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Sánchez-Ortega M, Garrido A, Cirauqui C, Sanz-Gonzalez L, Hernández MC, González-García A, Obregon K, Ferrer I, Paz-Ares L, Carrera AC. A potential therapeutic strategy based on acute oxidative stress induction for wild-type NRF2/KEAP1 lung squamous cell carcinoma. Redox Biol 2024; 75:103305. [PMID: 39137583 PMCID: PMC11372719 DOI: 10.1016/j.redox.2024.103305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Extensive efforts have been conducted in the search for new targetable drivers of lung squamous cell carcinoma (LUSC); to date, however, candidates remain mostly unsuccessful. One of the oncogenic pathways frequently found to be active in LUSC is NFE2L2 (NRF2 transcription factor), the levels of which are regulated by KEAP1. Mutations in NFE2L2 or KEAP1 trigger NRF2 activation, an essential protector against reactive oxygen species (ROS). We hypothesized that the frequency of NRF2 activation in LUSC (∼35 %) may reflect a sensitivity of LUSC to ROS. Results from this study reveal that whereas tumors containing active forms of NRF2 were protected, ROS induction in wild-type NFE2L2/KEAP1 LUSC cells triggered ferroptosis. The mechanism of ROS action in normal-NRF2 LUSC cells involved transient NRF2 activation, miR-126-3p/miR-126-5p upregulation, and reduction of p85β and SETD5 levels. SETD5 levels reduction triggered pentose pathway gene levels increase to toxic values. Simultaneous depletion of p85βPI3K and SETD5 triggered LUSC cell death, while p85βPI3K and SETD5 overexpression rescued survival of ROS-treated normal-NRF2 LUSC cells. This shows that the cascade involving NRF2 > miR-126-3p, miR-126-5p > p85βPI3K and SETD5 is responsible for ROS-induced cell death in normal-NRF2 LUSC. Transient ROS-induced cell death is shown in 3D spheroids, patient-derived organoids, and in xenografts of wild-type NFE2L2/KEAP1 LUSC cells, supporting the potential of acute local ROS induction as a therapeutic strategy for LUSC patients with normal-NRF2.
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Affiliation(s)
- M Sánchez-Ortega
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain
| | - A Garrido
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain; Department of Biosciences, School of Biomedical and Health Sciences, European University of Madrid, Villaviciosa de Odón, Madrid, E-28670, Spain.
| | - C Cirauqui
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre, Spanish National Cancer Research Center (CNIO), Madrid, E28029, Spain
| | - L Sanz-Gonzalez
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain
| | - M C Hernández
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain
| | - A González-García
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain
| | - K Obregon
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain
| | - I Ferrer
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre, Spanish National Cancer Research Center (CNIO), Madrid, E28029, Spain
| | - L Paz-Ares
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre, Spanish National Cancer Research Center (CNIO), Madrid, E28029, Spain
| | - A C Carrera
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Autonomous University of Madrid, Cantoblanco, Madrid, E-28049, Spain.
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2
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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024; 23:2986-2998. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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4
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Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Machyna M, Pintado-Urbanc AP, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature 2023; 622:173-179. [PMID: 37731000 PMCID: PMC10845139 DOI: 10.1038/s41586-023-06565-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
Lysine residues in histones and other proteins can be modified by post-translational modifications that encode regulatory information1. Lysine acetylation and methylation are especially important for regulating chromatin and gene expression2-4. Pathways involving these post-translational modifications are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here we report cellular lysine residues that are both methylated and acetylated on the same side chain to form Nε-acetyl-Nε-methyllysine (Kacme). We show that Kacme is found on histone H4 (H4Kacme) across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. H4Kacme can be installed by enzymatic acetylation of monomethyllysine peptides and is resistant to deacetylation by some HDACs in vitro. Kacme can be bound by chromatin proteins that recognize modified lysine residues, as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a cellular post-translational modification with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a post-translational modification with fundamental importance to chromatin biology.
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Affiliation(s)
- William J Lu-Culligan
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Leah J Connor
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Babatunde E Ekundayo
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Brendan T Rose
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Andreas P Pintado-Urbanc
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Isaac W Vock
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Franziska Bleichert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA.
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5
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Remines M, Schoonover M, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544294. [PMID: 37333147 PMCID: PMC10274911 DOI: 10.1101/2023.06.09.544294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Makailyn Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kellyn M. Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Erin D. Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
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6
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Hamey JJ, Wilkins MR. The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification. Proc Natl Acad Sci U S A 2023; 120:e2215431120. [PMID: 37252976 PMCID: PMC10265986 DOI: 10.1073/pnas.2215431120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Defining all sites for a post-translational modification in the cell, and identifying their upstream modifying enzymes, is essential for a complete understanding of a modification's function. However, the complete mapping of a modification in the proteome and definition of its associated enzyme-substrate network is rarely achieved. Here, we present the protein methylation network for Saccharomyces cerevisiae. Through a formal process of defining and quantifying all potential sources of incompleteness, for both the methylation sites in the proteome and also protein methyltransferases, we prove that this protein methylation network is now near-complete. It contains 33 methylated proteins and 28 methyltransferases, comprising 44 enzyme-substrate relationships, and a predicted further three enzymes. While the precise molecular function of most methylation sites is unknown, and it remains possible that other sites and enzymes remain undiscovered, the completeness of this protein modification network is unprecedented and allows us to holistically explore the role and evolution of protein methylation in the eukaryotic cell. We show that while no single protein methylation event is essential in yeast, the vast majority of methylated proteins are themselves essential, being primarily involved in the core cellular processes of transcription, RNA processing, and translation. This suggests that protein methylation in lower eukaryotes exists to fine-tune proteins whose sequences are evolutionarily constrained, providing an improvement in the efficiency of their cognate processes. The approach described here, for the construction and evaluation of post-translational modification networks and their constituent enzymes and substrates, defines a formal process of utility for other post-translational modifications.
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Affiliation(s)
- Joshua J. Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
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7
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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Ye PL, Yuan B, Wang XQ, Zhang MM, Zhao XQ. Modification of Phosphorylation Sites in the Yeast Lysine Methyltransferase Set5 Exerts Influences on the Mitogen-Activated Protein Kinase Hog1 under Prolonged Acetic Acid Stress. Microbiol Spectr 2023; 11:e0301122. [PMID: 36975803 PMCID: PMC10100857 DOI: 10.1128/spectrum.03011-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Responses to acetic acid toxicity in the budding yeast Saccharomyces cerevisiae have widespread implications in the biorefinery of lignocellulosic biomass and food preservation. Our previous studies revealed that Set5, the yeast lysine methyltransferase and histone H4 methyltransferase, was involved in acetic acid stress tolerance. However, it is still mysterious how Set5 functions and interacts with the known stress signaling network. Here, we revealed that elevated phosphorylation of Set5 during acetic acid stress is accompanied by enhanced expression of the mitogen-activated protein kinase (MAPK) Hog1. Further experiments uncovered that the phosphomimetic mutation of Set5 endowed yeast cells with improved growth and fermentation performance and altered transcription of specific stress-responsive genes. Intriguingly, Set5 was found to bind the coding region of HOG1 and regulate its transcription, along with increased expression and phosphorylation of Hog1. A protein-protein interaction between Set5 and Hog1 was also revealed. In addition, modification of Set5 phosphosites was shown to regulate reactive oxygen species (ROS) accumulation, which is known to affect yeast acetic acid stress tolerance. The findings in this study imply that Set5 may function together with the central kinase Hog1 to coordinate cell growth and metabolism in response to stress. IMPORTANCE Hog1 is the yeast homolog of p38 MAPK in mammals that is conserved across eukaryotes, and it plays crucial roles in stress tolerance, fungal pathogenesis, and disease treatments. Here, we provide evidence that modification of Set5 phosphorylation sites regulates the expression and phosphorylation of Hog1, which expands current knowledge on upstream regulation of the Hog1 stress signaling network. Set5 and its homologous proteins are present in humans and various eukaryotes. The newly identified effects of Set5 phosphorylation site modifications in this study benefit an in-depth understanding of eukaryotic stress signaling, as well as the treatment of human diseases.
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Affiliation(s)
- Pei-Liang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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9
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Chou KY, Lee JY, Kim KB, Kim E, Lee HS, Ryu HY. Histone modification in Saccharomyces cerevisiae: A review of the current status. Comput Struct Biotechnol J 2023; 21:1843-1850. [PMID: 36915383 PMCID: PMC10006725 DOI: 10.1016/j.csbj.2023.02.037] [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: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a well-characterized and popular model system for investigating histone modifications and the inheritance of chromatin states. The data obtained from this model organism have provided essential and critical information for understanding the complexity of epigenetic interactions and regulation in eukaryotes. Recent advances in biotechnology have facilitated the detection and quantitation of protein post-translational modification (PTM), including acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, and acylation, and led to the identification of several novel modification sites in histones. Determining the cellular function of these new histone markers is essential for understanding epigenetic mechanisms and their impact on various biological processes. In this review, we describe recent advances and current views on histone modifications and their effects on chromatin dynamics in S. cerevisiae.
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Key Words
- AdoMet, S-adenosylmethionine
- CAF-1, chromatin assembly factor-1
- CTD, C-terminal domain
- DSB, double-strand break
- E Glu, glutamic acid
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- Histone acetylation
- Histone acylation
- Histone methylation
- Histone phosphorylation
- Histone sumoylation
- Histone ubiquitylation
- JMJC, Jumonji C
- K Lys, lysine
- PTM, post-translational modification
- R Arg, arginine
- S, serine
- SAGA, Spt-Ada-Gcn5 acetyltransferase
- STUbL, SUMO-targeted ubiquitin ligase
- SUMO, small ubiquitin-like modifier
- T, threonine
- Y, tyrosine
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Affiliation(s)
- Kwon Young Chou
- School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Yeong Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kee-Beom Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eunjeong Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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10
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Phylogenomic and Evolutionary Analyses Reveal Diversifications of SET-Domain Proteins in Fungi. J Fungi (Basel) 2022; 8:jof8111159. [DOI: 10.3390/jof8111159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
In recent years, many publications have established histone lysine methylation as a central epigenetic modification in the regulation of chromatin and transcription. The histone lysine methyltransferases contain a conserved SET domain and are widely distributed in various organisms. However, a comprehensive study on the origin and diversification of the SET-domain-containing genes in fungi has not been conducted. In this study, a total of 3816 SET-domain-containing genes, which were identified and characterized using HmmSearch from 229 whole genomes sequenced fungal species, were used to ascertain their evolution and diversification in fungi. Using the CLANS program, all the SET-domain-containing genes were grouped into three main clusters, and each cluster contains several groups. Domain organization analysis showed that genes belonging to the same group have similar sequence structures. In contrast, different groups process domain organizations or locations differently, suggesting the SET-domain-containing genes belonging to different groups may have obtained distinctive regulatory mechanisms during their evolution. These genes that conduct the histone methylations (such as H3K4me, H3K9me, H3K27me, H4K20me, H3K36me) are mainly grouped into Cluster 1 while the other genes grouped into Clusters 2 and 3 are still functionally undetermined. Our results also showed that numerous gene duplication and loss events have happened during the evolution of those fungal SET-domain-containing proteins. Our results provide novel insights into the roles of SET-domain genes in fungal evolution and pave a fundamental path to further understanding the epigenetic basis of gene regulation in fungi.
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11
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Bhakt P, Raney M, Kaur R. The SET-domain protein CgSet4 negatively regulates antifungal drug resistance via the ergosterol biosynthesis transcriptional regulator CgUpc2a. J Biol Chem 2022; 298:102485. [PMID: 36108742 PMCID: PMC9576903 DOI: 10.1016/j.jbc.2022.102485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/27/2022] Open
Abstract
Invasive fungal infections, which pose a serious threat to human health, are increasingly associated with a high mortality rate and elevated health care costs, owing to rising resistance to current antifungals and emergence of multidrug-resistant fungal species. Candida glabrata is the second to fourth common cause of Candida bloodstream infections. Its high propensity to acquire resistance toward two mainstream drugs, azoles (inhibit ergosterol biosynthesis) and echinocandins (target cell wall), in clinical settings, and its inherent low azole susceptibility render antifungal therapy unsuccessful in many cases. Here, we demonstrate a pivotal role for the SET {suppressor of variegation 3 to 9 [Su(var)3-9], enhancer of zeste [E(z)], and trithorax (Trx)} domain-containing protein, CgSet4, in azole and echinocandin resistance via negative regulation of multidrug transporter-encoding and ergosterol biosynthesis (ERG) genes through the master transcriptional factors CgPdr1 and CgUpc2A, respectively. RNA-Seq analysis revealed that C. glabrata responds to caspofungin (CSP; echinocandin antifungal) stress by downregulation and upregulation of ERG and cell wall organization genes, respectively. Although CgSet4 acts as a repressor of the ergosterol biosynthesis pathway via CgUPC2A transcriptional downregulation, the CSP-induced ERG gene repression is not dependent on CgSet4, as CgSet4 showed diminished abundance on the CgUPC2A promoter in CSP-treated cells. Furthermore, we show a role for the last three enzymes of the ergosterol biosynthesis pathway, CgErg3, CgErg5, and CgErg4, in antifungal susceptibility and virulence in C. glabrata. Altogether, our results unveil the link between ergosterol biosynthesis and echinocandin resistance and have implications for combination antifungal therapy.
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Affiliation(s)
- Priyanka Bhakt
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Mayur Raney
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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12
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Maree JP, Tvardovskiy A, Ravnsborg T, Jensen ON, Rudenko G, Patterton HG. Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A. Nucleic Acids Res 2022; 50:9705-9723. [PMID: 36095123 PMCID: PMC9508842 DOI: 10.1093/nar/gkac759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/09/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.
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Affiliation(s)
- Johannes P Maree
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hugh-G Patterton
- Center for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7600, South Africa
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13
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Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem 2021; 297:100939. [PMID: 34224729 PMCID: PMC8329514 DOI: 10.1016/j.jbc.2021.100939] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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14
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Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem 2021; 296:100192. [PMID: 33334889 PMCID: PMC7948420 DOI: 10.1074/jbc.ra120.015995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/06/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
Histone methylation is central to the regulation of eukaryotic transcription. In Saccharomyces cerevisiae, it is controlled by a system of four methyltransferases (Set1p, Set2p, Set5p, and Dot1p) and four demethylases (Jhd1p, Jhd2p, Rph1p, and Gis1p). While the histone targets for these enzymes are well characterized, the connection of the enzymes with the intracellular signaling network and thus their regulation is poorly understood; this also applies to all other eukaryotes. Here we report the detailed characterization of the eight S. cerevisiae enzymes and show that they carry a total of 75 phosphorylation sites, 92 acetylation sites, and two ubiquitination sites. All enzymes are subject to phosphorylation, although demethylases Jhd1p and Jhd2p contained one and five sites respectively, whereas other enzymes carried 14 to 36 sites. Phosphorylation was absent or underrepresented on catalytic and other domains but strongly enriched for regions of disorder on methyltransferases, suggesting a role in the modulation of protein-protein interactions. Through mutagenesis studies, we show that phosphosites within the acidic and disordered N-terminus of Set2p affect H3K36 methylation levels in vivo, illustrating the functional importance of such sites. While most kinases upstream of the yeast histone methylation enzymes remain unknown, we model the possible connections between the cellular signaling network and the histone-based gene regulatory system and propose an integrated regulatory structure. Our results provide a foundation for future, detailed exploration of the role of specific kinases and phosphosites in the regulation of histone methylation.
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Affiliation(s)
- Ryan J Separovich
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mandy W M Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tyler R Chapman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Eve Slavich
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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15
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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16
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Zhao X, Tang B, Xu J, Wang N, Zhou Z, Zhang J. A SET domain-containing protein involved in cell wall integrity signaling and peroxisome biogenesis is essential for appressorium formation and pathogenicity of Colletotrichum gloeosporioides. Fungal Genet Biol 2020; 145:103474. [PMID: 33007450 DOI: 10.1016/j.fgb.2020.103474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/18/2020] [Accepted: 09/24/2020] [Indexed: 11/19/2022]
Abstract
The chromatin modulator Set5 plays important regulatory roles in both cell growth and stress responses of Saccharomyces cerevisiae. However, its function in filamentous fungi remains poorly understood. Here, we report the pathogenicity-related gene CgSET5 discovered in a T-DNA insertional mutant M285 of Colletotrichum gloeosporioides. Bioinformatic analysis revealed that CgSET5 encodes a SET domain-containing protein that is a homolog of the budding yeast S. cerevisiae Set5. CgSET5 is important for hyphae growth and conidiation and is necessary for appressorium formation and pathogenicity. CgSet5 regulates appressorium formation in a mitogen-activated protein kinase-independent manner. Inactivation of CgSET5 resulted in a significant reduction in chitin content within the cell wall, indicating CgSet5 plays a vital role in cell wall integrity. CgSet5 is involved in peroxisome biogenesis. We identified CgSet5 as the histone H4 methyltransferase, which methylates the critical H4 lysine residues 5 and 8 in C. gloeosporioides. We carried out a yeast two-hybrid screen to find CgSet5 interacting partners. We found CgSet5 putatively interacts with an inorganic pyrophosphatase named CgPpa1, which co-localized in the cytoplasm with CgSet5. Finally, CgPpa1 was found to strongly interact with CgSet5 in vivo during appressorium formation by bimolecular fluorescence complementation assays. These data corroborate a complex control function of CgSet5 acting as a core pathogenic regulator, which connects cell wall integrity and peroxisome biogenesis in C. gloeosporioides.
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Affiliation(s)
- Xuanzhu Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture, Xingcheng 125100, China
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park NR4 7UH, UK
| | - Jie Xu
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Na Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Zongshan Zhou
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China
| | - Junxiang Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture, Xingcheng 125100, China.
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17
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Ray A, Khan P, Nag Chaudhuri R. Deacetylation of H4 lysine16 affects acetylation of lysine residues in histone H3 and H4 and promotes transcription of constitutive genes. Epigenetics 2020; 16:597-617. [PMID: 32795161 DOI: 10.1080/15592294.2020.1809896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Histone modification map of H4 N-terminal tail residues in Saccharomyces cerevisiae reveals the prominence of lysine acetylation. Previous reports have indicated the importance of lysine acetylation in maintaining chromatin structure and function. H4K16, a residue with highly regulated acetylation dynamics has unique functions not overlapping with the other H4 N- terminal acetylable residues. The present work unravels the role of H4K16 acetylation in regulating expression of constitutive genes. H4K16 gets distinctly deacetylated over the coding region of constitutively expressed genes. Deacetylation of H4K16 reduces H3K9 acetylation at the cellular and gene level. Reduced H3K9 acetylation however did not negatively correlate with active gene transcription. Significantly, H4K16 deacetylation was found to be associated with hypoacetylated H4K12 throughout the locus of constitutive genes. H4K16 and K12 deacetylation is known to favour active transcription. Sas2, the HAT mutant showed similar patterns of hypoacetylated H3K9 and H4K12 at the active loci, clearly implying that the modifications were associated with deacetylation state of H4K16. Deacetylation of H4K16 was also concurrent with increased H3K56 acetylation in the promoter region and ORF of the constitutive genes. Combination of all these histone modifications significantly reduced H3 occupancy, increased promoter accessibility and enhanced RNAPII recruitment at the constitutively active loci. Consequently, we found that expression of active genes was higher in H4K16R mutant which mimic deacetylated state, but not in H4K16Q mimicking constitutive acetylation. To summarize, H4K16 deacetylation linked with H4K12 and H3K9 hypoacetylation along with H3K56 hyperacetylation generate a chromatin landscape that is conducive for transcription of constitutive genes.
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Affiliation(s)
- Anagh Ray
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Preeti Khan
- Department of Biotechnology, St. Xavier's College, Kolkata, India
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18
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Lamour J, Wan C, Zhang M, Zhao X, Den Haan R. Overexpression of endogenous stress-tolerance related genes in Saccharomyces cerevisiae improved strain robustness and production of heterologous cellobiohydrolase. FEMS Yeast Res 2020; 19:5479884. [PMID: 31073597 DOI: 10.1093/femsyr/foz035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
To enable Saccharomyces cerevisiae to produce renewable fuels from lignocellulose in a consolidated bioprocess, a heterologous cellulase system must be engineered into this yeast. In addition, inherently low secretion titers and sensitivity to adverse environmental conditions must be overcome. Here, two native S. cerevisiae genes related to yeast stress tolerance, YHB1 and SET5, were overexpressed under transcriptional control of the constitutive PGK1 promoter and their effects on heterologous secretion of Talaromyces emersonii cel7A cellobiohydrolase was investigated. Transformants showed increased secreted enzyme activity that ranged from 22% to 55% higher compared to the parental strains and this did not lead to deleterious growth effects. The recombinant strains overexpressing either YHB1 or SET5 also demonstrated multi-tolerant characteristics desirable in bioethanol production, i.e. improved tolerance to osmotic and heat stress. Quantitative reverse transcriptase PCR analysis in these strains showed decreased transcription of secretion pathway genes. However, decreased unfolded protein response was also observed, suggesting novel mechanisms for enhancing enzyme production through stress modulation. Overexpression of YHB1 in an unrelated diploid strain also enhanced stress tolerance and improved ethanol productivity in medium containing acetic acid. To our knowledge, this is the first demonstration that improved heterologous secretion and environmental stress tolerance could be engineered into yeast simultaneously.
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Affiliation(s)
- Jarryd Lamour
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Chun Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan Den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
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Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5. Mol Cell Biol 2020; 40:MCB.00341-19. [PMID: 31685550 DOI: 10.1128/mcb.00341-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
SMYD lysine methyltransferases target histones and nonhistone proteins for methylation and are critical regulators of muscle development and implicated in neoplastic transformation. They are characterized by a split catalytic SET domain and an intervening MYND zinc finger domain, as well as an extended C-terminal domain. Saccharomyces cerevisiae contains two SMYD proteins, Set5 and Set6, which share structural elements with the mammalian SMYD enzymes. Set5 is a histone H4 lysine 5, 8, and 12 methyltransferase, implicated in the regulation of stress responses and genome stability. While the SMYD proteins have diverse roles in cells, there are many gaps in our understanding of how these enzymes are regulated. Here, we performed mutational analysis of Set5, combined with phosphoproteomics, to identify regulatory mechanisms for its enzymatic activity and subcellular localization. Our results indicate that the MYND domain promotes Set5 chromatin association in cells and is required for its role in repressing subtelomeric genes. Phosphoproteomics revealed extensive phosphorylation of Set5, and phosphomimetic mutations enhance Set5 catalytic activity but diminish its ability to interact with chromatin in cells. These studies uncover multiple regions within Set5 that regulate its localization and activity and highlight potential avenues for understanding mechanisms controlling the diverse roles of SMYD enzymes.
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20
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Abstract
Although central to regulating the access to genetic information, most lysine methyltransferases remain poorly characterised relative to other family of enzymes. Herein, I report new substrates for the lysine methyltransferase SETD6. Based on the SETD6-catalysed site on the histone variant H2AZ, I identified similar sequences in the canonical histones H2A, H3, and H4 that are modified by SETD6 in vitro, and putative non-histone substrates. I herein expend the repertoire of substrates for methylation by SETD6.
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Affiliation(s)
- Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, England
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21
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Jezek M, Green EM. Histone Modifications and the Maintenance of Telomere Integrity. Cells 2019; 8:E199. [PMID: 30823596 PMCID: PMC6407025 DOI: 10.3390/cells8020199] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/09/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022] Open
Abstract
Telomeres, the nucleoprotein structures at the ends of eukaryotic chromosomes, play an integral role in protecting linear DNA from degradation. Dysregulation of telomeres can result in genomic instability and has been implicated in increased rates of cellular senescence and many diseases, including cancer. The integrity of telomeres is maintained by a coordinated network of proteins and RNAs, such as the telomerase holoenzyme and protective proteins that prevent the recognition of the telomere ends as a DNA double-strand breaks. The structure of chromatin at telomeres and within adjacent subtelomeres has been implicated in telomere maintenance pathways in model systems and humans. Specific post-translational modifications of histones, including methylation, acetylation, and ubiquitination, have been shown to be necessary for maintaining a chromatin environment that promotes telomere integrity. Here we review the current knowledge regarding the role of histone modifications in maintaining telomeric and subtelomeric chromatin, discuss the implications of histone modification marks as they relate to human disease, and highlight key areas for future research.
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Affiliation(s)
- Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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22
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Hoffmann G, Samel-Pommerencke A, Weber J, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE. A role for CENP-A/Cse4 phosphorylation on serine 33 in deposition at the centromere. FEMS Yeast Res 2019; 18:4768140. [PMID: 29272409 DOI: 10.1093/femsyr/fox094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
Centromeres are the sites of assembly of the kinetochore, which connect the chromatids to the microtubules for sister chromatid segregation during cell division. Centromeres are characterized by the presence of the histone H3 variant CENP-A (termed Cse4 in Saccharomyces cerevisiae). Here, we investigated the function of serine 33 phosphorylation of Cse4 (Cse4-S33ph) in S. cerevisiae, which lies within the essential N-terminal domain (END) of the extended Cse4 N-terminus. Significantly, we identified histone H4-K5, 8, 12R to cause a temperature-sensitive growth defect with mutations in Cse4-S33 and sensitivity to nocodazole and hydroxyurea. Furthermore, the absence of Cse4-S33ph reduced the levels of Cse4 at centromeric sequences, suggesting that Cse4 deposition is defective in the absence of S33 phosphorylation. We furthermore identified synthetic genetic interactions with histone H2A-E57A and H2A-L66A, which both cause a reduced interaction with the histone chaperone FACT and reduced H2A/H2B levels in chromatin, again supporting the notion that a combined defect of H2A/H2B and Cse4 deposition causes centromeric defects. Altogether, our data highlight the importance of correct histone deposition in building a functional centromeric nucleosome and suggests a role for Cse4-S33ph in this process.
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Affiliation(s)
- Gesine Hoffmann
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | | | - Jan Weber
- Biozentrum Köln, Universität zu Köln, 50674 Köln, Germany
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milano, Italy
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23
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SET domains and stress: uncovering new functions for yeast Set4. Curr Genet 2018; 65:643-648. [PMID: 30523388 DOI: 10.1007/s00294-018-0917-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022]
Abstract
Chromatin dynamics are central to the regulation of gene expression and genome stability, particularly in the presence of environmental signals or stresses that prompt rapid reprogramming of the genome to promote survival or differentiation. While numerous chromatin regulators have been implicated in modulating cellular responses to stress, gaps in our mechanistic understanding of chromatin-based changes during stress suggest that additional proteins are likely critical to these responses and the molecular details underlying their activities are unclear in many cases. We recently identified a role for the relatively uncharacterized SET domain protein Set4 in promoting cell survival during oxidative stress in Saccharomyces cerevisiae. Set4 is a member of the Set3 subfamily of SET domain proteins which are defined by the presence of a PHD finger and divergent SET domain sequences. Here, we integrate our new observations on the function of Set4 with known roles for other related family members, including yeast Set3, fly UpSET and mammalian proteins MLL5 and SETD5. We discuss outstanding questions regarding the molecular mechanisms by which these proteins control gene expression and their potential contributions to cellular responses to environmental stress.
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Tran K, Jethmalani Y, Jaiswal D, Green EM. Set4 is a chromatin-associated protein, promotes survival during oxidative stress, and regulates stress response genes in yeast. J Biol Chem 2018; 293:14429-14443. [PMID: 30082318 PMCID: PMC6139553 DOI: 10.1074/jbc.ra118.003078] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
The Set4 protein in the yeast Saccharomyces cerevisiae contains both a PHD finger and a SET domain, a common signature of chromatin-associated proteins, and shares sequence homology with the yeast protein Set3, the fly protein UpSET, and the human protein mixed-lineage leukemia 5 (MLL5). However, the biological role for Set4 and its potential function in chromatin regulation has not been well defined. Here, we analyzed yeast cell phenotypes associated with loss of Set4 or its overexpression, which revealed that Set4 protects against oxidative stress induced by hydrogen peroxide. Gene expression analysis indicated that Set4 promotes the activation of stress response genes in the presence of oxidative insults. Using ChIP analysis and other biochemical assays, we also found that Set4 interacts with chromatin and directly localizes to stress response genes upon oxidative stress. However, recombinant Set4 did not show detectable methyltransferase activity on histones. Our findings also suggest that Set4 abundance in the cell is balanced under normal and stress conditions to promote survival. Overall, these results suggest a model in which Set4 is a stress-responsive, chromatin-associated protein that activates gene expression programs required for cellular protection against oxidative stress. This work advances our understanding of mechanisms that protect cells during oxidative stress and further defines the role of the Set3-Set4 subfamily of SET domain-containing proteins in controlling gene expression in response to adverse environmental conditions.
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Affiliation(s)
- Khoa Tran
- From the Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Yogita Jethmalani
- From the Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Deepika Jaiswal
- From the Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Erin M Green
- From the Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
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25
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Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification. J Mol Biol 2017; 430:102-118. [PMID: 29183786 DOI: 10.1016/j.jmb.2017.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 01/24/2023]
Abstract
Protein methylation is one of the major post-translational modifications (PTMs) in the cell. In Saccharomyces cerevisiae, over 20 protein methyltransferases (MTases) and their respective substrates have been identified. However, the way in which these MTases are modified and potentially subject to regulation remains poorly understood. Here, we investigated six overexpressed S. cerevisiae protein MTases (Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1) to identify PTMs of potential functional relevance. We identified 48 PTM sites across the six MTases, including phosphorylation, acetylation and methylation. Forty-two sites are novel. We contextualized the PTM sites in structural models of the MTases and revealed that many fell in catalytic pockets or enzyme-substrate interfaces. These may regulate MTase activity. Finally, we compared PTMs on Hmt1 with those on its human homologs PRMT1, PRMT3, CARM1, PRMT6 and PRMT8. This revealed that several PTMs are conserved from yeast to human, whereas others are only found in Hmt1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD006767.
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26
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Fulton MD, Zhang J, He M, Ho MC, Zheng YG. Intricate Effects of α-Amino and Lysine Modifications on Arginine Methylation of the N-Terminal Tail of Histone H4. Biochemistry 2017. [PMID: 28644004 DOI: 10.1021/acs.biochem.7b00450] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical modifications of the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) of the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and >450 histone PTMs that have been discovered, and the PTMs of lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood. In this study, we investigated how naturally occurring N-terminal acetylation and PTMs of histone H4 lysine-5 (H4K5) affect arginine-3 methylation catalyzed by both type I and type II PRMTs at the biochemical level. Our studies found that acylations of H4K5 resulted in decreased levels of arginine methylation by PRMT1, PRMT3, and PRMT8. In contrast, PRMT5 exhibits an increased rate of arginine methylation upon H4K5 acetylation, propionylation, and crotonylation, but not upon H4K5 methylation, butyrylation, or 2-hydroxyisobutyrylation. Methylation of H4K5 did not affect arginine methylation by PRMT1 or PRMT5. There was a small increase in the rate of arginine methylation by PRMT8. Strikingly, a marked increase in the rate of arginine methylation was observed for PRMT3. Finally, N-terminal acetylation reduced the rate of arginine methylation by PRMT3 but had little influence on PRMT1, -5, and -8 activity. These results together highlight the underlying mechanistic differences in substrate recognition among different PRMTs and pave the way for the elucidation of the complex interplay of histone modifications.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Maomao He
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia , Athens, Georgia 30602, United States
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27
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Morimoto A, Kannari M, Tsuchida Y, Sasaki S, Saito C, Matsuta T, Maeda T, Akiyama M, Nakamura T, Sakaguchi M, Nameki N, Gonzalez FJ, Inoue Y. An HNF4α-microRNA-194/192 signaling axis maintains hepatic cell function. J Biol Chem 2017; 292:10574-10585. [PMID: 28465351 DOI: 10.1074/jbc.m117.785592] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatocyte nuclear factor 4α (HNF4α) controls the expression of liver-specific protein-coding genes. However, some microRNAs are also modulated by HNF4α, and it is not known whether they are direct targets of HNF4α and whether they influence hepatic function. In this study, we found that HNF4α regulates microRNAs, indicated by marked down-regulation of miR-194 and miR-192 (miR-194/192) in liver-specific Hnf4a-null (Hnf4aΔH) mice. Transactivation of the shared miR-194/192 promoter was dependent on HNF4α expression, indicating that miR-194/192 is a target gene of HNF4α. Screening of potential mRNAs targeted by miR-194/192 revealed that expression of genes involved in glucose metabolism (glycogenin 1 (Gyg1)), cell adhesion and migration (activated leukocyte cell adhesion molecule (Alcam)), tumorigenesis and tumor progression (Rap2b and epiregulin (Ereg)), protein SUMOylation (Sumo2), epigenetic regulation (Setd5 and Cullin 4B (Cln4b)), and the epithelial-mesenchymal transition (moesin (Msn)) was up-regulated in Hnf4aΔH mice. Moreover, we also found that miR-194/192 binds the 3'-UTR of these mRNAs. siRNA knockdown of HNF4α suppressed miR-194/192 expression in human hepatocellular carcinoma (HCC) cells and resulted in up-regulation of their mRNA targets. Inhibition and overexpression experiments with miR-194/192 revealed that Gyg1, Setd5, Sumo2, Cln4b, and Rap2b are miR-194 targets, whereas Ereg, Alcam, and Msn are miR-192 targets. These findings reveal a novel HNF4α network controlled by miR-194/192 that may play a critical role in maintaining the hepatocyte-differentiated state by inhibiting expression of genes involved in dedifferentiation and tumorigenesis. These insights may contribute to the development of diagnostic markers for early HCC detection, and targeting of the miR-194/192 pathway could be useful for managing HCC.
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Affiliation(s)
- Aoi Morimoto
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Mana Kannari
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Yuichi Tsuchida
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Shota Sasaki
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Chinatsu Saito
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Tsuyoshi Matsuta
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Tsukasa Maeda
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Megumi Akiyama
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Takahiro Nakamura
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Masakiyo Sakaguchi
- the Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan, and
| | - Nobukazu Nameki
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Frank J Gonzalez
- the Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20852
| | - Yusuke Inoue
- From the Laboratory of Molecular Life Science, Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan,
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28
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Nie L, Shuai L, Zhu M, Liu P, Xie ZF, Jiang S, Jiang HW, Li J, Zhao Y, Li JY, Tan M. The Landscape of Histone Modifications in a High-Fat Diet-Induced Obese (DIO) Mouse Model. Mol Cell Proteomics 2017; 16:1324-1334. [PMID: 28450421 DOI: 10.1074/mcp.m117.067553] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Indexed: 12/24/2022] Open
Abstract
Type 2 diabetes (T2D) is a major chronic healthcare concern worldwide. Emerging evidence suggests that a histone-modification-mediated epigenetic mechanism underlies T2D. Nevertheless, the dynamics of histone marks in T2D have not yet been carefully analyzed. Using a mass spectrometry-based label-free and chemical stable isotope labeling quantitative proteomic approach, we systematically profiled liver histone post-translational modifications (PTMs) in a prediabetic high-fat diet-induced obese (DIO) mouse model. We identified 170 histone marks, 30 of which were previously unknown. Interestingly, about 30% of the histone marks identified in DIO mouse liver belonged to a set of recently reported lysine acylation modifications, including propionylation, butyrylation, malonylation, and succinylation, suggesting possible roles of these newly identified histone acylations in diabetes and obesity. These histone marks were detected without prior affinity enrichment with an antibody, demonstrating that the histone acylation marks are present at reasonably high stoichiometry. Fifteen histone marks differed in abundance in DIO mouse liver compared with liver from chow-fed mice in label-free quantification, and six histone marks in stable isotope labeling quantification. Analysis of hepatic histone modifications from metformin-treated DIO mice revealed that metformin, a drug widely used for T2D, could reverse DIO-stimulated histone H3K36me2 in prediabetes, suggesting that this mark is likely associated with T2D development. Our study thus offers a comprehensive landscape of histone marks in a prediabetic mouse model, provides a resource for studying epigenetic functions of histone modifications in obesity and T2D, and suggest a new epigenetic mechanism for the physiological function of metformin.
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Affiliation(s)
- Litong Nie
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lin Shuai
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Mingrui Zhu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ping Liu
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Zhi-Fu Xie
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,¶University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shangwen Jiang
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Hao-Wen Jiang
- ‖College of Chemistry and Molecular Engineering, East China Normal University, China, 200062
| | - Jia Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
| | - Yingming Zhao
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203.,**Ben May Department for Cancer Research, University of Chicago, Chicago, IL
| | - Jing-Ya Li
- §State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203;
| | - Minjia Tan
- From the ‡The Chemical Proteomics Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203; .,§State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China, 201203
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29
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Huang L, Xu AM. SET and MYND domain containing protein 3 in cancer. Am J Transl Res 2017; 9:1-14. [PMID: 28123630 PMCID: PMC5250700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Lysine methylation plays a vital role in histone modification. Deregulations of lysine methyltransferases and demethylases have been frequently observed in human cancers. The SET and MYND domain containing protein 3 (SMYD3) is a novel histone lysine methyltransferase and it functions by regulating chromatin during the development of myocardial and skeletal muscle. It has been recently unveiled to play significant roles in human cancer genesis and progression via regulating various key cancer-associated genes and pathways and promoting cell proliferation and migration. Upregulation of SMYD3 expression is present in multiple cancer types, suggesting it as a potential prognostic marker. Herein the structure, substrates and targets of SMYD3, and its effects on initiation, invasion and metastasis of diverse tumors (e.g., esophageal squamous cell carcinoma, gastric cancer, hepatocellular carcinoma, cholangiocarcinoma, breast cancer, prostate cancer, and leukemia) are systematically reviewed, providing clues for the development of novel SMYD3-specific personalized anti-cancer therapy. SMYD3 inhibitors (e.g., BCI-121 and novobiocin) could hopefully fight against tumors with efficacy.
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Affiliation(s)
- Lei Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
- German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - A-Man Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical UniversityHefei, China
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30
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Jezek M, Gast A, Choi G, Kulkarni R, Quijote J, Graham-Yooll A, Park D, Green EM. The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance. Epigenetics 2016; 12:93-104. [PMID: 27911222 DOI: 10.1080/15592294.2016.1265712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of Saccharomyces cerevisiae have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
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Affiliation(s)
- Meagan Jezek
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Alison Gast
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Grace Choi
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Rushmie Kulkarni
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Jeremiah Quijote
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Andrew Graham-Yooll
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - DoHwan Park
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Erin M Green
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
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31
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Choose Your Own Adventure: The Role of Histone Modifications in Yeast Cell Fate. J Mol Biol 2016; 429:1946-1957. [PMID: 27769718 DOI: 10.1016/j.jmb.2016.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/07/2016] [Accepted: 10/07/2016] [Indexed: 12/16/2022]
Abstract
When yeast cells are challenged by a fluctuating environment, signaling networks activate differentiation programs that promote their individual or collective survival. These programs include the initiation of meiotic sporulation, the formation of filamentous growth structures, and the activation of programmed cell death pathways. The establishment and maintenance of these distinct cell fates are driven by massive gene expression programs that promote the necessary changes in morphology and physiology. While these genomic reprogramming events depend on a specialized network of transcription factors, a diverse set of chromatin regulators, including histone-modifying enzymes, chromatin remodelers, and histone variants, also play essential roles. Here, we review the broad functions of histone modifications in initiating cell fate transitions, with particular focus on their contribution to the control of expression of key genes required for the differentiation programs and chromatin reorganization that accompanies these cell fates.
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32
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Mazur PK, Gozani O, Sage J, Reynoird N. Novel insights into the oncogenic function of the SMYD3 lysine methyltransferase. Transl Cancer Res 2016; 5:330-333. [PMID: 30713830 DOI: 10.21037/tcr.2016.06.26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pawel K Mazur
- Departments of Pediatrics, Stanford University School of Medicine, CA 94305, USA.,Departments of Genetics, Stanford University School of Medicine, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, CA 94305, USA
| | - Julien Sage
- Departments of Pediatrics, Stanford University School of Medicine, CA 94305, USA.,Departments of Genetics, Stanford University School of Medicine, CA 94305, USA
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble Cedex, France
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33
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Zhang MM, Zhao XQ, Cheng C, Bai FW. Improved growth and ethanol fermentation of Saccharomyces cerevisiae in the presence of acetic acid by overexpression of SET5 and PPR1. Biotechnol J 2015; 10:1903-11. [PMID: 26479519 DOI: 10.1002/biot.201500508] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 11/12/2022]
Abstract
To better understand the contribution of zinc-finger proteins to environmental stress tolerance, particularly inhibition from acetic acid, which is a potent inhibitor for cellulosic ethanol production by microbial fermentations, SET5 and PPR1 were overexpressed in Saccharomyces cerevisiae BY4741. With 5 g/L acetic acid addition, engineered strains BY4741/SET5 and BY4741/PPR1 showed improved growth and enhanced ethanol fermentation performance compared to that with the control strain. Similar results were also observed in ethanol production using corn stover hydrolysate. Further studies indicated that SET5 and PPR1 overexpression in S. cerevisiae significantly improved activities of antioxidant enzymes and ATP generation in the presence of acetic acid, and consequently decreased intracellular accumulation of reactive oxygen species (50.9 and 45.7%, respectively). These results revealed the novel functions of SET5 and PPR1 for the improvement of yeast acetic acid tolerance, and also implicated the involvement of these proteins in oxidative stress defense and energy metabolism in S. cerevisiae. This work also demonstrated that overexpression of SET5 and PPR1 would be a feasible strategy to increase cellulosic ethanol production efficiency.
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Affiliation(s)
- Ming-Ming Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Feng-Wu Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.,State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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34
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Zhao Y, Garcia BA. Comprehensive Catalog of Currently Documented Histone Modifications. Cold Spring Harb Perspect Biol 2015; 7:a025064. [PMID: 26330523 DOI: 10.1101/cshperspect.a025064] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
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Affiliation(s)
- Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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35
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Huang Z, Cai L, Tu BP. Dietary control of chromatin. Curr Opin Cell Biol 2015; 34:69-74. [PMID: 26094239 DOI: 10.1016/j.ceb.2015.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/28/2022]
Abstract
Organisms must be able to rapidly alter gene expression in response to changes in their nutrient environment. This review summarizes evidence that epigenetic modifications of chromatin depend on particular metabolites of intermediary metabolism, enabling the facile regulation of gene expression in tune with metabolic state. Nutritional or dietary control of chromatin is an often-overlooked, yet fundamental regulatory mechanism directly linked to human physiology. Nutrient-sensitive epigenetic marks are dynamic, suggesting rapid turnover, and may have functions beyond the regulation of gene transcription, including pH regulation and as carbon sources in cancer cells.
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Affiliation(s)
- Zhiguang Huang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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36
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Fine-tuning of histone H3 Lys4 methylation during pseudohyphal differentiation by the CDK submodule of RNA polymerase II. Genetics 2014; 199:435-53. [PMID: 25467068 DOI: 10.1534/genetics.114.172841] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcriptional regulation is dependent upon the interactions between the RNA pol II holoenzyme complex and chromatin. RNA pol II is part of a highly conserved multiprotein complex that includes the core mediator and CDK8 subcomplex. In Saccharomyces cerevisiae, the CDK8 subcomplex, composed of Ssn2p, Ssn3p, Ssn8p, and Srb8p, is thought to play important roles in mediating transcriptional control of stress-responsive genes. Also central to transcriptional control are histone post-translational modifications. Lysine methylation, dynamically balanced by lysine methyltransferases and demethylases, has been intensively studied, uncovering significant functions in transcriptional control. A key question remains in understanding how these enzymes are targeted during stress response. To determine the relationship between lysine methylation, the CDK8 complex, and transcriptional control, we performed phenotype analyses of yeast lacking known lysine methyltransferases or demethylases in isolation or in tandem with SSN8 deletions. We show that the RNA pol II CDK8 submodule components SSN8/SSN3 and the histone demethylase JHD2 are required to inhibit pseudohyphal growth-a differentiation pathway induced during nutrient limitation-under rich conditions. Yeast lacking both SSN8 and JHD2 constitutively express FLO11, a major regulator of pseudohyphal growth. Interestingly, deleting known FLO11 activators including FLO8, MSS11, MFG1, TEC1, SNF1, KSS1, and GCN4 results in a range of phenotypic suppression. Using chromatin immunoprecipitation, we found that SSN8 inhibits H3 Lys4 trimethylation independently of JHD2 at the FLO11 locus, suggesting that H3 Lys4 hypermethylation is locking FLO11 into a transcriptionally active state. These studies implicate the CDK8 subcomplex in fine-tuning H3 Lys4 methylation levels during pseudohyphal differentiation.
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Martín GM, King DA, Garcia-Nieto PE, Morrison AJ. Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression. GENOMICS DATA 2014; 2:216-218. [PMID: 25152866 PMCID: PMC4140983 DOI: 10.1016/j.gdata.2014.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cells regulate transcription by coordinating the activities of multiple histone modifying complexes. We recently identified the yeast histone H4 methyltransferase Set5 and discovered functional overlap with the histone H3 methyltransferase Set1 in gene expression. Specifically, using next-generation RNA sequencing (RNA-Seq), we found that Set5 and Set1 function synergistically to regulate specific transcriptional programs at subtelomeres and transposable elements. Here we provide a comprehensive description of the methodology and analysis tools corresponding to the data deposited in NCBI's Gene Expression Omnibus (GEO) under the accession number GSE52086. This data complements the experimental methods described in Mas Martín G et al. (2014) and provides the means to explore the cooperative functions of histone H3 and H4 methyltransferases in the regulation of transcription. Furthermore, a fully annotated R code is included to enable researchers to use the following computational tools: comparison of significant differential expression (SDE) profiles; gene ontology enrichment of SDE; and enrichment of SDE relative to chromosomal features, such as centromeres, telomeres, and transposable elements. Overall, we present a bioinformatics platform that can be generally implemented for similar analyses with different datasets and in different organisms.
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Affiliation(s)
- Glòria Mas Martín
- Department of Biology, Stanford University, Stanford 94305, California, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford 94305, California, USA
| | | | - Ashby J Morrison
- Department of Biology, Stanford University, Stanford 94305, California, USA
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Mazur PK, Reynoird N, Khatri P, Jansen PWTC, Wilkinson AW, Liu S, Barbash O, Van Aller GS, Huddleston M, Dhanak D, Tummino PJ, Kruger RG, Garcia BA, Butte AJ, Vermeulen M, Sage J, Gozani O. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature 2014; 510:283-7. [PMID: 24847881 PMCID: PMC4122675 DOI: 10.1038/nature13320] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/11/2014] [Indexed: 12/12/2022]
Abstract
Deregulation in lysine methylation signaling has emerged as a common etiologic factor in cancer pathogenesis, with inhibitors of several histone lysine methyltransferases (KMTs) being developed as chemotherapeutics1. The largely cytoplasmic KMT SMYD3 (SET and MYND domain containing protein 3) is overexpressed in numerous human tumors2-4. However, the molecular mechanism by which SMYD3 regulates cancer pathways and its relationship to tumorigenesis in vivo are largely unknown. Here we show that methylation of MAP3K2 by SMYD3 increases MAP Kinase signaling and promotes the formation of Ras-driven carcinomas. Using mouse models for pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LAC), we found that abrogating SMYD3 catalytic activity inhibits tumor development in response to oncogenic Ras. We employed protein array technology to identify the MAP3K2 kinase as a target of SMYD3. In cancer cell lines, SMYD3-mediated methylation of MAP3K2 at lysine 260 potentiates activation of the Ras/Raf/MEK/ERK signaling module. Finally, the PP2A phosphatase complex, a key negative regulator of the MAP Kinase pathway, binds to MAP3K2 and this interaction is blocked by methylation. Together, our results elucidate a new role for lysine methylation in integrating cytoplasmic kinase-signaling cascades and establish a pivotal role for SMYD3 in the regulation of oncogenic Ras signaling.
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Affiliation(s)
- Pawel K Mazur
- 1] Department of Pediatrics, Stanford University School of Medicine, California 94305, USA [2] Department of Genetics, Stanford University School of Medicine, California 94305, USA [3]
| | - Nicolas Reynoird
- 1] Department of Biology, Stanford University, California 94305, USA [2]
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, and Department of Medicine, Stanford University School of Medicine, California 94305, USA
| | - Pascal W T C Jansen
- Department of Molecular Cancer Research and Department of Medical Oncology, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
| | - Alex W Wilkinson
- Department of Biology, Stanford University, California 94305, USA
| | - Shichong Liu
- Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Olena Barbash
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA
| | - Glenn S Van Aller
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA
| | - Michael Huddleston
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA
| | - Dashyant Dhanak
- 1] Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA [2] Janssen Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, USA (D.D.); Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands (M.V.)
| | - Peter J Tummino
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA
| | - Ryan G Kruger
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania 19426 USA
| | - Benjamin A Garcia
- Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Atul J Butte
- 1] Department of Pediatrics, Stanford University School of Medicine, California 94305, USA [2] Department of Genetics, Stanford University School of Medicine, California 94305, USA
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research and Department of Medical Oncology, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands [2] Janssen Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, USA (D.D.); Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands (M.V.)
| | - Julien Sage
- 1] Department of Pediatrics, Stanford University School of Medicine, California 94305, USA [2] Department of Genetics, Stanford University School of Medicine, California 94305, USA [3]
| | - Or Gozani
- 1] Department of Biology, Stanford University, California 94305, USA [2]
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Szczepińska T, Kutner J, Kopczyński M, Pawłowski K, Dziembowski A, Kudlicki A, Ginalski K, Rowicka M. Probabilistic approach to predicting substrate specificity of methyltransferases. PLoS Comput Biol 2014; 10:e1003514. [PMID: 24651469 PMCID: PMC3961171 DOI: 10.1371/journal.pcbi.1003514] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/01/2014] [Indexed: 11/18/2022] Open
Abstract
We present a general probabilistic framework for predicting the substrate specificity of enzymes. We designed this approach to be easily applicable to different organisms and enzymes. Therefore, our predictive models do not rely on species-specific properties and use mostly sequence-derived data. Maximum Likelihood optimization is used to fine-tune model parameters and the Akaike Information Criterion is employed to overcome the issue of correlated variables. As a proof-of-principle, we apply our approach to predicting general substrate specificity of yeast methyltransferases (MTases). As input, we use several physico-chemical and biological properties of MTases: structural fold, isoelectric point, expression pattern and cellular localization. Our method accurately predicts whether a yeast MTase methylates a protein, RNA or another molecule. Among our experimentally tested predictions, 89% were confirmed, including the surprising prediction that YOR021C is the first known MTase with a SPOUT fold that methylates a substrate other than RNA (protein). Our approach not only allows for highly accurate prediction of functional specificity of MTases, but also provides insight into general rules governing MTase substrate specificity.
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Affiliation(s)
- Teresa Szczepińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jan Kutner
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michał Kopczyński
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Pawłowski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Warsaw University of Life Sciences, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
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40
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Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ. Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. Epigenetics 2014; 9:513-22. [PMID: 24442241 DOI: 10.4161/epi.27645] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity.
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Affiliation(s)
| | - Devin A King
- Department of Biology; Stanford University; Stanford, CA USA
| | - Erin M Green
- Department of Biology; Stanford University; Stanford, CA USA
| | | | - Richard Alexander
- Department of Cellular and Molecular Pharmacology; University of California San Francisco; San Francisco, CA USA
| | - Sean R Collins
- Department of Chemical and Systems Biology; Stanford University; Stanford, CA USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology; University of California San Francisco; San Francisco, CA USA
| | - Or P Gozani
- Department of Biology; Stanford University; Stanford, CA USA
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Sadhu MJ, Guan Q, Li F, Sales-Lee J, Iavarone AT, Hammond MC, Cande WZ, Rine J. Nutritional control of epigenetic processes in yeast and human cells. Genetics 2013; 195:831-44. [PMID: 23979574 PMCID: PMC3813867 DOI: 10.1534/genetics.113.153981] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/12/2013] [Indexed: 02/02/2023] Open
Abstract
The vitamin folate is required for methionine homeostasis in all organisms. In addition to its role in protein synthesis, methionine is the precursor to S-adenosyl-methionine (SAM), which is used in myriad cellular methylation reactions, including all histone methylation reactions. Here, we demonstrate that folate and methionine deficiency led to reduced methylation of lysine 4 of histone H3 (H3K4) in Saccharomyces cerevisiae. The effect of nutritional deficiency on H3K79 methylation was less pronounced, but was exacerbated in S. cerevisiae carrying a hypomorphic allele of Dot1, the enzyme responsible for H3K79 methylation. This result suggested a hierarchy of epigenetic modifications in terms of their susceptibility to nutritional limitations. Folate deficiency caused changes in gene transcription that mirrored the effect of complete loss of H3K4 methylation. Histone methylation was also found to respond to nutritional deficiency in the fission yeast Schizosaccharomyces pombe and in human cells in culture.
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Affiliation(s)
- Meru J. Sadhu
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Qiaoning Guan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Fei Li
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
| | - Jade Sales-Lee
- Department of Chemistry, University of California, Berkeley, California 94720-3220
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
| | - Ming C. Hammond
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- Department of Chemistry, University of California, Berkeley, California 94720-3220
| | - W. Zacheus Cande
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-3220
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42
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Schiza V, Molina-Serrano D, Kyriakou D, Hadjiantoniou A, Kirmizis A. N-alpha-terminal acetylation of histone H4 regulates arginine methylation and ribosomal DNA silencing. PLoS Genet 2013; 9:e1003805. [PMID: 24068969 PMCID: PMC3778019 DOI: 10.1371/journal.pgen.1003805] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/03/2013] [Indexed: 11/24/2022] Open
Abstract
Post-translational modifications of histones play a key role in DNA-based processes, like transcription, by modulating chromatin structure. N-terminal acetylation is unique among the numerous histone modifications because it is deposited on the N-alpha amino group of the first residue instead of the side-chain of amino acids. The function of this modification and its interplay with other internal histone marks has not been previously addressed. Here, we identified N-terminal acetylation of H4 (N-acH4) as a novel regulator of arginine methylation and chromatin silencing in Saccharomyces cerevisiae. Lack of the H4 N-alpha acetyltransferase (Nat4) activity results specifically in increased deposition of asymmetric dimethylation of histone H4 arginine 3 (H4R3me2a) and in enhanced ribosomal-DNA silencing. Consistent with this, H4 N-terminal acetylation impairs the activity of the Hmt1 methyltransferase towards H4R3 in vitro. Furthermore, combinatorial loss of N-acH4 with internal histone acetylation at lysines 5, 8 and 12 has a synergistic induction of H4R3me2a deposition and rDNA silencing that leads to a severe growth defect. This defect is completely rescued by mutating arginine 3 to lysine (H4R3K), suggesting that abnormal deposition of a single histone modification, H4R3me2a, can impact on cell growth. Notably, the cross-talk between N-acH4 and H4R3me2a, which regulates rDNA silencing, is induced under calorie restriction conditions. Collectively, these findings unveil a molecular and biological function for H4 N-terminal acetylation, identify its interplay with internal histone modifications, and provide general mechanistic implications for N-alpha-terminal acetylation, one of the most common protein modifications in eukaryotes. The genome of eukaryotic cells is packaged into nucleosomes consisting of an octamer of histone proteins that is wrapped around by DNA. Histone proteins are often modified with chemical groups that can influence the arrangement of nucleosomes and thereby affect DNA-based processes like transcription. Histone N-terminal acetylation, which comprises the addition of a chemical group at the tip of the histone tail, is an abundant modification whose function is unknown. In this work, we show that N-terminal acetylation of histone H4 can strongly inhibit the occurrence of a neighboring modification, namely dimethylation at the third arginine. To do this, N-terminal acetylation cooperates with other internal lysine acetylation marks. We find that the communication amongst these histone modifications is necessary for controlling the expression of ribosomal RNA genes that are required for protein synthesis and cell growth. Our experiments show that in the absence of both N-terminal acetylation and lysine acetylation there is a strong increase in H4 arginine 3 dimethylation levels leading to cell lethality. This growth defect can be rescued by a point mutation on H4 that blocks methylation at position 3. Together, our results unveil a molecular and biological function for the previously uncharacterized N-terminal acetylation of histones.
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Affiliation(s)
- Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail:
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43
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Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem Sci 2013; 38:243-52. [PMID: 23490039 DOI: 10.1016/j.tibs.2013.02.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 01/31/2013] [Accepted: 02/05/2013] [Indexed: 01/08/2023]
Abstract
Methylated lysine and arginine residues in histones represent a crucial part of the histone code, and recognition of these methylated residues by protein interaction domains modulates transcription. Although some methylating enzymes appear to be histone specific, many can modify histone and non-histone substrates and an increasing number are specific for non-histone substrates. Some of the non-histone substrates can also be involved in transcription, but a distinct subset of protein methylation reactions occurs at residues buried deeply in ribosomal proteins that may function in protein-RNA interactions rather than protein-protein interactions. Additionally, recent work has identified enzymes that catalyze protein methylation reactions at new sites in ribosomal and other proteins. These reactions include modifications of histidine and cysteine residues as well as the N terminus.
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44
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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Green EM, Morrison AJ, Gozani O. New marks on the block: Set5 methylates H4 lysines 5, 8 and 12. Nucleus 2012; 3:335-9. [PMID: 22688645 DOI: 10.4161/nucl.20695] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The methylation of lysine residues in the N-terminal tails of histones is a highly conserved mechanism that regulates critical functions of chromatin, such as the control of gene expression. Using a biochemical approach, we recently identified new methylation marks on the histone H4 tail in budding yeast at lysines 5, 8 and 12, catalyzed by the previously-uncharacterized enzyme Set5. Genetic studies revealed that Set5 functions in cellular processes that also rely on the global chromatin modifying complexes COMPASS and NuA4, which methylate H3 lysine 4 and acetylate H4 lysines 5, 8 and 12, respectively. The identification of new methylation events on the H4 tail raises many intriguing questions regarding their function and their interaction with known histone modifications. Here, we analyze the insights gained about the new enzyme Set5 and the implications for new functionality added to the H4 tail.
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Affiliation(s)
- Erin M Green
- Department of Biology, Stanford University, Stanford, CA, USA.
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