Marín
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Jero Vicente-Soler
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Francisco Prieto-Ruiz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Teresa Soto
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Alejandro Franco
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - José Cansado
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Marisa Madrid
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
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Staneva D, Vasileva B, Podlesniy P, Miloshev G, Georgieva M. Yeast Chromatin Mutants Reveal Altered mtDNA Copy Number and Impaired Mitochondrial Membrane Potential. J Fungi (Basel) 2023; 9:jof9030329. [PMID: 36983497 PMCID: PMC10058930 DOI: 10.3390/jof9030329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4-Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petar Podlesniy
- CiberNed (Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas), 28029 Barcelona, Spain
| | - George Miloshev
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Rickard BP, Overchuk M, Obaid G, Ruhi MK, Demirci U, Fenton SE, Santos JH, Kessel D, Rizvi I. Photochemical Targeting of Mitochondria to Overcome Chemoresistance in Ovarian Cancer †. Photochem Photobiol 2023; 99:448-468. [PMID: 36117466 PMCID: PMC10043796 DOI: 10.1111/php.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
Abstract
Ovarian cancer is the most lethal gynecologic malignancy with a stubborn mortality rate of ~65%. The persistent failure of multiline chemotherapy, and significant tumor heterogeneity, has made it challenging to improve outcomes. A target of increasing interest is the mitochondrion because of its essential role in critical cellular functions, and the significance of metabolic adaptation in chemoresistance. This review describes mitochondrial processes, including metabolic reprogramming, mitochondrial transfer and mitochondrial dynamics in ovarian cancer progression and chemoresistance. The effect of malignant ascites, or excess peritoneal fluid, on mitochondrial function is discussed. The role of photodynamic therapy (PDT) in overcoming mitochondria-mediated resistance is presented. PDT, a photochemistry-based modality, involves the light-based activation of a photosensitizer leading to the production of short-lived reactive molecular species and spatiotemporally confined photodamage to nearby organelles and biological targets. The consequential effects range from subcytotoxic priming of target cells for increased sensitivity to subsequent treatments, such as chemotherapy, to direct cell killing. This review discusses how PDT-based approaches can address key limitations of current treatments. Specifically, an overview of the mechanisms by which PDT alters mitochondrial function, and a summary of preclinical advancements and clinical PDT experience in ovarian cancer are provided.
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Affiliation(s)
- Brittany P. Rickard
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marta Overchuk
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; North Carolina State University, Raleigh, NC 27606, USA
| | - Girgis Obaid
- Department of Bioengineering, University of Texas at Dallas, Richardson TX 95080, USA
| | - Mustafa Kemal Ruhi
- Institute of Biomedical Engineering, Boğaziçi University, Istanbul, Turkey
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Suzanne E. Fenton
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Janine H. Santos
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - David Kessel
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Imran Rizvi
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; North Carolina State University, Raleigh, NC 27606, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Center for Environmental Health and Susceptibility, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Pouzet S, Cruz-Ramón J, Le Bec M, Cordier C, Banderas A, Barral S, Castaño-Cerezo S, Lautier T, Truan G, Hersen P. Optogenetic control of beta-carotene bioproduction in yeast across multiple lab-scales. Front Bioeng Biotechnol 2023; 11:1085268. [PMID: 36814715 PMCID: PMC9939774 DOI: 10.3389/fbioe.2023.1085268] [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: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Optogenetics arises as a valuable tool to precisely control genetic circuits in microbial cell factories. Light control holds the promise of optimizing bioproduction methods and maximizing yields, but its implementation at different steps of the strain development process and at different culture scales remains challenging. In this study, we aim to control beta-carotene bioproduction using optogenetics in Saccharomyces cerevisiae and investigate how its performance translates across culture scales. We built four lab-scale illumination devices, each handling different culture volumes, and each having specific illumination characteristics and cultivating conditions. We evaluated optogenetic activation and beta-carotene production across devices and optimized them both independently. Then, we combined optogenetic induction and beta-carotene production to make a light-inducible beta-carotene producer strain. This was achieved by placing the transcription of the bifunctional lycopene cyclase/phytoene synthase CrtYB under the control of the pC120 optogenetic promoter regulated by the EL222-VP16 light-activated transcription factor, while other carotenogenic enzymes (CrtI, CrtE, tHMG) were expressed constitutively. We show that illumination, culture volume and shaking impact differently optogenetic activation and beta-carotene production across devices. This enabled us to determine the best culture conditions to maximize light-induced beta-carotene production in each of the devices. Our study exemplifies the stakes of scaling up optogenetics in devices of different lab scales and sheds light on the interplays and potential conflicts between optogenetic control and metabolic pathway efficiency. As a general principle, we propose that it is important to first optimize both components of the system independently, before combining them into optogenetic producing strains to avoid extensive troubleshooting. We anticipate that our results can help designing both strains and devices that could eventually lead to larger scale systems in an effort to bring optogenetics to the industrial scale.
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Affiliation(s)
- Sylvain Pouzet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jessica Cruz-Ramón
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Matthias Le Bec
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Céline Cordier
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Alvaro Banderas
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Simon Barral
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Sara Castaño-Cerezo
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France
| | - Thomas Lautier
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France,CNRS@CREATE, Singapore Institute of Food and Biotechnology Innovation, Agency for Science Technology and Research, Singapore, Singapore
| | - Gilles Truan
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l′Agriculture, l′Alimentation et l′Environnement (INRAE), Institut National des Sciences Appliquées (INSA), Toulouse, France
| | - Pascal Hersen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Pascal Hersen,
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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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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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Tchamani Piame L, Kaktcham PM, Foko Kouam EM, Fotso Techeu UD, Ngouénam RJ, Zambou Ngoufack F. Technological characterisation and probiotic traits of yeasts isolated from Sha'a, a Cameroonian maize-based traditional fermented beverage. Heliyon 2022; 8:e10850. [PMID: 36247120 PMCID: PMC9557902 DOI: 10.1016/j.heliyon.2022.e10850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/12/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
The current trend in starter selection is to combine both technological and probiotic properties to standardise and make functional artisanal fermented beverages such as Sha'a whose properties are very variable due to the lack of a known starter. The objective of this work was to study technological and probiotic properties of yeasts isolated from Sha'a sold in Bamenda, Bafoussam, Bonabérie, Dschang, Foumbot, Mbouda and Njombé (Cameroon). The isolated yeasts were studied for their ability to produce CO2 from glucose, to grow in the presence of 8% ethanol, 20% glucose and pH 3, to assimilate maltose and to produce ethanol. Then, the survival of the pre-selected isolates was assessed in simulated gastric (pH 2 and 3) and intestinal juices, followed by self-aggregation, co-aggregation, hydrophobicity, haemolysin, gelatinase, biogenic amine production, antibiotic and antifungal susceptibility, bile salt hydrolase and antiradical activity. The selected isolates were identified by sequencing the 5.8S/28S rRNA gene. From the 98 isolates obtained, 66 produced CO2 from glucose and 16 were then selected for their ability to grow in the presence of 8% ethanol, 20% glucose, pH 3 and maltose. The overall survival of isolates ranged from 4.12 ± 1.63 to 104.25 ± 0.19% (LT16) and from 0.56 ± 0.20 to 96.74 ± 1.60% (LT66) at pH 3 and pH 2 respectively. All of them have remarkable surface hydrophobicity properties. Based on principal component analysis, 5 isolates were selected as the best. However, only 3 of them, LT16 (the most promising), LT25 identified as Saccharomyces cerevisiae and LT80 as Nakaseomyces delphensis, do not produce a virulence factor. The latter can deconjugate bile salts with a maximum percentage of 60.54 ± 0.12% (LT16) and the highest inhibition of DPPH° radicals was 55.94 ± 1.14% (LT25). In summary, the yeast flora of Sha'a contains yeasts capable of fermenting and producing ethanol while producing bioactive compounds that would benefit the consumer.
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Fonseca GG. Metabolic engineering of Kluyveromyces marxianus for biomass-based applications. 3 Biotech 2022; 12:259. [PMID: 36068842 PMCID: PMC9440961 DOI: 10.1007/s13205-022-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/22/2022] [Indexed: 11/01/2022] Open
Abstract
Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03324-x.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Business and Science, University of Akureyri, Borgir v. Nordurslod, 600 Akureyri, Iceland
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40
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Nasuno R, Yoshikawa Y, Takagi H. Acetaldehyde reacts with a fluorescent nitric oxide probe harboring an o-phenylenediamine structure that interferes with fluorometry. Free Radic Biol Med 2022; 187:29-37. [PMID: 35605899 DOI: 10.1016/j.freeradbiomed.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Nitric oxide (NO) is a ubiquitous signaling molecule, and thus a variety of methods have been developed for its detection and quantification. Fluorometric analyses using a fluorescent NO probe harboring an o-phenylenediamine (OPD) structure are widely used for NO analyses in various organisms, including yeast. Here, we discovered that an NO-independent fluorophore (UNK436) was generated from a fluorescent NO probe 4-amino-5-methylamino-2',7'-difluorofluorescein (DAF-FM), which has an OPD structure, in yeast cells. The molecules responsible for this undesirable fluorescence and their reaction mechanisms were analyzed. Our mass spectrometric analysis showed that two carbon atoms from glucose were incorporated into UNK436. Subsequent analyses indicated that a non-proteinous small compound leads to the synthesis of UNK436 through an oxidative reaction. Furthermore, our LC/MS/MS analysis of the reaction mixture of DAF-FM with acetaldehyde in combination with stable isotope labeling demonstrated that acetaldehyde reacts with DAF-FM oxidatively, generating UNK436. Another NO probe with an OPD structure, diaminorhodamine-4M, reacted with acetaldehyde in the same way to emit fluorescence. Based on our findings, we recommend that in researches using OPD-based fluorescent NO probes, alternative analyses also be performed to identify the reaction products of the probes with NO to avoid false-positives.
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Affiliation(s)
- Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan.
| | - Yuki Yoshikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
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41
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Li F, Yuan L, Lu H, Li G, Chen Y, Engqvist MKM, Kerkhoven EJ, Nielsen J. Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction. Nat Catal 2022. [DOI: 10.1038/s41929-022-00798-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractEnzyme turnover numbers (kcat) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured kcat data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput kcat prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture kcat changes for mutated enzymes and identify amino acid residues with a strong impact on kcat values. We applied this approach to predict genome-scale kcat values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted kcat values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.
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42
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Sengupta S, Nath R, Bhuyan R, Bhattacharjee A. Variation in glucose metabolism under acidified sodium nitrite mediated nitrosative stress in Saccharomyces cerevisiae. J Appl Microbiol 2022; 133:1660-1675. [PMID: 35702895 DOI: 10.1111/jam.15669] [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: 03/25/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
AIMS The work aimed to understand the important changes during glucose metabolism in Saccharomyces cerevisiae under acidified sodium nitrite (ac.NaNO2 ) mediated nitrosative stress. METHODS AND RESULTS Confocal microscopy and fluorescence-activated cell sorting analysis were performed to investigate the generation of reactive nitrogen and oxygen species, and redox homeostasis under nitrosative stress was also characterized. Quantitative PCR analysis revealed that the expression of ADH genes was upregulated under such condition, whereas the ACO2 gene was downregulated. Some of the enzymes of the tricarboxylic acid cycle were partially inhibited, whereas malate metabolism and alcoholic fermentation were increased under nitrosative stress. Kinetics of ethanol production was also characterized. A network analysis was conducted to validate our findings. In the presence of ac.NaNO2 , in vitro protein tyrosine nitration formation was checked by western blotting using pure alcohol dehydrogenase and aconitase. CONCLUSIONS Alcoholic fermentation rate was increased under stress condition and this altered metabolism might be conjoined with the defence machinery to overcome the nitrosative stress. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first work of this kind where the role of metabolism under nitrosative stress has been characterized in S. cerevisiae and it will provide a base to develop an alternative method of industrial ethanol production.
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Affiliation(s)
- Swarnab Sengupta
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
| | - Rohan Nath
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
| | - Rajabrata Bhuyan
- Department of Bio-Science and Biotechnology, Banasthali Vidyapith (Deemed) University, Banasthali, Rajasthan, India
| | - Arindam Bhattacharjee
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
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43
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Sautchuk R, Eliseev RA. Cell energy metabolism and bone formation. Bone Rep 2022; 16:101594. [PMID: 35669927 PMCID: PMC9162940 DOI: 10.1016/j.bonr.2022.101594] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/19/2022] Open
Abstract
Energy metabolism plays an important role in cell and tissue ability to effectively function, maintain homeostasis, and perform repair. Yet, the role of energy metabolism in skeletal tissues in general and in bone, in particular, remains understudied. We, here, review the aspects of cell energy metabolism relevant to bone tissue, such as: i) availability of substrates and oxygen; ii) metabolism regulatory mechanisms most active in bone tissue, e.g. HIF and BMP; iii) crosstalk of cell bioenergetics with other cell functions, e.g. proliferation and differentiation; iv) role of glycolysis and mitochondrial oxidative phosphorylation in osteogenic lineage; and v) most significant changes in bone energy metabolism observed in aging and other pathologies. In addition, we review available methods to study energy metabolism on a subcellular, cellular, tissue, and live animal levels.
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Affiliation(s)
- Rubens Sautchuk
- Center for Musculoskeletal Research, University of Rochester School of Medicine & Dentistry, 601 Elmwood Ave, Rochester, NY 14642, United States
| | - Roman A. Eliseev
- Center for Musculoskeletal Research, University of Rochester School of Medicine & Dentistry, 601 Elmwood Ave, Rochester, NY 14642, United States
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Ding H, Jambunathan K, Jiang G, Margolis DM, Leng I, Ihnat M, Ma JX, Mirsalis J, Zhang Y. 3D Spheroids of Human Primary Urine-Derived Stem Cells in the Assessment of Drug-Induced Mitochondrial Toxicity. Pharmaceutics 2022; 14:1042. [PMID: 35631624 PMCID: PMC9145543 DOI: 10.3390/pharmaceutics14051042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondrial toxicity (Mito-Tox) risk has increased due to the administration of several classes of drugs, particularly some life-long antiretroviral drugs for HIV+ individuals. However, no suitable in vitro assays are available to test long-term Mito-Tox (≥4 weeks). The goal of this study is to develop a 3D spheroid system of human primary urine-derived stem cells (USC) for the prediction of drug-induced delayed Mito-Tox. The cytotoxicity and Mito-Tox were assessed in 3D USC spheroids 4 weeks after treatment with antiretroviral drugs: zalcitabine (ddC; 0.1, 1 and 10 µM), tenofovir (TFV; 3, 30 and 300 µM) or Raltegravir (RAL; 2, 20 and 200 µM). Rotenone (RTNN, 10 µM) and 0.1% DMSO served as positive and negative controls. Despite only mild cytotoxicity, ddC significantly inhibited the expression of oxidative phosphorylation enzyme Complexes I, III, and IV; and RAL transiently reduced the level of Complex IV. A significant increase in caspase 3 and ROS/RNS level but a decrease in total ATP were observed in USC treated with ddC, TFV, RAL, and RTNN. Levels of mtDNA content and mitochondrial mass were decreased in ddC but minimally or not in TFV- and RAL-treated spheroids. Thus, 3D USC spheroid using antiretroviral drugs as a model offers an alternative platform to assess drug-induced late Mito-Tox.
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Affiliation(s)
- Huifen Ding
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA;
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, China
| | - Kalyani Jambunathan
- SRI Biosciences, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA; (K.J.); (J.M.)
| | - Guochun Jiang
- University of North Carolina HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (G.J.); (D.M.M.)
| | - David M. Margolis
- University of North Carolina HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (G.J.); (D.M.M.)
| | - Iris Leng
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - Michael Ihnat
- Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, OK 73117, USA;
| | - Jian-Xing Ma
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA;
| | - Jon Mirsalis
- SRI Biosciences, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA; (K.J.); (J.M.)
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA;
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Beer production potentiality of some non-Saccharomyces yeast obtained from a traditional beer starter emao. Braz J Microbiol 2022; 53:1515-1531. [PMID: 35488168 PMCID: PMC9433491 DOI: 10.1007/s42770-022-00765-7] [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: 09/08/2021] [Accepted: 04/16/2022] [Indexed: 11/02/2022] Open
Abstract
The recent realisation regarding the potentiality of the long-neglected non-Saccharomyces yeasts in improving the flavour profile and functionality of alcoholic beverages has pushed researchers to search for such potent strains in many sources. We studied the fungal diversity and the rice beer production capability of the fungal strains isolated from emao-a traditional rice beer starter culture of the Boro community. Fifty distinct colonies were picked from mixed-culture plates, of which ten representative morphotypes were selected for species identification, and simultaneous saccharification and beer fermentation (SSBF) assay. The representative isolates were identified as Hyphopichia burtonii (Hbur-FI38, Hbur-FI44, Hbur-FI47 & Hbur-FI68), Saccharomyces cerevisiae (Scer-FI51), Wickerhamomyces anomalus (Wano-FI52), Candida carpophila (Ccar-FI53), Mucor circinelloides (Mcir-FI60), and Saccharomycopsis malanga (Smal-FI77 and Smal-FI84). The non-Saccharomyces yeast strains Hbur-FI38, Hbur-FI44, Ccar-FI53, and Smal-FI77 showed SSBF capacity on rice substrate producing beer that contained 7-10% (v/v) ethanol. A scaled-up fermentation assay was performed to assess the strain-wise fermentation behaviour in large-scale production. The nutritional, functional, and sensory qualities of the SSBF strain fermented beer were compared to the beer produced by emao. All the strains produced beer with reduced alcohol and energy value while compared to the traditional starter emao. Beer produced by both the strains of H. burtonii stood out with higher ascorbic acid, phenol, and antioxidant property, and improved sensory profile in addition to reduced alcohol and energy value. Such SSBF strains are advantageous over the non-SSBF S. cerevisiae strains as the former can be used for direct beer production from rice substrates.
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Simm C, Weerasinghe H, Thomas DR, Harrison PF, Newton HJ, Beilharz TH, Traven A. Disruption of Iron Homeostasis and Mitochondrial Metabolism Are Promising Targets to Inhibit Candida auris. Microbiol Spectr 2022; 10:e0010022. [PMID: 35412372 PMCID: PMC9045333 DOI: 10.1128/spectrum.00100-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022] Open
Abstract
Fungal infections are a global threat, but treatments are limited due to a paucity in antifungal drug targets and the emergence of drug-resistant fungi such as Candida auris. Metabolic adaptations enable microbial growth in nutrient-scarce host niches, and they further control immune responses to pathogens, thereby offering opportunities for therapeutic targeting. Because it is a relatively new pathogen, little is known about the metabolic requirements for C. auris growth and its adaptations to counter host defenses. Here, we establish that triggering metabolic dysfunction is a promising strategy against C. auris. Treatment with pyrvinium pamoate (PP) induced metabolic reprogramming and mitochondrial dysfunction evident in disrupted mitochondrial morphology and reduced tricarboxylic acid (TCA) cycle enzyme activity. PP also induced changes consistent with disrupted iron homeostasis. Nutrient supplementation experiments support the proposition that PP-induced metabolic dysfunction is driven by disrupted iron homeostasis, which compromises carbon and lipid metabolism and mitochondria. PP inhibited C. auris replication in macrophages, which is a relevant host niche for this yeast pathogen. We propose that PP causes a multipronged metabolic hit to C. auris: it restricts the micronutrient iron to potentiate nutritional immunity imposed by immune cells, and it further causes metabolic dysfunction that compromises the utilization of macronutrients, thereby curbing the metabolic plasticity needed for growth in host environments. Our study offers a new avenue for therapeutic development against drug-resistant C. auris, shows how complex metabolic dysfunction can be caused by a single compound triggering antifungal inhibition, and provides insights into the metabolic needs of C. auris in immune cell environments. IMPORTANCE Over the last decade, Candida auris has emerged as a human pathogen around the world causing life-threatening infections with wide-spread antifungal drug resistance, including pandrug resistance in some cases. In this study, we addressed the mechanism of action of the antiparasitic drug pyrvinium pamoate against C. auris and show how metabolism could be inhibited to curb C. auris proliferation. We show that pyrvinium pamoate triggers sweeping metabolic and mitochondrial changes and disrupts iron homeostasis. PP-induced metabolic dysfunction compromises the utilization of both micro- and macronutrients by C. auris and reduces its growth in vitro and in immune phagocytes. Our findings provide insights into the metabolic requirements for C. auris growth and define the mechanisms of action of pyrvinium pamoate against C. auris, demonstrating how this compound works by inhibiting the metabolic flexibility of the pathogen. As such, our study characterizes credible avenues for new antifungal approaches against C. auris.
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Affiliation(s)
- Claudia Simm
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
| | - Harshini Weerasinghe
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
| | - David R. Thomas
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Hayley J. Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Ana Traven
- Infection Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
- Centre to Impact AMR, Monash University, Victoria, Australia
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47
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Evaluation of microtiter plate as a high-throughput screening platform for beer fermentation. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-04009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractDownscaling the anaerobic fermentation in a microtiter plate (MTP) facilitates high throughput screening (HTS) applications. This study investigates the impacts of MTP configurations (scale, shaking, and cover) on the S. pastorianus beer fermentation compared to that in the shaking flask (SF) and European Brewing Convention (EBC) tube regarding fermentation performances and flavor attributes. The lager strains in MTPs accelerated cells reproduction and vitalization, sugar consumption, and glycerol accumulation. The microscale beer fermentation was closer to the SF but differed greatly from EBC tube fermentation depending on the MTP configurations. The downscaling from 2 mL to 0.2 mL in MTP increased the cell growth rate and vitality but did not change the maximum cell density. The shaking MTP did not promote early growth but sustained significantly higher cell numbers at the later fermentation stage. More than 1.5-folds acetaldehyde and higher alcohols, yet less than half esters, were obtained from the MTP and SF fermentations relative to that in the EBC tube. The air-tight MTP cover, as compared to the gas-permeable cover, not only balanced the above volatile flavors but also maintained integrity to the endogenous carbon dioxide pressure during beer fermentation. Additionally, fermentative activities were reduced by excluding air in either the material or the headspace of MTP. Hence, MTP configurations influenced S. pastorianus beer fermentation. These influences were partly attributed to their impacts on air accessibility. Conscious of the impacts, this study helps interpret the minimized fermentation and sheds light on the development of MTP based HTS platform for anaerobic cultivations.
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48
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Microbial pathways for advanced biofuel production. Biochem Soc Trans 2022; 50:987-1001. [PMID: 35411379 PMCID: PMC9162456 DOI: 10.1042/bst20210764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 01/16/2023]
Abstract
Decarbonisation of the transport sector is essential to mitigate anthropogenic climate change. Microbial metabolisms are already integral to the production of renewable, sustainable fuels and, building on that foundation, are being re-engineered to generate the advanced biofuels that will maintain mobility of people and goods during the energy transition. This review surveys the range of natural and engineered microbial systems for advanced biofuels production and summarises some of the techno-economic challenges associated with their implementation at industrial scales.
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49
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Boro N, Narzary D. Amylolytic Fungi in the Ethnic Beer Starter “emao” and Their Beer-Producing Attributes. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.869430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Naturally occurring autochthonous microbes associated with ethnic beer starters are diverse and important as they play different functional roles in beer fermentations. The study on culturable microbes from the ethnic rice beer starter “emao” of the Bodo community of Assam is limited. Here we isolated and identified the culturable fungal diversity associated with emao and screened them for beer-producing capability from glucose and starch substrates. Based on morphology and molecular characterization, the species identified were Candida glabrata (Cgla_RF2), Cyberlindnera fabianii (Cfab_RF37), Hyphopichia burtonii (Hbur_RF19), Mucor circinelloides (Mcir_RF48), Mucor indicus (Mind_RF25), Penicillium citrinum (Pcit_RF32), Rhodosporidiobolus ruineniae (Rrui_RF4 & Rrui_RF43), Saccharomyces cerevisiae (Scer_RF6), Saccharomycopsis fibuligera (Sfib_RF11), and Wickerhamomyces anomalus (Wano_RF3) among which the relative abundance (RA) of W. anomalus was the highest (24%) followed by C. glabrata and H. burtonii (16% in each). Five (Hbur_RF19, Sfib_RF11, Mind_RF25, Mcir_RF48, and Pcit_RF32) of eleven isolates showed amylase positive in the starch medium. Scer_RF6 showed the highest ethanol tolerance (14% v/v) followed by Hbur_RF19 (12% v/v), Cgla_RF2 (11% v/v) and Wano_RF3 (11% v/v). The amylase-positive strains produced beer-containing ethanol in the range of 3.17–7.3 (% v/v) from rice substrate. Although the rice beer produced by amylase-positive strains showed negligible pH difference, other parameters like ethanol, ascorbic acid, total phenol, and antioxidant properties were varied from beer to beer. Antibacterial activities shown by Mcir_RF48 and Pcit_RF32 against the test bacteria were higher with a 23–35 mm zone of inhibition than the other isolates. The present findings reveal the presence of fungi with antibacterial, amylolytic, ethanol fermenting, and antioxidant producing capacity in emao which could the source for future bioprospection.
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50
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Harrouard J, Eberlein C, Ballestra P, Dols-Lafargue M, Masneuf-Pomarede I, Miot-Sertier C, Schacherer J, Albertin W. Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast. Mol Ecol 2022; 32:2374-2395. [PMID: 35318747 DOI: 10.1111/mec.16439] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022]
Abstract
Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.
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Affiliation(s)
- Jules Harrouard
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Chris Eberlein
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Patricia Ballestra
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Isabelle Masneuf-Pomarede
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,BSA, 33170, Gradignan
| | - Cécile Miot-Sertier
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
| | - Warren Albertin
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
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