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Cheung S, Ng L, Xie P, Kocur O, Elias R, Schlegel P, Rosenwaks Z, Palermo GD. Genetic profiling of azoospermic men to identify the etiology and predict reproductive potential. J Assist Reprod Genet 2024; 41:1111-1124. [PMID: 38403804 PMCID: PMC11052749 DOI: 10.1007/s10815-024-03045-5] [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: 09/19/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
PURPOSE To identify germline mutations related to azoospermia etiology and reproductive potential of surgically retrieved spermatozoa, and to investigate the feasibility of predicting seminiferous tubule function of nonobstructive azoospermic men by transcriptomic profiling of ejaculates. MATERIALS AND METHODS Sperm specimens were obtained from 30 men (38.4 ± 6 years) undergoing epididymal sperm aspiration for obstructive azoospermia (OA, n = 19) acquired by vasectomy, or testicular biopsy for nonobstructive azoospermia (NOA, n = 11). To evaluate for a correlation with azoospermia etiology, DNAseq was performed on surgically retrieved spermatozoa, and cell-free RNAseq on seminal fluid (n = 23) was performed to predict spermatogenesis in the seminiferous tubule. RESULTS Overall, surgically retrieved sperm aneuploidy rates were 1.7% and 1.8% among OA and NOA cohorts, respectively. OA men carried housekeeping-related gene mutations, while NOA men displayed mutations on genes involved in crucial spermiogenic functions (AP1S2, AP1G2, APOE). We categorized couples within each cohort according to ICSI clinical outcomes to investigate genetic causes that may affect reproductive potential. All OA-fertile men (n = 9) carried mutations in ZNF749 (sperm production), whereas OA-infertile men (n = 10) harbored mutations in PRB1, which is essential for DNA replication. NOA-fertile men (n = 8) carried mutations in MPIG6B (stem cell lineage differentiation), whereas NOA-infertile individuals (n = 3) harbored mutations in genes involved in spermato/spermio-genesis (ADAM29, SPATA31E1, MAK, POLG, IFT43, ATG9B) and early embryonic development (MBD5, CCAR1, PMEPA1, POLK, REC8, REPIN1, MAPRE3, ARL4C). Transcriptomic assessment of cell-free RNAs in seminal fluid from NOA men allowed the prediction of residual spermatogenic foci. CONCLUSIONS Sperm genome profiling provides invaluable information on azoospermia etiology and identifies gene-related mechanistic links to reproductive performance. Moreover, RNAseq assessment of seminal fluid from NOA men can help predict sperm retrieval during testicular biopsies.
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Affiliation(s)
- Stephanie Cheung
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Lily Ng
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Philip Xie
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Olena Kocur
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Rony Elias
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Peter Schlegel
- Department of Urology, James Buchanan Brady Foundation and Cornell Reproductive Medicine Institute, Weill Cornell Medicine, New York, NY, USA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA
| | - Gianpiero D Palermo
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, 1305 York Avenue, Y720, New York, NY, 10021, USA.
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2
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Homsi C, Rajan RE, Minati R, St-Hilaire E, Bonneil E, Dufresne SF, Wurtele H, Verreault A, Thibault P. A Rapid and Efficient Method for the Extraction of Histone Proteins. J Proteome Res 2023; 22:2765-2773. [PMID: 37463329 PMCID: PMC10408643 DOI: 10.1021/acs.jproteome.3c00266] [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: 05/03/2023] [Indexed: 07/20/2023]
Abstract
Current protocols used to extract and purify histones are notoriously tedious, especially when using yeast cells. Here, we describe the use of a simple filter-aided sample preparation approach enabling histone extraction from yeast and mammalian cells using acidified ethanol, which not only improves extraction but also inactivates histone-modifying enzymes. We show that our improved method prevents N-terminal clipping of H3, an artifact frequently observed in yeast cells using standard histone extraction protocols. Our method is scalable and provides efficient recovery of histones when extracts are prepared from as few as two million yeast cells. We further demonstrate the application of this approach for the analysis of histone modifications in fungal clinical isolates available in a limited quantity. Compared with standard protocols, our method enables the study of histones and their modifications in a faster, simpler, and more robust manner.
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Affiliation(s)
- Charles Homsi
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Molecular
Biology Program, Université de Montréal, Montréal, Québec H3C3J7, Canada
| | - Roshan Elizabeth Rajan
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Robin Minati
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Molecular
Biology Program, Université de Montréal, Montréal, Québec H3C3J7, Canada
| | - Edlie St-Hilaire
- Maisonneuve-Rosemont
Hospital Research Center, Montréal, Québec H1T 2M4, Canada
| | - Eric Bonneil
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Simon F. Dufresne
- Division
of Infectious Diseases and Clinical Microbiology, Department of Medicine, Maisonneuve-Rosemont Hospital, Montréal, Québec H1T 2M4, Canada
| | - Hugo Wurtele
- Department
of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Department
of Pathology and Cell Biology, Université
de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Alain Verreault
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Department
of Pathology and Cell Biology, Université
de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Pierre Thibault
- Institute
for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
- Department
of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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3
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Gong X, Srivastava V, Naicker P, Khan A, Ahmad A. Candida parapsilosis Cell Wall Proteome Characterization and Effectiveness against Hematogenously Disseminated Candidiasis in a Murine Model. Vaccines (Basel) 2023; 11:vaccines11030674. [PMID: 36992262 DOI: 10.3390/vaccines11030674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Candida parapsilosis poses huge treatment challenges in the clinical settings of South Africa, and often causes infections among immunocompromised patients and underweight neonates. Cell wall proteins have been known to play vital roles in fungal pathogenesis, as these are the first points of contact toward environments, the host, and the immune system. This study characterized the cell wall immunodominant proteins of pathogenic yeast C. parapsilosis and evaluated their protective effects in mice, which could add value in vaccine development against the rising C. parapsilosis infections. Among different clinical strains, the most pathogenic and multidrug-resistant C. parapsilosis isolate was selected based on their susceptibility towards antifungal drugs, proteinase, and phospholipase secretions. Cell wall antigens were prepared by β-mercaptoethanol/ammonium bicarbonate extraction from selected C. parapsilosis strains. Antigenic proteins were identified using LC–MS/MS, where 933 proteins were found, with 34 being immunodominant. The protective effect of the cell wall immunodominant proteins was observed by immunizing BALB/c mice with cell wall protein extracts. After the immunization and booster, the BALC/c mice were challenged with a lethal dose of C. parapsilosis. In vivo results demonstrated increased survival rates and lower fungal burden in vital organs in the immunized mice compared to the unimmunized mice, thereby confirming the immunogenic property of cell wall-associated proteins of C. parapsilosis. Therefore, these results advocated the potential of these cell wall proteins to act as biomarkers for the development of diagnostic assays and/or vaccines against infections caused by C. parapsilosis.
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Affiliation(s)
- Xiaolong Gong
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Vartika Srivastava
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Amber Khan
- The Scintillon Institute, 6404 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg 2193, South Africa
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4
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Wei F, Pan B, Diao J, Wang Y, Sheng Y, Gao S. The micronuclear histone H3 clipping in the unicellular eukaryote Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:584-594. [PMID: 37078088 PMCID: PMC10077241 DOI: 10.1007/s42995-022-00151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/07/2022] [Indexed: 05/02/2023]
Abstract
Clipping of the histone H3 N-terminal tail has been implicated in multiple fundamental biological processes for a growing list of eukaryotes. H3 clipping, serving as an irreversible process to permanently remove some post-translational modifications (PTMs), may lead to noticeable changes in chromatin dynamics or gene expression. The eukaryotic model organism Tetrahymena thermophila is among the first few eukaryotes that exhibits H3 clipping activity, wherein the first six amino acids of H3 are cleaved off during vegetative growth. Clipping only occurs in the transcriptionally silent micronucleus of the binucleated T. thermophila, thus offering a unique opportunity to reveal the role of H3 clipping in epigenetic regulation. However, the physiological functions of the truncated H3 and its protease(s) for clipping remain elusive. Here, we review the major findings of H3 clipping in T. thermophila and highlight its association with histone modifications and cell cycle regulation. We also summarize the functions and mechanisms of H3 clipping in other eukaryotes, focusing on the high diversity in terms of protease families and cleavage sites. Finally, we predict several protease candidates in T. thermophila and provide insights for future studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00151-0.
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Affiliation(s)
- Fan Wei
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jinghan Diao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yuanyuan Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yalan Sheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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5
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Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation. Nat Immunol 2021; 22:711-722. [PMID: 34017121 PMCID: PMC8159908 DOI: 10.1038/s41590-021-00928-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/05/2021] [Indexed: 12/31/2022]
Abstract
Chromatin undergoes extensive reprogramming during immune cell differentiation. Here we report the repression of controlled histone H3 amino terminus proteolytic cleavage (H3ΔN) during monocyte-to-macrophage development. This abundant histone mark in human peripheral blood monocytes is catalyzed by neutrophil serine proteases (NSPs) cathepsin G, neutrophil elastase and proteinase 3. NSPs are repressed as monocytes mature into macrophages. Integrative epigenomic analysis reveals widespread H3ΔN distribution across the genome in a monocytic cell line and primary monocytes, which becomes largely undetectable in fully differentiated macrophages. H3ΔN is enriched at permissive chromatin and actively transcribed genes. Simultaneous NSP depletion in monocytic cells results in H3ΔN loss and further increase in chromatin accessibility, which likely primes the chromatin for gene expression reprogramming. Importantly, H3ΔN is reduced in monocytes from patients with systemic juvenile idiopathic arthritis, an autoinflammatory disease with prominent macrophage involvement. Overall, we uncover an epigenetic mechanism that primes the chromatin to facilitate macrophage development.
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6
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Proteomic Analysis of Saccharomyces cerevisiae Response to Oxidative Stress Mediated by Cocoa Polyphenols Extract. Molecules 2020; 25:molecules25030452. [PMID: 31973232 PMCID: PMC7037337 DOI: 10.3390/molecules25030452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
The present study addressed the protective effects against oxidative stress (OS) of a cocoa powder extract (CPEX) on the protein expression profile of S. cerevisiae. A proteomic analysis was performed after culture preincubation with CPEX either without stress (−OS) or under stress conditions (+OS) (5 mM of H2O2). LC-MS/MS identified 33 differentially expressed proteins (–OS: 14, +OS: 19) that were included By Gene Ontology analysis in biological processes: biosynthesis of amino acids, carbohydrate metabolism and reactive oxygen species metabolic process. In a gene-knockout strains study, eight proteins were identified as putative candidates for being involved in the protective mechanism of cocoa polyphenols against OS induced by H2O2. CPEX was able to exert its antioxidant activity in yeast mainly through the regulation of: (a) amino acids metabolism proteins by modulating the production of molecules with known antioxidant roles; (b) stress-responsive protein Yhb1, but we were unable to fully understand its down-regulation; (c) protein Prb1, which can act by clipping Histone H3 N-terminal tails that are related to cellular resistance to DNA damaging agents.
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7
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Mara P, Fragiadakis GS, Gkountromichos F, Alexandraki D. The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:170. [PMID: 30384856 PMCID: PMC6211499 DOI: 10.1186/s12934-018-1018-4] [Citation(s) in RCA: 23] [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: 08/14/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
Ammonium assimilation is linked to fundamental cellular processes that include the synthesis of non-essential amino acids like glutamate and glutamine. In Saccharomyces cerevisiae glutamate can be synthesized from α-ketoglutarate and ammonium through the action of NADP-dependent glutamate dehydrogenases Gdh1 and Gdh3. Gdh1 and Gdh3 are evolutionarily adapted isoforms and cover the anabolic role of the GDH-pathway. Here, we review the role and function of the GDH pathway in glutamate metabolism and we discuss the additional contributions of the pathway in chromatin regulation, nitrogen catabolite repression, ROS-mediated apoptosis, iron deficiency and sphingolipid-dependent actin cytoskeleton modulation in S.cerevisiae. The pleiotropic effects of GDH pathway in yeast biology highlight the importance of glutamate homeostasis in vital cellular processes and reveal new features for conserved enzymes that were primarily characterized for their metabolic capacity. These newly described features constitute insights that can be utilized for challenges regarding genetic engineering of glutamate homeostasis and maintenance of redox balances, biosynthesis of important metabolites and production of organic substrates. We also conclude that the discussed pleiotropic features intersect with basic metabolism and set a new background for further glutamate-dependent applied research of biotechnological interest.
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Affiliation(s)
- P. Mara
- Department of Chemistry, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Present Address: Woods Hole Oceanographic Institution, Woods Hole, MA 02543 USA
| | - G. S. Fragiadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
| | - F. Gkountromichos
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Faculty of Biology, Biocenter, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - D. Alexandraki
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
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8
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Abstract
Chromatin is an intelligent building block that can express either external or internal needs through structural changes. To date, three methods to change chromatin structure and regulate gene expression have been well-documented: histone modification, histone exchange, and ATP-dependent chromatin remodeling. Recently, a growing body of literature has suggested that histone tail cleavage is related to various cellular processes including stem cell differentiation, osteoclast differentiation, granulocyte differentiation, mammary gland differentiation, viral infection, aging, and yeast sporulation. Although the underlying mechanisms suggesting how histone cleavage affects gene expression in view of chromatin structure are only beginning to be understood, it is clear that this process is a novel transcriptional epigenetic mechanism involving chromatin dynamics. In this review, we describe the functional properties of the known histone tail cleavage with its proteolytic enzymes, discuss how histone cleavage impacts gene expression, and present future directions for this area of study.
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Affiliation(s)
- Sun-Ju Yi
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea
| | - Kyunghwan Kim
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea
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9
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Kerstens W, Van Dijck P. A Cinderella story: how the vacuolar proteases Pep4 and Prb1 do more than cleaning up the cell's mass degradation processes. MICROBIAL CELL 2018; 5:438-443. [PMID: 30386788 PMCID: PMC6206407 DOI: 10.15698/mic2018.10.650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recently, several research groups have assigned non-vacuolar functions to the well-known Saccharomyces cerevisiae vacuolar proteases Pep4 and Prb1, which are also known as proteinases A and B. These non-vacuolar activities seem to be autophagy-independent and stress-induced and suggest an unexplored but possibly prominent role for the proteases outside the vacuole. The functions range from the involvement in programmed cell death, to protection from hazardous protein forms and regulation of gene expression. We propose that a deeper understanding of these molecular processes will provide new insights that will be important for both fungal biology as well as studies in mammalian cells, as they might open up perspectives in the search for novel drug targets. To illustrate this, we summarize the recent literature on non-vacuolar Pep4 and Prb1 functions in S. cerevisiae and review the current data on the protein homologs in pathogenic fungi.
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Affiliation(s)
- Winnie Kerstens
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium.,Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium.,Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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10
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Okamoto A, Hosoda N, Tanaka A, Newnam GP, Chernoff YO, Hoshino SI. Proteolysis suppresses spontaneous prion generation in yeast. J Biol Chem 2017; 292:20113-20124. [PMID: 29038292 DOI: 10.1074/jbc.m117.811323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/05/2017] [Indexed: 11/06/2022] Open
Abstract
Prions are infectious proteins that cause fatal neurodegenerative disorders including Creutzfeldt-Jakob and bovine spongiform encephalopathy (mad cow) diseases. The yeast [PSI+] prion is formed by the translation-termination factor Sup35, is the best-studied prion, and provides a useful model system for studying such diseases. However, despite recent progress in the understanding of prion diseases, the cellular defense mechanism against prions has not been elucidated. Here, we report that proteolytic cleavage of Sup35 suppresses spontaneous de novo generation of the [PSI+] prion. We found that during yeast growth in glucose media, a maximum of 40% of Sup35 is cleaved at its N-terminal prion domain. This cleavage requires the vacuolar proteases PrA-PrB. Cleavage occurs in a manner dependent on translation but independently of autophagy between the glutamine/asparagine-rich (Q/N-rich) stretch critical for prion formation and the oligopeptide-repeat region required for prion maintenance, resulting in the removal of the Q/N-rich stretch from the Sup35 N terminus. The complete inhibition of Sup35 cleavage, by knocking out either PrA (pep4Δ) or PrB (prb1Δ), increased the rate of de novo formation of [PSI+] prion up to ∼5-fold, whereas the activation of Sup35 cleavage, by overproducing PrB, inhibited [PSI+] formation. On the other hand, activation of the PrB pathway neither cleaved the amyloid conformers of Sup35 in [PSI+] strains nor eliminated preexisting [PSI+]. These findings point to a mechanism antagonizing prion generation in yeast. Our results underscore the usefulness of the yeast [PSI+] prion as a model system to investigate defense mechanisms against prion diseases and other amyloidoses.
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Affiliation(s)
- Atsushi Okamoto
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Anri Tanaka
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Gary P Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332-2000
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332-2000; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan.
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11
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Shen J, Xiang X, Chen L, Wang H, Wu L, Sun Y, Ma L, Gu X, Liu H, Wang L, Yu YN, Shao J, Huang C, Chin YE. JMJD5 cleaves monomethylated histone H3 N-tail under DNA damaging stress. EMBO Rep 2017; 18:2131-2143. [PMID: 28982940 DOI: 10.15252/embr.201743892] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
The histone H3 N-terminal protein domain (N-tail) is regulated by multiple posttranslational modifications, including methylation, acetylation, phosphorylation, and by proteolytic cleavage. However, the mechanism underlying H3 N-tail proteolytic cleavage is largely elusive. Here, we report that JMJD5, a Jumonji C (JmjC) domain-containing protein, is a Cathepsin L-type protease that mediates histone H3 N-tail proteolytic cleavage under stress conditions that cause a DNA damage response. JMJD5 clips the H3 N-tail at the carboxyl side of monomethyl-lysine (Kme1) residues. In vitro H3 peptide digestion reveals that JMJD5 exclusively cleaves Kme1 H3 peptides, while little or no cleavage effect of JMJD5 on dimethyl-lysine (Kme2), trimethyl-lysine (Kme3), or unmethyl-lysine (Kme0) H3 peptides is observed. Although H3 Kme1 peptides of K4, K9, K27, and K36 can all be cleaved by JMJD5 in vitro, K9 of H3 is the major cleavage site in vivo, and H3.3 is the major H3 target of JMJD5 cleavage. Cleavage is enhanced at gene promoters bound and repressed by JMJD5 suggesting a role for H3 N-tail cleavage in gene expression regulation.
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Affiliation(s)
- Jing Shen
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
| | - Xueping Xiang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
| | - Lihan Chen
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Haiyi Wang
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Li Wu
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Yanyun Sun
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Li Ma
- Department of Surgery, Brown University School of Medicine-Rhode Island Hospital, Providence, RI, USA
| | - Xiuting Gu
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Hong Liu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
| | - Lishun Wang
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Ying-Nian Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
| | - Jimin Shao
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou Zhejiang, China
| | - Chao Huang
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China .,Translation Medicine Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Y Eugene Chin
- Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China .,Department of Surgery, Brown University School of Medicine-Rhode Island Hospital, Providence, RI, USA.,Translation Medicine Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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12
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Chauhan S, Mandal P, Tomar RS. Biochemical Analysis Reveals the Multifactorial Mechanism of Histone H3 Clipping by Chicken Liver Histone H3 Protease. Biochemistry 2016; 55:5464-82. [PMID: 27586699 DOI: 10.1021/acs.biochem.6b00625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolytic clipping of histone H3 has been identified in many organisms. Despite several studies, the mechanism of clipping, the substrate specificity, and the significance of this poorly understood epigenetic mechanism are not clear. We have previously reported histone H3 specific proteolytic clipping and a protein inhibitor in chicken liver. However, the sites of clipping are still not known very well. In this study, we attempt to identify clipping sites in histone H3 and to determine the mechanism of inhibition by stefin B protein, a cysteine protease inhibitor. By employing site-directed mutagenesis and in vitro biochemical assays, we have identified three distinct clipping sites in recombinant human histone H3 and its variants (H3.1, H3.3, and H3t). However, post-translationally modified histones isolated from chicken liver and Saccharomyces cerevisiae wild-type cells showed different clipping patterns. Clipping of histone H3 N-terminal tail at three sites occurs in a sequential manner. We have further observed that clipping sites are regulated by the structure of the N-terminal tail as well as the globular domain of histone H3. We also have identified the QVVAG region of stefin B protein to be very crucial for inhibition of the protease activity. Altogether, our comprehensive biochemical studies have revealed three distinct clipping sites in histone H3 and their regulation by the structure of histone H3, histone modifications marks, and stefin B.
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Affiliation(s)
- Sakshi Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
| | - Papita Mandal
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
| | - Raghuvir S Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
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Sandoval-Basilio J, Serafín-Higuera N, Reyes-Hernandez OD, Serafín-Higuera I, Leija-Montoya G, Blanco-Morales M, Sierra-Martínez M, Ramos-Mondragon R, García S, López-Hernández LB, Yocupicio-Monroy M, Alcaraz-Estrada SL. Low Proteolytic Clipping of Histone H3 in Cervical Cancer. J Cancer 2016; 7:1856-1860. [PMID: 27698925 PMCID: PMC5039369 DOI: 10.7150/jca.15605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/10/2016] [Indexed: 11/11/2022] Open
Abstract
Chromatin in cervical cancer (CC) undergoes chemical and structural changes that alter the expression pattern of genes. Recently, a potential mechanism, which regulates gene expression at transcriptional levels is the proteolytic clipping of histone H3. However, until now this process in CC has not been reported. Using HeLa cells as a model of CC and human samples from patients with CC, we identify that the H3 cleavage was lower in CC compared with control tissue. Additionally, the histone H3 clipping was performed by serine and aspartyl proteases in HeLa cells. These results suggest that histone H3 clipping operates as part of post-translational modification system in CC.
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Affiliation(s)
- Jorge Sandoval-Basilio
- Área de investigación clínica, Unidad de Innovación Clínica y Epidemiológica de la Secretaría de Salud del estado de Guerrero, Acapulco, Gro., México.; Laboratorio de Biología Molecular, Universidad Hipócrates, Acapulco, Gro., México
| | - Nicolás Serafín-Higuera
- Laboratorio de Biología Celular, Unidad Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California Mexicali, BC, México
| | - Octavio D Reyes-Hernandez
- Laboratorio de Genética y Diagnóstico Molecular, Unidad de Investigación, Hospital Juárez de México, Ciudad de México, México.; Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Idanya Serafín-Higuera
- Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México
| | - Gabriela Leija-Montoya
- Laboratorio de Bioquímica, Unidad Ciencias de la Salud, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California Mexicali, BC, México
| | - Magali Blanco-Morales
- Área de investigación clínica, Unidad de Innovación Clínica y Epidemiológica de la Secretaría de Salud del estado de Guerrero, Acapulco, Gro., México
| | - Monica Sierra-Martínez
- Laboratorio de Genética y Diagnóstico Molecular, Unidad de Investigación, Hospital Juárez de México, Ciudad de México, México
| | | | - Silvia García
- Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Ciudad de México, México
| | - Luz Berenice López-Hernández
- Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Ciudad de México, México
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Sofia L Alcaraz-Estrada
- Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Ciudad de México, México
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14
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Azad GK, Tomar RS. Partial purification of histone H3 proteolytic activity from the budding yeastSaccharomyces cerevisiae. Yeast 2016; 33:217-26. [DOI: 10.1002/yea.3153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gajendra Kumar Azad
- Laboratory of Chromatin Biology; Department of Biological Sciences, Indian Institute of Science Education and Research; Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology; Department of Biological Sciences, Indian Institute of Science Education and Research; Bhopal India
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15
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Abstract
Growing evidence demonstrates that metabolism and chromatin dynamics are not separate processes but that they functionally intersect in many ways. For example, the lysine biosynthetic enzyme homocitrate synthase was recently shown to have unexpected functions in DNA damage repair, raising the question of whether other amino acid metabolic enzymes participate in chromatin regulation. Using an in silico screen combined with reporter assays, we discovered that a diverse range of metabolic enzymes function in heterochromatin regulation. Extended analysis of the glutamate dehydrogenase 1 (Gdh1) revealed that it regulates silent information regulator complex recruitment to telomeres and ribosomal DNA. Enhanced N-terminal histone H3 proteolysis is observed in GDH1 mutants, consistent with telomeric silencing defects. A conserved catalytic Asp residue is required for Gdh1's functions in telomeric silencing and H3 clipping. Genetic modulation of α-ketoglutarate levels demonstrates a key regulatory role for this metabolite in telomeric silencing. The metabolic activity of glutamate dehydrogenase thus has important and previously unsuspected roles in regulating chromatin-related processes.
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Kim K, Punj V, Kim JM, Lee S, Ulmer TS, Lu W, Rice JC, An W. MMP-9 facilitates selective proteolysis of the histone H3 tail at genes necessary for proficient osteoclastogenesis. Genes Dev 2016; 30:208-19. [PMID: 26744418 PMCID: PMC4719310 DOI: 10.1101/gad.268714.115] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/07/2015] [Indexed: 12/15/2022]
Abstract
Kim et al. discovered that histone H3 N-terminal tail (H3NT) proteolysis is selectively targeted near transcription start sites of a small group of genes and that most H3NT-cleaved genes displayed significant expression changes during osteoclastogenesis. The principal H3NT protease of osteoclastogenesis is matrix metalloproteinase 9 (MMP-9). Although limited proteolysis of the histone H3 N-terminal tail (H3NT) is frequently observed during mammalian differentiation, the specific genomic sites targeted for H3NT proteolysis and the functional significance of H3NT cleavage remain largely unknown. Here we report the first method to identify and examine H3NT-cleaved regions in mammals, called chromatin immunoprecipitation (ChIP) of acetylated chromatin (ChIPac). By applying ChIPac combined with deep sequencing (ChIPac-seq) to an established cell model of osteoclast differentiation, we discovered that H3NT proteolysis is selectively targeted near transcription start sites of a small group of genes and that most H3NT-cleaved genes displayed significant expression changes during osteoclastogenesis. We also discovered that the principal H3NT protease of osteoclastogenesis is matrix metalloproteinase 9 (MMP-9). In contrast to other known H3NT proteases, MMP-9 primarily cleaved H3K18-Q19 in vitro and in cells. Furthermore, our results support CBP/p300-mediated acetylation of H3K18 as a central regulator of MMP-9 H3NT protease activity both in vitro and at H3NT cleavage sites during osteoclastogenesis. Importantly, we found that abrogation of H3NT proteolysis impaired osteoclastogenic gene activation concomitant with defective osteoclast differentiation. Our collective results support the necessity of MMP-9-dependent H3NT proteolysis in regulating gene pathways required for proficient osteoclastogenesis.
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Affiliation(s)
- Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA; Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Vasu Punj
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Jin-Man Kim
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Sunyoung Lee
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Tobias S Ulmer
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Judd C Rice
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
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Zhou P, Wu E, Alam HB, Li Y. Histone cleavage as a mechanism for epigenetic regulation: current insights and perspectives. Curr Mol Med 2015; 14:1164-72. [PMID: 25323999 DOI: 10.2174/1566524014666141015155630] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 11/22/2022]
Abstract
Discovered over a century ago, histones constitute one of the oldest families of proteins and have been remarkably conserved throughout eukaryotic evolution. However, only for the past 30 years have histones demonstrated that their influence extends far beyond packaging DNA. To create the various chromatin structures that are necessary for DNA function in higher eukaryotes, histones undergo posttranslational modifications. While many such modifications are well documented, others, such as histone tail cleavage are less understood. Recent studies have discovered several proteases that cleave histones and have suggested roles for clipped histones in stem cell differentiation and aging in addition to infection and inflammation; the underlying mechanisms, however, are uncertain. One histone class in particular, histone H3, has received outstanding interest due to its numerous N-terminal modification sites and prevalence in regulating homeostatic processes. Here, with special consideration of H3, we will discuss the novel findings regarding histone proteolytic cleavage as well as their significance in the studies of immunology and epigenetics.
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Affiliation(s)
| | | | | | - Y Li
- University of Michigan Medical School, Section of General Surgery, University of Michigan Hospital, Ann Arbor, MI 48109, USA.
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18
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Núñez A, Dulude D, Jbel M, Rokeach LA. Calnexin is essential for survival under nitrogen starvation and stationary phase in Schizosaccharomyces pombe. PLoS One 2015; 10:e0121059. [PMID: 25803873 PMCID: PMC4372366 DOI: 10.1371/journal.pone.0121059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/06/2015] [Indexed: 12/04/2022] Open
Abstract
Cell fate is determined by the balance of conserved molecular mechanisms regulating death (apoptosis) and survival (autophagy). Autophagy is a process by which cells recycle their organelles and macromolecules through degradation within the vacuole in yeast and plants, and lysosome in metazoa. In the yeast Schizosaccharomyces pombe, autophagy is strongly induced under nitrogen starvation and in aging cells. Previously, we demonstrated that calnexin (Cnx1p), a highly conserved transmembrane chaperone of the endoplasmic reticulum (ER), regulates apoptosis under ER stress or inositol starvation. Moreover, we showed that in stationary phase, Cnx1p is cleaved into two moieties, L_Cnx1p and S_Cnx1p. Here, we show that the processing of Cnx1p is regulated by autophagy, induced by nitrogen starvation or cell aging. The cleavage of Cnx1p involves two vacuolar proteases: Isp6, which is essential for autophagy, and its paralogue Psp3. Blocking autophagy through the knockout of autophagy-related genes (atg) results in inhibition of both, the cleavage and the trafficking of Cnx1p from the ER to the vacuole. We demonstrate that Cnx1p is required for cell survival under nitrogen-starvation and in chronological aging cultures. The death of the mini_cnx1 mutant (overlapping S_cnx1p) cells is accompanied by accumulation of high levels of reactive-oxygen species (ROS), a slowdown in endocytosis and severe cell-wall defects. Moreover, mutant cells expressing only S_Cnx1p showed cell wall defects. Co-expressing mutant overlapping the L_Cnx1p and S_Cnx1p cleavage products reverses the death, ROS phenotype and cell wall defect to wild-type levels. As it is involved in both apoptosis and autophagy, Cnx1p could be a nexus for the crosstalk between these pro-death and pro-survival mechanisms. Ours, and observations in mammalian systems, suggest that the multiple roles of calnexin depend on its sub-cellular localization and on its cleavage. The use of S. pombe should assist in further shedding light on the multiple roles of calnexin.
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Affiliation(s)
- Andrés Núñez
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Dominic Dulude
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Mehdi Jbel
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Luis A. Rokeach
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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19
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Howe CG, Gamble MV. Enzymatic cleavage of histone H3: a new consideration when measuring histone modifications in human samples. Clin Epigenetics 2015; 7:7. [PMID: 25628766 PMCID: PMC4307743 DOI: 10.1186/s13148-014-0041-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/22/2014] [Indexed: 11/25/2022] Open
Abstract
Histone modifications are increasingly being used as biomarkers of cancer prognosis and survival. However, we identified a cleavage product of histone H3 in human peripheral blood mononuclear cells, which interferes with measures of certain H3 modifications. Therefore, the potential for enzymatic cleavage of histones should be considered when measuring histone modifications in human samples. Furthermore, the enzymatic cleavage of human H3 is itself a fascinating area of research and two important questions remain to be answered: 1) Does cleavage of human H3 occur in vivo, as it does in other organisms? and 2) Does it serve a biologically important function?
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Affiliation(s)
- Caitlin G Howe
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 650 W. 168th Street, Room 1618, New York, NY 10032 USA
| | - Mary V Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 W. 168th Street, Room 1107E, New York, NY 10032 USA
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Dhaenens M, Glibert P, Meert P, Vossaert L, Deforce D. Histone proteolysis: a proposal for categorization into 'clipping' and 'degradation'. Bioessays 2014; 37:70-9. [PMID: 25350939 PMCID: PMC4305269 DOI: 10.1002/bies.201400118] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We propose for the first time to divide histone proteolysis into "histone degradation" and the epigenetically connoted "histone clipping". Our initial observation is that these two different classes are very hard to distinguish both experimentally and biologically, because they can both be mediated by the same enzymes. Since the first report decades ago, proteolysis has been found in a broad spectrum of eukaryotic organisms. However, the authors often not clearly distinguish or determine whether degradation or clipping was studied. Given the importance of histone modifications in epigenetic regulation we further elaborate on the different ways in which histone proteolysis could play a role in epigenetics. Finally, unanticipated histone proteolysis has probably left a mark on many studies of histones in the past. In conclusion, we emphasize the significance of reviving the study of histone proteolysis both from a biological and an experimental perspective. Also watch the Video Abstract.
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Affiliation(s)
- Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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22
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Mandal P, Chauhan S, Tomar RS. H3 clipping activity of glutamate dehydrogenase is regulated by stefin B and chromatin structure. FEBS J 2014; 281:5292-308. [PMID: 25263734 DOI: 10.1111/febs.13069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 08/15/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
Glutamate dehydrogenase has been recently identified as a tissue-specific histone H3-specific clipping enzyme. We have previously shown that it cleaves free as well as chromatin-bound histone H3. However, the physiological significance of this enzyme is still not clear. The present study aimed to improve our understanding of its significance in vivo. Using biochemical and cell biological approaches, we show that glutamate dehydrogenase is primarily associated with euchromatin, and it re-localizes from the nuclear periphery to the nucleolus upon DNA damage. The cysteine protease inhibitor stefin B regulates the H3 clipping activity of the enzyme. Chromatin structure and certain histone modifications influence H3 clipping activity. Interestingly, we also observed that an in vivo truncated form of H3 lacks H3K56 acetylation, which is a code for the DNA damage response. Together, these results suggest that glutamate dehydrogenase is a euchromatin-associated enzyme, and its H3 clipping activity is regulated by chromatin structure, histone modifications and an in vivo inhibitor. In response to DNA damage, it re-localizes to the nuclei, and hence may be involved in regulation of gene expression in vivo.
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Affiliation(s)
- Papita Mandal
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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23
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Vossaert L, Meert P, Scheerlinck E, Glibert P, Van Roy N, Heindryckx B, De Sutter P, Dhaenens M, Deforce D. Identification of histone H3 clipping activity in human embryonic stem cells. Stem Cell Res 2014; 13:123-34. [PMID: 24874291 DOI: 10.1016/j.scr.2014.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 01/17/2023] Open
Abstract
Posttranslational histone modifications are essential features in epigenetic regulatory networks. One of these modifications has remained largely understudied: regulated histone proteolysis. In analogy to the histone H3 clipping during early mouse embryonic stem cell differentiation, we report for the first time that also in human embryonic stem cells this phenomenon takes place in the two different analyzed cell lines. Employing complementary techniques, different cleavage sites could be identified, namely A21, R26 and residue 31. The enzyme responsible for this cleavage is found to be a serine protease. The formation of cleaved H3 follows a considerably variable pattern, depending on the timeframe, culture conditions and culture media applied. Contrary to earlier findings on H3 clipping, our results disconnect the link between declining Oct4 expression and H3 cleavage.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Paulien Meert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen Scheerlinck
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Glibert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Department of Medical Genetics, Ghent University, Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
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