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Xie CY, Su RR, Wu B, Sun ZY, Tang YQ. Response mechanisms of different Saccharomyces cerevisiae strains to succinic acid. BMC Microbiol 2024; 24:158. [PMID: 38720268 PMCID: PMC11077785 DOI: 10.1186/s12866-024-03314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The production of succinic acid (SA) from biomass has attracted worldwide interest. Saccharomyces cerevisiae is preferred for SA production due to its strong tolerance to low pH conditions, ease of genetic manipulation, and extensive application in industrial processes. However, when compared with bacterial producers, the SA titers and productivities achieved by engineered S. cerevisiae strains were relatively low. To develop efficient SA-producing strains, it's necessary to clearly understand how S. cerevisiae cells respond to SA. RESULTS In this study, we cultivated five S. cerevisiae strains with different genetic backgrounds under different concentrations of SA. Among them, KF7 and NBRC1958 demonstrated high tolerance to SA, whereas NBRC2018 displayed the least tolerance. Therefore, these three strains were chosen to study how S. cerevisiae responds to SA. Under a concentration of 20 g/L SA, only a few differentially expressed genes were observed in three strains. At the higher concentration of 60 g/L SA, the response mechanisms of the three strains diverged notably. For KF7, genes involved in the glyoxylate cycle were significantly downregulated, whereas genes involved in gluconeogenesis, the pentose phosphate pathway, protein folding, and meiosis were significantly upregulated. For NBRC1958, genes related to the biosynthesis of vitamin B6, thiamin, and purine were significantly downregulated, whereas genes related to protein folding, toxin efflux, and cell wall remodeling were significantly upregulated. For NBRC2018, there was a significant upregulation of genes connected to the pentose phosphate pathway, gluconeogenesis, fatty acid utilization, and protein folding, except for the small heat shock protein gene HSP26. Overexpression of HSP26 and HSP42 notably enhanced the cell growth of NBRC1958 both in the presence and absence of SA. CONCLUSIONS The inherent activities of small heat shock proteins, the levels of acetyl-CoA and the strains' potential capacity to consume SA all seem to affect the responses and tolerances of S. cerevisiae strains to SA. These factors should be taken into consideration when choosing host strains for SA production. This study provides a theoretical basis and identifies potential host strains for the development of robust and efficient SA-producing strains.
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Affiliation(s)
- Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Ran-Ran Su
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Renmin Rd. 4-13, Chengdu, 610041, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
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Using high-throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s43393-020-00003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3
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Jové M, Pradas I, Mota-Martorell N, Cabré R, Ayala V, Ferrer I, Pamplona R. Succination of Protein Thiols in Human Brain Aging. Front Aging Neurosci 2020; 12:52. [PMID: 32210786 PMCID: PMC7068737 DOI: 10.3389/fnagi.2020.00052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/17/2020] [Indexed: 01/07/2023] Open
Abstract
Human brain evolution toward complexity has been achieved with increasing energy supply as the main adaptation in brain metabolism. Energy metabolism, like other biochemical reactions in aerobic cells, is under enzymatic control and strictly regulated. Nevertheless, physiologically uncontrolled and deleterious reactions take place. It has been proposed that these reactions constitute the basic molecular mechanisms that underlie the maintenance or loss-of-function of neurons and, by extension, cerebral functions during brain aging. In this review article, we focus attention on the role of the nonenzymatic and irreversible adduction of fumarate to the protein thiols, which leads to the formation of S-(2-succino)cysteine (2SC; protein succination) in the human brain. In particular, we first offer a brief approach to the succination reaction, features related to the specificity of protein succination, methods for their detection and quantification, the bases for considering 2SC as a biomarker of mitochondrial stress, the succinated proteome, the cross-regional differences in 2SC content, and changes during brain aging, as well as the potential regulatory significance of fumarate and 2SC. We propose that 2SC defines cross-regional differences of metabolic mitochondrial stress in the human brain and that mitochondrial stress is sustained throughout the healthy adult lifespan in order to preserve neuronal function and survival.
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Affiliation(s)
- Mariona Jové
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Irene Pradas
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Rosanna Cabré
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Victoria Ayala
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Biomedical Research Institute of Bellvitge (IDIBELL), L'Hospitalet de Llobregat (Barcelona), Barcelona, Spain.,Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
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Saatchi F, Kirchmaier AL. Tolerance of DNA Replication Stress Is Promoted by Fumarate Through Modulation of Histone Demethylation and Enhancement of Replicative Intermediate Processing in Saccharomyces cerevisiae. Genetics 2019; 212:631-654. [PMID: 31123043 PMCID: PMC6614904 DOI: 10.1534/genetics.119.302238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Fumarase is a well-characterized TCA cycle enzyme that catalyzes the reversible conversion of fumarate to malate. In mammals, fumarase acts as a tumor suppressor, and loss-of-function mutations in the FH gene in hereditary leiomyomatosis and renal cell cancer result in the accumulation of intracellular fumarate-an inhibitor of α-ketoglutarate-dependent dioxygenases. Fumarase promotes DNA repair by nonhomologous end joining in mammalian cells through interaction with the histone variant H2A.Z, and inhibition of KDM2B, a H3 K36-specific histone demethylase. Here, we report that Saccharomyces cerevisiae fumarase, Fum1p, acts as a response factor during DNA replication stress, and fumarate enhances survival of yeast lacking Htz1p (H2A.Z in mammals). We observed that exposure to DNA replication stress led to upregulation as well as nuclear enrichment of Fum1p, and raising levels of fumarate in cells via deletion of FUM1 or addition of exogenous fumarate suppressed the sensitivity to DNA replication stress of htz1Δ mutants. This suppression was independent of modulating nucleotide pool levels. Rather, our results are consistent with fumarate conferring resistance to DNA replication stress in htz1Δ mutants by inhibiting the H3 K4-specific histone demethylase Jhd2p, and increasing H3 K4 methylation. Although the timing of checkpoint activation and deactivation remained largely unaffected by fumarate, sensors and mediators of the DNA replication checkpoint were required for fumarate-dependent resistance to replication stress in the htz1Δ mutants. Together, our findings imply metabolic enzymes and metabolites aid in processing replicative intermediates by affecting chromatin modification states, thereby promoting genome integrity.
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Affiliation(s)
- Faeze Saatchi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
| | - Ann L Kirchmaier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
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5
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Muid KA, Kimyon Ö, Reza SH, Karakaya HC, Koc A. Characterization of long living yeast deletion mutants that lack mitochondrial metabolism genes DSS1, PPA2 and AFG3. Gene 2019; 706:172-180. [PMID: 31082499 DOI: 10.1016/j.gene.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023]
Abstract
Molecular mechanisms of aging and longevity are still mostly unknown. Mitochondria play central roles in cellular metabolism and aging. In this study, we identified three deletion mutants of mitochondrial metabolism genes (ppa2∆, dss1∆, and afg3∆) that live longer than wild-type cells. These long-lived cells harbored significantly decreased amount of mitochondrial DNA (mtDNA) and reactive oxygen species (ROS). Compared to the serpentine nature of wild-type mitochondria, a different dynamics and distribution pattern of mitochondria were observed in the mutants. Both young and old long-lived cells produced relatively low but adequate levels of ATP for cellular activities. The status of the retrograde signaling was checked by expression of CIT2 gene and found activated in long-lived mutants. The mutant cells were also profiled for their gene expression patterns, and genes that were differentially regulated were determined. All long-lived cells comprised similar pleiotropic phenotype regarding mitochondrial dynamics and functions. Thus, this study suggests that DSS1, PPA2, and AFG3 genes modulate the lifespan by altering the mitochondrial morphology and functions.
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Affiliation(s)
- K A Muid
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Önder Kimyon
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Shahadat Hasan Reza
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Huseyin Caglar Karakaya
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Ahmet Koc
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey; Inonu University, Medical School, Department of Medical Biology and Genetics, Battalgazi, Malatya, Turkey.
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6
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Raja V, Salsaa M, Joshi AS, Li Y, van Roermund CWT, Saadat N, Lazcano P, Schmidtke M, Hüttemann M, Gupta SV, Wanders RJA, Greenberg ML. Cardiolipin-deficient cells depend on anaplerotic pathways to ameliorate defective TCA cycle function. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:654-661. [PMID: 30731133 DOI: 10.1016/j.bbalip.2019.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/22/2018] [Accepted: 02/02/2019] [Indexed: 01/01/2023]
Abstract
Previous studies have shown that the cardiolipin (CL)-deficient yeast mutant, crd1Δ, has decreased levels of acetyl-CoA and decreased activities of the TCA cycle enzymes aconitase and succinate dehydrogenase. These biochemical phenotypes are expected to lead to defective TCA cycle function. In this study, we report that signaling and anaplerotic metabolic pathways that supplement defects in the TCA cycle are essential in crd1Δ mutant cells. The crd1Δ mutant is synthetically lethal with mutants in the TCA cycle, retrograde (RTG) pathway, glyoxylate cycle, and pyruvate carboxylase 1. Glutamate levels were decreased, and the mutant exhibited glutamate auxotrophy. Glyoxylate cycle genes were up-regulated, and the levels of glyoxylate metabolites succinate and citrate were increased in crd1Δ. Import of acetyl-CoA from the cytosol into mitochondria is essential in crd1Δ, as deletion of the carnitine-acetylcarnitine translocase led to lethality in the CL mutant. β-oxidation was functional in the mutant, and oleate supplementation rescued growth defects. These findings suggest that TCA cycle deficiency caused by the absence of CL necessitates activation of anaplerotic pathways to replenish acetyl-CoA and TCA cycle intermediates. Implications for Barth syndrome, a genetic disorder of CL metabolism, are discussed.
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Affiliation(s)
- Vaishnavi Raja
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Amit S Joshi
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, Amsterdam, the Netherlands
| | - Nadia Saadat
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, United States of America
| | - Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Michael Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Smiti V Gupta
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, United States of America
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, Amsterdam, the Netherlands
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America.
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7
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Liu J, Li J, Liu Y, Shin HD, Ledesma-Amaro R, Du G, Chen J, Liu L. Synergistic Rewiring of Carbon Metabolism and Redox Metabolism in Cytoplasm and Mitochondria of Aspergillus oryzae for Increased l-Malate Production. ACS Synth Biol 2018; 7:2139-2147. [PMID: 30092627 DOI: 10.1021/acssynbio.8b00130] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
l-Malate is an important platform chemical that has extensive applications in the food, feed, and wine industries. Here, we synergistically engineered the carbon metabolism and redox metabolism in the cytosol and mitochondria of a previously engineered Aspergillus oryzae to further improve the l-malate titer and decrease the byproduct succinate concentration. First, the accumulation of the intermediate pyruvate was eliminated by overexpressing a pyruvate carboxylase from Rhizopus oryzae in the cytosol and mitochondria of A. oryzae, and consequently, the l-malate titer increased 7.5%. Then, malate synthesis via glyoxylate bypass in the mitochondria was enhanced, and citrate synthase in the oxidative TCA cycle was downregulated by RNAi, enhancing the l-malate titer by 10.7%. Next, the exchange of byproducts (succinate and fumarate) between the cytosol and mitochondria was regulated by the expression of a dicarboxylate carrier Sfc1p from Saccharomyces cerevisiae in the mitochondria, which increased l-malate titer 3.5% and decreased succinate concentration 36.8%. Finally, an NADH oxidase from Lactococcus lactis was overexpressed to decrease the NADH/NAD+ ratio, and the engineered A. oryzae strain produced 117.2 g/L l-malate and 3.8 g/L succinate, with an l-malate yield of 0.9 g/g corn starch and a productivity of 1.17 g/L/h. Our results showed that synergistic engineering of the carbon and redox metabolisms in the cytosol and mitochondria of A. oryzae effectively increased the l-malate titer, while simultaneously decreasing the concentration of the byproduct succinate. The strategies used in our work may be useful for the metabolic engineering of fungi to produce other industrially important chemicals.
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Affiliation(s)
- Jingjing Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Hyun-dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | | | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Taïeb D, Pacak K. New Insights into the Nuclear Imaging Phenotypes of Cluster 1 Pheochromocytoma and Paraganglioma. Trends Endocrinol Metab 2017; 28:807-817. [PMID: 28867159 PMCID: PMC5673583 DOI: 10.1016/j.tem.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022]
Abstract
Pheochromocytomas and paragangliomas (PPGLs) belong to the family of neural crest cell-derived neoplasms. In up to 70% of cases they are associated with germline and somatic mutations in 15 well-characterized PPGL driver or fusion genes. PPGLs can be grouped into three main clusters, where cluster 1 includes PPGLs characterized by a pseudohypoxic signature. Although cluster 1 tumors share several common features, they exhibit unique behaviors. We present here unique insights into the imaging phenotypes of cluster 1 PPGLs based on glucose uptake, catecholamine metabolism, and somatostatin receptor expression. Recent data suggest that succinate is a major player in the imaging phenotype of succinate dehydrogenase-deficient PPGLs. This review emphasizes the emerging stromal cell-succinate interaction and highlights new perspectives in PPGL theranostics.
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Affiliation(s)
- David Taïeb
- Department of Nuclear Medicine, La Timone University Hospital, European Center for Research in Medical Imaging (CERIMED), Aix-Marseille University, Marseille, France.
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Garrigue P, Bodin-Hullin A, Balasse L, Fernandez S, Essamet W, Dignat-George F, Pacak K, Guillet B, Taïeb D. The Evolving Role of Succinate in Tumor Metabolism: An 18F-FDG-Based Study. J Nucl Med 2017; 58:1749-1755. [PMID: 28619735 DOI: 10.2967/jnumed.117.192674] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/24/2017] [Indexed: 12/27/2022] Open
Abstract
In recent years, inherited and acquired mutations in the tricarboxylic acid (TCA) cycle enzymes have been reported in diverse cancers. Pheochromocytomas and paragangliomas often exhibit dysregulation of glucose metabolism, which is also driven by mutations in genes encoding the TCA cycle enzymes or by activation of hypoxia signaling. Pheochromocytomas and paragangliomas associated with succinate dehydrogenase (SDH) deficiency are characterized by high 18F-FDG avidity. This association is currently only partially explained. Therefore, we hypothesized that accumulation of succinate due to the TCA cycle defect could be the major connecting hub between SDH-mutated tumors and the 18F-FDG uptake profile. Methods: To test whether succinate modifies the 18F-FDG metabolic profile of tumors, we performed in vitro and in vivo (small-animal PET/CT imaging and autoradiography) experiments in the presence of succinate, fumarate, and phosphate-buffered saline (PBS) in different cell models. As a control, we also evaluated the impact of succinate on 18F-fluorocholine uptake and retention. Glucose transporter 1 (GLUT1) immunohistochemistry was performed to assess whether 18F-FDG uptake correlates with GLUT1 staining. Results: Intratumoral injection of succinate significantly increased 18F-FDG uptake at 24 h on small-animal PET/CT imaging and autoradiography. No effect of succinate was observed on cancer cells in vitro, but interestingly, we found that succinate caused increased 18F-FDG uptake by human umbilical vein endothelial cells in a concentration-dependent manner. No significant effect was observed after intratumoral injection of fumarate or PBS. Succinate, fumarate, and PBS have no effect on cell viability, regardless of cell lineage. Intramuscular injection of succinate also significantly increases 18F-FDG uptake by muscle when compared with either PBS or fumarate, highlighting the effect of succinate on connective tissues. No difference was observed between PBS and succinate on 18F-fluorocholine uptake in the tumor and muscle and on hind limb blood flow. GLUT1 expression quantification did not significantly differ between the study groups. Conclusion: The present study shows that succinate stimulates 18F-FDG uptake by endothelial cells, a finding that partially explains the 18F-FDG metabotype observed in tumors with SDH deficiency. Although this study is an 18F-FDG-based approach, it provides an impetus to better characterize the determinants of 18F-FDG uptake in various tumors and their surrounding microenvironment, with a special emphasis on the role of tumor-specific oncometabolites.
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Affiliation(s)
- Philippe Garrigue
- Aix-Marseille University, INSERM, UMR-S 1076, Marseille, France.,Aix-Marseille University, CERIMED, Marseille, France.,Department of Nuclear Medicine, Aix-Marseille University, Marseille, France
| | | | - Laure Balasse
- Aix-Marseille University, INSERM, UMR-S 1076, Marseille, France.,Aix-Marseille University, CERIMED, Marseille, France
| | | | - Wassim Essamet
- Department of Neuropathology, APHM Timone, Marseille, France; and
| | | | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Benjamin Guillet
- Aix-Marseille University, INSERM, UMR-S 1076, Marseille, France.,Aix-Marseille University, CERIMED, Marseille, France.,Department of Nuclear Medicine, Aix-Marseille University, Marseille, France
| | - David Taïeb
- Aix-Marseille University, CERIMED, Marseille, France .,Department of Nuclear Medicine, Aix-Marseille University, Marseille, France
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SLC25 Family Member Genetic Interactions Identify a Role for HEM25 in Yeast Electron Transport Chain Stability. G3-GENES GENOMES GENETICS 2017; 7:1861-1873. [PMID: 28404662 PMCID: PMC5473764 DOI: 10.1534/g3.117.041194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The SLC25 family member SLC25A38 (Hem25 in yeast) was recently identified as a mitochondrial glycine transporter that provides substrate to initiate heme/hemoglobin synthesis. Mutations in the human SLC25A38 gene cause congenital sideroblastic anemia. The full extent to which SLC25 family members coregulate heme synthesis with other mitochondrial functions is not clear. In this study, we surveyed 29 nonessential SLC25 family members in Saccharomyces cerevisiae for their ability to support growth in the presence and absence of HEM25. Six SLC25 family members were identified that were required for growth or for heme synthesis in cells lacking Hem25 function. Importantly, we determined that loss of function of the SLC25 family member Flx1, which imports FAD into mitochondria, together with loss of function of Hem25, resulted in inability to grow on media that required yeast cells to supply energy using mitochondrial respiration. We report that specific components of complexes of the electron transport chain are decreased in the absence of Flx1 and Hem25 function. In addition, we show that mitochondria from flx1Δ hem25Δ cells contain uncharacterized Cox2-containing high molecular weight aggregates. The functions of Flx1 and Hem25 provide a facile explanation for the decrease in heme level, and in specific electron transport chain complex components.
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11
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González B, Mas A, Beltran G, Cullen PJ, Torija MJ. Role of Mitochondrial Retrograde Pathway in Regulating Ethanol-Inducible Filamentous Growth in Yeast. Front Physiol 2017; 8:148. [PMID: 28424625 PMCID: PMC5372830 DOI: 10.3389/fphys.2017.00148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
In yeast, ethanol is produced as a by-product of fermentation through glycolysis. Ethanol also stimulates a developmental foraging response called filamentous growth and is thought to act as a quorum-sensing molecule. Ethanol-inducible filamentous growth was examined in a small collection of wine/European strains, which validated ethanol as an inducer of filamentous growth. Wine strains also showed variability in their filamentation responses, which illustrates the striking phenotypic differences that can occur among individuals. Ethanol-inducible filamentous growth in Σ1278b strains was independent of several of the major filamentation regulatory pathways [including fMAPK, RAS-cAMP, Snf1, Rpd3(L), and Rim101] but required the mitochondrial retrograde (RTG) pathway, an inter-organellar signaling pathway that controls the nuclear response to defects in mitochondrial function. The RTG pathway regulated ethanol-dependent filamentous growth by maintaining flux through the TCA cycle. The ethanol-dependent invasive growth response required the polarisome and transcriptional induction of the cell adhesion molecule Flo11p. Our results validate established stimuli that trigger filamentous growth and show how stimuli can trigger highly specific responses among individuals. Our results also connect an inter-organellar pathway to a quorum sensing response in fungi.
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Affiliation(s)
- Beatriz González
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
| | - Paul J Cullen
- Department of Biological Sciences, University at BuffaloBuffalo, NY, USA
| | - María Jesús Torija
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i VirgiliTarragona, Spain
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Unrean P, Jeennor S, Laoteng K. Systematic development of biomass overproducing Scheffersomyces stipitis for high-cell-density fermentations. Synth Syst Biotechnol 2016; 1:47-55. [PMID: 29062927 PMCID: PMC5640594 DOI: 10.1016/j.synbio.2016.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 01/05/2016] [Accepted: 01/10/2016] [Indexed: 11/28/2022] Open
Abstract
The development of economically feasible bio-based process requires efficient cell factories capable of producing the desired product at high titer under high-cell-density fermentation. Herein we present a combinatorial approach based on systems metabolic engineering and metabolic evolution for the development of efficient biomass-producing strain. Systems metabolic engineering guided by flux balance analysis (FBA) was first employed to rationally design mutant strains of Scheffersomyces stipitis with high biomass yield. By experimentally implementing these mutations, the biomass yield was improved by 30% in GPD1, 25% in TKL1, 30% in CIT1, and 44% in ZWF1 overexpressed mutants compared to wild-type. These designed mutants were further fine-tuned through metabolic evolution resulting in the maximal biomass yield of 0.49 g-cdw/g-glucose, which matches well with predicted yield phenotype. The constructed mutants are beneficial for biotechnology applications dealing with high cell titer cultivations. This work demonstrates a solid confirmation of systems metabolic engineering in combination with metabolic evolution approach for efficient strain development, which could assist in rapid optimization of cell factory for an economically viable and sustainable bio-based process.
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Affiliation(s)
- Pornkamol Unrean
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Sukanya Jeennor
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
| | - Kobkul Laoteng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand
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Martinez-Moya P, Niehaus K, Alcaíno J, Baeza M, Cifuentes V. Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources. BMC Genomics 2015; 16:289. [PMID: 25887121 PMCID: PMC4404605 DOI: 10.1186/s12864-015-1484-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/25/2015] [Indexed: 11/27/2022] Open
Abstract
Background Astaxanthin is a potent antioxidant with increasing biotechnological interest. In Xanthophyllomyces dendrorhous, a natural source of this pigment, carotenogenesis is a complex process regulated through several mechanisms, including the carbon source. X. dendrorhous produces more astaxanthin when grown on a non-fermentable carbon source, while decreased astaxanthin production is observed in the presence of high glucose concentrations. In the present study, we used a comparative proteomic and metabolomic analysis to characterize the yeast response when cultured in minimal medium supplemented with glucose (fermentable) or succinate (non-fermentable). Results A total of 329 proteins were identified from the proteomic profiles, and most of these proteins were associated with carotenogenesis, lipid and carbohydrate metabolism, and redox and stress responses. The metabolite profiles revealed 92 metabolites primarily associated with glycolysis, the tricarboxylic acid cycle, amino acids, organic acids, sugars and phosphates. We determined the abundance of proteins and metabolites of the central pathways of yeast metabolism and examined the influence of these molecules on carotenogenesis. Similar to previous proteomic-stress response studies, we observed modulation of abundance from several redox, stress response, carbohydrate and lipid enzymes. Additionally, the accumulation of trehalose, absence of key ROS response enzymes, an increased abundance of the metabolites of the pentose phosphate pathway and tricarboxylic acid cycle suggested an association between the accumulation of astaxanthin and oxidative stress in the yeast. Moreover, we observed the increased abundance of late carotenogenesis enzymes during astaxanthin accumulation under succinate growth conditions. Conclusions The use of succinate as a carbon source in X. dendrorhous cultures increases the availability of acetyl-CoA for the astaxanthin production compared with glucose, likely reflecting the positive regulation of metabolic enzymes of the tricarboxylic acid and glyoxylate cycles. The high metabolite level generated in this pathway could increase the cellular respiration rate, producing reactive oxygen species, which induces carotenogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1484-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pilar Martinez-Moya
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Karsten Niehaus
- Department of Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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Mitochondrial dysfunction in cancer chemoresistance. Biochem Pharmacol 2014; 92:62-72. [DOI: 10.1016/j.bcp.2014.07.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 12/19/2022]
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Tang X, Feng H, Zhang J, Chen WN. Comparative proteomics analysis of engineered Saccharomyces cerevisiae with enhanced biofuel precursor production. PLoS One 2013; 8:e84661. [PMID: 24376832 PMCID: PMC3871657 DOI: 10.1371/journal.pone.0084661] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
The yeast Saccharomyces cerevisiae was metabolically modified for enhanced biofuel precursor production by knocking out genes encoding mitochondrial isocitrate dehydrogenase and over-expression of a heterologous ATP-citrate lyase. A comparative iTRAQ-coupled 2D LC-MS/MS analysis was performed to obtain a global overview of ubiquitous protein expression changes in S. cerevisiae engineered strains. More than 300 proteins were identified. Among these proteins, 37 were found differentially expressed in engineered strains and they were classified into specific categories based on their enzyme functions. Most of the proteins involved in glycolytic and pyruvate branch-point pathways were found to be up-regulated and the proteins involved in respiration and glyoxylate pathway were however found to be down-regulated in engineered strains. Moreover, the metabolic modification of S. cerevisiae cells resulted in a number of up-regulated proteins involved in stress response and differentially expressed proteins involved in amino acid metabolism and protein biosynthesis pathways. These LC-MS/MS based proteomics analysis results not only offered extensive information in identifying potential protein-protein interactions, signal pathways and ubiquitous cellular changes elicited by the engineered pathways, but also provided a meaningful biological information platform serving further modification of yeast cells for enhanced biofuel production.
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Affiliation(s)
- Xiaoling Tang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Huixing Feng
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianhua Zhang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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