1
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Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E. Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem 2022; 65:4182-4200. [PMID: 35191694 DOI: 10.1021/acs.jmedchem.1c01999] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bromodomains regulate chromatin remodeling and gene transcription through recognition of acetylated lysines on histones and other proteins. Bromodomain-containing protein TAF1, a subunit of general transcription factor TFIID, initiates preinitiation complex formation and cellular transcription. TAF1 serves as a cofactor for certain oncogenic transcription factors and is implicated in regulating the p53 tumor suppressor. Therefore, TAF1 is a potential target to develop small molecule therapeutics for diseases arising from dysregulated transcription, such as cancer. Here, we report the ATR kinase inhibitor AZD6738 (Ceralasertib) and analogues thereof as bona fide inhibitors of TAF1. Crystallographic and small-angle X-ray scattering studies established that newly identified and previously reported inhibitors stabilize distinct structural states of the TAF1 tandem bromodomain through "open-closed" transitions and dimerization. Combined with functional studies on p53 signaling in cancer cell lines, the data provide new insights into the feasibility and challenges of TAF1 inhibitors as chemical probes and therapeutics.
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Affiliation(s)
- Rezaul Md Karim
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Leixiang Yang
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Lihong Chen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Melissa J Bikowitz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Junhao Lu
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Dylan Grassie
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Zachary P Shultz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Justin M Lopchuk
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Jiandong Chen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
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2
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Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nat Commun 2022; 13:749. [PMID: 35136069 PMCID: PMC8826447 DOI: 10.1038/s41467-022-28427-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/25/2022] [Indexed: 12/26/2022] Open
Abstract
Tousled-like kinases (TLKs) are nuclear serine-threonine kinases essential for genome maintenance and proper cell division in animals and plants. A major function of TLKs is to phosphorylate the histone chaperone proteins ASF1a and ASF1b to facilitate DNA replication-coupled nucleosome assembly, but how TLKs selectively target these critical substrates is unknown. Here, we show that TLK2 selectivity towards ASF1 substrates is achieved in two ways. First, the TLK2 catalytic domain recognizes consensus phosphorylation site motifs in the ASF1 C-terminal tail. Second, a short sequence at the TLK2 N-terminus docks onto the ASF1a globular N-terminal domain in a manner that mimics its histone H3 client. Disrupting either catalytic or non-catalytic interactions through mutagenesis hampers ASF1 phosphorylation by TLK2 and cell growth. Our results suggest that the stringent selectivity of TLKs for ASF1 is enforced by an unusual interaction mode involving mutual recognition of a short sequence motifs by both kinase and substrate. Tousled-like kinase 2 (TLK2) phosphorylates ASF1 histone chaperones to promote nucleosome assembly in S phase. Here, the authors show that TLK2 targets ASF1 by simulating its client protein histone H3, exploiting a primordial protein interaction surface for regulatory control.
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Affiliation(s)
- Bertrand Simon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - David A Calderwood
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA. .,Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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3
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Zhang Y, Tao H, Huang SY. Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1. Int J Mol Sci 2019; 20:ijms20133325. [PMID: 31284555 PMCID: PMC6651421 DOI: 10.3390/ijms20133325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
The recruitment and transference of proteins through protein-protein interactions is a general process involved in various biological functions in cells. Despite the importance of this general process, the dynamic mechanism of how proteins are recruited and transferred from one interacting partner to another remains unclear. In this study, we investigated the dynamic mechanisms of recruitment and translocation of histone chaperone CIA/ASF1 for nucleosome disassembly by exploring the conformational space and the free energy profile of unbound DBD(CCG1) and CIA/ASF1-bound DBD(CCG1) systems through extensive molecular dynamics simulations. It was found that there exists three metastable conformational states for DBD(CCG1), an unbound closed state, a CIA/ASF1-bound half-open state, and an open state. The free energy landscape shows that the closed state and the half-open state are separated by a high free energy barrier, while the half-open state and the open state are connected with a moderate free energy increase. The high free energy barrier between the closed and half-open states explains why DBD(CCG1) can recruit CIA/ASF1 and remain in the binding state during the transportation. In addition, the asymmetric binding of CIA/ASF1 on DBD(CCG1) allows DBD(CCG1) to adopt the open state by moving one of its two domains, such that the exposed domain of DBD(CCG1) is able to recognize the acetylated histone H4 tails. As such, CIA/ASF1 has a chance to translocate from DBD(CCG1) to histone, which is also facilitated by the moderate energy increase from the bound half-open state to the open state of DBD(CCG1). These findings suggest that the recruitment and transference of histone chaperone CIA/ASF1 is highly favored by its interaction with DBD(CCG1) via conformational selection and asymmetric binding, which may represent a general mechanism of similar biological processes.
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Affiliation(s)
- Yanjun Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China.
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4
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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5
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Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
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Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
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6
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Takeuchi K, Senda M, Lo YH, Kofuji S, Ikeda Y, Sasaki AT, Senda T. Structural reverse genetics study of the PI5P4Kβ-nucleotide complexes reveals the presence of the GTP bioenergetic system in mammalian cells. FEBS J 2017; 283:3556-3562. [PMID: 27090388 DOI: 10.1111/febs.13739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/12/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022]
Abstract
Reverse genetic analysis can connect a gene and its protein counterpart to a biological function(s) by knockout or knockdown of the specific gene. However, when a protein has multiple biochemical activities, the conventional genetics strategy is incapable of distinguishing which biochemical activity of the protein is critical for the particular biological function(s). Here, we propose a structural reverse genetics strategy to overcome this problem. In a structural reverse genetics study, multiple biochemical activities of a protein are segregated by mapping those activities to a structural element(s) in the atomic resolution tertiary structure. Based on the structural mapping, a mutant lacking one biochemical activity of interest can be produced with the other activities kept intact. Expression of the mutant by knockin or ectopic expression in the knockout strain along with the following analysis can connect the single biochemical activity of interest to a biological function. Using the structural reverse genetics strategy, we have dissected the newly identified GTP-dependent activity of a lipid kinase PI5P4Kβ from its ATP-dependent activity. The GTP-insensitive mutant has demonstrated the existence of the GTP bioenergetic sensor system in mammalian cells and its critical role in tumorigenesis. As structural reverse genetics can identify in vivo significance of individual biochemical activity, it is a powerful approach to reveal hidden biological functions, which could be a novel pharmacological target for therapeutic intervention. Given the recent expansion of choices in structural biological methods and advances in genome editing technologies, the time is ripe for structural reverse genetics strategies.
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Affiliation(s)
- Koh Takeuchi
- Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan.,JST, PRESTO, Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Satoshi Kofuji
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA. .,Department of Cancer Biology, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA. .,Department of Neurosurgery, Brain Tumor Center, Neuroscience Institute, University of Cincinnati College of Medicine, OH, USA.
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan. .,Department of Materials Structure Science, School of High Energy Accelerator Science, The graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki, Japan.
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7
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Paul PK, Rabaglia ME, Wang CY, Stapleton DS, Leng N, Kendziorski C, Lewis PW, Keller MP, Attie AD. Histone chaperone ASF1B promotes human β-cell proliferation via recruitment of histone H3.3. Cell Cycle 2016; 15:3191-3202. [PMID: 27753532 DOI: 10.1080/15384101.2016.1241914] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Anti-silencing function 1 (ASF1) is a histone H3-H4 chaperone involved in DNA replication and repair, and transcriptional regulation. Here, we identify ASF1B, the mammalian paralog to ASF1, as a proliferation-inducing histone chaperone in human β-cells. Overexpression of ASF1B led to distinct transcriptional signatures consistent with increased cellular proliferation and reduced cellular death. Using multiple methods of monitoring proliferation and mitotic progression, we show that overexpression of ASF1B is sufficient to induce human β-cell proliferation. Co-expression of histone H3.3 further augmented β-cell proliferation, whereas suppression of endogenous H3.3 attenuated the stimulatory effect of ASF1B. Using the histone binding-deficient mutant of ASF1B (V94R), we show that histone binding to ASF1B is required for the induction of β-cell proliferation. In contrast to H3.3, overexpression of histone H3 variants H3.1 and H3.2 did not have an impact on ASF1B-mediated induction of proliferation. Our findings reveal a novel role of ASF1B in human β-cell replication and show that ASF1B and histone H3.3A synergistically stimulate human β-cell proliferation.
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Affiliation(s)
- Pradyut K Paul
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
| | - Mary E Rabaglia
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
| | - Chen-Yu Wang
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
| | - Donald S Stapleton
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
| | - Ning Leng
- b Department of Statistics , University of Wisconsin , Madison , WI , USA
| | - Christina Kendziorski
- c Department of Biostatistics and Medical Informatics , University of Wisconsin , Madison , WI , USA
| | - Peter W Lewis
- d Department of Biomolecular Chemistry , University of Wisconsin , Madison , WI , USA
| | - Mark P Keller
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
| | - Alan D Attie
- a Department of Biochemistry , University of Wisconsin , Madison , WI , USA
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8
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Messiaen S, Guiard J, Aigueperse C, Fliniaux I, Tourpin S, Barroca V, Allemand I, Fouchet P, Livera G, Vernet M. Loss of the histone chaperone ASF1B reduces female reproductive capacity in mice. Reproduction 2016; 151:477-89. [PMID: 26850882 DOI: 10.1530/rep-15-0327] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/04/2016] [Indexed: 12/12/2022]
Abstract
Anti-silencing function 1 (ASF1) is an evolutionarily conserved histone H3-H4 chaperone involved in the assembly/disassembly of nucleosome and histone modification. Two paralogous genes, Asf1a and Asf1b, exist in the mouse genome. Asf1a is ubiquitously expressed and its loss causes embryonic lethality. Conversely, Asf1b expression is more restricted and has been less studied. To determine the in vivo function of Asf1b, we generated a Asf1b-deficient mouse line (Asf1b(GT(ROSA-βgeo)437)) in which expression of the lacZ reporter gene is driven by the Asf1b promoter. Analysis of β-galactosidase activity at early embryonic stages indicated a correlation between Asf1b expression and cell differentiation potential. In the gonads of both male and female, Asf1b expression was specifically detected in the germ cell lineage with a peak expression correlated with meiosis. The viability of Asf1b-null mice suggests that Asf1b is dispensable for mouse development. However, these mice showed reduced reproductive capacity compared with wild-type controls. We present evidence that the timing of meiotic entry and the subsequent gonad development are affected more severely in Asf1b-null female mice than in male mice. In female mice, in addition to subfertility related to altered gamete formation, variable defects compromising the development and/or survival of their offspring were also observed. Altogether, our data indicate the importance of Asf1b expression at the time of meiotic entry, suggesting that chromatin modifications may play a central role in this process.
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Affiliation(s)
- S Messiaen
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France Laboratoire de développement des gonadesFontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - J Guiard
- CEADSV/iRTSV/Atelier de transgenèse, Grenoble F-38054 Cedex 9, France
| | - C Aigueperse
- CEADSV/iRTSV/Atelier de transgenèse, Grenoble F-38054 Cedex 9, France
| | - I Fliniaux
- CEADSV/iRTSV/Atelier de transgenèse, Grenoble F-38054 Cedex 9, France
| | - S Tourpin
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France Laboratoire de développement des gonadesFontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - V Barroca
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - I Allemand
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France Laboratoire de gamétogenèseapoptose et génotoxicité, Fontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - P Fouchet
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France Laboratoire de gamétogenèseapoptose et génotoxicité, Fontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - G Livera
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France Laboratoire de développement des gonadesFontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
| | - M Vernet
- CEADSV/iRCM/UMR S967 Stabilité génétique, cellules souches et radiations, Fontenay-aux-roses F-92265, France CEADSV/iRTSV/Atelier de transgenèse, Grenoble F-38054 Cedex 9, France Laboratoire de Recherche sur la réparation et la transcription dans les cellules souchesFontenay-aux-roses F-92265, France INSERMUMR 967, Fontenay-aux-roses F-92265, France Univ Paris DiderotSorbonne Paris cité, UMR S967, Fontenay-aux-roses F-92265, France Univ Paris-SudUMR S967, Fontenay-aux-roses F-92265, France
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9
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Abstract
Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.
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10
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Binding of the histone chaperone ASF1 to the CBP bromodomain promotes histone acetylation. Proc Natl Acad Sci U S A 2014; 111:E1072-81. [PMID: 24616510 DOI: 10.1073/pnas.1319122111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The multifunctional Creb-binding protein (CBP) protein plays a pivotal role in many critical cellular processes. Here we demonstrate that the bromodomain of CBP binds to histone H3 acetylated on lysine 56 (K56Ac) with higher affinity than to its other monoacetylated binding partners. We show that autoacetylation of CBP is critical for the bromodomain-H3 K56Ac interaction, and we propose that this interaction occurs via autoacetylation-induced conformation changes in CBP. Unexpectedly, the bromodomain promotes acetylation of H3 K56 on free histones. The CBP bromodomain also interacts with the histone chaperone anti-silencing function 1 (ASF1) via a nearby but distinct interface. This interaction is necessary for ASF1 to promote acetylation of H3 K56 by CBP, indicating that the ASF1-bromodomain interaction physically delivers the histones to the histone acetyl transferase domain of CBP. A CBP bromodomain mutation manifested in Rubinstein-Taybi syndrome has compromised binding to both H3 K56Ac and ASF1, suggesting that these interactions are important for the normal function of CBP.
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11
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Abstract
Currently, there is no method to distinguish between the roles of a subunit in one multisubunit protein complex from its roles in other complexes in vivo. This is because a mutation in a common subunit will affect all complexes containing that subunit. Here, we describe a unique method to discriminate between the functions of a common subunit in different multisubunit protein complexes. In this method, a common subunit in a multisubunit protein complex is genetically fused to a subunit that is specific to that complex and point mutated. The resulting phenotype(s) identify the specific function(s) of the subunit in that complex only. Histone H2B is a common subunit in nucleosomes containing H2A/H2B or Htz1/H2B dimers. The H2B was fused to H2A or Htz1 and point mutated. This strategy revealed that H2B has common and distinct functions in different nucleosomes. This method could be used to study common subunits in other multisubunit protein complexes.
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12
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Vischi Winck F, Arvidsson S, Riaño-Pachón DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, Rupprecht J, Mueller-Roeber B. Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One 2013; 8:e79909. [PMID: 24224019 PMCID: PMC3816576 DOI: 10.1371/journal.pone.0079909] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 10/01/2013] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
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Affiliation(s)
- Flavia Vischi Winck
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Samuel Arvidsson
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Mauricio Riaño-Pachón
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Sabrina Hempel
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
- Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Aneta Koseska
- University of Potsdam, Institute of Physics, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - David Alejandro Urbina Gomez
- Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | - Jens Rupprecht
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail:
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13
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Endo H, Nakabayashi Y, Kawashima S, Enomoto T, Seki M, Horikoshi M. Nucleosome surface containing nucleosomal DNA entry/exit site regulates H3-K36me3 via association with RNA polymerase II and Set2. Genes Cells 2013; 17:65-81. [PMID: 22212475 DOI: 10.1111/j.1365-2443.2011.01573.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A nucleosome is composed of intrinsically disordered histone tails and a structured nucleosome core surrounded by DNA. A variety of modifiable residues on the intrinsically disordered histone tails have been identified in the last decade. Mapping of the functional residues on the structured nucleosome core surface was recently initiated by global analysis of a comprehensive histone point mutant library (histone-GLibrary). It stands to reason that a functional relationship exists between modifiable residues on the intrinsically disordered histone tails and functional residues on the structured nucleosome core; however, this matter has been poorly explored. During transcription elongation, trimethylation of histone H3 at lysine 36 (H3-K36me3) is mediated by histone methyltransferase Set2, which binds to RNA polymerase II. Here, we used a histone-GLibrary that encompasses the nucleosomal DNA entry/exit site to show that six residues (H2A-G107, H2A-I112, H2A-L117, H3-T45, H3-R49 and H3-R52) form a surface on the structured nucleosome core and regulate H3-K36me3. Trimethylation at H3-K4 introduced by histone methyltransferase Set1 was not affected by the mutation of any of the six residues. Chromatin immunoprecipitation analysis showed that most of these residues are critical for the chromatin association of RNA polymerase II and Set2, suggesting that these components regulate H3-K36me3 through functional interactions with the structured nucleosome core surface.
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Affiliation(s)
- Hirohito Endo
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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14
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Elliott GO, Murphy KJ, Hayes JJ, Thiriet C. Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4. Nucleic Acids Res 2013; 41:2228-38. [PMID: 23303778 PMCID: PMC3575802 DOI: 10.1093/nar/gks1451] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We used a novel single-cell strategy to examine the fate of histones during G2-phase. Consistent with previous results, we find that in G2-phase, the majority of nuclear histones are assembled into chromatin, whereas a small fraction comprises an unassembled pool. Small increases in the amount of histones within the free pool affect the extent of exchange, suggesting that the free pool is in dynamic equilibrium with chromatin proteins. Unexpectedly, acetylated H4 is preferentially partitioned to the unassembled pool. Although an increase in global histone acetylation did not affect overall nucleosome dynamics, an H4 containing lysine to glutamine substitutions as mimics of acetylation significantly increased the rate of exchange, but did not affect the acetylation state of neighbouring nucleosomes. Interestingly, transcribed regions are particularly predisposed to exchange on incorporation of H4 acetylation mimics compared with surrounding regions. Our results support a model whereby histone acetylation on K8 and K16 specifically marks nucleosomes for eviction, with histones being rapidly deacetylated on reassembly.
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Affiliation(s)
- Giles O Elliott
- UFIP (FRE-CNRS 3478), Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France
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15
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Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Müller S, Pawson T, Gingras AC, Arrowsmith C, Knapp S. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 2012; 149:214-31. [PMID: 22464331 PMCID: PMC3326523 DOI: 10.1016/j.cell.2012.02.013] [Citation(s) in RCA: 1204] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/16/2011] [Accepted: 01/13/2012] [Indexed: 12/18/2022]
Abstract
Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.
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Affiliation(s)
- Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tracy Keates
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ildiko Felletar
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Tony Pawson
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Biochemistry and Molecular Biology, George Washington University, School of Medicine and Health Sciences, 2300 Eye Street, NW, Suite 530, Washington, DC, 20037, USA
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16
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Surprising complexity of the Asf1 histone chaperone-Rad53 kinase interaction. Proc Natl Acad Sci U S A 2012; 109:2866-71. [PMID: 22323608 DOI: 10.1073/pnas.1106023109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The histone chaperone Asf1 and the checkpoint kinase Rad53 are found in a complex in budding yeast cells in the absence of genotoxic stress. Our data suggest that this complex involves at least three interaction sites. One site involves the H3-binding surface of Asf11 with an as yet undefined surface of Rad53. A second site is formed by the Rad53-FHA1 domain binding to Asf1-T(270) phosphorylated by casein kinase II. The third site involves the C-terminal 21 amino acids of Rad53 bound to the conserved Asf1 N-terminal domain. The structure of this site showed that the Rad53 C-terminus binds Asf1 in a remarkably similar manner to peptides derived from the histone cochaperones HirA and CAF-I. We call this binding motif, (R/K)R(I/A/V) (L/P), the AIP box for Asf1-Interacting Protein box. Furthermore, C-terminal Rad53-F(820) binds the same pocket of Asf1 as does histone H4-F(100). Thus Rad53 competes with histones H3-H4 and cochaperones HirA/CAF-I for binding to Asf1. Rad53 is phosphorylated and activated upon genotoxic stress. The Asf1-Rad53 complex dissociated when cells were treated with hydroxyurea but not methyl-methane-sulfonate, suggesting a regulation of the complex as a function of the stress. We identified a rad53 mutation that destabilized the Asf1-Rad53 complex and increased the viability of rad9 and rad24 mutants in conditions of genotoxic stress, suggesting that complex stability impacts the DNA damage response.
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17
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Huang YC, Saito S, Yokoyama KK. Histone chaperone Jun dimerization protein 2 (JDP2): role in cellular senescence and aging. Kaohsiung J Med Sci 2012; 26:515-31. [PMID: 20950777 DOI: 10.1016/s1607-551x(10)70081-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/22/2010] [Indexed: 01/12/2023] Open
Abstract
Transcription factor Jun dimerization protein 2 (JDP2) binds directly to histones and DNA, and inhibits p300-mediated acetylation of core histones and reconstituted nucleosomes that contain JDP2-recognition DNA sequences. The region of JDP2 that encompasses its histone-binding domain and DNA-binding region is essential to inhibit histone acetylation by histone acetyltransferases. Moreover, assays of nucleosome assembly in vitro demonstrate that JDP2 also has histone-chaperone activity. The mutation of the region responsible for inhibition of histone acetyltransferase activity within JDP2 eliminates repression of transcription from the c-jun promoter by JDP2, as well as JDP2-mediated inhibition of retinoic-acid-induced differentiation. Thus JDP2 plays a key role as a repressor of cell differentiation by regulating the expression of genes with an activator protein 1 (AP-1) site via inhibition of histone acetylation and/or assembly and disassembly of nucleosomes. Senescent cells show a series of alterations, including flatten and enlarged morphology, increase in nonspecific acidic β-galactosidase activity, chromatin condensation, and changes in gene expression patterns. The onset and maintenance of senescence are regulated by two tumor suppressors, p53 and retinoblastoma proteins. The expression of p53 and retinoblastoma proteins is regulated by two distinct proteins, p16(Ink4a) and Arf, respectively, which are encoded by cdkn2a. JDP2 inhibits recruitment of the polycomb repressive complexes 1 and 2 (PRC-1 and PRC-2) to the promoter of the gene that encodes p16(Ink4a) and inhibits the methylation of lysine 27 of histone H3 (H3K27). The PRCs associate with the p16(Ink4a)/Arf locus in young proliferating cells and dissociate from it in senescent cells. Therefore, it seems that chromatin-remodeling factors that regulate association and dissociation of PRCs, and are controlled by JDP2, might play an important role in the senescence program. The molecular mechanisms that underlie the action of JDP2 in cellular aging and replicative senescence by mediating the dissociation of PRCs from the p16(Ink4a)/Arf locus are discussed.
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Affiliation(s)
- Yu-Chang Huang
- Center of Excellence for Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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18
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Ishikawa K, Ohsumi T, Tada S, Natsume R, Kundu LR, Nozaki N, Senda T, Enomoto T, Horikoshi M, Seki M. Roles of histone chaperone CIA/Asf1 in nascent DNA elongation during nucleosome replication. Genes Cells 2011; 16:1050-62. [DOI: 10.1111/j.1365-2443.2011.01549.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Wang Z, Patel DJ. Combinatorial readout of dual histone modifications by paired chromatin-associated modules. J Biol Chem 2011; 286:18363-8. [PMID: 21454653 DOI: 10.1074/jbc.r111.219139] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of histone modifications and their interaction with effector modules/proteins has attracted increasing attention in recent years. Accumulating evidence indicates that epigenetic regulation, which involves post-translational modification on histones and DNAs or the participation of RNAs, plays an important role in many cellular processes. Histone modifications can function individually but are also capable of functioning combinatorially as a pattern. Recently, much more attention has focused on interpreting combined histone patterns by their downstream effectors. Structure/function-based studies on paired module-mediated histone cross-talk have greatly enhanced our understanding of the plasticity of the "histone code" hypothesis.
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Affiliation(s)
- Zhanxin Wang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
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20
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Endo H, Kawashima S, Sato L, Lai MS, Enomoto T, Seki M, Horikoshi M. Chromatin dynamics mediated by histone modifiers and histone chaperones in postreplicative recombination. Genes Cells 2010; 15:945-58. [PMID: 20718939 DOI: 10.1111/j.1365-2443.2010.01435.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic chromatin is regulated by chromatin factors such as histone modification enzymes, chromatin remodeling complexes and histone chaperones in a variety of DNA-dependent reactions. Among these reactions, transcription in the chromatin context is well studied. On the other hand, how other DNA-dependent reactions, including postreplicative homologous recombination, are regulated in the chromatin context remains elusive. Here, histone H3 Lys56 acetylation, mediated by the histone acetyltransferase Rtt109 and the histone chaperone Cia1/Asf1, is shown to be required for postreplicative sister chromatid recombination. This recombination did not occur in the cia1/asf1-V94R mutant, which lacks histone binding and histone chaperone activities and which cannot promote the histone acetyltransferase activity of Rtt109. A defect in another histone chaperone, CAF-1, led to an increase in acetylated H3-K56 (H3-K56-Ac)-dependent postreplicative recombination. Some DNA lesions recognized by the putative ubiquitin ligase complex Rtt101-Mms1-Mms22, which is reported to act downstream of the H3-K56-Ac signaling pathway, seem to be increased in CAF-1 defective cells. Taken together, these data provide the framework for a postreplicative recombination mechanism controlled by histone modifiers and histone chaperones in multiple ways.
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Affiliation(s)
- Hirohito Endo
- Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi, Japan
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