1
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Gu Y, Zhang B, Tian J, Li L, He Y. Physiology, quorum sensing, and proteomics of lactic acid bacteria were affected by Saccharomyces cerevisiae YE4. Food Res Int 2023; 166:112612. [PMID: 36914328 DOI: 10.1016/j.foodres.2023.112612] [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: 11/24/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
The interaction mode between lactic acid bacteria (LAB) and yeast in a fermentation system directly determines the quality of the products, thus understanding their mode of interaction can improve product quality. The present study investigated the effects of Saccharomyces cerevisiae YE4 on LAB from the perspectives of physiology, quorum sensing (QS), and proteomics. The presence of S. cerevisiae YE4 slowed down the growth of Enterococcus faecium 8-3 but had no significant effect on acid production or biofilm formation. S. cerevisiae YE4 significantly reduced the activity of autoinducer-2 at 19 h in E. faecium 8-3 and at 7-13 h in Lactobacillus fermentum 2-1. Expression of the QS-related genes luxS and pfs was also inhibited at 7 h. Moreover, a total of 107 E. faecium 8-3 proteins differed significantly in coculture with S. cerevisiae YE4-these proteins are involved in metabolic pathways including biosynthesis of secondary metabolites; biosynthesis of amino acids; alanine, aspartate, and glutamate metabolism; fatty acid metabolism; and fatty acid biosynthesis. Among them, proteins involved in cell adhesion, cell wall formation, two-component systems, and ABC transporters were detected. Therefore, S. cerevisiae YE4 might affect the physiological metabolism of E. faecium 8-3 by affecting cell adhesion, cell wall formation, and cell-cell interactions.
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Affiliation(s)
- Yue Gu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, Inner Mongolia 010018, China
| | - Baojun Zhang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, Inner Mongolia 010018, China
| | - Jianjun Tian
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, Inner Mongolia 010018, China
| | - Lijie Li
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, Inner Mongolia 010018, China.
| | - Yinfeng He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, Inner Mongolia 010018, China.
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2
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Gu Y, Tian J, Zhang Y, Wu J, He Y. Effect of Saccharomyces cerevisiae cell-free supernatant on the physiology, quorum sensing, and protein synthesis of lactic acid bacteria. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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3
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Kiiskilä JM, Hassinen IE, Kettunen J, Kytövuori L, Mikkola I, Härkönen P, Jokelainen JJ, Keinänen-Kiukaanniemi S, Perola M, Majamaa K. Association between mitochondrial DNA haplogroups J and K, serum branched-chain amino acids and lowered capability for endurance exercise. BMC Sports Sci Med Rehabil 2022; 14:95. [PMID: 35619160 PMCID: PMC9137050 DOI: 10.1186/s13102-022-00485-3] [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: 10/07/2021] [Accepted: 05/17/2022] [Indexed: 11/11/2022]
Abstract
Background Endurance exercise training promotes the catabolism of branched-chain amino acids (BCAAs) in skeletal muscles. We have previously shown that mitochondrial DNA (mtDNA) haplogroups J and K are markers of low responders in endurance training. In this paper, we hypothesize that BCAA catabolism is a surrogate marker of lower respiratory chain activity attributed to these haplogroups. We evaluated whether exercise-induced changes in amino acid concentrations differ between subjects harbouring mtDNA haplogroups J or K and those with non-JK haplogroups. Methods Finnish male conscripts (N = 633) undertook the 12-min Cooper running test at the beginning and end of their military service. The intervention during the service mainly included endurance aerobic exercise and sports-related muscle training. Concentrations of seven amino acids were analysed in the serum using a high-throughput 1H NMR metabolomics platform. Total DNA was extracted from whole blood, and restriction fragment analysis was used to determine mtDNA haplogroups J and K. Results The concentrations of the seven amino acids were higher following the intervention, with the exception of phenylalanine; interestingly, the increase in the concentrations of three BCAAs was larger in subjects with haplogroup J or K than in subjects with non-JK haplogroups (p = 0.029). MtDNA haplogroups J and K share two common nonsynonymous variants. Structural analysis based on crystallographic data on bovine complexes I and III revealed that the Leu18 variant in cytochrome b encoded by m.14798T > C may interfere with ubiquinone binding at the Qi site in complex III. Conclusions The increase in the concentrations of serum BCAAs following exercise intervention differs between subjects harbouring mtDNA haplogroup J or K and those harbouring non-JK haplogroups. Lower response in endurance training and difference in exercise-induced increase in the concentrations of serum BCAAs suggest decreased respiratory chain activity. Haplogroups J and K share m.14798T > C in MT-CYB, which may hamper the function of complex III. Supplementary information The online version contains supplementary material available at 10.1186/s13102-022-00485-3.
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Affiliation(s)
- Jukka M Kiiskilä
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland. .,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland.
| | - Ilmo E Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | | | - Pirjo Härkönen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Jari J Jokelainen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Sirkka Keinänen-Kiukaanniemi
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Healthcare and Social Services of Selänne, Pyhäjärvi, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
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4
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Grasso C, Eccles DA, Boukalova S, Fabre MS, Dawson RH, Neuzil J, Herst PM, Berridge MV. Mitochondrial DNA Affects the Expression of Nuclear Genes Involved in Immune and Stress Responses in a Breast Cancer Model. Front Physiol 2020; 11:543962. [PMID: 33329014 PMCID: PMC7732479 DOI: 10.3389/fphys.2020.543962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/09/2020] [Indexed: 12/29/2022] Open
Abstract
Tumor cells without mitochondrial (mt) DNA (ρ0 cells) are auxotrophic for uridine, and their growth is supported by pyruvate. While ATP synthesis in ρ0 cells relies on glycolysis, they fail to form tumors unless they acquire mitochondria from stromal cells. Mitochondrial acquisition restores respiration that is essential for de novo pyrimidine biosynthesis and for mitochondrial ATP production. The physiological processes that underpin intercellular mitochondrial transfer to tumor cells lacking mtDNA and the metabolic remodeling and restored tumorigenic properties of cells that acquire mitochondria are not well understood. Here, we investigated the changes in mitochondrial and nuclear gene expression that accompany mtDNA deletion and acquisition in metastatic murine 4T1 breast cancer cells. Loss of mitochondrial gene expression in 4T1ρ0 cells was restored in cells recovered from subcutaneous tumors that grew from 4T1ρ0 cells following acquisition of mtDNA from host cells. In contrast, the expression of most nuclear genes that encode respiratory complex subunits and mitochondrial ribosomal subunits was not greatly affected by loss of mtDNA, indicating ineffective mitochondria-to-nucleus communication systems for these nuclear genes. Further, analysis of nuclear genes whose expression was compromised in 4T1ρ0 cells showed that immune- and stress-related genes were the most highly differentially expressed, representing over 70% of those with greater than 16-fold higher expression in 4T1 compared with 4T1ρ0 cells. The monocyte recruiting chemokine, Ccl2, and Psmb8, a subunit of the immunoproteasome that generates MHCI-binding peptides, were the most highly differentially expressed. Early monocyte/macrophage recruitment into the tumor mass was compromised in 4T1ρ0 cells but recovered before mtDNA could be detected. Taken together, our results show that mitochondrial acquisition by tumor cells without mtDNA results in bioenergetic remodeling and re-expression of genes involved in immune function and stress adaptation.
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Affiliation(s)
- Carole Grasso
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - David A. Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Stepana Boukalova
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czechia
| | | | | | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czechia
- School of Medical Science, Griffith University, Southport, QLD, Australia
| | - Patries M. Herst
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Department of Radiation Therapy, University of Otago, Wellington, New Zealand
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5
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Xiao Y, Clima R, Busch J, Rabien A, Kilic E, Villegas SL, Timmermann B, Attimonelli M, Jung K, Meierhofer D. Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma. Cancer Res 2020; 80:3830-3840. [PMID: 32694149 DOI: 10.1158/0008-5472.can-20-0754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are closely related, rare kidney tumors. Mutations in complex I (CI)-encoding genes play an important role in dysfunction of the oxidative phosphorylation (OXPHOS) system in renal oncocytoma, but are less frequently observed in chRCC. As such, the relevance of OXPHOS status and role of CI mutations in chRCC remain unknown. To address this issue, we performed proteome and metabolome profiling as well as mitochondrial whole-exome sequencing to detect mitochondrial alterations in chRCC tissue specimens. Multiomic analysis revealed downregulation of electron transport chain (ETC) components in chRCC that differed from the expression profile in renal oncocytoma. A decrease in mitochondrial (mt)DNA content, rather than CI mutations, was the main cause for reduced OXPHOS in chRCC. There was a negative correlation between protein and transcript levels of nuclear DNA- but not mtDNA-encoded ETC complex subunits in chRCC. In addition, the reactive oxygen species scavenger glutathione (GSH) was upregulated in chRCC due to decreased expression of proteins involved in GSH degradation. These results demonstrate that distinct mechanisms of OXPHOS exist in chRCC and renal oncocytoma and that expression levels of ETC complex subunits can serve as a diagnostic marker for this rare malignancy. SIGNIFICANCE: These findings establish potential diagnostic markers to distinguish malignant chRCC from its highly similar but benign counterpart, renal oncocytoma.
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Affiliation(s)
- Yi Xiao
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rosanna Clima
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari, Bari, Italy.,Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, Bologna, Italy
| | - Jonas Busch
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Anja Rabien
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
| | - Ergin Kilic
- Institut für Pathologie am Klinikum Leverkusen, Leverkusen, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sonia L Villegas
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari, Bari, Italy
| | - Klaus Jung
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
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6
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Pendleton AL, Antolic AT, Kelly AC, Davis MA, Camacho LE, Doubleday K, Anderson MJ, Langlais PR, Lynch RM, Limesand SW. Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. Am J Physiol Endocrinol Metab 2020; 319:E67-E80. [PMID: 32396498 PMCID: PMC7468780 DOI: 10.1152/ajpendo.00057.2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/25/2023]
Abstract
Fetal sheep with placental insufficiency-induced intrauterine growth restriction (IUGR) have lower hindlimb oxygen consumption rates (OCRs), indicating depressed mitochondrial oxidative phosphorylation capacity in their skeletal muscle. We hypothesized that OCRs are lower in skeletal muscle mitochondria from IUGR fetuses, due to reduced electron transport chain (ETC) activity and lower abundances of tricarboxylic acid (TCA) cycle enzymes. IUGR sheep fetuses (n = 12) were created with mid-gestation maternal hyperthermia and compared with control fetuses (n = 12). At 132 ± 1 days of gestation, biceps femoris muscles were collected, and the mitochondria were isolated. Mitochondria from IUGR muscle have 47% lower State 3 (Complex I-dependent) OCRs than controls, whereas State 4 (proton leak) OCRs were not different between groups. Furthermore, Complex I, but not Complex II or IV, enzymatic activity was lower in IUGR fetuses compared with controls. Proteomic analysis (n = 6/group) identified 160 differentially expressed proteins between groups, with 107 upregulated and 53 downregulated mitochondria proteins in IUGR fetuses compared with controls. Although no differences were identified in ETC subunit protein abundances, abundances of key TCA cycle enzymes [isocitrate dehydrogenase (NAD+) 3 noncatalytic subunit β (IDH3B), succinate-CoA ligase ADP-forming subunit-β (SUCLA2), and oxoglutarate dehydrogenase (OGDH)] were lower in IUGR mitochondria. IUGR mitochondria had a greater abundance of a hypoxia-inducible protein, NADH dehydrogenase 1α subcomplex 4-like 2, which is known to incorporate into Complex I and lower Complex I-mediated NADH oxidation. Our findings show that mitochondria from IUGR skeletal muscle adapt to hypoxemia and hypoglycemia by lowering Complex I activity and TCA cycle enzyme concentrations, which together, act to lower OCR and NADH production/oxidation in IUGR skeletal muscle.
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Affiliation(s)
- Alexander L Pendleton
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona
| | - Andrew T Antolic
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Amy C Kelly
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Melissa A Davis
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Leticia E Camacho
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Kevin Doubleday
- Department of Epidemiology and Biostatistics, College of Public Health, University of Arizona, Tucson, Arizona
| | - Miranda J Anderson
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Paul R Langlais
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona
- Department of Medicine, University of Arizona, Tucson, Arizona
| | - Ronald M Lynch
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona
- Department of Physiology, University of Arizona, Tucson, Arizona
| | - Sean W Limesand
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
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7
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Achour B, Al-Majdoub ZM, Rostami-Hodjegan A, Barber J. Mass Spectrometry of Human Transporters. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:223-247. [PMID: 32084322 DOI: 10.1146/annurev-anchem-091719-024553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
- Certara, Princeton, New Jersey 08540, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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8
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Gu Y, Wu J, Tian J, Li L, Zhang B, Zhang Y, He Y. Effects of Exogenous Synthetic Autoinducer-2 on Physiological Behaviors and Proteome of Lactic Acid Bacteria. ACS OMEGA 2020; 5:1326-1335. [PMID: 32010802 PMCID: PMC6990425 DOI: 10.1021/acsomega.9b01021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Bacterial populations use a cell-to-cell communication system to coordinate community-wide regulation processes, which is termed quorum sensing (QS). Autoinducer-2 (AI-2) is a universal signal molecule that mediates inter- and intraspecies QS systems among different bacteria. In this study, the effects of exogenous addition of AI-2 synthesized in vitro on physiological behaviors and proteome were investigated in lactic acid bacteria strains. Exogenous AI-2 had a concentration-dependent effect on the Enterococcus faecium 8-3 cell density. There was no significant influence on biofilm formation and individual morphology of cells upon 60 μM AI-2 addition in E. faecium 8-3 and Lactobacillus fermentum 2-1. However, it improved the acid and alkali resistance of E. faecium 8-3. With the addition of AI-2, 15 differentially expressed proteins were identified in E. faecium 8-3, which participate in RNA transport signaling, RNA polymerase, ribosome, oxidative phosphorylation, cysteine and methionine metabolism, pyrimidine metabolism, ATP-binding cassette (ABC) transporters, purine metabolism, biosynthesis of the amino acid pathway, etc. Among them, the expression of 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase, which is known to be involved in AI-2 synthesis and cysteine and amino acid metabolism, was upregulated. These findings will lay the foundation to clarify the mechanism of cell-to-cell communication and bacterial physiological behaviors mediated by AI-2.
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9
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Ni Y, Hagras MA, Konstantopoulou V, Mayr JA, Stuchebrukhov AA, Meierhofer D. Mutations in NDUFS1 Cause Metabolic Reprogramming and Disruption of the Electron Transfer. Cells 2019; 8:cells8101149. [PMID: 31557978 PMCID: PMC6829531 DOI: 10.3390/cells8101149] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
Complex I (CI) is the first enzyme of the mitochondrial respiratory chain and couples the electron transfer with proton pumping. Mutations in genes encoding CI subunits can frequently cause inborn metabolic errors. We applied proteome and metabolome profiling of patient-derived cells harboring pathogenic mutations in two distinct CI genes to elucidate underlying pathomechanisms on the molecular level. Our results indicated that the electron transfer within CI was interrupted in both patients by different mechanisms. We showed that the biallelic mutations in NDUFS1 led to a decreased stability of the entire N-module of CI and disrupted the electron transfer between two iron–sulfur clusters. Strikingly interesting and in contrast to the proteome, metabolome profiling illustrated that the pattern of dysregulated metabolites was almost identical in both patients, such as the inhibitory feedback on the TCA cycle and altered glutathione levels, indicative for reactive oxygen species (ROS) stress. Our findings deciphered pathological mechanisms of CI deficiency to better understand inborn metabolic errors.
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Affiliation(s)
- Yang Ni
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Present address: Laboratory of Angiogenesis and Vascular Metabolism, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
| | - Muhammad A. Hagras
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA; (M.A.H.); (A.A.S.)
- Present address: Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vassiliki Konstantopoulou
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria;
| | - Johannes A. Mayr
- Department of Pediatrics, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria;
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA; (M.A.H.); (A.A.S.)
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
- Correspondence: ; Tel.: +49-30-8413-1567
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10
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Xiao Y, Meierhofer D. Glutathione Metabolism in Renal Cell Carcinoma Progression and Implications for Therapies. Int J Mol Sci 2019; 20:E3672. [PMID: 31357507 PMCID: PMC6696504 DOI: 10.3390/ijms20153672] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
A significantly increased level of the reactive oxygen species (ROS) scavenger glutathione (GSH) has been identified as a hallmark of renal cell carcinoma (RCC). The proposed mechanism for increased GSH levels is to counteract damaging ROS to sustain the viability and growth of the malignancy. Here, we review the current knowledge about the three main RCC subtypes, namely clear cell RCC (ccRCC), papillary RCC (pRCC), and chromophobe RCC (chRCC), at the genetic, transcript, protein, and metabolite level and highlight their mutual influence on GSH metabolism. A further discussion addresses the question of how the manipulation of GSH levels can be exploited as a potential treatment strategy for RCC.
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Affiliation(s)
- Yi Xiao
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Takustraße 3, 14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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11
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Li M, Jin X, Guo F, Wu G, Wu L, Deng S. Integrative analyses of key genes and regulatory elements in fluoride-affected osteosarcoma. J Cell Biochem 2019; 120:15397-15409. [PMID: 31037778 DOI: 10.1002/jcb.28807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/30/2019] [Accepted: 04/08/2019] [Indexed: 12/17/2022]
Abstract
Osteosarcoma is one of the most malignant tumors in adolescents with severe outcomes while fluoride is one of the most abundant elements in the environment. Epidemiological evidence has elucidated the relationship between fluoride and osteosarcoma, but the molecular mechanisms are extremely complicated. Microarray profiles were downloaded from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) in the progression of fluoride-affected osteosarcoma. The functional enrichment analysis was performed, a protein-protein interaction network, a microRNA-messenger RNA (mRNA) and a transcription factors-mRNA regulatory network were constructed and performed using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape. A total of 171 DEGs were identified. The functions and pathways of the DEGs were enriched in nucleolus, protein ubiquitination, protein binding, RNA transport, and the spliceosome. Eighteen hub genes were identified and functional analysis revealed that these genes are mainly enriched in protein binding, nucleoplasm, and ribosomal RNA processing. Survival analysis showed that the hub genes may be involved in the invasion or recurrence of osteosarcoma. In conclusion, the DEGs and hub genes with their regulatory elements identified in this study will help us understand the molecular mechanisms underlying fluoride-affected osteosarcoma and provide candidate targets for future research.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Jin
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengjing Guo
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Wu
- Geriatrics Department, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sisi Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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12
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Ubiquitin System. Int J Mol Sci 2018; 19:ijms19041080. [PMID: 29617326 PMCID: PMC5979459 DOI: 10.3390/ijms19041080] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 02/06/2023] Open
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13
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Medina AB, Banaszczak M, Ni Y, Aretz I, Meierhofer D. ρ⁰ Cells Feature De-Ubiquitination of SLC Transporters and Increased Levels and Fluxes of Amino Acids. Int J Mol Sci 2017; 18:ijms18040879. [PMID: 28425971 PMCID: PMC5412460 DOI: 10.3390/ijms18040879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 01/28/2023] Open
Abstract
Solute carrier (SLC) transporters are a diverse group of membrane transporter proteins that regulate the cellular flux and distribution of endogenous and xenobiotic compounds. Post-translational modifications (PTMs), such as ubiquitination, have recently emerged as one of the major regulatory mechanisms in protein function and localization. Previously, we showed that SLC amino acid transporters were on average 6-fold de-ubiquitinated and increased amino acid levels were detected in ρ0 cells (lacking mitochondrial DNA, mtDNA) compared to parental cells. Here, we elucidated the altered functionality of SLC transporters and their dynamic ubiquitination status by measuring the uptake of several isotopically labeled amino acids in both human osteosarcoma 143B.TK- and ρ0 cells. Our pulse chase analysis indicated that de-ubiquitinated amino acid transporters in ρ0 cells were accompanied by an increased transport rate, which leads to higher levels of amino acids in the cell. Finding SLC transport enhancers is an aim of the pharmaceutical industry in order to compensate for loss of function mutations in these genes. Thus, the ubiquitination status of SLC transporters could be an indicator for their functionality, but evidence for a direct connection between de-ubiquitination and transporter activity has to be further elucidated.
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Affiliation(s)
| | - Marcin Banaszczak
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
- Department of Biochemistry and Human Nutrition, Pomeranian Medical University, Broniewskiego 24, 71-460 Szczecin, Poland.
| | - Yang Ni
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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Seidel G, Meierhofer D, Şen NE, Guenther A, Krobitsch S, Auburger G. Quantitative Global Proteomics of Yeast PBP1 Deletion Mutants and Their Stress Responses Identifies Glucose Metabolism, Mitochondrial, and Stress Granule Changes. J Proteome Res 2016; 16:504-515. [PMID: 27966978 DOI: 10.1021/acs.jproteome.6b00647] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The yeast protein PBP1 is implicated in very diverse pathways. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors. Here, we performed label-free quantitative global proteomics to identify crucial downstream factors, either without stress or under cell stress conditions (heat and NaN3). Compared to the wildtype BY4741 strain, PBP1 deletion always triggered downregulation of the key bioenergetics enzyme KGD2 and the prion protein RNQ1 as well as upregulation of the leucine biosynthesis enzyme LEU1. Without stress, enrichment of stress response factors was consistently detected for both deletion mutants; upon stress, these factors were more pronounced. The selective analysis of components of stress granules and P-bodies revealed a prominent downregulation of GIS2. Our yeast data are in good agreement with a global proteomics and metabolomics publication that the PBP1 ortholog ATAXIN-2 (ATXN2) knockout (KO) in mouse results in mitochondrial deficits in leucine/fatty acid catabolism and bioenergetics, with an obesity phenotype. Furthermore, our data provide the completely novel insight that PBP1 mutations in stress periods involve GIS2, a plausible scenario in view of previous data that both PBP1 and GIS2 relocalize from ribosomes to stress granules, interact with poly(A)-binding protein in translation regulation and prevent mitochondrial precursor overaccumulation stress (mPOS). This may be relevant for human diseases like spinocerebellar ataxias, amyotrophic lateral sclerosis, and the metabolic syndrome.
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Affiliation(s)
- Gunnar Seidel
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Nesli-Ece Şen
- Experimental Neurology, Goethe University Medical School , Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Anika Guenther
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Sylvia Krobitsch
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School , Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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