1
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Cleere MM, Gardner KH. Optogenetic control of phosphate-responsive genes using single component fusion proteins in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.605841. [PMID: 39131330 PMCID: PMC11312615 DOI: 10.1101/2024.08.02.605841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Blue light illumination can be detected by Light-Oxygen-Voltage (LOV) photosensing proteins and translated into a range of biochemical responses, facilitating the generation of novel optogenetic tools to control cellular function. Here we develop new variants of our previously described VP-EL222 light-dependent transcription factor and apply them to study the phosphate-responsive signaling (PHO) pathway in the budding yeast Saccharomyces cerevisiae, exemplifying the utilities of these new tools. Focusing first on the VP-EL222 protein itself, we quantified the tunability of gene expression as a function of light intensity and duration, and demonstrated that this system can tolerate the addition of substantially larger effector domains without impacting function. We further demonstrated the utility of several EL222-driven transcriptional controllers in both plasmid and genomic settings, using the PHO5 and PHO84 promoters in their native chromosomal contexts as examples. These studies highlight the utility of light-controlled gene activation using EL222 tethered to either artificial transcription domains or yeast activator proteins (Pho4). Similarly, we demonstrate the ability to optogenetically repress gene expression with EL222 fused to the yeast Ume6 protein. We finally investigated the effects of moving EL222 recruitment sites to different locations within the PHO5 and PHO84 promoters, as well as determining how this artificial light-controlled regulation could be integrated with the native controls dependent on inorganic phosphate (Pi) availability. Taken together, our work expands the applicability of these versatile optogenetic tools in the types of functionality they can deliver and biological questions that can be probed.
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Affiliation(s)
- Matthew M Cleere
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biochemistry, Chemistry, and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY 10016
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
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2
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Chen L, Ruan J, Li Y, Liu M, Liu Y, Guan Y, Mao Z, Wang W, Yang HQ, Guo T. ADA2b acts to positively regulate blue light-mediated photomorphogenesis in Arabidopsis. Biochem Biophys Res Commun 2024; 717:150050. [PMID: 38718571 DOI: 10.1016/j.bbrc.2024.150050] [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: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024]
Abstract
Cryptochromes (CRYs) act as blue light photoreceptors to regulate various plant physiological processes including photomorphogenesis and repair of DNA double strand breaks (DSBs). ADA2b is a conserved transcription co-activator that is involved in multiple plant developmental processes. It is known that ADA2b interacts with CRYs to mediate blue light-promoted DSBs repair. Whether ADA2b may participate in CRYs-mediated photomorphogenesis is unknown. Here we show that ADA2b acts to inhibit hypocotyl elongation and hypocotyl cell elongation in blue light. We found that the SWIRM domain-containing C-terminus mediates the blue light-dependent interaction of ADA2b with CRYs in blue light. Moreover, ADA2b and CRYs act to co-regulate the expression of hypocotyl elongation-related genes in blue light. Based on previous studies and these results, we propose that ADA2b plays dual functions in blue light-mediated DNA damage repair and photomorphogenesis.
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Affiliation(s)
- Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jiaqi Ruan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yupeng Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Minqing Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yan Guan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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3
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Chen YJC, Bhaskara GB, Lu Y, Lin K, Dent SYR. The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586811. [PMID: 38585845 PMCID: PMC10996596 DOI: 10.1101/2024.03.26.586811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse, and clonal heterogeneity in MM, but our knowledge on epigenetic mechanisms underlying MM development is far from complete. The SAGA complex serves as a coactivator in transcription and catalyzes acetylation and deubiquitylation. Analyses of datasets in the Cancer Dependency Map Project revealed many SAGA components are selective dependencies in MM. To define SAGA-specific functions, we focused on ADA2B, the only subunit in the lysine acetyltransferase (KAT) module that specifically functions in SAGA. Integration of RNA-seq, ATAC-seq, and CUT&RUN results identified pathways directly regulated by ADA2B include MTORC1 signaling, MYC, E2F, and MM-specific MAF oncogenic programs. We discovered that ADA2B is recruited to MAF and MYC gene targets, and that MAF shares a majority of its targets with MYC in MM cells. Furthermore, we found the SANT domain of ADA2B is required for interaction with both GCN5 and PCAF acetyltransferases, incorporation into SAGA, and ADA2B protein stability. Our findings uncover previously unknown SAGA KAT module-dependent mechanisms controlling MM cell growth, revealing a vulnerability that might be exploited for future development of MM therapy.
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Affiliation(s)
- Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Govinal Badiger Bhaskara
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y. R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Yu Y, Zhao F, Yue Y, Zhao Y, Zhou DX. Lysine acetylation of histone acetyltransferase adaptor protein ADA2 is a mechanism of metabolic control of chromatin modification in plants. NATURE PLANTS 2024; 10:439-452. [PMID: 38326652 DOI: 10.1038/s41477-024-01623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Histone acetylation is a predominant active chromatin mark deposited by histone acetyltransferases (HATs) that transfer the acetyl group from acetyl coenzyme A (acetyl-CoA) to lysine ε-amino groups in histones. GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is one of the best-characterized HATs and functions in association with several adaptor proteins such as ADA2 within multiprotein HAT complexes. ADA2-GCN5 interaction increases GCN5 binding to acetyl-CoA and stimulates its HAT activity. It remains unclear whether the HAT activity of GCN5 (which acetylates not only histones but also cellular proteins) is regulated by acetyl-CoA levels, which vary greatly in cells under different metabolic and nutrition conditions. Here we show that the ADA2 protein itself is acetylated by GCN5 in rice cells. Lysine acetylation exposes ADA2 to a specific E3 ubiquitin ligase and reduces its protein stability. In rice plants, ADA2 protein accumulation reversely parallels its lysine acetylation and acetyl-CoA levels, both of which are dynamically regulated under varying growth conditions. Stress-induced ADA2 accumulation could stimulate GCN5 HAT activity to compensate for the reduced acetyl-CoA levels for histone acetylation. These results indicate that ADA2 lysine acetylation that senses cellular acetyl-CoA variations is a mechanism to regulate HAT activity and histone acetylation homeostasis in plants under changing environments.
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Affiliation(s)
- Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, France.
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5
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Patel AB, He Y, Radhakrishnan I. Histone acetylation and deacetylation - Mechanistic insights from structural biology. Gene 2024; 890:147798. [PMID: 37726026 PMCID: PMC11253779 DOI: 10.1016/j.gene.2023.147798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Histones are subject to a diverse array of post-translational modifications. Among them, lysine acetylation is not only the most pervasive and dynamic modification but also highly consequential for regulating gene transcription. Although enzymes responsible for the addition and removal of acetyl groups were discovered almost 30 years ago, high-resolution structures of the enzymes in the context of their native complexes are only now beginning to become available, thanks to revolutionary technologies in protein structure determination and prediction. Here, we will review our current understanding of the molecular mechanisms of acetylation and deacetylation engendered by chromatin-modifying complexes, compare and contrast shared features, and discuss some of the pressing questions for future studies.
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Affiliation(s)
- Avinash B Patel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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6
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Yu CK, Stephenson CJ, Villamor TC, Dyba TG, Schulz BL, Fraser JA. SAGA Complex Subunit Hfi1 Is Important in the Stress Response and Pathogenesis of Cryptococcus neoformans. J Fungi (Basel) 2023; 9:1198. [PMID: 38132798 PMCID: PMC10744473 DOI: 10.3390/jof9121198] [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: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
The Spt-Ada-Gcn Acetyltransferase (SAGA) complex is a highly conserved co-activator found across eukaryotes. It is composed of a number of modules which can vary between species, but all contain the core module. Hfi1 (known as TADA1 in Homo sapiens) is one of the proteins that forms the core module, and has been shown to play an important role in maintaining complex structural integrity in both brewer's yeast and humans. In this study we successfully identified the gene encoding this protein in the important fungal pathogen, Cryptococcus neoformans, and named it HFI1. The hfi1Δ mutant is highly pleiotropic in vitro, influencing phenotypes, ranging from temperature sensitivity and melanin production to caffeine resistance and titan cell morphogenesis. In the absence of Hfi1, the transcription of several other SAGA genes is impacted, as is the acetylation and deubiquination of several histone residues. Importantly, loss of the gene significantly impacts virulence in a murine inhalation model of cryptococcosis. In summary, we have established that Hfi1 modulates multiple pathways that directly affect virulence and survival in C. neoformans, and provided deeper insight into the importance of the non-enzymatic components of the SAGA complex.
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Affiliation(s)
| | | | | | | | | | - James A. Fraser
- School of Chemistry & Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia; (C.K.Y.); (C.J.S.); (T.C.V.); (T.G.D.); (B.L.S.)
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7
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Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
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Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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8
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Fraser OA, Namitz KEW, Showalter SA. Advances in direct detection of lysine methylation and acetylation by nuclear magnetic resonance using 13C-enriched cofactors. Methods 2023; 218:72-83. [PMID: 37524235 PMCID: PMC10528339 DOI: 10.1016/j.ymeth.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
Post-translational modifications (PTMs) are reversible chemical modifications that can modulate protein structure and function. Methylation and acetylation are two such PTMs with integral and well-characterized biological roles, including modulation of chromatin structure; and unknown or poorly understood roles, exemplified by the influence of these PTMs on transcription factor structure and function. The need for biological insights into the function of these PTMs motivates the development of a nondestructive and label-free method that enables pursuit of molecular mechanisms. Here, we present a protocol for implementing nuclear magnetic resonance (NMR) methods that allow for unambiguous detection of methylation and acetylation events and demonstrate their utility by observing these marks on histone H3 tail as a model system. We leverage strategic isotopic enrichment of cofactor and peptide for visualization by [1H, 13C]-HSQC and 13C direct-detect NMR measurements. Finally, we present 13C-labeling schemes that facilitate one-dimensional NMR experiments, which combine reduced measurement time relative to two-dimensional spectroscopy with robust filtering of background signals that would otherwise create spectral crowding or limit detection of low-abundance analytes.
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Affiliation(s)
- Olivia A Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
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9
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Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA. J Mol Biol 2023; 435:168192. [PMID: 37394032 PMCID: PMC10529903 DOI: 10.1016/j.jmb.2023.168192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg2+, and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg2+. Two sABs from these selections, C12 and C18, showed different degrees of Mg2+-sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg2+-depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg2+-depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg2+] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.
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Affiliation(s)
- Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Piotr Tokarz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Bharat G Reddy
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Blazej M Skrobek
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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10
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Lin CC, Lee WJ, Zeng CY, Chou MY, Lin TJ, Lin CS, Ho MC, Shih MC. SUB1A-1 anchors a regulatory cascade for epigenetic and transcriptional controls of submergence tolerance in rice. PNAS NEXUS 2023; 2:pgad229. [PMID: 37492276 PMCID: PMC10364326 DOI: 10.1093/pnasnexus/pgad229] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/28/2023] [Indexed: 07/27/2023]
Abstract
Most rice (Oryza sativa) cultivars cannot survive under prolonged submergence. However, some O. sativa ssp. indica cultivars, such as FR13A, are highly tolerant owing to the SUBMERGENCE 1A-1 (SUB1A-1) allele, which encodes a Group VII ethylene-responsive factor (ERFVII) protein; other submergence-intolerant cultivars contain a SUB1A-2 allele. The two alleles differ only by a single substitution at the 186th amino acid position from serine in SUB1A-1 to proline in SUB1A-2 resulting in only SUB1A-1 being able to be phosphorylated. Two other ERFVIIs, ERF66 and ERF67, function downstream of SUB1A-1 to form a regulatory cascade in response to submergence stress. Here, we show that SUB1A-1, but not SUB1A-2, interacts with ADA2b of the ADA2b-GCN5 acetyltransferase complex, in which GCN5 functions as a histone acetyltransferase. Phosphorylation of SUB1A-1 at serine 186 enhances the interaction of SUB1A-1 with ADA2b. ADA2b and GCN5 expression was induced under submergence, suggesting that these two genes might play roles in response to submergence stress. In transient assays, binding of SUB1A-1 to the ERF67 promoter and ERF67 transcription were highly induced when SUB1A-1 was expressed together with the ADA2b-GCN5 acetyltransferase complex. Taken together, these results suggest that phospho-SUB1A-1 recruits the ADA2-GCN5 acetyltransferase complex to modify the chromatin structure of the ERF66/ERF67 promoter regions and activate gene expression, which in turn enhances rice submergence tolerance.
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Affiliation(s)
| | | | - Cyong-Yu Zeng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Mei-Yi Chou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ting-Jhen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Meng-Chiao Ho
- To whom correspondence should be addressed: (M.C.S.); (M.C.H.)
| | - Ming-Che Shih
- To whom correspondence should be addressed: (M.C.S.); (M.C.H.)
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11
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Haile ST, Rahman S, Fields JK, Orsburn BC, Bumpus NN, Wolberger C. The SAGA HAT module is tethered by its SWIRM domain and modulates activity of the SAGA DUB module. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194929. [PMID: 36965704 PMCID: PMC10226619 DOI: 10.1016/j.bbagrm.2023.194929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/12/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is a transcriptional co-activator that both acetylates and deubiquitinates histones. The histone acetyltransferase (HAT) subunit, Gcn5, is part of a subcomplex of SAGA called the HAT module. A minimal HAT module complex containing Gcn5 bound to Ada2 and Ada3 is required for full Gcn5 activity on nucleosomes. Deletion studies have suggested that the Ada2 SWIRM domain plays a role in tethering the HAT module to the remainder of SAGA. While recent cryo-EM studies have resolved the structure of the core of the SAGA complex, the HAT module subunits and molecular details of its interactions with the SAGA core could not be resolved. Here we show that the SWIRM domain is required for incorporation of the HAT module into the yeast SAGA complex, but not the ADA complex, a distinct six-protein acetyltransferase complex that includes the SAGA HAT module proteins. In the isolated Gcn5/Ada2/Ada3 HAT module, deletion of the SWIRM domain modestly increased activity but had negligible effect on nucleosome binding. Loss of the HAT module due to deletion of the SWIRM domain decreases the H2B deubiquitinating activity of SAGA, indicating a role for the HAT module in regulating SAGA DUB module activity. A model of the HAT module created with Alphafold Multimer provides insights into the structural basis for our biochemical data, as well as prior deletion studies.
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Affiliation(s)
- Sara T Haile
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - James K Fields
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, United States of America.
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12
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Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. Conformation-specific synthetic antibodies discriminate multiple functional states of the ion channel CorA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539746. [PMID: 37205530 PMCID: PMC10187328 DOI: 10.1101/2023.05.07.539746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg 2+ , and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg 2+ . Two sABs from these selections, C12 and C18, showed different degrees of Mg 2+ -sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg 2+ -depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg 2+ -depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg 2+ ] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.
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Sato G, Kuroda K. Overcoming the Limitations of CRISPR-Cas9 Systems in Saccharomyces cerevisiae: Off-Target Effects, Epigenome, and Mitochondrial Editing. Microorganisms 2023; 11:microorganisms11041040. [PMID: 37110464 PMCID: PMC10145089 DOI: 10.3390/microorganisms11041040] [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: 02/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Modification of the genome of the yeast Saccharomyces cerevisiae has great potential for application in biological research and biotechnological advancements, and the CRISPR-Cas9 system has been increasingly employed for these purposes. The CRISPR-Cas9 system enables the precise and simultaneous modification of any genomic region of the yeast to a desired sequence by altering only a 20-nucleotide sequence within the guide RNA expression constructs. However, the conventional CRISPR-Cas9 system has several limitations. In this review, we describe the methods that were developed to overcome these limitations using yeast cells. We focus on three types of developments: reducing the frequency of unintended editing to both non-target and target sequences in the genome, inducing desired changes in the epigenetic state of the target region, and challenging the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles such as mitochondria. These developments using yeast cells to overcome the limitations of the CRISPR-Cas9 system are a key factor driving the advancement of the field of genome editing.
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Affiliation(s)
- Genki Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
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14
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Lin CJ, Yang SY, Hsu LH, Yu SJ, Chen YL. The Gcn5-Ada2-Ada3 histone acetyltransferase module has divergent roles in pathogenesis of Candida glabrata. Med Mycol 2023; 61:myad004. [PMID: 36715154 DOI: 10.1093/mmy/myad004] [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: 10/05/2022] [Revised: 01/04/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Candida glabrata is an opportunistic fungal pathogen and the second most prevalent species isolated from candidiasis patients. C. glabrata has intrinsic tolerance to antifungal drugs and oxidative stresses and the ability to adhere to mucocutaneous surfaces. However, knowledge about the regulation of its virulence traits is limited. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex modulates gene transcription by histone acetylation through the histone acetyltransferase (HAT) module comprised of Gcn5-Ada2-Ada3. Previously, we showed that the ada2 mutant was hypervirulent but displayed decreased tolerance to antifungal drugs and cell wall perturbing agents. In this study, we further characterized the functions of Ada3 and Gcn5 in C. glabrata. We found that single, double, or triple deletions of the HAT module, as expected, resulted in a decreased level of acetylation on histone H3 lysine 9 (H3K9) and defective growth. These mutants were more susceptible to antifungal drugs, oxidative stresses, and cell wall perturbing agents compared with the wild-type. In addition, HAT module mutants exhibited enhanced agar invasion and upregulation of adhesin and proteases encoding genes, whereas the biofilm formation of those mutants was impaired. Interestingly, HAT module mutants exhibited enhanced induction of catalases (CTA1) expression upon treatment with H2O2 compared with the wild-type. Lastly, although ada3 and gcn5 exhibited marginal hypervirulence, the HAT double and triple mutants were hypervirulent in a murine model of candidiasis. In conclusion, the HAT module of the SAGA complex plays unique roles in H3K9 acetylation, drug tolerance, oxidative stress response, adherence, and virulence in C. glabrata.
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Affiliation(s)
- Chi-Jan Lin
- Institute of Molecular Biology, National Chung Hsing University, 40227 Taichung, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Sheng-Yung Yang
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Li-Hang Hsu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Shang-Jie Yu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
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15
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Zhao H, Ge Z, Zhou M, Bai R, Zeng H, Wei Y, He C, Shi H. Histone acetyltransferase HAM1 interacts with molecular chaperone DNAJA2 and confers immune responses through salicylic acid biosynthetic genes in cassava. PLANT, CELL & ENVIRONMENT 2023; 46:635-649. [PMID: 36451539 DOI: 10.1111/pce.14501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Cassava bacterial blight (CBB) is one of the most serious diseases in cassava production, so it is essential to explore the underlying mechanism of immune responses. Histone acetylation is an important epigenetic modification, however, its relationship with cassava disease resistance remains unclear. Here, we identified 10 histone acetyltransferases in cassava and found that the transcript of MeHAM1 showed the highest induction to CBB. Functional analysis showed that MeHAM1 positively regulated disease resistance to CBB through modulation of salicylic acid (SA) accumulation. Further investigation revealed that MeHAM1 directly activated SA biosynthetic genes' expression via promoting lysine 9 of histone 3 (H3K9) acetylation and lysine 5 of histone 4 (H4K5) acetylation of these genes. In addition, molecular chaperone MeDNAJA2 physically interacted with MeHAM1, and MeDNAJA2 also regulated plant immune responses and SA biosynthetic genes. In conclusion, this study illustrates that MeHAM1 and MeDNAJA2 confer immune responses through transcriptional programming of SA biosynthetic genes via histone acetylation. The MeHAM1 & MeDNAJA2-SA biosynthesis module not only constructs the direct relationship between histone acetylation and cassava disease resistance, but also provides gene network with potential value for genetic improvement of cassava disease resistance.
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Affiliation(s)
- Huiping Zhao
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
| | - Zhongyuan Ge
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
| | - Mengmeng Zhou
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
| | - Ruoyu Bai
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Chaozu He
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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16
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Fraser OA, Dewing SM, Usher ET, George C, Showalter SA. A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins. Front Mol Biosci 2023; 9:1074743. [PMID: 36685286 PMCID: PMC9853081 DOI: 10.3389/fmolb.2022.1074743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.
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Affiliation(s)
- Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Sophia M. Dewing
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Emery T. Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Christy George
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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17
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Abstract
General control nonderepressible 5 protein (Gcn5) and its homologs, including p300/CBP-associated factor (PCAF), are lysine acetyltransferases that modify both histone and non-histone proteins using acetyl coenzyme A as a donor substrate. While decades of studies have uncovered a vast network of cellular processes impacted by these acetyltransferases, including gene transcription and metabolism, far less is known about how these enzymes are themselves regulated. In this review, we summarize the type and functions of posttranslational modifications proposed to control Gcn5 in both yeast and human cells. We further outline common themes, open questions, and strategies to guide future work.
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18
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Jiang H, Meng F, Lu D, Chen Y, Luo G, Chen Y, Chen J, Chen C, Zhang X, Su D. High-throughput FastCloning technology: A low-cost method for parallel cloning. PLoS One 2022; 17:e0273873. [PMID: 36084059 PMCID: PMC9462701 DOI: 10.1371/journal.pone.0273873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
FastCloning, a reliable cloning technique for plasmid construction, is a widely used protocol in biomedical research laboratories. Only two-step molecular manipulations are required to add a gene (cDNA) of interest into the desired vector. However, parallel cloning of the gene into multiple vectors is still a labor-intensive operation, which requires a range of primers for different vectors in high-throughput cloning projects. The situation could even be worse if multiple fragments of DNA are required to be added into one plasmid. Here, we describe a high-throughput FastCloning (HTFC) method, a protocol for parallel cloning by adding an adaptor sequence into all vectors. The target gene and vectors were PCR amplified separately to obtain the insert product and linear vectors with 18-base overlapping at each end of the DNAs required for FastCloning. Furthermore, a method for generating polycistronic bacterial constructs based on the same strategy as that used for HTFC was developed. Thus, the HTFC technique is a simple, effective, reliable, and low-cost tool for parallel cloning.
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Affiliation(s)
- Hua Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Fan Meng
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Deren Lu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yanjuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Guilin Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yuejun Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Jun Chen
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Cheng Chen
- Department of Gynecology and Obstetrics, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P.R. China
| | - Xi Zhang
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, P.R. China
- * E-mail:
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19
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Yamamoto R, Sato G, Amai T, Ueda M, Kuroda K. Development of Artificial System to Induce Chromatin Loosening in Saccharomyces cerevisiae. Biomolecules 2022; 12:1138. [PMID: 36009033 PMCID: PMC9406041 DOI: 10.3390/biom12081138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 12/05/2022] Open
Abstract
In eukaryotic cells, loosening of chromatin causes changes in transcription and DNA replication. The artificial conversion of tightly packed chromatin (heterochromatin) to loosely packed chromatin (euchromatin) enables gene expression and regulates cell differentiation. Although some chemicals convert chromatin structures through histone modifications, they lack sequence specificity. This study attempted to establish a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae. We focused on histone acetylation, which is one of the mechanisms of euchromatin induction. The sequence-recognizing ability of the dead Cas9 (dCas9) and guide RNA (gRNA) complex was used to promote histone acetylation at a targeted genomic locus. We constructed a plasmid to produce a fusion protein consisting of dCas9 and histone acetyltransferase Gcn5 and a plasmid to express gRNA recognizing the upstream region of heterochromatic URA3. Confocal microscopy revealed that the fusion proteins were localized in the nucleus. The yeast strain producing the fusion protein and gRNA grew well in the uracil-deficient medium, while the strain harboring empty plasmids or the strain containing the mutations that cause loss of nucleosomal histone acetylation activity of Gcn5 did not. This suggests that the heterochromatin was loosened as much as euchromatin through nucleosomal histone acetylation. The amount of euchromatic DNA at the target locus increased, indicating that chromatin loosening was induced by our system. Nucleosomal histone acetylation in heterochromatic loci by our developed system is a promising method for inducing euchromatic state in a target locus.
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Affiliation(s)
| | | | | | | | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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20
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Vasyliuk D, Felt J, Zhong ED, Berger B, Davis JH, Yip CK. Conformational landscape of the yeast SAGA complex as revealed by cryo-EM. Sci Rep 2022; 12:12306. [PMID: 35853968 PMCID: PMC9296673 DOI: 10.1038/s41598-022-16391-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
Spt-Ada-Gcn5-Acetyltransferase (SAGA) is a conserved multi-subunit complex that activates RNA polymerase II-mediated transcription by acetylating and deubiquitinating nucleosomal histones and by recruiting TATA box binding protein (TBP) to DNA. The prototypical yeast Saccharomyces cerevisiae SAGA contains 19 subunits that are organized into Tra1, core, histone acetyltransferase, and deubiquitination modules. Recent cryo-electron microscopy studies have generated high-resolution structural information on the Tra1 and core modules of yeast SAGA. However, the two catalytical modules were poorly resolved due to conformational flexibility of the full assembly. Furthermore, the high sample requirement created a formidable barrier to further structural investigations of SAGA. Here, we report a workflow for isolating/stabilizing yeast SAGA and preparing cryo-EM specimens at low protein concentration using a graphene oxide support layer. With this procedure, we were able to determine a cryo-EM reconstruction of yeast SAGA at 3.1 Å resolution and examine its conformational landscape with the neural network-based algorithm cryoDRGN. Our analysis revealed that SAGA adopts a range of conformations with its HAT module and central core in different orientations relative to Tra1.
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Affiliation(s)
- Diana Vasyliuk
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Joeseph Felt
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Ellen D Zhong
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph H Davis
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, V6T 1Z3, Canada.
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21
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Global profiling of regulatory elements in the histone benzoylation pathway. Nat Commun 2022; 13:1369. [PMID: 35296687 PMCID: PMC8927147 DOI: 10.1038/s41467-022-29057-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 02/24/2022] [Indexed: 11/08/2022] Open
Abstract
Lysine benzoylation (Kbz) is a recently discovered post-translational modification associated with active transcription. However, the proteins for maintaining and interpreting Kbz and the physiological roles of Kbz remain elusive. Here, we systematically characterize writer, eraser, and reader proteins of histone Kbz in S. cerevisiae using proteomic, biochemical, and structural approaches. Our study identifies 27 Kbz sites on yeast histones that can be regulated by cellular metabolic states. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and NAD+-dependent histone deacetylase Hst2 could function as the writer and eraser of histone Kbz, respectively. Crystal structures of Hst2 complexes reveal the molecular basis for Kbz recognition and catalysis by Hst2. In addition, we demonstrate that a subset of YEATS domains and bromodomains serve as Kbz readers, and structural analyses reveal how YEATS and bromodomains recognize Kbz marks. Moreover, the proteome-wide screening of Kbz-modified proteins identifies 207 Kbz sites on 149 non-histone proteins enriched in ribosome biogenesis, glycolysis/gluconeogenesis, and rRNA processing pathways. Our studies identify regulatory elements for the Kbz pathway and provide a framework for dissecting the biological functions of lysine benzoylation. Lysine benzoylation (Kbz) is a recently discovered histone modification. Here, the authors characterize writers, erasers and readers of histone Kbz in S. cerevisiae and identify non-histone proteins bearing Kbz, laying foundations to dissect the roles of Kbz in diverse cellular processes.
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22
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Huang J, Dai W, Xiao D, Xiong Q, Liu C, Hu J, Ge F, Yu X, Li S. Acetylation-dependent SAGA complex dimerization promotes nucleosome acetylation and gene transcription. Nat Struct Mol Biol 2022; 29:261-273. [PMID: 35301489 DOI: 10.1038/s41594-022-00736-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/30/2021] [Accepted: 02/02/2022] [Indexed: 11/09/2022]
Abstract
Cells reprogram their transcriptomes to adapt to external conditions. The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is a highly conserved transcriptional coactivator that plays essential roles in cell growth and development, in part by acetylating histones. Here, we uncover an autoregulatory mechanism of the Saccharomyces cerevisiae SAGA complex in response to environmental changes. Specifically, the SAGA complex acetylates its Ada3 subunit at three sites (lysines 8, 14 and 182) that are dynamically deacetylated by Rpd3. The acetylated Ada3 lysine residues are bound by bromodomains within SAGA subunits Gcn5 and Spt7 that synergistically facilitate formation of SAGA homo-dimers. Ada3-mediated dimerization is enhanced when cells are grown under sucrose or under phosphate-starvation conditions. Once dimerized, SAGA efficiently acetylates nucleosomes, promotes gene transcription and enhances cell resistance to stress. Collectively, our work reveals a mechanism for regulation of SAGA structure and activity and provides insights into how cells adapt to environmental conditions.
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Affiliation(s)
- Junhua Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Wenjing Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Duncheng Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.
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23
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Davydova EK. Protein Engineering: Advances in Phage Display for Basic Science and Medical Research. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S146-S110. [PMID: 35501993 PMCID: PMC8802281 DOI: 10.1134/s0006297922140127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Functional Protein Engineering became the hallmark in biomolecule manipulation in the new millennium, building on and surpassing the underlying structural DNA manipulation and recombination techniques developed and employed in the last decades of 20th century. Because of their prominence in almost all biological processes, proteins represent extremely important targets for engineering enhanced or altered properties that can lead to improvements exploitable in healthcare, medicine, research, biotechnology, and industry. Synthetic protein structures and functions can now be designed on a computer and/or evolved using molecular display or directed evolution methods in the laboratory. This review will focus on the recent trends in protein engineering and the impact of this technology on recent progress in science, cancer- and immunotherapies, with the emphasis on the current achievements in basic protein research using synthetic antibody (sABs) produced by phage display pipeline in the Kossiakoff laboratory at the University of Chicago (KossLab). Finally, engineering of the highly specific binding modules, such as variants of Streptococcal protein G with ultra-high orthogonal affinity for natural and engineered antibody scaffolds, and their possible applications as a plug-and-play platform for research and immunotherapy will be described.
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Affiliation(s)
- Elena K Davydova
- The University of Chicago, Department of Biochemistry and Molecular Biology, Chicago, IL 60637, USA.
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24
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The GCN5: its biological functions and therapeutic potentials. Clin Sci (Lond) 2021; 135:231-257. [PMID: 33443284 DOI: 10.1042/cs20200986] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
General control non-depressible 5 (GCN5) or lysine acetyltransferase 2A (KAT2A) is one of the most highly studied histone acetyltransferases. It acts as both histone acetyltransferase (HAT) and lysine acetyltransferase (KAT). As an HAT it plays a pivotal role in the epigenetic landscape and chromatin modification. Besides, GCN5 regulates a wide range of biological events such as gene regulation, cellular proliferation, metabolism and inflammation. Imbalance in the GCN5 activity has been reported in many disorders such as cancer, metabolic disorders, autoimmune disorders and neurological disorders. Therefore, unravelling the role of GCN5 in different diseases progression is a prerequisite for both understanding and developing novel therapeutic agents of these diseases. In this review, we have discussed the structural features, the biological function of GCN5 and the mechanical link with the diseases associated with its imbalance. Moreover, the present GCN5 modulators and their limitations will be presented in a medicinal chemistry perspective.
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25
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Liu L, Ge W, Zhang Z, Li Y, Xie M, Zhao C, Yao C, Luo C, Wu Z, Wang W, Zhao D, Zhang J, Qiu W, Wang Y. Sublytic C5b-9 triggers glomerular mesangial cell proliferation via enhancing FGF1 and PDGFα gene transcription mediated by GCN5-dependent SOX9 acetylation in rat Thy-1 nephritis. FASEB J 2021; 35:e21751. [PMID: 34156114 DOI: 10.1096/fj.202002814rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022]
Abstract
Rat Thy-1 nephritis (Thy-1N) is an animal model of human mesangioproliferative glomerulonephritis (MsPGN), accompanied by glomerular mesangial cell (GMC) proliferation and extracellular matrix (ECM) deposition. Although sublytic C5b-9 formed on GMC membrane could induce cell proliferation, the mechanism is still unclear. In this study, we first demonstrated that the level of SRY related HMG-BOX gene 9 (SOX9), general control nonderepressible 5 (GCN5), fibroblast growth factor 1 (FGF1) and platelet-derived growth factor α (PDGFα) was all elevated both in the renal tissues of Thy-1N rats (in vivo) and in the GMCs (in vitro) with sublytic C5b-9 stimulation. Then, we not only discovered that sublytic C5b-9 caused GMC proliferation through increasing SOX9, GCN5, FGF1 and PDGFα expression, but also proved that SOX9 and GCN5 formed a complex and combined with FGF1 and PDGFα promoters, leading to FGF1 and PDGFα gene transcription. More importantly, GCN5 could mediate SOX9 acetylation at lysine 62 (K62) to enhance SOX9 binding to FGF1 or PDGFα promoter and promote FGF1 or PDGFα synthesis and GMC proliferation. Besides, the experiments in vivo also showed that FGF1 and PDGFα expression, GMC proliferation and urinary protein secretion in Thy-1N rats were greatly reduced by silencing renal SOX9, GCN5, FGF1 or PDGFα gene. Furthermore, the renal tissues of MsPGN patients also exhibited positive expression of these genes mentioned above. Collectively, our findings indicate that GCN5, SOX9 and FGF1/PDGFα can form an axis and play an essential role in sublytic C5b-9-triggered GMC proliferation, which might provide a novel insight into the pathogenesis of Thy-1N and MsPGN.
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Affiliation(s)
- Longfei Liu
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China.,Department of Central Laboratory, The Affiliated Huaian No. 1 People's Hospital, Nanjing Medical University, Huai'an, China
| | - Wen Ge
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Zhiwei Zhang
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Ya Li
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Mengxiao Xie
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenhui Zhao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunlei Yao
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Can Luo
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Zhijiao Wu
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Wenbo Wang
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Dan Zhao
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Jing Zhang
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Wen Qiu
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Antibody Technology of Ministry of Health, Nanjing Medical University, Nanjing, China
| | - Yingwei Wang
- Key Laboratory of Immunological Environment and Disease, Department of Immunology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Antibody Technology of Ministry of Health, Nanjing Medical University, Nanjing, China
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26
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Wu CJ, Liu ZZ, Wei L, Zhou JX, Cai XW, Su YN, Li L, Chen S, He XJ. Three functionally redundant plant-specific paralogs are core subunits of the SAGA histone acetyltransferase complex in Arabidopsis. MOLECULAR PLANT 2021; 14:1071-1087. [PMID: 33737195 DOI: 10.1016/j.molp.2021.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/25/2021] [Accepted: 03/12/2021] [Indexed: 05/29/2023]
Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved histone acetyltransferase complex that has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. In this study, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits but also four plant-specific subunits: three functionally redundant paralogs, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. Mutations in SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the genes encoding conserved SAGA subunits HAG1 and ADA2B, including delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. Furthermore, we demonstrated that SCS1/2A/2B are required for the function of the SAGA complex in histone acetylation, thereby promoting the transcription of development-related genes. These results together suggest that SCS1/2A/2B are core subunits of the SAGA complex in Arabidopsis. Compared with SAGA complexes in other eukaryotes, the SAGA complexes in plants have evolved unique features that are necessary for normal growth and development.
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Affiliation(s)
- Chan-Juan Wu
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Long Wei
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10084, China
| | - Xin-Jian He
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10084, China.
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27
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Soffers JHM, Workman JL. The SAGA chromatin-modifying complex: the sum of its parts is greater than the whole. Genes Dev 2021; 34:1287-1303. [PMID: 33004486 PMCID: PMC7528701 DOI: 10.1101/gad.341156.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review, Soffers and Workman discuss the initial discovery of the canonical SAGA complex, the subsequent studies that have shaped our view on the internal organization of its subunits into modules, and the latest structural work that visualizes the modules and provides insights into their function. There are many large protein complexes involved in transcription in a chromatin context. However, recent studies on the SAGA coactivator complex are generating new paradigms for how the components of these complexes function, both independently and in concert. This review highlights the initial discovery of the canonical SAGA complex 23 years ago, our evolving understanding of its modular structure and the relevance of its modular nature for its coactivator function in gene regulation.
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Affiliation(s)
- Jelly H M Soffers
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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28
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Adamus K, Reboul C, Voss J, Huang C, Schittenhelm RB, Le SN, Ellisdon AM, Elmlund H, Boudes M, Elmlund D. SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent. J Biol Chem 2021; 296:100671. [PMID: 33864814 PMCID: PMC8131915 DOI: 10.1016/j.jbc.2021.100671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/03/2022] Open
Abstract
The SAGA-like complex SLIK is a modified version of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. SLIK is formed through C-terminal truncation of the Spt7 SAGA subunit, causing loss of Spt8, one of the subunits that interacts with the TATA-binding protein (TBP). SLIK and SAGA are both coactivators of RNA polymerase II transcription in yeast, and both SAGA and SLIK perform chromatin modifications. The two complexes have been speculated to uniquely contribute to transcriptional regulation, but their respective contributions are not clear. To investigate, we assayed the chromatin modifying functions of SAGA and SLIK, revealing identical kinetics on minimal substrates in vitro. We also examined the binding of SAGA and SLIK to TBP and concluded that interestingly, both protein complexes have similar affinity for TBP. Additionally, despite the loss of Spt8 and C-terminus of Spt7 in SLIK, TBP prebound to SLIK is not released in the presence of TATA-box DNA, just like TBP prebound to SAGA. Furthermore, we determined a low-resolution cryo-EM structure of SLIK, revealing a modular architecture identical to SAGA. Finally, we performed a comprehensive study of DNA-binding properties of both coactivators. Purified SAGA and SLIK both associate with ssDNA and dsDNA with high affinity (KD = 10–17 nM), and the binding is sequence-independent. In conclusion, our study shows that the cleavage of Spt7 and the absence of the Spt8 subunit in SLIK neither drive any major conformational differences in its structure compared with SAGA, nor significantly affect HAT, DUB, or DNA-binding activities in vitro.
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Affiliation(s)
- Klaudia Adamus
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Cyril Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jarrod Voss
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Cheng Huang
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sarah N Le
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Andrew M Ellisdon
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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29
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Yu Y, Tencer A, Xuan H, Kutateladze TG, Shi X. ZZEF1 is a Histone Reader and Transcriptional Coregulator of Krüppel-Like Factors. J Mol Biol 2020; 433:166722. [PMID: 33227311 DOI: 10.1016/j.jmb.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
Abstract
The ZZ-type zinc finger and EF-hand domain protein 1 (ZZEF1) is a multidomain-containing protein. Mutations of ZZEF1 has been implicated in several kinds of human diseases such as diabetes and cancers. However, the function of the ZZEF protein remains largely unknown. Here we show that ZZEF1 functions as a histone H3 reader. The second ZZ domain of ZZEF1 (ZZEF1ZZ2) binds to the N-terminus of histone H3 and is capable of accommodating common epigenetic marks on the H3 tail. The N-terminal amino acids, especially Ala1, of H3 and an acidic cavity of ZZEF1ZZ2 are critical for the ZZ-H3 interaction. RNA-seq analysis in human lung cancer cell line H1299 reveals that downregulated genes upon ZZEF1 depletion are specifically enriched in genes regulated by Krüppel-like factors. Indeed, ZZEF1 physically interacts with KLF9 and KLF6, and regulates a common set of target genes of these transcription factors. Together, our findings suggest a model in which ZZEF1 binds to histone H3 tail and promotes KLF9/6-mediated gene regulation.
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Affiliation(s)
- Yucong Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Adam Tencer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hongwen Xuan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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30
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Ben-Shem A, Papai G, Schultz P. Architecture of the multi-functional SAGA complex and the molecular mechanism of holding TBP. FEBS J 2020; 288:3135-3147. [PMID: 32946670 DOI: 10.1111/febs.15563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/11/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022]
Abstract
In eukaryotes, transcription of protein encoding genes is initiated by the controlled deposition of the TATA-box binding protein TBP onto gene promoters, followed by the ordered assembly of a pre-initiation complex. The SAGA co-activator is a 19-subunit complex that stimulates transcription by the action of two chromatin-modifying enzymatic modules, a transcription activator binding module, and by delivering TBP. Recent cryo electron microscopy structures of yeast SAGA with bound nucleosome or TBP reveal the architecture of the different functional domains of the co-activator. An octamer of histone fold domains is found at the core of SAGA. This octamer, which deviates considerably from the symmetrical analogue forming the nucleosome, establishes a peripheral site for TBP binding where steric hindrance represses interaction with spurious DNA. The structures point to a mechanism for TBP delivery and release from SAGA that requires TFIIA and whose efficiency correlates with the affinity of DNA to TBP. These results provide a structural basis for understanding specific TBP delivery onto gene promoters and the role played by SAGA in regulating gene expression. The properties of the TBP delivery machine harboured by SAGA are compared with the TBP loading device present in the TFIID complex and show multiple similitudes.
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Affiliation(s)
- Adam Ben-Shem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Université de Strasbourg, France.,Equipe labellisée Ligue Contre le Cancer, France
| | - Gabor Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Université de Strasbourg, France.,Equipe labellisée Ligue Contre le Cancer, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Université de Strasbourg, France.,Equipe labellisée Ligue Contre le Cancer, France
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31
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Espinola-Lopez JM, Tan S. The Ada2/Ada3/Gcn5/Sgf29 histone acetyltransferase module. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194629. [PMID: 32890768 DOI: 10.1016/j.bbagrm.2020.194629] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/14/2023]
Abstract
Histone post-translational modifications are essential for the regulation of gene expression in eukaryotes. Gcn5 (KAT2A) is a histone acetyltransferase that catalyzes the post-translational modification at multiple positions of histone H3 through the transfer of acetyl groups to the free amino group of lysine residues. Gcn5 catalyzes histone acetylation in the context of a HAT module containing the Ada2, Ada3 and Sgf29 subunits of the parent megadalton SAGA transcriptional coactivator complex. Biochemical and structural studies have elucidated mechanisms for Gcn5's acetyl- and other acyltransferase activities on histone substrates, for histone H3 phosphorylation and histone H3 methylation crosstalks with histone H3 acetylation, and for how Ada2 increases Gcn5's histone acetyltransferase activity. Other studies have identified Ada2 isoforms in SAGA-related complexes and characterized variant Gcn5 HAT modules containing these Ada2 isoforms. In this review, we highlight biochemical and structural studies of Gcn5 and its functional interactions with Ada2, Ada3 and Sgf29.
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Affiliation(s)
- Jose M Espinola-Lopez
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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32
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Catalysis by protein acetyltransferase Gcn5. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194627. [PMID: 32841743 DOI: 10.1016/j.bbagrm.2020.194627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 02/04/2023]
Abstract
Gcn5 serves as the defining member of the Gcn5-related N-acetyltransferase (GNAT) superfamily of proteins that display a common structural fold and catalytic mechanism involving the transfer of the acyl-group, primarily acetyl-, from CoA to an acceptor nucleophile. In the case of Gcn5, the target is the ε-amino group of lysine primarily on histones. Over the years, studies on Gcn5 structure-function have often formed the basis by which we understand the complex activities and regulation of the entire protein acetyltransferase family. It is now appreciated that protein acetylation occurs on thousands of proteins and can reversibly regulate the function of many cellular processes. In this review, we provide an overview of our fundamental understanding of catalysis, regulation of activity and substrate selection, and inhibitor development for this archetypal acetyltransferase.
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33
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What do the structures of GCN5-containing complexes teach us about their function? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194614. [PMID: 32739556 DOI: 10.1016/j.bbagrm.2020.194614] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. It involves the assembly of general transcription factors and RNA polymerase II into a functional pre-initiation complex at core promoters. The degree of chromatin compaction controls the accessibility of the transcription machinery to template DNA. Co-activators have critical roles in this process by actively regulating chromatin accessibility. Many transcriptional coactivators are multisubunit complexes, organized into distinct structural and functional modules and carrying multiple regulatory activities. The first nuclear histone acetyltransferase (HAT) characterized was General Control Non-derepressible 5 (Gcn5). Gcn5 was subsequently identified as a subunit of the HAT module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which is an experimental paradigm for multifunctional co-activators. We know today that Gcn5 is the catalytic subunit of multiple distinct co-activator complexes with specific functions. In this review, we summarize recent advances in the structure of Gcn5-containing co-activator complexes, most notably SAGA, and discuss how these new structural insights contribute to better understand their functions.
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34
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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35
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Liu J, Xue Z, Zhang Y, Vann KR, Shi X, Kutateladze TG. Structural Insight into Binding of the ZZ Domain of HERC2 to Histone H3 and SUMO1. Structure 2020; 28:1225-1230.e3. [PMID: 32726574 DOI: 10.1016/j.str.2020.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/10/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022]
Abstract
Human ubiquitin ligase HERC2, a component of the DNA repair machinery, has been linked to neurological diseases and cancer. Here, we show that the ZZ domain of HERC2 (HERC2ZZ) binds to histone H3 tail and tolerates posttranslational modifications commonly present in H3. The crystal structure of the HERC2ZZ:H3 complex provides the molecular basis for this interaction and highlights a critical role of the negatively charged site of HERC2ZZ in capturing of A1 of H3. NMR, mutagenesis, and fluorescence data reveal that HERC2ZZ binds to H3 and the N-terminal tail of SUMO1, a previously reported ligand of HERC2ZZ, with comparable affinities. Like H3, the N-terminal tail of SUMO1 occupies the same negatively charged site of HERC2ZZ in the crystal structure of the complex, although in contrast to H3 it adopts an α-helical conformation. Our data suggest that HERC2ZZ may play a role in mediating the association of HERC2 with chromatin.
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Affiliation(s)
- Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zhaoyu Xue
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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36
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Cheon Y, Kim H, Park K, Kim M, Lee D. Dynamic modules of the coactivator SAGA in eukaryotic transcription. Exp Mol Med 2020; 52:991-1003. [PMID: 32616828 PMCID: PMC8080568 DOI: 10.1038/s12276-020-0463-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) is a highly conserved transcriptional coactivator that consists of four functionally independent modules. Its two distinct enzymatic activities, histone acetylation and deubiquitylation, establish specific epigenetic patterns on chromatin and thereby regulate gene expression. Whereas earlier studies emphasized the importance of SAGA in regulating global transcription, more recent reports have indicated that SAGA is involved in other aspects of gene expression and thus plays a more comprehensive role in regulating the overall process. Here, we discuss recent structural and functional studies of each SAGA module and compare the subunit compositions of SAGA with related complexes in yeast and metazoans. We discuss the regulatory role of the SAGA deubiquitylating module (DUBm) in mRNA surveillance and export, and in transcription initiation and elongation. The findings suggest that SAGA plays numerous roles in multiple stages of transcription. Further, we describe how SAGA is related to human disease. Overall, in this report, we illustrate the newly revealed understanding of SAGA in transcription regulation and disease implications for fine-tuning gene expression. A protein that helps add epigenetic information to genome, SAGA, controls many aspects of gene activation, potentially making it a target for cancer therapies. To fit inside the tiny cell nucleus, the genome is tightly packaged, and genes must be unpacked before they can be activated. Known to be important in genome opening, SAGA has now been shown to also play many roles in gene activation. Daeyoup Lee at the KAIST, Daejeon, South Korea, and co-workers have reviewed recent discoveries about SAGA’s structure, function, and roles in disease. They report that SAGA’s complex (19 subunits organized into four modules) allows it to play so many roles, genome opening, initiating transcription, and efficiently exporting mRNAs. Its master role means that malfunction of SAGA may be linked to many diseases.
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Affiliation(s)
- Youngseo Cheon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Harim Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Kyubin Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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Mitropoulou AN, Ceska T, Heads JT, Beavil AJ, Henry AJ, McDonnell JM, Sutton BJ, Davies AM. Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization. Acta Crystallogr F Struct Biol Commun 2020; 76:116-129. [PMID: 32133997 PMCID: PMC7057348 DOI: 10.1107/s2053230x20001466] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/03/2020] [Indexed: 12/01/2022] Open
Abstract
Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by FcεRI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and FcεRI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with FcεRI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.
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Affiliation(s)
- Alkistis N. Mitropoulou
- Randall Centre for Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London SE1 1UL, UK
- Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Tom Ceska
- UCB Celltech, 208 Bath Road, Slough SL1 3WE, UK
| | | | - Andrew J. Beavil
- Randall Centre for Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London SE1 1UL, UK
- Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | | | - James M. McDonnell
- Randall Centre for Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London SE1 1UL, UK
- Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Brian J. Sutton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London SE1 1UL, UK
- Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Anna M. Davies
- Randall Centre for Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London SE1 1UL, UK
- Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
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Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A. Structure of SAGA and mechanism of TBP deposition on gene promoters. Nature 2020; 577:711-716. [PMID: 31969704 DOI: 10.1038/s41586-020-1944-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/19/2019] [Indexed: 11/09/2022]
Abstract
SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes1. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.
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Affiliation(s)
- Gabor Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Alexandre Frechard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olga Kolesnikova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
| | - Adam Ben-Shem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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Wang H, Dienemann C, Stützer A, Urlaub H, Cheung ACM, Cramer P. Structure of the transcription coactivator SAGA. Nature 2020; 577:717-720. [PMID: 31969703 PMCID: PMC6994259 DOI: 10.1038/s41586-020-1933-5] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/27/2019] [Indexed: 01/13/2023]
Abstract
Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase)1,2 and transcription factor IID (TFIID)2-4. SAGA is required for all regulated transcription5 and is conserved among eukaryotes6. SAGA contains four modules7-9: the activator-binding Tra1 module, the core module, the histone acetyltransferase (HAT) module and the histone deubiquitination (DUB) module. Previous studies provided partial structures10-14, but the structure of the central core module is unknown. Here we present the cryo-electron microscopy structure of SAGA from the yeast Saccharomyces cerevisiae and resolve the core module at 3.3 Å resolution. The core module consists of subunits Taf5, Sgf73 and Spt20, and a histone octamer-like fold. The octamer-like fold comprises the heterodimers Taf6-Taf9, Taf10-Spt7 and Taf12-Ada1, and two histone-fold domains in Spt3. Spt3 and the adjacent subunit Spt8 interact with the TATA box-binding protein (TBP)2,7,15-17. The octamer-like fold and its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt distinct conformations. Taf12 and Spt20 form flexible connections to the Tra1 module, whereas Sgf73 tethers the DUB module. Binding of a nucleosome to SAGA displaces the HAT and DUB modules from the core-module surface, allowing the DUB module to bind one face of an ubiquitinated nucleosome.
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Affiliation(s)
- Haibo Wang
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Alexandra Stützer
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen, Germany
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany
| | - Alan C M Cheung
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, UK
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
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40
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Rössl A, Denoncourt A, Lin MS, Downey M. A synthetic non-histone substrate to study substrate targeting by the Gcn5 HAT and sirtuin HDACs. J Biol Chem 2019; 294:6227-6239. [PMID: 30804216 DOI: 10.1074/jbc.ra118.006051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
Gcn5 and sirtuins are highly conserved histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes that were first characterized as regulators of gene expression. Although histone tails are important substrates of these enzymes, they also target many nonhistone proteins that function in diverse biological processes. However, the mechanisms used by these enzymes to choose their nonhistone substrates are unknown. Previously, we used SILAC-based MS to identify novel nonhistone substrates of Gcn5 and sirtuins in yeast and found a shared target consensus sequence. Here, we use a synthetic biology approach to demonstrate that this consensus sequence can direct acetylation and deacetylation targeting by these enzymes in vivo Remarkably, fusion of the sequence to a nonsubstrate confers de novo acetylation that is regulated by both Gcn5 and sirtuins. We exploit this synthetic fusion substrate as a tool to define subunits of the Gcn5-containing SAGA and ADA complexes required for nonhistone protein acetylation. In particular, we find a key role for the Ada2 and Ada3 subunits in regulating acetylations on our fusion substrate. In contrast, other subunits tested were largely dispensable, including those required for SAGA stability. In an extended analysis, defects in proteome-wide acetylation observed in ada3Δ mutants mirror those in ada2Δ mutants. Altogether, our work argues that nonhistone protein acetylation by Gcn5 is determined in part by specific amino acids surrounding target lysines but that even optimal sequences require both Ada2 and Ada3 for robust acetylation. The synthetic fusion substrate we describe can serve as a tool to further dissect the regulation of both Gcn5 and sirtuin activities in vivo.
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Affiliation(s)
- Anthony Rössl
- From the Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada, and
| | - Alix Denoncourt
- From the Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada, and
| | | | - Michael Downey
- From the Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada, .,Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada, and
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Zhang Y, Mi W, Xue Y, Shi X, Kutateladze TG. The ZZ domain as a new epigenetic reader and a degradation signal sensor. Crit Rev Biochem Mol Biol 2019; 54:1-10. [PMID: 30691308 DOI: 10.1080/10409238.2018.1564730] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although relatively small in size, the ZZ-type zinc finger (ZZ) domain is a versatile signaling module that is implicated in a diverse set of cell signaling events. Here, we highlight the most recent studies focused on the ZZ domain function as a histone reader and a sensor of protein degradation signals. We review and compare the molecular and structural mechanisms underlying targeting the amino-terminal sequences of histone H3 and arginylated substrates by the ZZ domain. We also discuss the ZZ domain sensitivity to histone PTMs and summarize biological outcomes associated with the recognition of histone and non-histone ligands by the ZZ domain-containing proteins and complexes.
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Affiliation(s)
- Yi Zhang
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Wenyi Mi
- b Center for Epigenetics Van Andel Research Institute , Grand Rapids , MI , USA
| | - Yongming Xue
- c Genetics and Epigenetics Graduate Program , The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences , Houston , TX , USA
| | - Xiaobing Shi
- b Center for Epigenetics Van Andel Research Institute , Grand Rapids , MI , USA
| | - Tatiana G Kutateladze
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
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