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Cheng C, McCauley BS, Matulionis N, Vogelauer M, Camacho D, Christofk HR, Dang W, Irwin NAT, Kurdistani SK. Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae. SCIENCE ADVANCES 2025; 11:eadv4082. [PMID: 40215312 PMCID: PMC11988410 DOI: 10.1126/sciadv.adv4082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 03/06/2025] [Indexed: 04/14/2025]
Abstract
The discovery of histone H3 copper reductase activity provides a novel metabolic framework for understanding the functions of core histone residues, which, unlike N-terminal residues, have remained largely unexplored. We previously demonstrated that histone H3 cysteine 110 (H3C110) contributes to cupric (Cu2+) ion binding and its reduction to the cuprous (Cu1+) form. However, this residue is absent in Saccharomyces cerevisiae, raising questions about its evolutionary and functional significance. Here, we report that H3C110 has been lost in many fungal lineages despite near-universal conservation across eukaryotes. Introduction of H3C110 into S. cerevisiae increased intracellular Cu1+ levels and ameliorated the iron homeostasis defects caused by inactivation of the Cup1 metallothionein or glutathione depletion. Enhanced histone copper reductase activity also extended replicative life span under oxidative growth conditions but reduced it under fermentative conditions. Our findings suggest that a trade-off between histone copper reductase activity, iron metabolism, and life span may underlie the loss or retention of H3C110 across eukaryotes.
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Affiliation(s)
- Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brenna S. McCauley
- Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dimitrios Camacho
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weiwei Dang
- Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas A. T. Irwin
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Pena IA, Shi JS, Chang SM, Yang J, Block S, Adelmann CH, Keys HR, Ge P, Bathla S, Witham IH, Sienski G, Nairn AC, Sabatini DM, Lewis CA, Kory N, Vander Heiden MG, Heiman M. SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation. Nat Commun 2025; 16:978. [PMID: 39856062 PMCID: PMC11760969 DOI: 10.1038/s41467-025-56130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 01/08/2025] [Indexed: 01/30/2025] Open
Abstract
Many essential proteins require pyridoxal 5'-phosphate, the active form of vitamin B6, as a cofactor for their activity. These include enzymes important for amino acid metabolism, one-carbon metabolism, polyamine synthesis, erythropoiesis, and neurotransmitter metabolism. A third of all mammalian pyridoxal 5'-phosphate-dependent enzymes are localized in the mitochondria; however, the molecular machinery involved in the regulation of mitochondrial pyridoxal 5'-phosphate levels in mammals remains unknown. In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5'-phosphate. Loss of SLC25A38 causes depletion of mitochondrial, but not cellular, pyridoxal 5'-phosphate, and impairs cellular proliferation under both physiological and low vitamin B6 conditions. Metabolic changes associated with SLC25A38 loss suggest impaired mitochondrial pyridoxal 5'-phosphate-dependent enzymatic reactions, including serine to glycine conversion catalyzed by serine hydroxymethyltransferase-2 as well as ornithine aminotransferase. The proliferation defect of SLC25A38-null K562 cells in physiological and low vitamin B6 media can be explained by the loss of serine hydroxymethyltransferase-2-dependent production of one-carbon units and downstream de novo nucleotide synthesis. Our work points to a role for SLC25A38 in mitochondrial pyridoxal 5'-phosphate accumulation and provides insights into the pathology of congenital sideroblastic anemia.
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Affiliation(s)
- Izabella A Pena
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Ottawa, ON, Canada.
| | - Jeffrey S Shi
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
| | - Sarah M Chang
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Jason Yang
- Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel Block
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Charles H Adelmann
- Department of Biology, MIT, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Preston Ge
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Shveta Bathla
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Isabella H Witham
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Angus C Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - David M Sabatini
- Institute of Organic Chemistry and Biochemistry, IOCB, Prague, Czechia
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- UMass Chan Medical School, Program in Molecular Medicine, Worcester, MA, USA
| | - Nora Kory
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Vander Heiden
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myriam Heiman
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
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Xu N, Xu Y, Smith N, Chen H, Guo Z, Lee J, Wu X. MTM1 displays a new function in the regulation of nickel resistance in Saccharomyces cerevisiae. Metallomics 2022; 14:6711704. [PMID: 36138538 PMCID: PMC9989664 DOI: 10.1093/mtomcs/mfac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023]
Abstract
Nickel (Ni) is an essential yet toxic trace element. Although a cofactor for many metalloenzymes, nickel function and metabolism is not fully explored in eukaryotes. Molecular biology and metallomic methods were utilized to explore the new physiological functions of nickel in Saccharomyces cerevisiae. Here we showed that MTM1 knockout cells displayed much stronger nickel tolerance than wild-type cells and mitochondrial accumulations of Ni and Fe of mtm1Δ cells dramatically decreased compared to wild-type cells when exposed to excess nickel. Superoxide dismutase 2 (Sod2p) activity in mtm1Δ cells was severely attenuated and restored through Ni supplementation in media or total protein. SOD2 mRNA level of mtm1Δ cells was significantly higher than that in the wild-type strain but was decreased by Ni supplementation. MTM1 knockout afforded resistance to excess nickel mediated through reactive oxygen species levels. Meanwhile, additional Ni showed no significant effect on the localization of Mtm1p. Our study reveals the MTM1 gene plays an important role in nickel homeostasis and identifies a novel function of nickel in promoting Sod2p activity in yeast cells.
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Affiliation(s)
- Naifeng Xu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yuan Xu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nathan Smith
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln 68588-0664, Nebraska
| | - Huizhu Chen
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ziguo Guo
- Hubei Inspection Center for Quality and Safety of Agricultural Food, Wuhan 430070, China
| | - Jaekwon Lee
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln 68588-0664, Nebraska
| | - Xiaobin Wu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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Bian J, Wang L, Wu J, Simth N, Zhang L, Wang Y, Wu X. MTM1 plays an important role in the regulation of zinc tolerance in Saccharomyces cerevisiae. J Trace Elem Med Biol 2021; 66:126759. [PMID: 33872833 DOI: 10.1016/j.jtemb.2021.126759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Acquisition and distribution of zinc supports a number of biological processes. Various molecular factors are involved in zinc metabolism but not fully explored. BASIC PROCEDURES Spontaneous mutants were generated in yeast with excess zinc culture followed by whole genome DNA sequencing to discover zinc metabolism related genes by bioinformatics. An identified mutant was characterized through metallomic and molecular biology methods. MAIN FINDINGS Here we reported that MTM1 knockout cells displayed much stronger zinc tolerance than wild type cells on SC medium when exposed to excess zinc. Zn accumulation of mtm1Δ cells was dramatically decreased compared to wild type cells under excessive zinc condition due to MTM1 deletion reduced zinc uptake. ZRC1 mRNA level of mtm1Δ cells was significantly higher than that in the wild-type strain leading to increased vacuolar zinc accumulations in mtm1Δ cells. The mRNA levels of ZRT1 and ZAP1 decreased in mtm1Δ cells contributing to less Zn uptake. The zrc1Δmtm1Δ double knockout strain exhibited Zn sensitivity. MTM1 knockout did not afford resistance to excess zinc through an effect mediated through an influence on levels of ROS. Superoxide dismutase 2 (Sod2p) activity in mtm1Δ cells was severely impaired and not restored through Zn supplementation. Meanwhile, additional Zn showed no significant effect on the localization and expression of Mtm1p. PRINCIPAL CONCLUSIONS Our study reveals the MTM1 gene plays an important role in the regulation of zinc homeostasis in yeast cells via changing zinc uptake and distribution. This discovery provides new insights for better understanding biochemical communication between vacuole and mitochondrial in relation to zinc-metabolism.
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Affiliation(s)
- Jiang Bian
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Department of Obstetrics and Gynecology, Shanghai Everjoy Medical Polyclinic, 675 Minbei Road, Shanghai, 201107, China
| | - Lingyun Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jie Wu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Nathan Simth
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, United States
| | - Lingzhi Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yuanfeng Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaobin Wu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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The cystic fibrosis transmembrane conductance regulator (CFTR) and its stability. Cell Mol Life Sci 2016; 74:23-38. [PMID: 27734094 PMCID: PMC5209436 DOI: 10.1007/s00018-016-2386-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is responsible for the disease cystic fibrosis (CF). It is a membrane protein belonging to the ABC transporter family functioning as a chloride/anion channel in epithelial cells around the body. There are over 1500 mutations that have been characterised as CF-causing; the most common of these, accounting for ~70 % of CF cases, is the deletion of a phenylalanine at position 508. This leads to instability of the nascent protein and the modified structure is recognised and then degraded by the ER quality control mechanism. However, even pharmacologically ‘rescued’ F508del CFTR displays instability at the cell’s surface, losing its channel function rapidly and it is rapidly removed from the plasma membrane for lysosomal degradation. This review will, therefore, explore the link between stability and structure/function relationships of membrane proteins and CFTR in particular and how approaches to study CFTR structure depend on its stability. We will also review the application of a fluorescence labelling method for the assessment of the thermostability and the tertiary structure of CFTR.
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Whittaker JW. Intracellular trafficking of the pyridoxal cofactor. Implications for health and metabolic disease. Arch Biochem Biophys 2015; 592:20-6. [PMID: 26619753 DOI: 10.1016/j.abb.2015.11.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/09/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023]
Abstract
The importance of the vitamin B6-derived pyridoxal cofactor for human health has been established through more than 70 years of intensive biochemical research, revealing its fundamental roles in metabolism. B6 deficiency, resulting from nutritional limitation or impaired uptake from dietary sources, is associated with epilepsy, neuromuscular disease and neurodegeneration. Hereditary disorders of B6 processing are also known, and genetic defects in pathways involved in transport of B6 into the cell and its transformation to the pyridoxal-5'-phosphate enzyme cofactor can contribute to cardiovascular disease by interfering with homocysteine metabolism and the biosynthesis of vasomodulatory polyamines. Compared to the processes involved in cellular uptake and processing of the B6 vitamers, trafficking of the PLP cofactor across intracellular membranes is very poorly understood, even though the availability of PLP within subcellular compartments (particularly the mitochondrion) may have important health implications. The aim of this review is to concisely summarize the state of current knowledge of intracellular trafficking of PLP and to identify key directions for future research.
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Affiliation(s)
- James W Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA.
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Whittaker MM, Penmatsa A, Whittaker JW. The Mtm1p carrier and pyridoxal 5'-phosphate cofactor trafficking in yeast mitochondria. Arch Biochem Biophys 2015; 568:64-70. [PMID: 25637770 DOI: 10.1016/j.abb.2015.01.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
Biochemical communication between the cytoplasmic and mitochondrial subsystems of the cell depends on solute carriers in the mitochondrial inner membrane that transport metabolites between the two compartments. We have expressed and purified a yeast mitochondrial carrier protein (Mtm1p, YGR257cp), originally identified as a manganese ion carrier, for biochemical characterization aimed at resolving its function. High affinity, stoichiometric pyridoxal 5'-phosphate (PLP) cofactor binding was characterized by fluorescence titration and calorimetry, and the biochemical effects of mtm1 gene deletion on yeast mitochondria were investigated. The PLP status of the mitochondrial proteome (the mitochondrial 'PLP-ome') was probed by immunoblot analysis of mitochondria isolated from wild type (MTM1(+)) and knockout (MTM1(-)) yeast, revealing depletion of mitochondrial PLP in the latter. A direct activity assay of the enzyme catalyzing the first committed step of heme biosynthesis, the PLP-dependent mitochondrial enzyme 5-aminolevulinate synthase, extends these results, providing a specific example of PLP cofactor limitation. Together, these experiments support a role for Mtm1p in mitochondrial PLP trafficking and highlight the link between PLP cofactor transport and iron metabolism, a remarkable illustration of metabolic integration.
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Affiliation(s)
- Mei M Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Aravind Penmatsa
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - James W Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA.
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