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Kufrin V, Seiler A, Brilloff S, Rothfuß H, Küchler S, Schäfer S, Rahimian E, Baumgarten J, Ding L, Buchholz F, Ball CR, Bornhäuser M, Glimm H, Bill M, Wurm AA. The histone modifier KAT2A presents a selective target in a subset of well-differentiated microsatellite-stable colorectal cancers. Cell Death Differ 2025:10.1038/s41418-025-01479-7. [PMID: 40140561 DOI: 10.1038/s41418-025-01479-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 01/27/2025] [Accepted: 03/14/2025] [Indexed: 03/28/2025] Open
Abstract
Lysine acetyltransferase 2 A (KAT2A) plays a pivotal role in epigenetic gene regulation across various types of cancer. In colorectal cancer (CRC), increased KAT2A expression is associated with a more aggressive phenotype. Our study aims to elucidate the molecular underpinnings of KAT2A dependency in CRC and assess the consequences of KAT2A depletion. We conducted a comprehensive analysis by integrating CRISPR-Cas9 screening data with genomics, transcriptomics, and global acetylation patterns in CRC cell lines to pinpoint molecular markers indicative of KAT2A dependency. Additionally, we characterized the phenotypic effect of a CRISPR-interference-mediated KAT2A knockdown in CRC cell lines and patient-derived 3D spheroid cultures. Moreover, we assessed the effect of KAT2A depletion within a patient-derived xenograft mouse model in vivo. Our findings reveal that KAT2A dependency is closely associated with microsatellite stability, lower mutational burden, and increased molecular differentiation signatures in CRC, independent of the KAT2A expression levels. KAT2A-dependent CRC cells display higher gene expression levels and enriched H3K27ac marks at gene loci linked to enterocytic differentiation. Furthermore, loss of KAT2A leads to decreased cell growth and viability in vitro and in vivo, downregulation of proliferation- and stem cell-associated genes, and induction of differentiation markers. Altogether, our data show that a specific subset of CRCs with a more differentiated phenotype relies on KAT2A. For these CRC cases, KAT2A might represent a promising novel therapeutic target.
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Affiliation(s)
- Vida Kufrin
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Annika Seiler
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Silke Brilloff
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Helen Rothfuß
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Sandra Küchler
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Silvia Schäfer
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Elahe Rahimian
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Jonas Baumgarten
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- TUD Dresden University of Technology, Faculty of Biology, Dresden, Germany
| | - Martin Bornhäuser
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marius Bill
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Alexander A Wurm
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- German Cancer Consortium (DKTK), Dresden, Germany.
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Zhu M, Lu X, Wang D, Ma J, Wang Y, Wang R, Wang H, Cheng W, Zhu Y. A narrative review of epigenetic marker in H3K27ac and its emerging potential as a therapeutic target in cancer. Epigenomics 2025; 17:263-279. [PMID: 39981972 PMCID: PMC11853624 DOI: 10.1080/17501911.2025.2460900] [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: 09/09/2024] [Accepted: 01/28/2025] [Indexed: 02/22/2025] Open
Abstract
Histone acetylation, particularly H3 K27 acetylation (H3K27ac), is a critical post-translational modification that regulates chromatin structure and gene expression, which plays a significant role in various cancers, including breast, colon, lung, hepatocellular, and prostate cancer. However, the mechanisms of H3K27ac in tumorigenesis are not yet comprehensive, especially its epigenetic mechanisms. This review endeavors to discuss findings on the involvement of H3K27ac in carcinogenesis within the past 5 years through a literature search using academic databases such as Web of Science. Firstly, we provide an overview of the diverse landscape of histone modifications, emphasizing the distinctive characteristics and critical significance of H3K27ac. Secondly, we summarize and compare advanced high-throughput sequencing technologies that have been utilized in the construction of the H3K27ac epigenetic map. Thirdly, we elucidate the role of H3K27ac in mediating gene transcription. Fourthly, we venture into the potential molecular mechanism of H3K27ac in cancer development. Finally, we engage in discussing future therapeutic approaches in oncology, with a spotlight on strategies that harness the potential of H3K27 modifications. In conclusion, this review comprehensively summarizes the characteristics of H3K27ac and underscores its pivotal role in cancer, providing valuable insights into its potential as a therapeutic target for cancer intervention.
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Affiliation(s)
- Meizi Zhu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Xuejin Lu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Danhong Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Jinhu Ma
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yi Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Rui Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Hongye Wang
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Wenhui Cheng
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yaling Zhu
- Department of Pathophysiology, College of Basic Medical Science, Anhui Medical University, Hefei, China
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
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Lin L, Huang Y, McIntyre J, Chang CH, Colmenares S, Lee YCG. Prevalent Fast Evolution of Genes Involved in Heterochromatin Functions. Mol Biol Evol 2024; 41:msae181. [PMID: 39189646 PMCID: PMC11408610 DOI: 10.1093/molbev/msae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements. Given the importance of these functions, it is expected that genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions, purifying selection may have maintained the proportions of intrinsically disordered regions of these proteins. Together with the observed negative associations between the evolutionary rate of these genes and the genomic abundance of transposable elements, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of transposable elements may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
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Affiliation(s)
- Leila Lin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Jennifer McIntyre
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ching-Ho Chang
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Serafin Colmenares
- Department of Cell and Molecular Biology, University of California, Berkeley, CA, USA
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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4
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Huoh YS, Zhang Q, Törner R, Baca SC, Arthanari H, Hur S. Mechanism for controlled assembly of transcriptional condensates by Aire. Nat Immunol 2024; 25:1580-1592. [PMID: 39169234 PMCID: PMC11362013 DOI: 10.1038/s41590-024-01922-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024]
Abstract
Transcriptional condensates play a crucial role in gene expression and regulation, yet their assembly mechanisms remain poorly understood. Here, we report a multi-layered mechanism for condensate assembly by autoimmune regulator (Aire), an essential transcriptional regulator that orchestrates gene expression reprogramming for central T cell tolerance. Aire condensates assemble on enhancers, stimulating local transcriptional activities and connecting disparate inter-chromosomal loci. This functional condensate formation hinges upon the coordination between three Aire domains: polymerization domain caspase activation recruitment domain (CARD), histone-binding domain (first plant homeodomain (PHD1)), and C-terminal tail (CTT). Specifically, CTT binds coactivators CBP/p300, recruiting Aire to CBP/p300-rich enhancers and promoting CARD-mediated condensate assembly. Conversely, PHD1 binds to the ubiquitous histone mark H3K4me0, keeping Aire dispersed throughout the genome until Aire nucleates on enhancers. Our findings showed that the balance between PHD1-mediated suppression and CTT-mediated stimulation of Aire polymerization is crucial to form transcriptionally active condensates at target sites, providing new insights into controlled polymerization of transcriptional regulators.
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Affiliation(s)
- Yu-San Huoh
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Qianxia Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ricarda Törner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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Lin L, Huang Y, McIntyre J, Chang CH, Colmenares S, Lee YCG. Prevalent fast evolution of genes involved in heterochromatin functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583199. [PMID: 38496614 PMCID: PMC10942301 DOI: 10.1101/2024.03.03.583199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements (TEs). Given the importance of these functions, it is expected that the genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions (IDRs), purifying selection may have maintained the proportions of IDRs of these proteins. Together with the observed negative associations between evolutionary rates of these genes and genomic TE abundance, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of TEs may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
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Das C, Dash SR, Sinha S, Paul S, Das B, Bhal S, Sethy C, Kundu CN. Talazoparib enhances the quinacrine-mediated apoptosis in patient-derived oral mucosa CSCs by inhibiting BER pathway through the modulation of GCN5 and P300. Med Oncol 2023; 40:351. [PMID: 37940725 DOI: 10.1007/s12032-023-02222-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
The presence of cancer stem cells (CSCs) in the tumor microenvironment (TME) is majorly responsible for the development and recurrence of cancer. Earlier reports suggested that upon DNA damage, poly-(ADP-ribose) polymerase-1 (PARP-1) helps in chromatin modulation and DNA repair process, thereby promoting CSC survival. But whether a combination of DNA damaging agents along with PARP inhibitors can modulate chromatin assembly, inhibit DNA repair processes, and subsequently target CSCs is not known. Hence, we have investigated the effect of nontoxic bioactive compound quinacrine (QC) and a potent PARP inhibitor Talazoparib in patient-derived oral mucosa CSCs (OM-CSCs) and in vivo xenograft mice preclinical model systems. Data showed that QC + Talazoparib inhibited the PARP-1-mediated chromatin remodelers' recruitment and deregulated HAT activity of GCN5 (general control nonderepressible-5) and P300 at DNA damage site, thereby preventing the access of repair proteins to the damaged DNA. Additionally, this combination treatment inhibited topoisomerase activity, induced topological stress, and induced apoptosis in OM-CSCs. Similar results were observed in an in vivo xenograft mice model system. Collectively, the data suggested that QC + Talazoparib treatment inhibited BER pathway, induced genomic instability and triggered apoptosis in OM-CSCs through the deregulation of PARP-1-mediated chromatin remodelers (GCN5 and P300) activity. Schematic representation of QC + Talazoparib-induced apoptosis in oral mucosa CSCs. (1) Induction of DNA damage takes place after QC treatment (2) PARP1-mediated PARylation at the site of DNA damage, which recruits multiple chromatin remodelers (3) Acetylation at the histone tails relax the structure of chromatin and recruits the BER pathway proteins at the site of DNA damage. (4) BER pathway activated at the site of DNA damage. (5) CSCs survive after successful repair of DNA damage. (6) Treatment of QC-treated CSCs with PARP inhibitor Talazoparib (7) Inhibition of PARylation results in failure of chromatin remodelers to interact with PARP1. (8) Inhibition of acetylation status leads to chromatin compaction. (9) BER pathway proteins are not recruited at the site of DNA damage, resulting in inhibition of BER pathway and accumulation of unrepaired DNA damage, leading to apoptosis and cell death.
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Affiliation(s)
- Chinmay Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Somya Ranjan Dash
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Saptarshi Sinha
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Subarno Paul
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Subhasmita Bhal
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chinmayee Sethy
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India.
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Li K, Mocciaro G, Griffin JL, Zhang N. The Saccharomyces cerevisiae acetyltransferase Gcn5 exerts antagonistic pleiotropic effects on chronological ageing. Aging (Albany NY) 2023; 15:10915-10937. [PMID: 37874684 PMCID: PMC10637828 DOI: 10.18632/aging.205109] [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: 04/07/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023]
Abstract
Compared to replicative lifespan, epigenetic regulation of chronological lifespan (CLS) is less well understood in yeast. Here, by screening all the viable mutants of histone acetyltransferase (HAT) and histone deacetylase (HDAC), we demonstrate that Gcn5, functioning in the HAT module of the SAGA/SLIK complex, exhibits an epistatic relationship with the HDAC Hda1 to control the expression of starvation-induced stress response and respiratory cell growth. Surprisingly, the gcn5Δ mutants lose their colony-forming potential early in the stationary phase but display a longer maximum CLS than their WT counterparts, suggesting the contradictory roles of Gcn5 in lifespan regulation. Integrative analyses of the transcriptome, metabolome and ChIP assays reveal that Gcn5 is necessary for the activation of two regulons upon glucose starvation: the Msn2/4-/Gis1-dependent stress response and the Cat8-/Adr1-mediated metabolic reprogramming, to enable pro-longevity characteristics, including redox homeostasis, stress resistance and maximal storage of carbohydrates. The activation of Cat8-/Adr1-dependent regulon also promotes the pyruvate dehydrogenase (PDH) bypass, leading to acetyl-CoA synthesis, global and targeted H3K9 acetylation. Global H3K9 acetylation levels mediated by Gcn5 and Hda1 during the transition into stationary phase are positively correlated with senescent cell populations accumulated in the aged cell cultures. These data suggest that Gcn5 lies in the centre of a feed-forward loop between histone acetylation and starvation-induced gene expression, enabling stress resistance and homeostasis but also promoting chronological ageing concomitantly.
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Affiliation(s)
- Kaiqiang Li
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Gabriele Mocciaro
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jules L. Griffin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- The Rowett Institute, University of Aberdeen, Foresterhill Campus, Aberdeen AB25 2ZD, UK
| | - Nianshu Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Fraser OA, Namitz KEW, Showalter SA. Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors. Methods 2023; 218:72-83. [PMID: 37524235 PMCID: PMC10528339 DOI: 10.1016/j.ymeth.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
Post-translational modifications (PTMs) are reversible chemical modifications that can modulate protein structure and function. Methylation and acetylation are two such PTMs with integral and well-characterized biological roles, including modulation of chromatin structure; and unknown or poorly understood roles, exemplified by the influence of these PTMs on transcription factor structure and function. The need for biological insights into the function of these PTMs motivates the development of a nondestructive and label-free method that enables pursuit of molecular mechanisms. Here, we present a protocol for implementing nuclear magnetic resonance (NMR) methods that allow for unambiguous detection of methylation and acetylation events and demonstrate their utility by observing these marks on histone H3 tail as a model system. We leverage strategic isotopic enrichment of cofactor and peptide for visualization by [1H, 13C]-HSQC and 13C direct-detect NMR measurements. Finally, we present 13C-labeling schemes that facilitate one-dimensional NMR experiments, which combine reduced measurement time relative to two-dimensional spectroscopy with robust filtering of background signals that would otherwise create spectral crowding or limit detection of low-abundance analytes.
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Affiliation(s)
- Olivia A Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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Small EM, Osley MA. A screen for histone mutations that affect quiescence in S. cerevisiae. FEBS J 2023; 290:3539-3562. [PMID: 36871139 DOI: 10.1111/febs.16759] [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: 08/07/2022] [Revised: 12/15/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Quiescence or G0 is a reversible state in which cells cease division but retain the ability to resume proliferation. Quiescence occurs in all organisms and is essential for stem cell maintenance and tissue renewal. It is also related to chronological lifespan (CLS)-the survival of postmitotic quiescent cells (Q cells) over time-and thus contributes to longevity. Important questions remain regarding the mechanisms that control entry into quiescence, maintenance of quiescence and re-entry of Q cells into the cell cycle. S. cerevisiae has emerged as an excellent organism in which to address these questions because of the ease in which Q cells can be isolated. Following entry into G0, yeast cells remain viable for an extended period and can re-enter the cell cycle when exposed to growth-promoting signals. Histone acetylation is lost during the formation of Q cells and chromatin becomes highly condensed. This unique chromatin landscape regulates quiescence-specific transcriptional repression and has been linked to the formation and maintenance of Q cells. To ask whether other chromatin features regulate quiescence, we conducted two comprehensive screens of histone H3 and H4 mutants and identified mutants that show either altered quiescence entry or CLS. Examination of several quiescence entry mutants found that none of the mutants retain histone acetylation in Q cells but show differences in chromatin condensation. A comparison of H3 and H4 mutants with altered CLS to those with altered quiescence entry found that chromatin plays both overlapping and independent roles in the continuum of the quiescence program.
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Affiliation(s)
- Eric M Small
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Mary Ann Osley
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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10
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Haile ST, Rahman S, Fields JK, Orsburn BC, Bumpus NN, Wolberger C. The SAGA HAT module is tethered by its SWIRM domain and modulates activity of the SAGA DUB module. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194929. [PMID: 36965704 PMCID: PMC10226619 DOI: 10.1016/j.bbagrm.2023.194929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/12/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is a transcriptional co-activator that both acetylates and deubiquitinates histones. The histone acetyltransferase (HAT) subunit, Gcn5, is part of a subcomplex of SAGA called the HAT module. A minimal HAT module complex containing Gcn5 bound to Ada2 and Ada3 is required for full Gcn5 activity on nucleosomes. Deletion studies have suggested that the Ada2 SWIRM domain plays a role in tethering the HAT module to the remainder of SAGA. While recent cryo-EM studies have resolved the structure of the core of the SAGA complex, the HAT module subunits and molecular details of its interactions with the SAGA core could not be resolved. Here we show that the SWIRM domain is required for incorporation of the HAT module into the yeast SAGA complex, but not the ADA complex, a distinct six-protein acetyltransferase complex that includes the SAGA HAT module proteins. In the isolated Gcn5/Ada2/Ada3 HAT module, deletion of the SWIRM domain modestly increased activity but had negligible effect on nucleosome binding. Loss of the HAT module due to deletion of the SWIRM domain decreases the H2B deubiquitinating activity of SAGA, indicating a role for the HAT module in regulating SAGA DUB module activity. A model of the HAT module created with Alphafold Multimer provides insights into the structural basis for our biochemical data, as well as prior deletion studies.
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Affiliation(s)
- Sara T Haile
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - James K Fields
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America.
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11
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Izzo LT, Trefely S, Demetriadou C, Drummond JM, Mizukami T, Kuprasertkul N, Farria AT, Nguyen PT, Murali N, Reich L, Kantner DS, Shaffer J, Affronti H, Carrer A, Andrews A, Capell BC, Snyder NW, Wellen KE. Acetylcarnitine shuttling links mitochondrial metabolism to histone acetylation and lipogenesis. SCIENCE ADVANCES 2023; 9:eadf0115. [PMID: 37134161 PMCID: PMC10156126 DOI: 10.1126/sciadv.adf0115] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
The metabolite acetyl-CoA is necessary for both lipid synthesis in the cytosol and histone acetylation in the nucleus. The two canonical precursors to acetyl-CoA in the nuclear-cytoplasmic compartment are citrate and acetate, which are processed to acetyl-CoA by ATP-citrate lyase (ACLY) and acyl-CoA synthetase short-chain 2 (ACSS2), respectively. It is unclear whether other substantial routes to nuclear-cytosolic acetyl-CoA exist. To investigate this, we generated cancer cell lines lacking both ACLY and ACSS2 [double knockout (DKO) cells]. Using stable isotope tracing, we show that both glucose and fatty acids contribute to acetyl-CoA pools and histone acetylation in DKO cells and that acetylcarnitine shuttling can transfer two-carbon units from mitochondria to cytosol. Further, in the absence of ACLY, glucose can feed fatty acid synthesis in a carnitine responsive and carnitine acetyltransferase (CrAT)-dependent manner. The data define acetylcarnitine as an ACLY- and ACSS2-independent precursor to nuclear-cytosolic acetyl-CoA that can support acetylation, fatty acid synthesis, and cell growth.
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Affiliation(s)
- Luke T. Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Christina Demetriadou
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Jack M. Drummond
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Takuya Mizukami
- Department of Cancer Epigenetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Nina Kuprasertkul
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aimee T. Farria
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phuong T. T. Nguyen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nivitha Murali
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren Reich
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel S. Kantner
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Joshua Shaffer
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hayley Affronti
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Carrer
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Andrews
- Department of Cancer Epigenetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Kathryn E. Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Fraser OA, Dewing SM, Usher ET, George C, Showalter SA. A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins. Front Mol Biosci 2023; 9:1074743. [PMID: 36685286 PMCID: PMC9853081 DOI: 10.3389/fmolb.2022.1074743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.
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Affiliation(s)
- Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Sophia M. Dewing
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Emery T. Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Christy George
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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13
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Faragó A, Zsindely N, Farkas A, Neller A, Siági F, Szabó MR, Csont T, Bodai L. Acetylation State of Lysine 14 of Histone H3.3 Affects Mutant Huntingtin Induced Pathogenesis. Int J Mol Sci 2022; 23:15173. [PMID: 36499499 PMCID: PMC9738228 DOI: 10.3390/ijms232315173] [Citation(s) in RCA: 6] [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: 10/27/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a polyglutamine-coding CAG repeat in the Huntingtin gene. One of the main causes of neurodegeneration in HD is transcriptional dysregulation that, in part, is caused by the inhibition of histone acetyltransferase (HAT) enzymes. HD pathology can be alleviated by increasing the activity of specific HATs or by inhibiting histone deacetylase (HDAC) enzymes. To determine which histone's post-translational modifications (PTMs) might play crucial roles in HD pathology, we investigated the phenotype-modifying effects of PTM mimetic mutations of variant histone H3.3 in a Drosophila model of HD. Specifically, we studied the mutations (K→Q: acetylated; K→R: non-modified; and K→M: methylated) of lysine residues K9, K14, and K27 of transgenic H3.3. In the case of H3.3K14Q modification, we observed the amelioration of all tested phenotypes (viability, longevity, neurodegeneration, motor activity, and circadian rhythm defects), while H3.3K14R had the opposite effect. H3.3K14Q expression prevented the negative effects of reduced Gcn5 (a HAT acting on H3K14) on HD pathology, while it only partially hindered the positive effects of heterozygous Sirt1 (an HDAC acting on H3K14). Thus, we conclude that the Gcn5-dependent acetylation of H3.3K14 might be an important epigenetic contributor to HD pathology.
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Affiliation(s)
- Anikó Faragó
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Anita Farkas
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Alexandra Neller
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Fruzsina Siági
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Márton Richárd Szabó
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - Tamás Csont
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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14
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Histone Acetyltransferase CfGcn5-Mediated Autophagy Governs the Pathogenicity of Colletotrichum fructicola. mBio 2022; 13:e0195622. [PMID: 35975920 PMCID: PMC9600425 DOI: 10.1128/mbio.01956-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Camellia oleifera is a woody edible-oil plant in China, and anthracnose occurs wherever it is grown, causing serious losses each year. We previously identified that the histone acetyltransferase CfGcn5 orchestrates growth, development, and pathogenicity in Colletotrichum fructicola, the major causal agent of anthracnose on C. oleifera. To elucidate the underlying mechanism, we conducted a transcriptome analysis and found that CfGcn5 is mainly involved in ribosomes, catalytic and metabolic processes, primary metabolism, and autophagy. In addition, we provided evidence showing that CfGcn5 serves as an autophagy repressor to mediate the expression of many autophagy-related genes (ATG) and undergoes degradation during autophagy. Moreover, we found that the CfATG8 and CfATG9 gene-deletion mutants had defects in mitosis and autophagy, resulting in their decreased appressoria formation rates and lower turgor pressure. These combined effects caused the failure of their appressoria functions and caused defects on their pathogenicity, revealing the importance of autophagy in pathogenicity. Taken together, our study illustrates that the autophagy repressor CfGcn5 undergoes degradation in order to regulate autophagy-dependent pathogenicity in C. fructicola.
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15
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Yu S, Paderu P, Lee A, Eirekat S, Healey K, Chen L, Perlin DS, Zhao Y. Histone Acetylation Regulator Gcn5 Mediates Drug Resistance and Virulence of Candida glabrata. Microbiol Spectr 2022; 10:e0096322. [PMID: 35658596 PMCID: PMC9241792 DOI: 10.1128/spectrum.00963-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/17/2022] [Indexed: 01/08/2023] Open
Abstract
Candida glabrata is poised to adapt to drug pressure rapidly and acquire antifungal resistance leading to therapeutic failure. Given the limited antifungal armamentarium, there is an unmet need to explore new targets or therapeutic strategies for antifungal treatment. The lysine acetyltransferase Gcn5 has been implicated in the pathogenesis of C. albicans. Yet how Gcn5 functions and impacts antifungal resistance in C. glabrata is unknown. Disrupting GCN5 rendered C. glabrata cells more sensitive to various stressors, partially reverted resistance in drug-resistant mutants, and attenuated the emergence of resistance compared to wild-type cells. RNA sequencing (RNA-seq) analysis revealed transcriptomic changes involving multiple biological processes and different transcriptional responses to antifungal drugs in gcn5Δ cells compared to wild-type cells. GCN5 deletion also resulted in reduced intracellular survival within THP-1 macrophages. In summary, Gcn5 plays a critical role in modulating the virulence of C. glabrata and regulating its response to antifungal pressure and host defense. IMPORTANCE As an important and successful human pathogen, Candida glabrata is known for its swift adaptation and rapid acquisition of resistance to the most commonly used antifungal agents, resulting in therapeutic failure in clinical settings. Here, we describe that the histone acetyltransferase Gcn5 is a key factor in adapting to antifungal pressure and developing resistance in C. glabrata. The results provide new insights into epigenetic control over the drug response in C. glabrata and may be useful for drug target discovery and the development of new therapeutic strategies to combat fungal infections.
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Affiliation(s)
- Shuying Yu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, People’s Republic of China
| | - Padmaja Paderu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Annie Lee
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Sami Eirekat
- Department of Biology, William Paterson University, Wayne, New Jersey, USA
| | - Kelley Healey
- Department of Biology, William Paterson University, Wayne, New Jersey, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC, USA
| | - Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
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16
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Sanz AB, García R, Pavón-Vergés M, Rodríguez-Peña JM, Arroyo J. Control of Gene Expression via the Yeast CWI Pathway. Int J Mol Sci 2022; 23:ijms23031791. [PMID: 35163713 PMCID: PMC8836261 DOI: 10.3390/ijms23031791] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/18/2022] Open
Abstract
Living cells exposed to stressful environmental situations can elicit cellular responses that guarantee maximal cell survival. Most of these responses are mediated by mitogen-activated protein kinase (MAPK) cascades, which are highly conserved from yeast to humans. Cell wall damage conditions in the yeast Saccharomyces cerevisiae elicit rescue mechanisms mainly associated with reprogramming specific transcriptional responses via the cell wall integrity (CWI) pathway. Regulation of gene expression by this pathway is coordinated by the MAPK Slt2/Mpk1, mainly via Rlm1 and, to a lesser extent, through SBF (Swi4/Swi6) transcription factors. In this review, we summarize the molecular mechanisms controlling gene expression upon cell wall stress and the role of chromatin structure in these processes. Some of these mechanisms are also discussed in the context of other stresses governed by different yeast MAPK pathways. Slt2 regulates both transcriptional initiation and elongation by interacting with chromatin at the promoter and coding regions of CWI-responsive genes but using different mechanisms for Rlm1- and SBF-dependent genes. Since MAPK pathways are very well conserved in eukaryotic cells and are essential for controlling cellular physiology, improving our knowledge regarding how they regulate gene expression could impact the future identification of novel targets for therapeutic intervention.
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17
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Electromagnetized gold nanoparticles improve neurogenesis and cognition in the aged brain. Biomaterials 2021; 278:121157. [PMID: 34601195 DOI: 10.1016/j.biomaterials.2021.121157] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/17/2021] [Accepted: 09/26/2021] [Indexed: 12/30/2022]
Abstract
Adult neurogenesis is the lifelong process by which new neurons are generated in the dentate gyrus. However, adult neurogenesis capacity decreases with age, and this decrease is closely linked to cognitive and memory decline. Our study demonstrated that electromagnetized gold nanoparticles (AuNPs) promote adult hippocampal neurogenesis, thereby improving cognitive function and memory consolidation in aged mice. According to single-cell RNA sequencing data, the numbers of neural stem cells (NSCs) and neural progenitors were significantly increased by electromagnetized AuNPs. Additionally, electromagnetic stimulation resulted in specific activation of the histone acetyltransferase Kat2a, which led to histone H3K9 acetylation in adult NSCs. Moreover, in vivo electromagnetized AuNP stimulation efficiently increased hippocampal neurogenesis in aged and Hutchinson-Gilford progeria mouse brains, thereby alleviating the symptoms of aging. Therefore, our study provides a proof-of-concept for the in vivo stimulation of hippocampal neurogenesis using electromagnetized AuNPs as a promising therapeutic strategy for the treatment of age-related brain diseases.
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18
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Guo Q, Kang H, Wang J, Dong Y, Peng R, Zhao H, Wu W, Guan H, Li F. Inhibition of ACLY Leads to Suppression of Osteoclast Differentiation and Function Via Regulation of Histone Acetylation. J Bone Miner Res 2021; 36:2065-2080. [PMID: 34155695 DOI: 10.1002/jbmr.4399] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/17/2022]
Abstract
ATP-citrate lyase (ACLY), generating most of the nucleocytosolic acetyl coenzyme A (acetyl-CoA) for histone acetylation, links cell metabolism to epigenetic regulation. Recent investigations demonstrated that ACLY activated by metabolic reprogramming played an essential role in both M1 and M2 macrophage activation via histone acetylation. Previous studies also revealed that histone methylation and acetylation were critical for transcriptional regulation of osteoclast-specific genes. Considering that osteoclast differentiation also undergoes metabolic reprogramming and the activity of ACLY is always Akt-dependent, we inferred that receptor activator of NF-κB (RANK) activation might enhance the activity of ACLY through downstream pathways and ACLY might play a role in osteoclast formation. In the current study, we found that ACLY was gradually activated during RANK ligand (RANKL)-induced osteoclast differentiation from bone marrow-derived macrophages (BMMs). Both ACLY knock-down and small molecular ACLY inhibitor BMS-303141 significantly decreased nucleocytosolic acetyl-CoA in BMMs and osteoclasts and suppressed osteoclast formation in vitro. BMS-303141 also suppressed osteoclast formation in vivo and prevents ovariectomy (OVX)-induced bone loss. Further investigations showed that RANKL triggered ACLY translocation into nucleus, consistent with increasing histone H3 acetylation, which was correlated to ACLY. The H3 lysine residues influenced by ACLY were in accordance with GCN5 targets. Using GCN5 knock-down and overexpression, we showed that ACLY and GCN5 functioned in the same pathway for histone H3 acetylation. Analysis of pathways downstream of RANK activation revealed that ACLY was Akt-dependent and predominately affected Akt pathway. With the help of RNA-sequencing, we discovered Rac1 as a downstream regulator of ACLY, which was involved in shACLY-mediated suppression of osteoclast differentiation, cytoskeleton organization, and signal transduction and was transcriptionally regulated by ACLY via histone H3 acetylation. To summarize, our results proved that inhibition of ATP-citrate lyase led to suppression of osteoclast differentiation and function via regulation of histone acetylation. Rac1 could be a downstream regulator of ACLY. © 2021 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Qian Guo
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Honglei Kang
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Wang
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yimin Dong
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Renpeng Peng
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjian Zhao
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wu
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hanfeng Guan
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Li
- Department of Orthopedic Surgery and Biological Engineering and Regenerative Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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19
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Schachner LF, Tran DP, Lee A, McGee JP, Jooss K, Durbin K, Seckler HDS, Adams L, Cline E, Melani R, Ives AN, Des Soye B, Kelleher NL, Patrie SM. Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 465:116591. [PMID: 34539228 PMCID: PMC8445521 DOI: 10.1016/j.ijms.2021.116591] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The combined use of electrospray ionization run in so-called "native mode" with top-down mass spectrometry (nTDMS) is enhancing both structural biology and discovery proteomics by providing three levels of information in a single experiment: the intact mass of a protein or complex, the masses of its subunits and non-covalent cofactors, and fragment ion masses from direct dissociation of subunits that capture the primary sequence and combinations of diverse post-translational modifications (PTMs). While intact mass data are readily deconvoluted using well-known software options, the analysis of fragmentation data that result from a tandem MS experiment - essential for proteoform characterization - is not yet standardized. In this tutorial, we offer a decision-tree for the analysis of nTDMS experiments on protein complexes and diverse bioassemblies. We include an overview of strategies to navigate this type of analysis, provide example data sets, and highlight software for the hypothesis-driven interrogation of fragment ions for localization of PTMs, metals, and cofactors on native proteoforms. Throughout we have emphasized the key features (deconvolution, search mode, validation, other) that the reader can consider when deciding upon their specific experimental and data processing design using both open-access and commercial software.
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Affiliation(s)
- Luis F. Schachner
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Denise P. Tran
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Alexander Lee
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - John P. McGee
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Kevin Jooss
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Kenneth Durbin
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Henrique Dos Santos Seckler
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Lauren Adams
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Erika Cline
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Rafael Melani
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Ashley N. Ives
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Benjamin Des Soye
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
| | - Steven M. Patrie
- Departments of Chemistry, Chemical and Biological Engineering, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, 60208, Evanston, IL, USA
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20
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Dong J, LeBlanc C, Poulet A, Mermaz B, Villarino G, Webb KM, Joly V, Mendez J, Voigt P, Jacob Y. H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation. THE PLANT CELL 2021; 33:961-979. [PMID: 33793815 PMCID: PMC8226292 DOI: 10.1093/plcell/koaa027] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 05/17/2023]
Abstract
Epigenetic mechanisms play diverse roles in the regulation of genome stability in eukaryotes. In Arabidopsis thaliana, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6, which catalyze the deposition of K27me1 on replication-dependent H3.1 variants. The loss of H3.1K27me1 in atxr5 atxr6 double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the transcriptional co-activator and conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires the GCN5-interacting protein ADA2b and the chromatin remodeler CHR6 to mediate the heterochromatic defects in atxr5 atxr6 mutants. Our results also indicate that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variants, but H3.1K27 and H3.1K36 play essential functions in inducing genomic instability in the absence of H3.1K27me1. Finally, we show that H3.1K36 acetylation by GCN5 is negatively regulated by H3.1K27me1 in vitro. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining transcriptional silencing and genome stability in heterochromatin by restricting GCN5-mediated histone acetylation in plants.
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Affiliation(s)
- Jie Dong
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Axel Poulet
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Benoit Mermaz
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Gonzalo Villarino
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Valentin Joly
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Josefina Mendez
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
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21
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Giardina SF, Valdambrini E, Warren JD, Barany F. PROTACs: Promising Approaches for Epigenetic Strategies to Overcome Drug Resistance. Curr Cancer Drug Targets 2021; 21:306-325. [PMID: 33535953 DOI: 10.2174/1568009621666210203110857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/26/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
Epigenetic modulation of gene expression is essential for tissue-specific development and maintenance in mammalian cells. Disruption of epigenetic processes, and the subsequent alteration of gene functions, can result in inappropriate activation or inhibition of various cellular signaling pathways, leading to cancer. Recent advancements in the understanding of the role of epigenetics in cancer initiation and progression have uncovered functions for DNA methylation, histone modifications, nucleosome positioning, and non-coding RNAs. Epigenetic therapies have shown some promise for hematological malignancies, and a wide range of epigenetic-based drugs are undergoing clinical trials. However, in a dynamic survival strategy, cancer cells exploit their heterogeneous population which frequently results in the rapid acquisition of therapy resistance. Here, we describe novel approaches in drug discovery targeting the epigenome, highlighting recent advances the selective degradation of target proteins using Proteolysis Targeting Chimera (PROTAC) to address drug resistance.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
| | - Elena Valdambrini
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
| | - J David Warren
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, Box 63, New York, NY, 10065, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
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22
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Yu R, Cao X, Sun L, Zhu JY, Wasko BM, Liu W, Crutcher E, Liu H, Jo MC, Qin L, Kaeberlein M, Han Z, Dang W. Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism. Nat Commun 2021; 12:1981. [PMID: 33790287 PMCID: PMC8012573 DOI: 10.1038/s41467-021-22257-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Histone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.
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Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Xiaohua Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, USA
- University of Houston, Clear Lake, TX, USA
| | - Wei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Emeline Crutcher
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Haiying Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | | | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Zhe Han
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
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23
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Lowe BR, Yadav RK, Henry RA, Schreiner P, Matsuda A, Fernandez AG, Finkelstein D, Campbell M, Kallappagoudar S, Jablonowski CM, Andrews AJ, Hiraoka Y, Partridge JF. Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail. eLife 2021; 10:e65369. [PMID: 33522486 PMCID: PMC7872514 DOI: 10.7554/elife.65369] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/30/2021] [Indexed: 12/11/2022] Open
Abstract
Sequencing of cancer genomes has identified recurrent somatic mutations in histones, termed oncohistones, which are frequently poorly understood. Previously we showed that fission yeast expressing only the H3.3G34R mutant identified in aggressive pediatric glioma had reduced H3K36 trimethylation and acetylation, increased genomic instability and replicative stress, and defective homology-dependent DNA damage repair. Here we show that surprisingly distinct phenotypes result from G34V (also in glioma) and G34W (giant cell tumors of bone) mutations, differentially affecting H3K36 modifications, subtelomeric silencing, genomic stability; sensitivity to irradiation, alkylating agents, and hydroxyurea; and influencing DNA repair. In cancer, only 1 of 30 alleles encoding H3 is mutated. Whilst co-expression of wild-type H3 rescues most G34 mutant phenotypes, G34R causes dominant hydroxyurea sensitivity, homologous recombination defects, and dominant subtelomeric silencing. Together, these studies demonstrate the complexity associated with different substitutions at even a single residue in H3 and highlight the utility of genetically tractable systems for their analysis.
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Affiliation(s)
- Brandon R Lowe
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Rajesh K Yadav
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer CenterPhiladelphiaUnited States
| | - Patrick Schreiner
- Department of Bioinformatics, St. Jude Children’s Research HospitalMemphisUnited States
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobeJapan
- Graduate School of Frontier Biosciences, Osaka UniversitySuitaJapan
| | - Alfonso G Fernandez
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | - David Finkelstein
- Department of Bioinformatics, St. Jude Children’s Research HospitalMemphisUnited States
| | - Margaret Campbell
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
| | | | | | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer CenterPhiladelphiaUnited States
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobeJapan
- Graduate School of Frontier Biosciences, Osaka UniversitySuitaJapan
| | - Janet F Partridge
- Department of Pathology, St. Jude Children’s Research HospitalMemphisUnited States
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24
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Latorre-Muro P, Baeza J, Hurtado-Guerrero R, Hicks T, Delso I, Hernández-Ruiz C, Velázquez-Campoy A, Lawton AJ, Angulo J, Denu JM, Carrodeguas JA. Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity. J Biol Chem 2021; 296:100205. [PMID: 33334880 PMCID: PMC7948413 DOI: 10.1074/jbc.ra120.015103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry, saturation-transfer difference nuclear magnetic resonance and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. In addition, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemical reaction with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress.
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Affiliation(s)
- Pedro Latorre-Muro
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
| | - Josue Baeza
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Ignacio Delso
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, Zaragoza, Spain
| | - Cristina Hernández-Ruiz
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Adrian Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biomedical Research Network Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain; IIS Aragón, Zaragoza, Spain
| | - Alexis J Lawton
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich, UK; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-Universidad de Sevilla), Sevilla, Spain
| | - John M Denu
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - José A Carrodeguas
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; IIS Aragón, Zaragoza, Spain.
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25
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Chan JC, Maze I. Nothing Is Yet Set in (Hi)stone: Novel Post-Translational Modifications Regulating Chromatin Function. Trends Biochem Sci 2020; 45:829-844. [PMID: 32498971 PMCID: PMC7502514 DOI: 10.1016/j.tibs.2020.05.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/28/2020] [Accepted: 05/14/2020] [Indexed: 01/04/2023]
Abstract
Histone post-translational modifications (PTMs) have emerged as exciting mechanisms of biological regulation, impacting pathways related to cancer, immunity, brain function, and more. Over the past decade alone, several histone PTMs have been discovered, including acylation, lipidation, monoaminylation, and glycation, many of which appear to have crucial roles in nucleosome stability and transcriptional regulation. In this review, we discuss novel histone PTMs identified within the past 10 years, with an extended focus on enzymatic versus nonenzymatic mechanisms underlying modification and adduction. Furthermore, we consider how these novel histone PTMs might fit within the framework of a so-called 'histone code', emphasizing the physiological relevance of these PTMs in metabolism, development, and disease states.
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Affiliation(s)
- Jennifer C Chan
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ian Maze
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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26
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López AJ, Hecking JK, White AO. The Emerging Role of ATP-Dependent Chromatin Remodeling in Memory and Substance Use Disorders. Int J Mol Sci 2020; 21:E6816. [PMID: 32957495 PMCID: PMC7555352 DOI: 10.3390/ijms21186816] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Long-term memory formation requires coordinated regulation of gene expression and persistent changes in cell function. For decades, research has implicated histone modifications in regulating chromatin compaction necessary for experience-dependent changes to gene expression and cell function during memory formation. Recent evidence suggests that another epigenetic mechanism, ATP-dependent chromatin remodeling, works in concert with the histone-modifying enzymes to produce large-scale changes to chromatin structure. This review examines how histone-modifying enzymes and chromatin remodelers restructure chromatin to facilitate memory formation. We highlight the emerging evidence implicating ATP-dependent chromatin remodeling as an essential mechanism that mediates activity-dependent gene expression, plasticity, and cell function in developing and adult brains. Finally, we discuss how studies that target chromatin remodelers have expanded our understanding of the role that these complexes play in substance use disorders.
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Affiliation(s)
- Alberto J. López
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Julia K. Hecking
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
| | - André O. White
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA;
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27
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The evolving metabolic landscape of chromatin biology and epigenetics. Nat Rev Genet 2020; 21:737-753. [PMID: 32908249 DOI: 10.1038/s41576-020-0270-8] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These inputs - which include both nutrient availability as a result of diet and growth factor signalling - are implicated in linking the environment to the maintenance of cellular homeostasis and cell identity. Recent studies have demonstrated that these inputs are much broader than had previously been known, encompassing metabolism from a wide variety of sources, including alcohol and microbiotal metabolism. These factors modify DNA and histones and exert specific effects on cell biology, systemic physiology and pathology. In this Review, we discuss the nature of these molecular networks, highlight their role in mediating cellular responses and explore their modifiability through dietary and pharmacological interventions.
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28
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Espinola-Lopez JM, Tan S. The Ada2/Ada3/Gcn5/Sgf29 histone acetyltransferase module. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194629. [PMID: 32890768 DOI: 10.1016/j.bbagrm.2020.194629] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/14/2023]
Abstract
Histone post-translational modifications are essential for the regulation of gene expression in eukaryotes. Gcn5 (KAT2A) is a histone acetyltransferase that catalyzes the post-translational modification at multiple positions of histone H3 through the transfer of acetyl groups to the free amino group of lysine residues. Gcn5 catalyzes histone acetylation in the context of a HAT module containing the Ada2, Ada3 and Sgf29 subunits of the parent megadalton SAGA transcriptional coactivator complex. Biochemical and structural studies have elucidated mechanisms for Gcn5's acetyl- and other acyltransferase activities on histone substrates, for histone H3 phosphorylation and histone H3 methylation crosstalks with histone H3 acetylation, and for how Ada2 increases Gcn5's histone acetyltransferase activity. Other studies have identified Ada2 isoforms in SAGA-related complexes and characterized variant Gcn5 HAT modules containing these Ada2 isoforms. In this review, we highlight biochemical and structural studies of Gcn5 and its functional interactions with Ada2, Ada3 and Sgf29.
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Affiliation(s)
- Jose M Espinola-Lopez
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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29
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Proietti G, Wang Y, Rainone G, Mecinović J. Effect of lysine side chain length on histone lysine acetyltransferase catalysis. Sci Rep 2020; 10:13046. [PMID: 32747680 PMCID: PMC7400623 DOI: 10.1038/s41598-020-69510-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023] Open
Abstract
Histone lysine acetyltransferase (KAT)-catalyzed acetylation of lysine residues in histone tails plays a key role in regulating gene expression in eukaryotes. Here, we examined the role of lysine side chain length in the catalytic activity of human KATs by incorporating shorter and longer lysine analogs into synthetic histone H3 and H4 peptides. The enzymatic activity of MOF, PCAF and GCN5 acetyltransferases towards histone peptides bearing lysine analogs was evaluated using MALDI-TOF MS assays. Our results demonstrate that human KAT enzymes have an ability to catalyze an efficient acetylation of longer lysine analogs, whereas shorter lysine analogs are not substrates for KATs. Kinetics analyses showed that lysine is a superior KAT substrate to its analogs with altered chain length, implying that lysine has an optimal chain length for KAT-catalyzed acetylation reaction.
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Affiliation(s)
- Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yali Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Blood Transfusion, China-Japan Union Hospital, Jilin University, 126 Xiantai Street, Changchun, 130033, People's Republic of China
| | - Giorgio Rainone
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark. .,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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30
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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31
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Proietti G, Rainone G, Hintzen JCJ, Mecinović J. Exploring the Histone Acylome through Incorporation of γ-Thialysine on Histone Tails. Bioconjug Chem 2020; 31:844-851. [PMID: 32058696 DOI: 10.1021/acs.bioconjchem.0c00012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histone lysine acetyltransferases (KATs) catalyze the transfer of the acetyl group from acetyl Coenzyme A to lysine residues in histones and nonhistone proteins. Here, we report biomolecular studies on epigenetic acetylation and related acylation reactions of lysine and γ-thialysine, a cysteine-derived lysine mimic, which can be site-specifically introduced to histone peptides and histone proteins. Enzyme assays demonstrate that human KATs catalyze an efficient acetylation and propionylation of histone peptides that possess lysine and γ-thialysine. Enzyme kinetics analyses reveal that lysine- and γ-thialysine-containing histone peptides exhibit indistinguishable Km values, whereas small differences in kcat values were observed. This work highlights that γ-thialysine may act as a representative and easily accessible lysine mimic for chemical and biochemical examinations of post-translationally modified histones.
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Affiliation(s)
- Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Giorgio Rainone
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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32
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Domingues AF, Kulkarni R, Giotopoulos G, Gupta S, Vinnenberg L, Arede L, Foerner E, Khalili M, Adao RR, Johns A, Tan S, Zeka K, Huntly BJ, Prabakaran S, Pina C. Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells. eLife 2020; 9:e51754. [PMID: 31985402 PMCID: PMC7039681 DOI: 10.7554/elife.51754] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is an aggressive hematological malignancy with abnormal progenitor self-renewal and defective white blood cell differentiation. Its pathogenesis comprises subversion of transcriptional regulation, through mutation and by hijacking normal chromatin regulation. Kat2a is a histone acetyltransferase central to promoter activity, that we recently associated with stability of pluripotency networks, and identified as a genetic vulnerability in AML. Through combined chromatin profiling and single-cell transcriptomics of a conditional knockout mouse, we demonstrate that Kat2a contributes to leukemia propagation through preservation of leukemia stem-like cells. Kat2a loss impacts transcription factor binding and reduces transcriptional burst frequency in a subset of gene promoters, generating enhanced variability of transcript levels. Destabilization of target programs shifts leukemia cell fate out of self-renewal into differentiation. We propose that control of transcriptional variability is central to leukemia stem-like cell propagation, and establish a paradigm exploitable in different tumors and distinct stages of cancer evolution.
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Affiliation(s)
- Ana Filipa Domingues
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Rashmi Kulkarni
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - George Giotopoulos
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Shikha Gupta
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Laura Vinnenberg
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Liliana Arede
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Elena Foerner
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Mitra Khalili
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of Medical Genetics and Molecular Medicine, School of MedicineZanjan University of Medical Sciences (ZUMS)ZanjanIslamic Republic of Iran
| | - Rita Romano Adao
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Ayona Johns
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
| | - Shengjiang Tan
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Keti Zeka
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Brian J Huntly
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Sudhakaran Prabakaran
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Department of BiologyIISERPuneIndia
| | - Cristina Pina
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
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33
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Cote JM, Kuo YM, Henry RA, Scherman H, Krzizike DD, Andrews AJ. Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation. Nucleic Acids Res 2019; 47:7380-7391. [PMID: 31194870 DOI: 10.1093/nar/gkz508] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 05/27/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
The ability of histone chaperone Anti-silencing factor 1 (Asf1) to direct acetylation of lysine 56 of histone H3 (H3K56ac) represents an important regulatory step in genome replication and DNA repair. In Saccharomyces cerevisiae, Asf1 interacts functionally with a second chaperone, Vps75, and the lysine acetyltransferase (KAT) Rtt109. Both Asf1 and Vps75 can increase the specificity of histone acetylation by Rtt109, but neither alter selectivity. However, changes in acetylation selectivity have been observed in histones extracted from cells, which contain a plethora of post-translational modifications. In the present study, we use a series of singly acetylated histones to test the hypothesis that histone pre-acetylation and histone chaperones function together to drive preferential acetylation of H3K56. We show that pre-acetylated H3K14ac/H4 functions with Asf1 to drive specific acetylation of H3K56 by Rtt109-Vps75. Additionally, we identified an exosite containing an acidic patch in Asf1 and show that mutations to this region alter Asf1-mediated crosstalk that changes Rtt109-Vps75 selectivity. Our proposed mechanism suggests that Gcn5 acetylates H3K14, recruiting remodeler complexes, allowing for the Asf1-H3K14ac/H4 complex to be acetylated at H3K56 by Rtt109-Vps75. This mechanism explains the conflicting biochemical data and the genetic links between Rtt109, Vps75, Gcn5 and Asf1 in the acetylation of H3K56.
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Affiliation(s)
- Joy M Cote
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ryan A Henry
- Department of Chemistry and Biochemistry, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Hataichanok Scherman
- The Histone Source, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel D Krzizike
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Soffers JHM, Li X, Saraf A, Seidel CW, Florens L, Washburn MP, Abmayr SM, Workman JL. Characterization of a metazoan ADA acetyltransferase complex. Nucleic Acids Res 2019; 47:3383-3394. [PMID: 30715476 PMCID: PMC6468242 DOI: 10.1093/nar/gkz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/24/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
The Gcn5 acetyltransferase functions in multiple acetyltransferase complexes in yeast and metazoans. Yeast Gcn5 is part of the large SAGA (Spt-Ada-Gcn5 acetyltransferase) complex and a smaller ADA acetyltransferase complex. In flies and mammals, Gcn5 (and its homolog pCAF) is part of various versions of the SAGA complex and another large acetyltransferase complex, ATAC (Ada2A containing acetyltransferase complex). However, a complex analogous to the small ADA complex in yeast has never been described in metazoans. Previous studies in Drosophila hinted at the existence of a small complex which contains Ada2b, a partner of Gcn5 in the SAGA complex. Here we have purified and characterized the composition of this complex and show that it is composed of Gcn5, Ada2b, Ada3 and Sgf29. Hence, we have named it the metazoan 'ADA complex'. We demonstrate that the fly ADA complex has histone acetylation activity on histones and nucleosome substrates. Moreover, ChIP-Sequencing experiments identified Ada2b peaks that overlap with another SAGA subunit, Spt3, as well as Ada2b peaks that do not overlap with Spt3 suggesting that the ADA complex binds chromosomal sites independent of the larger SAGA complex.
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Affiliation(s)
| | - Xuanying Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Susan M Abmayr
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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The acetyltransferase GCN5 maintains ATRA-resistance in non-APL AML. Leukemia 2019; 33:2628-2639. [PMID: 31576004 DOI: 10.1038/s41375-019-0581-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023]
Abstract
To date, only one subtype of acute myeloid leukemia (AML), acute promyelocytic leukemia (APL) can be effectively treated by differentiation therapy utilizing all-trans retinoic acid (ATRA). Non-APL AMLs are resistant to ATRA. Here we demonstrate that the acetyltransferase GCN5 contributes to ATRA resistance in non-APL AML via aberrant acetylation of histone 3 lysine 9 (H3K9ac) residues maintaining the expression of stemness and leukemia associated genes. We show that inhibition of GCN5 unlocks an ATRA-driven therapeutic response. This response is potentiated by coinhibition of the lysine demethylase LSD1, leading to differentiation in most non-APL AML. Induction of differentiation was not correlated to a specific AML subtype, cytogenetic, or mutational status. Our study shows a previously uncharacterized role of GCN5 in maintaining the immature state of leukemic blasts and identifies GCN5 as a therapeutic target in AML. The high efficacy of the combined epigenetic treatment with GCN5 and LSD1 inhibitors may enable the use of ATRA for differentiation therapy of non-APL AML. Furthermore, it supports a strategy of combined targeting of epigenetic factors to improve treatment, a concept potentially applicable for a broad range of malignancies.
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36
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Discordant Effects of Putative Lysine Acetyltransferase Inhibitors in Biochemical and Living Systems. Cells 2019; 8:cells8091022. [PMID: 31480793 PMCID: PMC6770547 DOI: 10.3390/cells8091022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
Lysine acetyltransferases (KATs) are exquisitely fine-tuned to target specific lysine residues on many proteins, including histones, with aberrant acetylation at distinct lysines implicated in different pathologies. However, researchers face a lack of molecular tools to probe the importance of site-specific acetylation events in vivo. Because of this, there can be a disconnect between the predicted in silico or in vitro effects of a drug and the actual observable in vivo response. We have previously reported on how an in vitro biochemical analysis of the site-specific effects of the compound C646 in combination with the KAT p300 can accurately predict changes in histone acetylation induced by the same compound in cells. Here, we build on this effort by further analyzing a number of reported p300 modulators, while also extending the analysis to correlate the effects of these drugs to developmental and phenotypical changes, utilizing cellular and zebrafish model systems. While this study demonstrates the utility of biochemical models as a starting point for predicting in vivo activity of multi-site targeting KATs, it also highlights the need for the development of new enzyme inhibitors that are more specific to the regulation of KAT activity in vivo.
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37
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Duchatel RJ, Jackson ER, Alvaro F, Nixon B, Hondermarck H, Dun MD. Signal Transduction in Diffuse Intrinsic Pontine Glioma. Proteomics 2019; 19:e1800479. [DOI: 10.1002/pmic.201800479] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/03/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Frank Alvaro
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- John Hunter Children's Hospital Faculty of Health and Medicine University of Newcastle New Lambton Heights NSW 2305 Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia
| | - Hubert Hondermarck
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- Cancer Neurobiology Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
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38
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Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
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Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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40
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The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun 2019; 10:625. [PMID: 30733442 PMCID: PMC6367351 DOI: 10.1038/s41467-019-08579-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/18/2019] [Indexed: 11/19/2022] Open
Abstract
The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm5) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme. Elp3 is the catalytic subunit of the eukaryotic Elongator complex that catalyzes posttranscriptional tRNA modifications. Here the authors present the crystal structures of an acetyl-CoA analog bound bacterial Elp3 and a monomeric archaeal Elp3 and show that Elp3 functions as a tRNA modification enzyme in all domains of life.
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41
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Lozoya OA, Wang T, Grenet D, Wolfgang TC, Sobhany M, Ganini da Silva D, Riadi G, Chandel N, Woychik RP, Santos JH. Mitochondrial acetyl-CoA reversibly regulates locus-specific histone acetylation and gene expression. Life Sci Alliance 2019; 2:e201800228. [PMID: 30737248 PMCID: PMC6369536 DOI: 10.26508/lsa.201800228] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022] Open
Abstract
The impact of mitochondrial dysfunction in epigenetics is emerging, but our understanding of this relationship and its effect on gene expression remains incomplete. We previously showed that acute mitochondrial DNA (mtDNA) loss leads to histone hypoacetylation. It remains to be defined if these changes are maintained when mitochondrial dysfunction is chronic and if they alter gene expression. To fill these gaps of knowledge, we here studied a progressive and a chronic model of mtDNA depletion using biochemical, pharmacological, genomics, and genetic assays. We show that histones are primarily hypoacetylated in both models. We link these effects to decreased histone acetyltransferase activity unrelated to changes in ATP citrate lyase, acetyl coenzyme A synthetase 2, or pyruvate dehydrogenase activities, which can be reversibly modulated by altering the mitochondrial pool of acetyl-coenzyme A. Also, we determined that the accompanying changes in histone acetylation regulate locus-specific gene expression and physiological outcomes, including the production of prostaglandins. These results may be relevant to the pathophysiology of mtDNA depletion syndromes and to understanding the effects of environmental agents that lead to physical or functional mtDNA loss.
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Affiliation(s)
- Oswaldo A Lozoya
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Tianyuan Wang
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Dagoberto Grenet
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Taylor C Wolfgang
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Mack Sobhany
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Douglas Ganini da Silva
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Navdeep Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Richard P Woychik
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Janine H Santos
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
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Bakhos-Douaihy D, Desmaze C, Jeitany M, Gauthier LR, Biard D, Junier MP, Chneiweiss H, Boussin FD. ALT cancer cells are specifically sensitive to lysine acetyl transferase inhibition. Oncotarget 2019; 10:773-784. [PMID: 30774779 PMCID: PMC6366824 DOI: 10.18632/oncotarget.26616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 12/20/2018] [Indexed: 12/28/2022] Open
Abstract
Some cancer cells elongate their telomeres through the ALT (alternative lengthening of telomeres) pathway, which is based on homologous recombination for the addition of telomere repeats without telomerase activity. General control non-derepressible 5 (GCN5) and P300/CBP-associated factor (PCAF), two homologous lysine acetyltransferases, exert opposite effects on the ALT pathway, inhibiting or favoring it respectively. Here we show that ALT cells are particularly sensitive to the inhibition of acetyltransferases activities using Anacardic Acid (AA). AA treatment recapitulates the effect of PCAF knockdown on several ALT features, suggesting that AA decreased the ALT mechanism through the inhibition of lysine transferase activity of PCAF, but not that of GCN5. Furthermore, AA specifically sensitizes human ALT cells to radiation as compared to telomerase-positive cells suggesting that the inhibition of lysine acetyltransferases activity may be used to increase the radiotherapy efficiency against ALT cancers.
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Affiliation(s)
- Dalal Bakhos-Douaihy
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France.,INSERM U1276, Fontenay-aux-Roses, France.,Université Paris-Diderot, U1276, Fontenay-aux-Roses, France.,Université Paris-Sud, U1276, Fontenay-aux-Roses, France
| | - Chantal Desmaze
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France.,INSERM U1276, Fontenay-aux-Roses, France.,Université Paris-Diderot, U1276, Fontenay-aux-Roses, France.,Université Paris-Sud, U1276, Fontenay-aux-Roses, France
| | - Maya Jeitany
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France.,INSERM U1276, Fontenay-aux-Roses, France.,Université Paris-Diderot, U1276, Fontenay-aux-Roses, France.,Université Paris-Sud, U1276, Fontenay-aux-Roses, France
| | - Laurent R Gauthier
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France.,INSERM U1276, Fontenay-aux-Roses, France.,Université Paris-Diderot, U1276, Fontenay-aux-Roses, France.,Université Paris-Sud, U1276, Fontenay-aux-Roses, France
| | - Denis Biard
- CEA, Institut de Biologie François Jacob, SEPIA, Team Cellular Engineering and Human Syndromes, Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France
| | - Marie-Pierre Junier
- Neuroscience Paris Seine-IBPS, CNRS UMR8246, Inserm U1130, Sorbonne Université, Paris, France
| | - Hervé Chneiweiss
- Neuroscience Paris Seine-IBPS, CNRS UMR8246, Inserm U1130, Sorbonne Université, Paris, France
| | - François D Boussin
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France.,INSERM U1276, Fontenay-aux-Roses, France.,Université Paris-Diderot, U1276, Fontenay-aux-Roses, France.,Université Paris-Sud, U1276, Fontenay-aux-Roses, France
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43
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Application of modified histone peptide arrays in chromatin research. Arch Biochem Biophys 2019; 661:31-38. [DOI: 10.1016/j.abb.2018.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 01/15/2023]
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Label-Free Quantitative Proteomics of Lysine Acetylome Identifies Substrates of Gcn5 in Magnaporthe oryzae Autophagy and Epigenetic Regulation. mSystems 2018; 3:mSystems00270-18. [PMID: 30505942 PMCID: PMC6247014 DOI: 10.1128/msystems.00270-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 11/25/2022] Open
Abstract
Gcn5 is a histone acetyltransferase that was previously shown to regulate phototropic and starvation-induced autophagy in the rice blast fungus Magnaporthe oryzae, likely via modification on autophagy protein Atg7. In this study, we identified more potential substrates of Gcn5-mediated acetylation by quantitative and comparative acetylome analyses. By epifluorescence microscopy and biochemistry experiments, we verified that Gcn5 may regulate autophagy induction at both the epigenetic and posttranslational levels and regulate autophagic degradation of a critical metabolic enzyme pyruvate kinase (Pk) likely via acetylation. Overall, our findings reveal comprehensive posttranslational modification executed by Gcn5, in response to various external stimuli, to synergistically promote cellular differentiation in a fungal pathogen. The rice blast fungus Magnaporthe oryzae poses a great threat to global food security. During its conidiation (asexual spore formation) and appressorium (infecting structure) formation, autophagy is induced, serving glycogen breakdown or programmed cell death function, both essential for M. oryzae pathogenicity. Recently, we identified an M. oryzae histone acetyltransferase (HAT) Gcn5 as a key regulator in phototropic induction of autophagy and asexual spore formation while serving a cellular function other than autophagy induction during M. oryzae infection. To further understand the regulatory mechanism of Gcn5 on M. oryzae pathogenicity, we set out to identify more Gcn5 substrates by comparative acetylome between the wild-type (WT) and GCN5 overexpression (OX) mutant and between OX mutant and GCN5 deletion (knockout [KO]) mutant. Our results showed that Gcn5 regulates autophagy induction and other important aspects of fungal pathogenicity, including energy metabolism, stress response, cell toxicity and death, likely via both epigenetic regulation (histone acetylation) and posttranslational modification (nonhistone protein acetylation). IMPORTANCE Gcn5 is a histone acetyltransferase that was previously shown to regulate phototropic and starvation-induced autophagy in the rice blast fungus Magnaporthe oryzae, likely via modification on autophagy protein Atg7. In this study, we identified more potential substrates of Gcn5-mediated acetylation by quantitative and comparative acetylome analyses. By epifluorescence microscopy and biochemistry experiments, we verified that Gcn5 may regulate autophagy induction at both the epigenetic and posttranslational levels and regulate autophagic degradation of a critical metabolic enzyme pyruvate kinase (Pk) likely via acetylation. Overall, our findings reveal comprehensive posttranslational modification executed by Gcn5, in response to various external stimuli, to synergistically promote cellular differentiation in a fungal pathogen.
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Gaviard C, Broutin I, Cosette P, Dé E, Jouenne T, Hardouin J. Lysine Succinylation and Acetylation in Pseudomonas aeruginosa. J Proteome Res 2018; 17:2449-2459. [DOI: 10.1021/acs.jproteome.8b00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Isabelle Broutin
- LCRB, UMR 8015, CNRS, University Paris Descartes, Sorbonne Paris City, 75270 Paris Cedex 06, France
| | - Pascal Cosette
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
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Simithy J, Sidoli S, Garcia BA. Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. Proteomics 2018. [PMID: 29512899 DOI: 10.1002/pmic.201700309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromatin fiber is the control panel of eukaryotic cells. Chromatin is mostly composed of DNA, which contains the genetic instruction for cell phenotype, and histone proteins, which provide the scaffold for chromatin folding and part of the epigenetic inheritance. Histone writers/erasers "flag" chromatin regions by catalyzing/removing covalent histone post-translational modifications (PTMs). Histone PTMs chemically contribute to chromatin relaxation or compaction and recruit histone readers to modulate DNA readout. The precursors of protein PTMs are mostly small metabolites. For instance, acetyl-CoA is used for acetylation, ATP for phosphorylation, and S-adenosylmethionine for methylation. Interestingly, PTMs such as acetylation can occur at neutral pH also without their respective enzyme when the precursor is sufficiently concentrated. Therefore, it is essential to differentially quantify the contribution of histone writers/erasers versus the effect of local concentration of metabolites to understand the primary regulation of histone PTM abundance. Aberrant phenotypes such as cancer cells have misregulated metabolism and thus the composition and the modulation of chromatin is not only driven by enzymatic tuning. In this review, the latest advances in mass spectrometry (MS) to analyze histone PTMs and the most adopted quantification methods for related metabolites, both necessary to understand PTM relative changes, are discussed.
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Affiliation(s)
- Johayra Simithy
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics Chromatin 2018; 11:11. [PMID: 29548294 PMCID: PMC5856334 DOI: 10.1186/s13072-018-0181-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core-including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination-can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription. However, direct experimental investigation of the effects of these PTMs is very difficult. Theoretical models can rationalize existing observations, suggest working hypotheses for future experiments, and provide a unifying framework for connecting PTMs with the observed effects. RESULTS A physics-based framework is proposed that predicts the effect of charge-altering PTMs in the histone core, quantitatively for several types of lysine charge-neutralizing PTMs including acetylation, and qualitatively for all phosphorylations, on the nucleosome stability and subsequent changes in DNA accessibility, making a connection to resulting biological phenotypes. The framework takes into account multiple partially assembled states of the nucleosome at the atomic resolution. The framework is validated against experimentally known nucleosome stability changes due to the acetylation of specific lysines, and their effect on transcription. The predicted effect of charge-altering PTMs on DNA accessibility can vary dramatically, from virtually none to a strong, region-dependent increase in accessibility of the nucleosomal DNA; in some cases, e.g., H4K44, H2AK75, and H2BK57, the effect is significantly stronger than that of the extensively studied acetylation sites such H3K56, H3K115 or H3K122. Proximity to the DNA is suggestive of the strength of the PTM effect, but there are many exceptions. For the vast majority of charge-altering PTMs, the predicted increase in the DNA accessibility should be large enough to result in a measurable modulation of transcription. However, a few possible PTMs, such as acetylation of H4K77, counterintuitively decrease the DNA accessibility, suggestive of the repressed chromatin. A structural explanation for the phenomenon is provided. For the majority of charge-altering PTMs, the effect on DNA accessibility is simply additive (noncooperative), but there are exceptions, e.g., simultaneous acetylation of H4K79 and H3K122, where the combined effect is amplified. The amplification is a direct consequence of the nucleosome-DNA complex having more than two structural states. The effect of individual PTMs is classified based on changes in the accessibility of various regions throughout the nucleosomal DNA. The PTM's resulting imprint on the DNA accessibility, "PTMprint," is used to predict effects of many yet unexplored PTMs. For example, acetylation of H4K44 yields a PTMprint similar to the PTMprint of H3K56, and thus acetylation of H4K44 is predicted to lead to a wide range of strong biological effects. CONCLUSION Charge-altering post-translational modifications in the relatively unexplored globular histone core may provide a precision mechanism for controlling accessibility to the nucleosomal DNA.
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Affiliation(s)
- Andrew T. Fenley
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
| | | | - Yared H. Kidane
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
| | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
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Sein H, Reinmets K, Peil K, Kristjuhan K, Värv S, Kristjuhan A. Rpb9-deficient cells are defective in DNA damage response and require histone H3 acetylation for survival. Sci Rep 2018; 8:2949. [PMID: 29440683 PMCID: PMC5811553 DOI: 10.1038/s41598-018-21110-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/29/2018] [Indexed: 11/09/2022] Open
Abstract
Rpb9 is a non-essential subunit of RNA polymerase II that is involved in DNA transcription and repair. In budding yeast, deletion of RPB9 causes several phenotypes such as slow growth and temperature sensitivity. We found that simultaneous mutation of multiple N-terminal lysines within histone H3 was lethal in rpb9Δ cells. Our results indicate that hypoacetylation of H3 leads to inefficient repair of DNA double-strand breaks, while activation of the DNA damage checkpoint regulators γH2A and Rad53 is suppressed in Rpb9-deficient cells. Combination of H3 hypoacetylation with the loss of Rpb9 leads to genomic instability, aberrant segregation of chromosomes in mitosis, and eventually to cell death. These results indicate that H3 acetylation becomes essential for efficient DNA repair and cell survival if a DNA damage checkpoint is defective.
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Affiliation(s)
- Henel Sein
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Kristina Reinmets
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Kadri Peil
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Kersti Kristjuhan
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Signe Värv
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.,Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Arnold Kristjuhan
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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49
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Li X, Shao Y, Sha X, Fang P, Kuo YM, Andrews AJ, Li Y, Yang WY, Maddaloni M, Pascual DW, Luo JJ, Jiang X, Wang H, Yang X. IL-35 (Interleukin-35) Suppresses Endothelial Cell Activation by Inhibiting Mitochondrial Reactive Oxygen Species-Mediated Site-Specific Acetylation of H3K14 (Histone 3 Lysine 14). Arterioscler Thromb Vasc Biol 2018; 38:599-609. [PMID: 29371247 DOI: 10.1161/atvbaha.117.310626] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE IL-35 (interleukin-35) is an anti-inflammatory cytokine, which inhibits immune responses by inducing regulatory T cells and regulatory B cells and suppressing effector T cells and macrophages. It remains unknown whether atherogenic stimuli induce IL-35 and whether IL-35 inhibits atherogenic lipid-induced endothelial cell (EC) activation and atherosclerosis. EC activation induced by hyperlipidemia stimuli, including lysophosphatidylcholine is considered as an initiation step for monocyte recruitment and atherosclerosis. In this study, we examined the expression of IL-35 during early atherosclerosis and the roles and mechanisms of IL-35 in suppressing lysophosphatidylcholine-induced EC activation. APPROACH AND RESULTS Using microarray and ELISA, we found that IL-35 and its receptor are significantly induced during early atherosclerosis in the aortas and plasma of ApoE (apolipoprotein E) knockout mice-an atherosclerotic mouse model-and in the plasma of hypercholesterolemic patients. In addition, we found that IL-35 suppresses lysophosphatidylcholine-induced monocyte adhesion to human aortic ECs. Furthermore, our RNA-sequencing analysis shows that IL-35 selectively inhibits lysophosphatidylcholine-induced EC activation-related genes, such as ICAM-1 (intercellular adhesion molecule-1). Mechanistically, using flow cytometry, mass spectrometry, electron spin resonance analyses, and chromatin immunoprecipitation-sequencing analyses, we found that IL-35 blocks lysophosphatidylcholine-induced mitochondrial reactive oxygen species, which are required for the induction of site-specific H3K14 (histone 3 lysine 14) acetylation, increased binding of proinflammatory transcription factor AP-1 in the promoter of ICAM-1, and induction of ICAM-1 transcription in human aortic EC. Finally, IL-35 cytokine therapy suppresses atherosclerotic lesion development in ApoE knockout mice. CONCLUSIONS IL-35 is induced during atherosclerosis development and inhibits mitochondrial reactive oxygen species-H3K14 acetylation-AP-1-mediated EC activation.
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Affiliation(s)
- Xinyuan Li
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Ying Shao
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Xiaojin Sha
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Pu Fang
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Yin-Ming Kuo
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Andrew J Andrews
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Yafeng Li
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - William Y Yang
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Massimo Maddaloni
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - David W Pascual
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Jin J Luo
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Xiaohua Jiang
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Hong Wang
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.)
| | - Xiaofeng Yang
- From the Centers for Metabolic Disease Research, Cardiovascular Research, and Thrombosis Research (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), Department of Pharmacology (X.L., Y.S., X.S., P.F., Y.L., W.Y.Y., X.J., H.W., X.Y.), and Department of Neurology (J.J.L.), Temple University Lewis Katz School of Medicine, Philadelphia, PA; Department of Cancer Biology, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA (Y.-M.K., A.J.A.); and Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville (M.M., D.W.P.).
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Castañeda CA, Wolfson NA, Leng KR, Kuo YM, Andrews AJ, Fierke CA. HDAC8 substrate selectivity is determined by long- and short-range interactions leading to enhanced reactivity for full-length histone substrates compared with peptides. J Biol Chem 2017; 292:21568-21577. [PMID: 29109148 PMCID: PMC5766737 DOI: 10.1074/jbc.m117.811026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/05/2017] [Indexed: 01/03/2023] Open
Abstract
Histone deacetylases (HDACs) catalyze deacetylation of acetyl-lysine residues within proteins. To date, HDAC substrate specificity and selectivity have been largely estimated using peptide substrates. However, it is unclear whether peptide substrates accurately reflect the substrate selectivity of HDAC8 toward full-length proteins. Here, we compare HDAC8 substrate selectivity in the context of peptides, full-length proteins, and protein-nucleic acid complexes. We demonstrate that HDAC8 catalyzes deacetylation of tetrameric histone (H3/H4) substrates with catalytic efficiencies that are 40-300-fold higher than those for corresponding peptide substrates. Thus, we conclude that additional contacts with protein substrates enhance catalytic efficiency. However, the catalytic efficiency decreases for larger multiprotein complexes. These differences in HDAC8 substrate selectivity for peptides and full-length proteins suggest that HDAC8 substrate preference is based on a combination of short- and long-range interactions. In summary, this work presents detailed kinetics for HDAC8-catalyzed deacetylation of singly-acetylated, full-length protein substrates, revealing that HDAC8 substrate selectivity is determined by multiple factors. These insights provide a foundation for understanding recognition of full-length proteins by HDACs.
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Affiliation(s)
| | | | - Katherine R Leng
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Yin-Ming Kuo
- the Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | | | - Carol A Fierke
- From the Program in Chemical Biology and
- the Departments of Biological Chemistry and
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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