1
|
Breuer J, Ferreira DEA, Kramer M, Bollermann J, Nowrousian M. Functional analysis of chromatin-associated proteins in Sordaria macrospora reveals similar roles for RTT109 and ASF1 in development and DNA damage response. G3 (BETHESDA, MD.) 2024; 14:jkae019. [PMID: 38261383 PMCID: PMC10917505 DOI: 10.1093/g3journal/jkae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
We performed a functional analysis of two potential partners of ASF1, a highly conserved histone chaperone that plays a crucial role in the sexual development and DNA damage resistance in the ascomycete Sordaria macrospora. ASF1 is known to be involved in nucleosome assembly and disassembly, binding histones H3 and H4 during transcription, replication and DNA repair and has direct and indirect roles in histone recycling and modification as well as DNA methylation, acting as a chromatin modifier hub for a large network of chromatin-associated proteins. Here, we functionally characterized two of these proteins, RTT109 and CHK2. RTT109 is a fungal-specific histone acetyltransferase, while CHK2 is an ortholog to PRD-4, a checkpoint kinase of Neurospora crassa that performs similar cell cycle checkpoint functions as yeast RAD53. Through the generation and characterization of deletion mutants, we discovered striking similarities between RTT109 and ASF1 in terms of their contributions to sexual development, histone acetylation, and protection against DNA damage. Phenotypic observations revealed a developmental arrest at the same stage in Δrtt109 and Δasf1 strains, accompanied by a loss of H3K56 acetylation, as detected by western blot analysis. Deletion mutants of rtt109 and asf1 are sensitive to the DNA damaging agent methyl methanesulfonate, but not hydroxyurea. In contrast, chk2 mutants are fertile and resistant to methyl methanesulfonate, but not hydroxyurea. Our findings suggest a close functional association between ASF1 and RTT109 in the context of development, histone modification, and DNA damage response, while indicating a role for CHK2 in separate pathways of the DNA damage response.
Collapse
Affiliation(s)
- Jan Breuer
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | | | - Mike Kramer
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Jonas Bollermann
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| |
Collapse
|
2
|
Breuer J, Busche T, Kalinowski J, Nowrousian M. Histone binding of ASF1 is required for fruiting body development but not for genome stability in the filamentous fungus Sordaria macrospora. mBio 2024; 15:e0289623. [PMID: 38112417 PMCID: PMC10790691 DOI: 10.1128/mbio.02896-23] [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: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Histone chaperones are proteins that are involved in nucleosome assembly and disassembly and can therefore influence all DNA-dependent processes including transcription, DNA replication, and repair. ASF1 is a histone chaperone that is conserved throughout eukaryotes. In contrast to most other multicellular organisms, a deletion mutant of asf1 in the fungus Sordaria macrospora is viable; however, the mutant is sterile. In this study, we could show that the histone-binding ability of ASF1 is required for fertility in S. macrospora, whereas the function of ASF1 in maintenance of genome stability does not require histone binding. We also showed that the histone modifications H3K27me3 and H3K56ac are misregulated in the Δasf1 mutant. Furthermore, we identified a large duplication on chromosome 2 of the mutant strain that is genetically linked to the Δasf1 allele present on chromosome 6, suggesting that viability of the mutant might depend on the presence of the duplicated region.
Collapse
Affiliation(s)
- Jan Breuer
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
3
|
Shi R, Gong P, Luo Q, Chen W, Wang C. Histone Acetyltransferase Rtt109 Regulates Development, Morphogenesis, and Citrinin Biosynthesis in Monascus purpureus. J Fungi (Basel) 2023; 9:jof9050530. [PMID: 37233241 DOI: 10.3390/jof9050530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Histone acetyltransferase (HAT) has been reported to be pivotal for various physiological processes in many fungi. However, the functions that HAT Rtt109 perform in edible fungi Monascus and the underlying mechanism remains unclear. Here, we identified the rtt109 gene in Monascus, constructed the rtt109 knockout strain (Δrtt109) and its complementary strain (Δrtt109:com) by CRISPR/Cas9 methods, and functionally characterized the roles that Rtt109 play in Monascus. Deletion of rtt109 significantly reduced conidia formation and colony growth, whereas, it increased the yield of Monascus pigments (MPs) and citrinin (CTN). Further real-time quantitative PCR (RT-qPCR) analysis indicated that Rtt109 remarkably affected the transcriptional expression of key genes related to development, morphogenesis, and secondary metabolism of Monascus. Together, our results revealed the critical roles of HAT Rtt109 in Monascus, and enriched our current knowledge of the development and regulation of secondary metabolism in fungi, throwing light on restraining or eliminating citrinin in the development and industrial applications of Monascus.
Collapse
Affiliation(s)
- Ruoyu Shi
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming 650201, China
| | - Pengfei Gong
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Qiaoqiao Luo
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Wei Chen
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Chengtao Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| |
Collapse
|
4
|
Nowrousian M. The Role of Chromatin and Transcriptional Control in the Formation of Sexual Fruiting Bodies in Fungi. Microbiol Mol Biol Rev 2022; 86:e0010422. [PMID: 36409109 PMCID: PMC9769939 DOI: 10.1128/mmbr.00104-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fungal fruiting bodies are complex, three-dimensional structures that arise from a less complex vegetative mycelium. Their formation requires the coordinated action of many genes and their gene products, and fruiting body formation is accompanied by major changes in the transcriptome. In recent years, numerous transcription factor genes as well as chromatin modifier genes that play a role in fruiting body morphogenesis were identified, and through research on several model organisms, the underlying regulatory networks that integrate chromatin structure, gene expression, and cell differentiation are becoming clearer. This review gives a summary of the current state of research on the role of transcriptional control and chromatin structure in fruiting body development. In the first part, insights from transcriptomics analyses are described, with a focus on comparative transcriptomics. In the second part, examples of more detailed functional characterizations of the role of chromatin modifiers and/or transcription factors in several model organisms (Neurospora crassa, Aspergillus nidulans, Sordaria macrospora, Coprinopsis cinerea, and Schizophyllum commune) that have led to a better understanding of regulatory networks at the level of chromatin structure and transcription are discussed.
Collapse
Affiliation(s)
- Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Histone Acetylation in the Epigenetic Regulation of Bone Metabolism and Related Diseases. Stem Cells Int 2021; 2021:8043346. [PMID: 34326880 PMCID: PMC8310436 DOI: 10.1155/2021/8043346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
As the earliest studied epigenetic modification, acetylation has been explored a lot through the years. While bone tissue acts as an indispensable part of body, researches aimed at the relationship between the bone and acetylation became necessary. Some environmental factors like diet may affect the metabolism status that some metabolites especially nicotinamide adenine dinucleotide (NAD) were found able to regulate intracellular histone acetylation in bone metabolism. This review focuses on representing the interaction among acetylation, metabolism, and the bone. The results showed that acetylation connects a lot with bone metabolism, while the explorations about related metabolites like acetyl-CoA or different environmental exposures are still limited. Some acetylation-related therapy methods of bone diseases based on metabolic regulation or epigenetic enzymes were also reviewed.
Collapse
|
7
|
Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
Collapse
Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
| |
Collapse
|
8
|
Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans. mSystems 2021; 6:6/1/e01316-20. [PMID: 33500332 PMCID: PMC7842366 DOI: 10.1128/msystems.01316-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes lethal fungal infections in immunocompromised patients. Lysine crotonylation is a newly discovered PTM (posttranslational modification) epigenetic type that may play a critical role in regulating gene expression. In this study, we used an antibody-enrichment approach along with LC-MS/MS to carry out a quantitative crotonylome analysis in C. albicans We found a total of 5,242 crotonylation sites and 1,584 crotonylated proteins among 9,038 proteins in this organism. Of these crotonylated proteins, a few unique crotonylated motifs are noted such as D and E in positions +1, +2, or +3 or K and R in positions +5 or +6, while A, E, F, G, P, W, and Y are in the -1 position or A, K, and R are found in positions -5, -6, -7, or -8. Functional analysis has shown that a majority of the crotonylated proteins are related to biosynthetic events and carbon metabolism. When combined with previously collected data on acetylation and succinylation, PPI (protein-protein interaction network) analysis reveals that proteins with functions in ribosomal biogenesis, oxidative phosphorylation, nucleus activity, and proteasome formation are heavily modified by these three PTM types. To the best of our knowledge, this is the first crotonylome study carried out in C. albicans and is an important step to a better understanding of the biological and pathogenic impact of PTM in C. albicans IMPORTANCE C. albicans is a kind of pathogen of fungal infections that is found worldwide. Lysine crotonylation of proteins as a recently discovered PTM (posttranslational modification) may have a critical role in regulating cells. We first carried out large-scale analysis of crotonylated proteome and multiple PTM analysis (acetylation, succinylation, and crotonylation), then drew a diagram to show multiple PTM sites on histones in C. albicans of our study. This study about crotonylome in human pathogenic fungi is a milestone that first and deeply investigates the functional analysis of crotonylated proteins in C. albicans, which marks an important start for further research.
Collapse
|
9
|
Zhang XW, Feng N, Wang LC, Liu D, Hua YM, Zhang C, Tu PF, Zeng KW. Small-molecule arone protects from neuroinflammation in LPS-activated microglia BV-2 cells by targeting histone-remodeling chaperone ASF1a. Biochem Pharmacol 2020; 177:113932. [DOI: 10.1016/j.bcp.2020.113932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
|
10
|
Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
Collapse
Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| |
Collapse
|
11
|
Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T. Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Nat Commun 2019; 10:3435. [PMID: 31387991 PMCID: PMC6684614 DOI: 10.1038/s41467-019-11410-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/14/2019] [Indexed: 12/13/2022] Open
Abstract
Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.
Collapse
Affiliation(s)
- Nataliya Danilenko
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Schneiderberg 38, D-30167, Hannover, Germany
| | - Lukas Lercher
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Schneiderberg 38, D-30167, Hannover, Germany
| | - John Kirkpatrick
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Schneiderberg 38, D-30167, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, D-38124, Braunschweig, Germany
| | - Frank Gabel
- University Grenoble Alpes, CEA, CNRS IBS, 71 avenue des Martyrs, F-38044, Grenoble, France.,Institut Laue-Langevin, 71 avenue des Martyrs, F-38042, Grenoble, France
| | - Luca Codutti
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Schneiderberg 38, D-30167, Hannover, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Schneiderberg 38, D-30167, Hannover, Germany. .,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, D-38124, Braunschweig, Germany.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Kwon S, Lee J, Jeon J, Kim S, Park SY, Jeon J, Lee YH. Role of the Histone Acetyltransferase Rtt109 in Development and Pathogenicity of the Rice Blast Fungus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1200-1210. [PMID: 29856240 DOI: 10.1094/mpmi-01-18-0015-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated the implications of Rtt109-mediated response to DNA damage on development and pathogenesis of the rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog of Rtt109 in M. oryzae (MoRtt109) was found via sequence homology and its functionality was confirmed by phenotypic complementation of the Saccharomyces cerevisiae Rtt109 deletion strain. Targeted deletion of MoRtt109 resulted in a significant reduction in acetylation of H3K56 and rendered the fungus defective in hyphal growth and asexual reproduction. Furthermore, the deletion mutant displayed hypersensitivity to genotoxic agents, confirming the conserved importance of Rtt109 in genome integrity maintenance and genotoxic stress tolerance. Elevated expression of DNA repair genes and the results of the comet assay were consistent with constitutive endogenous DNA damage. Although the conidia produced from the mutant were not impaired in germination and appressorium morphogenesis, the mutant was significantly less pathogenic on rice leaves. Transcriptomic analysis provided insight into the factors underlying phenotypic defects that are associated with deficiency of H3K56 acetylation. Overall, our results indicate that MoRtt109 is a conserved histone acetyltransferase that affects proliferation and asexual fecundity of M. oryzae through maintenance of genome integrity and response to DNA damage.
Collapse
Affiliation(s)
- Seomun Kwon
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaejoon Lee
- 2 Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; and
| | - Jongbum Jeon
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Seongbeom Kim
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sook-Young Park
- 3 Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea
| | - Junhyun Jeon
- 2 Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; and
| | - Yong-Hwan Lee
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
14
|
Zhang L, Serra-Cardona A, Zhou H, Wang M, Yang N, Zhang Z, Xu RM. Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Cell 2018; 174:818-830.e11. [PMID: 30057113 DOI: 10.1016/j.cell.2018.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022]
Abstract
Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 αN, where K56 is normally located, and stabilization of the very C-terminal β strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.
Collapse
Affiliation(s)
- Lin Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mingzhu Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 300353 Tianjin, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
| |
Collapse
|