1
|
Vandermeulen MD, Lorenz MC, Cullen PJ. Conserved signaling modules regulate filamentous growth in fungi: a model for eukaryotic cell differentiation. Genetics 2024:iyae122. [PMID: 39239926 DOI: 10.1093/genetics/iyae122] [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: 06/11/2024] [Accepted: 07/20/2024] [Indexed: 09/07/2024] Open
Abstract
Eukaryotic organisms are composed of different cell types with defined shapes and functions. Specific cell types are produced by the process of cell differentiation, which is regulated by signal transduction pathways. Signaling pathways regulate cell differentiation by sensing cues and controlling the expression of target genes whose products generate cell types with specific attributes. In studying how cells differentiate, fungi have proved valuable models because of their ease of genetic manipulation and striking cell morphologies. Many fungal species undergo filamentous growth-a specialized growth pattern where cells produce elongated tube-like projections. Filamentous growth promotes expansion into new environments, including invasion into plant and animal hosts by fungal pathogens. The same signaling pathways that regulate filamentous growth in fungi also control cell differentiation throughout eukaryotes and include highly conserved mitogen-activated protein kinase (MAPK) pathways, which is the focus of this review. In many fungal species, mucin-type sensors regulate MAPK pathways to control filamentous growth in response to diverse stimuli. Once activated, MAPK pathways reorganize cell polarity, induce changes in cell adhesion, and promote the secretion of degradative enzymes that mediate access to new environments. However, MAPK pathway regulation is complicated because related pathways can share components with each other yet induce unique responses (i.e. signal specificity). In addition, MAPK pathways function in highly integrated networks with other regulatory pathways (i.e. signal integration). Here, we discuss signal specificity and integration in several yeast models (mainly Saccharomyces cerevisiae and Candida albicans) by focusing on the filamentation MAPK pathway. Because of the strong evolutionary ties between species, a deeper understanding of the regulation of filamentous growth in established models and increasingly diverse fungal species can reveal fundamentally new mechanisms underlying eukaryotic cell differentiation.
Collapse
Affiliation(s)
| | - Michael C Lorenz
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260-1300, USA
| |
Collapse
|
2
|
Ryan CJ, Devakumar LPS, Pettitt SJ, Lord CJ. Complex synthetic lethality in cancer. Nat Genet 2023; 55:2039-2048. [PMID: 38036785 DOI: 10.1038/s41588-023-01557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023]
Abstract
The concept of synthetic lethality has been widely applied to identify therapeutic targets in cancer, with varying degrees of success. The standard approach normally involves identifying genetic interactions between two genes, a driver and a target. In reality, however, most cancer synthetic lethal effects are likely complex and also polygenic, being influenced by the environment in addition to involving contributions from multiple genes. By acknowledging and delineating this complexity, we describe in this article how the success rate in cancer drug discovery and development could be improved.
Collapse
Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland.
| | - Lovely Paul Solomon Devakumar
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| |
Collapse
|
3
|
Bardani E, Kallemi P, Tselika M, Katsarou K, Kalantidis K. Spotlight on Plant Bromodomain Proteins. BIOLOGY 2023; 12:1076. [PMID: 37626962 PMCID: PMC10451976 DOI: 10.3390/biology12081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.
Collapse
Affiliation(s)
- Eirini Bardani
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Martha Tselika
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| |
Collapse
|
4
|
Conway TP, Moye-Rowley WS. Conditional Protein Depletion in the Analysis of Antifungal Drug Resistance in Candida glabrata. Methods Mol Biol 2023; 2658:191-200. [PMID: 37024703 DOI: 10.1007/978-1-0716-3155-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
This chapter illustrates a method to generate Candida glabrata conditional depletion mutants for SNF2, an ATPase subunit of the SWI/SNF chromatin remodeling complex with potential roles in the response to azole drugs. The strategy employed utilizes a plant-specific proteolysis pathway which allows for the rapid degradation of a target protein in the presence of the phytohormone, auxin. The steps taken to generate strains expressing the auxin-inducible plant F-box protein, Tir1, and in which the auxin-binding target, IAA17, is C-terminally fused to Snf2 are described. This acute depletion strategy is suitable for studying the effects of the loss of growth-critical proteins. The rapid depletion afforded by the auxin-induced degradation avoids the potential complications of a null allele causing a severe growth defect and allows a more rapid assessment of the consequences of reduced levels of a protein of interest.
Collapse
Affiliation(s)
- Thomas P Conway
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
5
|
Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (BETHESDA, MD.) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
Collapse
Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
| |
Collapse
|
6
|
Geng Q, Li H, Wang D, Sheng RC, Zhu H, Klosterman SJ, Subbarao KV, Chen JY, Chen FM, Zhang DD. The Verticillium dahliae Spt-Ada-Gcn5 Acetyltransferase Complex Subunit Ada1 Is Essential for Conidia and Microsclerotia Production and Contributes to Virulence. Front Microbiol 2022; 13:852571. [PMID: 35283850 PMCID: PMC8905346 DOI: 10.3389/fmicb.2022.852571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
Verticillium dahliae is a destructive soil-borne pathogen of many economically important dicots. The genetics of pathogenesis in V. dahliae has been extensively studied. Spt-Ada-Gcn5 acetyltransferase complex (SAGA) is an ATP-independent multifunctional chromatin remodeling complex that contributes to diverse transcriptional regulatory functions. As members of the core module in the SAGA complex in Saccharomyces cerevisiae, Ada1, together with Spt7 and Spt20, play an important role in maintaining the integrity of the complex. In this study, we identified homologs of the SAGA complex in V. dahliae and found that deletion of the Ada1 subunit (VdAda1) causes severe defects in the formation of conidia and microsclerotia, and in melanin biosynthesis and virulence. The effect of VdAda1 on histone acetylation in V. dahliae was confirmed by western blot analysis. The deletion of VdAda1 resulted in genome-wide alteration of the V. dahliae transcriptome, including genes encoding transcription factors and secreted proteins, suggesting its prominent role in the regulation of transcription and virulence. Overall, we demonstrated that VdAda1, a member of the SAGA complex, modulates multiple physiological processes by regulating global gene expression that impinge on virulence and survival in V. dahliae.
Collapse
Affiliation(s)
- Qi Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dan Wang
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruo-Cheng Sheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - He Zhu
- National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, The Cotton Research Center of Liaoning Academy of Agricultural Sciences, Liaoning Provincial Institute of Economic Crops, Liaoyang, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, United States
| | - Krishna V Subbarao
- Department of Plant Pathology, c/o U.S. Agricultural Research Station, University of California, Davis, Salinas, CA, United States
| | - Jie-Yin Chen
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng-Mao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dan-Dan Zhang
- Team of Crop Verticillium Wilt, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
7
|
Vandermeulen MD, Cullen PJ. Gene by Environment Interactions reveal new regulatory aspects of signaling network plasticity. PLoS Genet 2022; 18:e1009988. [PMID: 34982769 PMCID: PMC8759647 DOI: 10.1371/journal.pgen.1009988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Phenotypes can change during exposure to different environments through the regulation of signaling pathways that operate in integrated networks. How signaling networks produce different phenotypes in different settings is not fully understood. Here, Gene by Environment Interactions (GEIs) were used to explore the regulatory network that controls filamentous/invasive growth in the yeast Saccharomyces cerevisiae. GEI analysis revealed that the regulation of invasive growth is decentralized and varies extensively across environments. Different regulatory pathways were critical or dispensable depending on the environment, microenvironment, or time point tested, and the pathway that made the strongest contribution changed depending on the environment. Some regulators even showed conditional role reversals. Ranking pathways' roles across environments revealed an under-appreciated pathway (OPI1) as the single strongest regulator among the major pathways tested (RAS, RIM101, and MAPK). One mechanism that may explain the high degree of regulatory plasticity observed was conditional pathway interactions, such as conditional redundancy and conditional cross-pathway regulation. Another mechanism was that different pathways conditionally and differentially regulated gene expression, such as target genes that control separate cell adhesion mechanisms (FLO11 and SFG1). An exception to decentralized regulation of invasive growth was that morphogenetic changes (cell elongation and budding pattern) were primarily regulated by one pathway (MAPK). GEI analysis also uncovered a round-cell invasion phenotype. Our work suggests that GEI analysis is a simple and powerful approach to define the regulatory basis of complex phenotypes and may be applicable to many systems.
Collapse
Affiliation(s)
- Matthew D. Vandermeulen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| |
Collapse
|
8
|
Soffers JHM, Alcantara SGM, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters. PLoS Genet 2021; 17:e1009668. [PMID: 34807910 PMCID: PMC8648115 DOI: 10.1371/journal.pgen.1009668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/06/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022] Open
Abstract
The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene expression is not well understood. During Drosophila oogenesis, the enzymatic functions are not equally required, which may indicate that different genes require different enzymatic functions. An analogy for this phenomenon is the handyman principle: while a handyman has many tools, which tool he uses depends on what requires maintenance. Here we analyzed the role of the non-enzymatic core module during Drosophila oogenesis, which interacts with TBP. We show that depletion of SAGA-specific core subunits blocked egg chamber development at earlier stages than depletion of enzymatic subunits. These results, as well as additional genetic analyses, point to an interaction with TBP and suggest a differential role of SAGA modules at different promoter types. However, SAGA subunits co-occupied all promoter types of active genes in ChIP-seq and ChIP-nexus experiments, and the complex was not specifically associated with distinct promoter types in the ovary. The high-resolution genomic binding profiles were congruent with SAGA recruitment by activators upstream of the start site, and retention on chromatin by interactions with modified histones downstream of the start site. Our data illustrate that a distinct genetic requirement for specific components may conceal the fact that the entire complex is physically present and suggests that the biological context defines which module functions are critical. Embryonic development critically relies on the differential expression of genes in different tissues. This involves the dynamic interplay between DNA, sequence-specific transcription factors, coactivators and chromatin remodelers, which guide the transcription machinery to the appropriate promoters for productive transcription. To understand how this happens at the molecular level, we need to understand when and how coactivator complexes such as SAGA function. SAGA consists of multiple modules with well characterized enzymatic functions. This study shows that the non-enzymatic core module of SAGA is required for Drosophila oogenesis, while the enzymatic functions are largely dispensable. Despite this differential requirement, SAGA subunits appear to be broadly recruited to all promoter types, consistent with the biochemical integrity of the complex. These results suggest that genetic requirements for different modules depend on the developmental demands.
Collapse
Affiliation(s)
- Jelly H. M. Soffers
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sergio G-M Alcantara
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Xuanying Li
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Wanqing Shao
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Christopher W. Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
| | - Susan M. Abmayr
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- * E-mail:
| |
Collapse
|
9
|
Stanek TJ, Gennaro VJ, Tracewell MA, Di Marcantonio D, Pauley KL, Butt S, McNair C, Wang F, Kossenkov AV, Knudsen KE, Butt T, Sykes SM, McMahon SB. The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J 2021; 40:e102509. [PMID: 34155658 PMCID: PMC8365265 DOI: 10.15252/embj.2019102509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/10/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.
Collapse
Affiliation(s)
- Timothy J Stanek
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Victoria J Gennaro
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Mason A Tracewell
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Kristen L Pauley
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Sabrina Butt
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Christopher McNair
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | | | - Karen E Knudsen
- Department of Cancer BiologySidney Kimmel Medical College and Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Stephen M Sykes
- Blood Cell Development and Function ProgramFox Chase Cancer CenterPhiladelphiaPAUSA
| | - Steven B McMahon
- Department of Biochemistry and Molecular BiologySidney Kimmel Medical CollegeThomas Jefferson UniversityPhiladelphiaPAUSA
| |
Collapse
|
10
|
Peng H, Zhang S, Peng Y, Zhu S, Zhao X, Zhao X, Yang S, Liu G, Dong Y, Gan X, Li Q, Zhang X, Pei H, Chen X. Yeast Bromodomain Factor 1 and Its Human Homolog TAF1 Play Conserved Roles in Promoting Homologous Recombination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100753. [PMID: 34056863 PMCID: PMC8336524 DOI: 10.1002/advs.202100753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Indexed: 05/12/2023]
Abstract
Histone acetylation is a key histone post-translational modification that shapes chromatin structure, dynamics, and function. Bromodomain (BRD) proteins, the readers of acetyl-lysines, are located in the center of the histone acetylation-signaling network. How they regulate DNA repair and genome stability remains poorly understood. Here, a conserved function of the yeast Bromodomain Factor 1 (Bdf1) and its human counterpart TAF1 is reported in promoting DNA double-stranded break repair by homologous recombination (HR). Depletion of either yeast BDF1 or human TAF1, or disruption of their BRDs impairs DNA end resection, Replication Protein A (RPA) and Rad51 loading, and HR repair, causing genome instability and hypersensitivity to DNA damage. Mechanistically, it is shown that Bdf1 preferentially binds the DNA damage-induced histone H4 acetylation (H4Ac) via the BRD motifs, leading to its chromatin recruitment. Meanwhile, Bdf1 physically interacts with RPA, and this interaction facilitates RPA loading in the chromatin context and the subsequent HR repair. Similarly, TAF1 also interacts with H4Ac or RPA. Thus, Bdf1 and TAF1 appear to share a conserved mechanism in linking the HR repair to chromatin acetylation in preserving genome integrity.
Collapse
Affiliation(s)
- Haoyang Peng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Simin Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yihan Peng
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Shuangyi Zhu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xin Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaocong Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Shuangshuang Yang
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Guangxue Liu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yang Dong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaoli Gan
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Huadong Pei
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| |
Collapse
|
11
|
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: 33] [Impact Index Per Article: 11.0] [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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Lim S, Ahn H, Duan R, Liu Y, Ryu HY, Ahn SH. The Spt7 subunit of the SAGA complex is required for the regulation of lifespan in both dividing and nondividing yeast cells. Mech Ageing Dev 2021; 196:111480. [PMID: 33831401 DOI: 10.1016/j.mad.2021.111480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Spt7 belongs to the suppressor of Ty (SPT) module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and is known as the yeast ortholog of human STAF65γ. Spt7 lacks intrinsic enzymatic activity but is responsible for the integrity and proper assembly of the SAGA complex. Here, we determined the role of the SAGA Spt7 subunit in cellular aging. We found that Spt7 was indispensable for a normal lifespan in both dividing and nondividing yeast cells. In the quiescent state of cells, Spt7 was required for the control of overall mRNA levels. In mitotically active cells, deletion of the SPT module had little effect on the recombination rate within heterochromatic ribosomal DNA (rDNA) loci, but loss of Spt7 profoundly elevated the plasmid-based DNA recombination frequency. Consistently, loss of Spt7 increased spontaneous Rad52 foci by approximately two-fold upon entry into S phase. These results provide evidence that Spt7 contributes to the regulation of the normal replicative lifespan (RLS) and chronological lifespan (CLS), possibly by controlling the DNA recombination rate and overall mRNA expression. We propose that the regulation of SAGA complex integrity by Spt7 might be involved in the conserved regulatory pathway for lifespan regulation in eukaryotes.
Collapse
Affiliation(s)
- Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hyojeong Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Ruxin Duan
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea.
| |
Collapse
|
14
|
Grant PA, Winston F, Berger SL. The biochemical and genetic discovery of the SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194669. [PMID: 33338653 DOI: 10.1016/j.bbagrm.2020.194669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
One of the major advances in our understanding of gene regulation in eukaryotes was the discovery of factors that regulate transcription by controlling chromatin structure. Prominent among these discoveries was the demonstration that Gcn5 is a histone acetyltransferase, establishing a direct connection between transcriptional activation and histone acetylation. This breakthrough was soon followed by the purification of a protein complex that contains Gcn5, the SAGA complex. In this article, we review the early genetic and biochemical experiments that led to the discovery of SAGA and the elucidation of its multiple activities.
Collapse
Affiliation(s)
- Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, United States of America
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States of America.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Department of Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| |
Collapse
|
15
|
Nuño-Cabanes C, Rodríguez-Navarro S. The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194607. [PMID: 32712338 DOI: 10.1016/j.bbagrm.2020.194607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Gene expression, the decoding of DNA information into accessible instructions for protein synthesis, is a complex process in which multiple steps, including transcription, mRNA processing and mRNA export, are regulated by different factors. One of the first steps in this process involves chemical and structural changes in chromatin to allow transcription. For such changes to occur, histone tail and DNA epigenetic modifications foster the binding of transcription factors to promoter regions. The SAGA coactivator complex plays a crucial role in this process by mediating histone acetylation through Gcn5, and histone deubiquitination through Ubp8 enzymes. However, most SAGA subunits interact physically with other proteins beyond the SAGA complex. These interactions could represent SAGA-independent functions or a mechanism to widen SAGA multifunctionality. Among the different mechanisms to perform more than one function, protein moonlighting defines unrelated molecular activities for the same polypeptide sequence. Unlike pleiotropy, where a single gene can affect different phenotypes, moonlighting necessarily involves separate functions of a protein at the molecular level. In this review we describe in detail some of the alternative physical interactions of several SAGA subunits. In some cases, the alternative role constitutes a clear moonlighting function, whereas in most of them the lack of molecular evidence means that we can only define these interactions as promiscuous that require further work to verify if these are moonlighting functions.
Collapse
Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain.
| |
Collapse
|
16
|
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: 29] [Impact Index Per Article: 7.3] [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.
Collapse
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.
| |
Collapse
|
17
|
Yarrington RM, Yu Y, Yan C, Bai L, Stillman DJ. A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae. Genetics 2020; 215:407-420. [PMID: 32327563 PMCID: PMC7268993 DOI: 10.1534/genetics.120.303254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/21/2020] [Indexed: 01/12/2023] Open
Abstract
Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we analyze expression of the Saccharomyces cerevisiaeHO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested that the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.
Collapse
Affiliation(s)
- Robert M Yarrington
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Yaxin Yu
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Chao Yan
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lu Bai
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| |
Collapse
|
18
|
Wang L, Chen R, Weng Q, Lin S, Wang H, Li L, Fuchs BB, Tan X, Mylonakis E. SPT20 Regulates the Hog1-MAPK Pathway and Is Involved in Candida albicans Response to Hyperosmotic Stress. Front Microbiol 2020; 11:213. [PMID: 32153525 PMCID: PMC7047840 DOI: 10.3389/fmicb.2020.00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 11/22/2022] Open
Abstract
Candida albicans is the most common fungal pathogen and relies on the Hog1-MAPK pathway to resist osmotic stress posed by the environment or during host invasions. Here, we investigated the role of SPT20 in response to osmotic stress. Testing a C. albicans spt20Δ/Δ mutant, we found it was sensitive to osmotic stress. Using sequence alignment, we identified the conserved functional domains between CaSpt20 and ScSpt20. Reconstitution of the Spt20 function in a spt20Δ/CaSPT20 complemented strain found CaSPT20 can suppress the high sensitivity to hyperosmotic stressors, a cell wall stress agent, and antifungal drugs in the Saccharomyces cerevisiae spt20Δ/Δ mutant background. We measured the cellular glycerol accumulation and found it was significantly lower in the C. albicans spt20Δ/Δ mutant strain, compared to the wild type strain SC5314 (P < 0.001). This result was also supported by quantitative reverse transcription-PCR, which showed the expression levels of gene contributing to glycerol accumulation were reduced in Caspt20Δ/Δ compared to wild type (GPD2 and TGL1, P < 0.001), while ADH7 and AGP2, whose expression can lead to glycerol decrease, were induced when cells were exposed to high osmolarity (ADH7, P < 0.001; AGP2, P = 0.002). In addition, we tested the transcription levels of Hog1-dependent osmotic stress response genes, and found that they were significantly upregulated in wild type cells encountering hyperosmolarity, while the expression of HGT10, SKO1, CAT1, and SLP3 were not induced when SPT20 was deleted. Although the transcript of ORF19.3661 and ORF19.4370 in Caspt20Δ/Δ was induced in the presence of 1 M NaCl, the levels were less than what was observed in the wild type (ORF19.3661, P = 0.007; ORF19.4370, P = 0.011). Moreover, the deletion of CaSPT20 in C. albicans reduced phosphorylation levels of Hog1. These findings suggested that SPT20 is conserved between yeast and C. albicans and plays an important role in adapting to osmotic stress through regulating Hog1-MAPK pathway.
Collapse
Affiliation(s)
- Lianfang Wang
- Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ruilan Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Intensive Care Unit, Fangcun Branch of Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Qiuting Weng
- Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shaoming Lin
- Department of Respiratory, Longhua District People’s Hospital, Shenzhen, China
| | - Huijun Wang
- Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Li
- Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Beth Burgwyn Fuchs
- Department of Medicine, Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Xiaojiang Tan
- Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Eleftherios Mylonakis
- Department of Medicine, Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, United States
| |
Collapse
|
19
|
Petty EL, Evpak M, Pillus L. Connecting GCN5's centromeric SAGA to the mitotic tension-sensing checkpoint. Mol Biol Cell 2018; 29:2201-2212. [PMID: 29995571 PMCID: PMC6249797 DOI: 10.1091/mbc.e17-12-0701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Multiple interdependent mechanisms ensure faithful segregation of chromosomes during cell division. Among these, the spindle assembly checkpoint monitors attachment of spindle microtubules to the centromere of each chromosome, whereas the tension-sensing checkpoint monitors the opposing forces between sister chromatid centromeres for proper biorientation. We report here a new function for the deeply conserved Gcn5 acetyltransferase in the centromeric localization of Rts1, a key player in the tension-sensing checkpoint. Rts1 is a regulatory component of protein phopshatase 2A, a near universal phosphatase complex, which is recruited to centromeres by the Shugoshin (Sgo) checkpoint component under low-tension conditions to maintain sister chromatid cohesion. We report that loss of Gcn5 disrupts centromeric localization of Rts1. Increased RTS1 dosage robustly suppresses gcn5∆ cell cycle and chromosome segregation defects, including restoration of Rts1 to centromeres. Sgo1’s Rts1-binding function also plays a key role in RTS1 dosage suppression of gcn5∆ phenotypes. Notably, we have identified residues of the centromere histone H3 variant Cse4 that function in these chromosome segregation-related roles of RTS1. Together, these findings expand the understanding of the mechanistic roles of Gcn5 and Cse4 in chromosome segregation.
Collapse
Affiliation(s)
- Emily L Petty
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
| | - Masha Evpak
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
| | - Lorraine Pillus
- Division of Biological Sciences, Molecular Biology, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA 92103
| |
Collapse
|
20
|
Baptista T, Grünberg S, Minoungou N, Koster MJE, Timmers HTM, Hahn S, Devys D, Tora L. SAGA Is a General Cofactor for RNA Polymerase II Transcription. Mol Cell 2017; 68:130-143.e5. [PMID: 28918903 PMCID: PMC5632562 DOI: 10.1016/j.molcel.2017.08.016] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/28/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
Abstract
Prior studies suggested that SAGA and TFIID are alternative factors that promote RNA polymerase II transcription with about 10% of genes in S. cerevisiae dependent on SAGA. We reassessed the role of SAGA by mapping its genome-wide location and role in global transcription in budding yeast. We find that SAGA maps to the UAS elements of most genes, overlapping with Mediator binding and irrespective of previous designations of SAGA or TFIID-dominated genes. Disruption of SAGA through mutation or rapid subunit depletion reduces transcription from nearly all genes, measured by newly-synthesized RNA. We also find that the acetyltransferase Gcn5 synergizes with Spt3 to promote global transcription and that Spt3 functions to stimulate TBP recruitment at all tested genes. Our data demonstrate that SAGA acts as a general cofactor required for essentially all RNA polymerase II transcription and is not consistent with the previous classification of SAGA and TFIID-dominated genes.
Collapse
Affiliation(s)
- Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Sebastian Grünberg
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nadège Minoungou
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Maria J E Koster
- Molecular Cancer Research and Stem Cell Section, Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht c/o Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - H T Marc Timmers
- Molecular Cancer Research and Stem Cell Section, Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht c/o Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Steve Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
| |
Collapse
|
21
|
Sinha I, Kumar S, Poonia P, Sawhney S, Natarajan K. Functional specialization of two paralogous TAF12 variants by their selective association with SAGA and TFIID transcriptional regulatory complexes. J Biol Chem 2017; 292:6047-6055. [PMID: 28275052 PMCID: PMC5391738 DOI: 10.1074/jbc.c116.768549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
TATA box-binding protein (TBP)-associated factors (TAFs), evolutionarily conserved from yeast to humans, play a central role during transcription initiation. A subset of TAF proteins is shared in transcription factor II D (TFIID) and SAGA transcription regulatory complexes. Although higher eukaryotes contain multiple TAF variants that specify tissue- and developmental stage-specific organization of TFIID or SAGA complexes, in unicellular genomes, however, each TAF is encoded by a single gene. Surprisingly, we found that the genome of Candida albicans, the predominant human fungal pathogen, contains two paralogous TAF12 genes, CaTAF12L and CaTAF12, encoding H2B-like histone-fold domain-containing variants. Of the available fungal genome sequences, only seven other closely related diploid pathogenic Candida genomes encode the two TAF12 paralogs. Using affinity purifications from C. albicans cell extracts, we demonstrate that CaTAF12L uniquely associates with the SAGA complex and CaTAF12 associates with the TFIID complex. We further show that CaTAF12, but not CaTAF12L, is essential for C. albicans growth. Conditional depletion of the two TAF12 variant proteins caused distinct cellular and colony phenotypes. Together our results define a specialized organization of the TAF12 variants and non-redundant roles for the two TAF12 variants in the unicellular C. albicans genome.
Collapse
Affiliation(s)
- Ishani Sinha
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shambhu Kumar
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Poonia
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonal Sawhney
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Krishnamurthy Natarajan
- From the Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
22
|
Abstract
Chromatin is a highly dynamic structure that imparts structural organization to the genome and regulates the gene expression underneath. The decade long research in deciphering the significance of epigenetics in maintaining cellular integrity has embarked the focus on chromatin remodeling enzymes. These drivers have been categorized as readers, writers and erasers with each having significance of their own. Largely, on the basis of structure, ATP dependent chromatin remodelers have been grouped into 4 families; SWI/SNF, ISWI, IN080 and CHD. It is still unclear to what degree these enzymes are swayed by local DNA sequences when shifting a nucleosome to different positions. The ability of regulating active and repressive transcriptional state via open and close chromatin architecture has been well studied however, the significance of chromatin remodelers in regulating transcription at each step i.e. initiation, elongation and termination require further attention. The authors have highlighted the significance and role of different chromatin remodelers in transcription, DNA repair and histone variant deposition.
Collapse
Affiliation(s)
- Monica Tyagi
- a Kusuma School of Biological Sciences, Indian Institute of Technology Delhi Hauz Khas , New Delhi , India
| | | | | | | |
Collapse
|
23
|
Kwon Y, Cha J, Chiang J, Tran G, Nislow C, Hur JS, Kwak YS. Lichen-forming fungus Caloplaca flavoruscens inhibits transcription factors and chromatin remodeling system in fungi. FEMS Microbiol Lett 2016; 363:fnw113. [PMID: 27190156 DOI: 10.1093/femsle/fnw113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 11/14/2022] Open
Abstract
Lichen-forming fungi and extracts derived from them have been used as alternative medicine sources for millennia and recently there has been a renewed interest in their known bioactive properties for anticancer agents, cosmetics and antibiotics. Although lichen-forming fungus-derived compounds are biologically and commercially valuable, few studies have been performed to determine their modes of action. This study used chemical-genetic and chemogenomic high-throughput analyses to gain insight into the modes of action of Caloplaca flavoruscens extracts. High-throughput screening of 575 lichen extracts was performed and 39 extracts were identified which inhibited yeast growth. A C. flavoruscens extract was selected as a promising antifungal and was subjected to genome-wide haploinsufficiency profiling and homozygous profiling assays. These screens revealed that yeast deletion strains lacking Rsc8, Pro1 and Toa2 were sensitive to three concentrations (IC25.5, IC25 and IC50, respectively) of C. flavoruscens extract. Gene-enrichment analysis of the data showed that C. flavoruscens extracts appear to perturb transcription and chromatin remodeling.
Collapse
Affiliation(s)
- Youngho Kwon
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaeyul Cha
- Department of Plant Medicine and Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jennifer Chiang
- Pharmaceutical Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Grant Tran
- Pharmaceutical Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Suncheon National University, Suncheon 57922, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea Department of Plant Medicine and Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| |
Collapse
|
24
|
Nocetti N, Whitehouse I. Nucleosome repositioning underlies dynamic gene expression. Genes Dev 2016; 30:660-72. [PMID: 26966245 PMCID: PMC4803052 DOI: 10.1101/gad.274910.115] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/09/2016] [Indexed: 11/25/2022]
Abstract
Nocetti and Whitehouse report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. Nucleosome repositioning at gene promoters is a fundamental aspect of the regulation of gene expression. However, the extent to which nucleosome repositioning is used within eukaryotic genomes is poorly understood. Here we report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. We present evidence of extensive nucleosome repositioning at thousands of gene promoters as genes are activated and repressed. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. The extent of nucleosome shifting is closely related to the dynamic range of gene transcription and generally related to DNA sequence properties and use of the coactivators TFIID or SAGA. However, dynamic gene expression is not limited to SAGA-regulated promoters and is an inherent feature of most genes. While nucleosome repositioning occurs pervasively, we found that a class of genes required for growth experience acute nucleosome shifting as cells enter the cell cycle. Significantly, our data identify that the ATP-dependent chromatin-remodeling enzyme Snf2 plays a fundamental role in nucleosome repositioning and the expression of growth genes. We also reveal that nucleosome organization changes extensively in concert with phases of the cell cycle, with large, regularly spaced nucleosome arrays being established in mitosis. Collectively, our data and analysis provide a framework for understanding nucleosome dynamics in relation to fundamental DNA-dependent transactions.
Collapse
Affiliation(s)
- Nicolas Nocetti
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; BCMB Graduate Program, Weill Cornell Medical College, New York, New York 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
25
|
Randise-Hinchliff C, Coukos R, Sood V, Sumner MC, Zdraljevic S, Meldi Sholl L, Garvey Brickner D, Ahmed S, Watchmaker L, Brickner JH. Strategies to regulate transcription factor-mediated gene positioning and interchromosomal clustering at the nuclear periphery. J Cell Biol 2016; 212:633-46. [PMID: 26953353 PMCID: PMC4792077 DOI: 10.1083/jcb.201508068] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/02/2016] [Indexed: 11/23/2022] Open
Abstract
In yeast, transcription factors mediate gene positioning at the nuclear periphery and interchromosomal clustering. These phenomena are regulated by several different strategies that lead to dynamic changes in the spatial arrangement of genes over different time scales. In budding yeast, targeting of active genes to the nuclear pore complex (NPC) and interchromosomal clustering is mediated by transcription factor (TF) binding sites in the gene promoters. For example, the binding sites for the TFs Put3, Ste12, and Gcn4 are necessary and sufficient to promote positioning at the nuclear periphery and interchromosomal clustering. However, in all three cases, gene positioning and interchromosomal clustering are regulated. Under uninducing conditions, local recruitment of the Rpd3(L) histone deacetylase by transcriptional repressors blocks Put3 DNA binding. This is a general function of yeast repressors: 16 of 21 repressors blocked Put3-mediated subnuclear positioning; 11 of these required Rpd3. In contrast, Ste12-mediated gene positioning is regulated independently of DNA binding by mitogen-activated protein kinase phosphorylation of the Dig2 inhibitor, and Gcn4-dependent targeting is up-regulated by increasing Gcn4 protein levels. These different regulatory strategies provide either qualitative switch-like control or quantitative control of gene positioning over different time scales.
Collapse
Affiliation(s)
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Varun Sood
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Michael Chas Sumner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Lauren Meldi Sholl
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | | | - Sara Ahmed
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Lauren Watchmaker
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201
| |
Collapse
|
26
|
Shanle EK, Andrews FH, Meriesh H, McDaniel SL, Dronamraju R, DiFiore JV, Jha D, Wozniak GG, Bridgers JB, Kerschner JL, Krajewski K, Martín GM, Morrison AJ, Kutateladze TG, Strahl BD. Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response. Genes Dev 2015; 29:1795-800. [PMID: 26341557 PMCID: PMC4573853 DOI: 10.1101/gad.269977.115] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The YEATS domain, found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation. Here, we show that the YEATS domain of Taf14, a member of key transcriptional and chromatin-modifying complexes in yeast, is a selective reader of histone H3 Lys9 acetylation (H3K9ac). Structural analysis reveals that acetylated Lys9 is sandwiched in an aromatic cage formed by F62 and W81. Disruption of this binding in cells impairs gene transcription and the DNA damage response. Our findings establish a highly conserved acetyllysine reader function for the YEATS domain protein family and highlight the significance of this interaction for Taf14.
Collapse
Affiliation(s)
- Erin K Shanle
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Hashem Meriesh
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Stephen L McDaniel
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Raghuvar Dronamraju
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Julia V DiFiore
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Deepak Jha
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Glenn G Wozniak
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Joseph B Bridgers
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Jenny L Kerschner
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Glòria Mas Martín
- Department of Biology, Stanford University, Stanford, California 94305 USA
| | - Ashby J Morrison
- Department of Biology, Stanford University, Stanford, California 94305 USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA; Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| |
Collapse
|
27
|
Qiu H, Chereji RV, Hu C, Cole HA, Rawal Y, Clark DJ, Hinnebusch AG. Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation. Genome Res 2015; 26:211-25. [PMID: 26602697 PMCID: PMC4728374 DOI: 10.1101/gr.196337.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/18/2015] [Indexed: 12/27/2022]
Abstract
Chaperones, nucleosome remodeling complexes, and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these cofactors function ubiquitously, as well as the impact of nucleosome eviction on transcription genome-wide, is poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple cofactors to address these issues for about 200 genes belonging to the Gcn4 transcriptome, of which about 70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation. Examining four target genes in a panel of mutants indicated that SWI/SNF, Gcn5, the Hsp70 cochaperone Ydj1, and chromatin-associated factor Yta7 are required downstream from Gcn4 binding, whereas Asf1/Rtt109, Nap1, RSC, and H2AZ are dispensable for robust H3 eviction in otherwise wild-type cells. Using ChIP-seq to interrogate all 70 exemplar genes in single, double, and triple mutants implicated Gcn5, Snf2, and Ydj1 in H3 eviction at most, but not all, Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these three cofactors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in cofactor mutants was coupled with reduced Pol II occupancies for the Gcn4 transcriptome and the most highly expressed uninduced genes, but the relative Pol II levels at most genes were unaffected or even elevated. These findings indicate that nucleosome eviction is crucial for robust transcription of highly expressed genes but that other steps in gene activation are more rate-limiting for most other yeast genes.
Collapse
Affiliation(s)
- Hongfang Qiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Răzvan V Chereji
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cuihua Hu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hope A Cole
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yashpal Rawal
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David J Clark
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
28
|
Dutta A, Gogol M, Kim JH, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn MP, Workman JL. Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions. Genes Dev 2014; 28:2314-30. [PMID: 25319830 PMCID: PMC4201291 DOI: 10.1101/gad.243584.114] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. Dutta et al. find that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. The intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. The presence of histone acetylation and activator-dependent recruitment and retention of Swi/Snf is important for its efficient function. It is not understood, however, why such mechanisms are required to enhance Swi/Snf activity on nucleosomes. Snf2, the catalytic subunit of the Swi/Snf remodeling complex, has been shown to be a target of the Gcn5 acetyltransferase. Our study found that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. Also, the intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Interestingly, the presence of transcription activators mitigates the effects of the reduced affinity of acetylated Snf2 for acetylated nucleosomes. Supporting our in vitro results, we found that activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. Our studies demonstrate that competing effects of (1) Swi/Snf retention by activators or high levels of histone acetylation and (2) Snf2 acetylation-mediated release regulate dynamics of Swi/Snf occupancy at target genes.
Collapse
Affiliation(s)
- Arnob Dutta
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeong-Hoon Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, Korea
| | - Michaela Smolle
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | - Joshua Gilmore
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| |
Collapse
|
29
|
Adaptive response and tolerance to sugar and salt stress in the food yeast Zygosaccharomyces rouxii. Int J Food Microbiol 2014; 185:140-57. [DOI: 10.1016/j.ijfoodmicro.2014.05.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/18/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
|
30
|
Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:728-36. [PMID: 24583555 DOI: 10.1016/j.bbagrm.2014.02.013] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 01/08/2023]
Abstract
Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
Collapse
Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
31
|
Burke TL, Miller JL, Grant PA. Direct inhibition of Gcn5 protein catalytic activity by polyglutamine-expanded ataxin-7. J Biol Chem 2013; 288:34266-34275. [PMID: 24129567 DOI: 10.1074/jbc.m113.487538] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease caused by polyglutamine (polyQ) expansion within the N-terminal region of the ataxin-7 protein, a known subunit of the SAGA complex. Although the mechanisms of SCA7 pathogenesis remain poorly understood, previous studies have shown perturbations in SAGA histone acetyltransferase function and transcriptional alterations. We sought to determine whether and how polyQ-expanded ataxin-7 affects SAGA catalytic activity. Here, we determined that polyQ-expanded ataxin-7 directly bound the Gcn5 catalytic core of SAGA while in association with its regulatory proteins, Ada2 and Ada3. This caused a significant decrease in Gcn5 histone acetyltransferase activity in vitro and in vivo at two SAGA-regulated galactose genes, GAL1 and GAL7. However, Gcn5 occupancy at the GAL1 and GAL7 promoters was increased in these cells, revealing a dominant-negative phenotype of the polyQ-expanded ataxin-7-incorporated, catalytically inactive SAGA. These findings suggest a dominant mechanism of polyQ-mediated SAGA inhibition that potentially contributes to SCA7 disease pathogenesis.
Collapse
Affiliation(s)
- Tara L Burke
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Jaime L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Patrick A Grant
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908.
| |
Collapse
|
32
|
The yeast AMPK homolog SNF1 regulates acetyl coenzyme A homeostasis and histone acetylation. Mol Cell Biol 2013; 33:4701-17. [PMID: 24081331 DOI: 10.1128/mcb.00198-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetyl coenzyme A (acetyl-CoA) is a key metabolite at the crossroads of metabolism, signaling, chromatin structure, and transcription. Concentration of acetyl-CoA affects histone acetylation and links intermediary metabolism and transcriptional regulation. Here we show that SNF1, the budding yeast ortholog of the mammalian AMP-activated protein kinase (AMPK), plays a role in the regulation of acetyl-CoA homeostasis and global histone acetylation. SNF1 phosphorylates and inhibits acetyl-CoA carboxylase, which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the first and rate-limiting reaction in the de novo synthesis of fatty acids. Inactivation of SNF1 results in a reduced pool of cellular acetyl-CoA, globally decreased histone acetylation, and reduced fitness and stress resistance. The histone acetylation and transcriptional defects can be partially suppressed and the overall fitness improved in snf1Δ mutant cells by increasing the cellular concentration of acetyl-CoA, indicating that the regulation of acetyl-CoA homeostasis represents another mechanism in the SNF1 regulatory repertoire.
Collapse
|
33
|
Galdieri L, Chang J, Mehrotra S, Vancura A. Yeast phospholipase C is required for normal acetyl-CoA homeostasis and global histone acetylation. J Biol Chem 2013; 288:27986-98. [PMID: 23913687 DOI: 10.1074/jbc.m113.492348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Phospholipase C (Plc1p) is required for the initial step of inositol polyphosphate (InsP) synthesis, and yeast cells with deletion of the PLC1 gene are completely devoid of any InsPs and display aberrations in transcriptional regulation. Here we show that Plc1p is required for a normal level of histone acetylation; plc1Δ cells that do not synthesize any InsPs display decreased acetylation of bulk histones and global hypoacetylation of chromatin histones. In accordance with the role of Plc1p in supporting histone acetylation, plc1Δ mutation is synthetically lethal with mutations in several subunits of SAGA and NuA4 histone acetyltransferase (HAT) complexes. Conversely, the growth rate, sensitivity to multiple stresses, and the transcriptional defects of plc1Δ cells are partially suppressed by deletion of histone deacetylase HDA1. The histone hypoacetylation in plc1Δ cells is due to the defect in degradation of repressor Mth1p, and consequently lower expression of HXT genes and reduced conversion of glucose to acetyl-CoA, a substrate for HATs. The histone acetylation and transcriptional defects can be partially suppressed and the overall fitness improved in plc1Δ cells by increasing the cellular concentration of acetyl-CoA. Together, our data indicate that Plc1p and InsPs are required for normal acetyl-CoA homeostasis, which, in turn, regulates global histone acetylation.
Collapse
Affiliation(s)
- Luciano Galdieri
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | | | | | | |
Collapse
|
34
|
Balancing chromatin remodeling and histone modifications in transcription. Trends Genet 2013; 29:621-9. [PMID: 23870137 DOI: 10.1016/j.tig.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/29/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
Abstract
Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive crosstalk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relations between nucleosome remodeling and modifying machineries. Defining the combined functions of the complexes that alter nucleosome interactions, position, and stability is key to understanding processes that require access to DNA, particularly with growing appreciation of their contributions to human health and disease. Here, we highlight recent advances in the interactions between histone modifications and the imitation-switch (ISWI) and chromodomain helicase DNA-binding protein 1 (CHD1) chromatin remodelers from studies in budding yeast, fission yeast, flies, and mammalian cells, with a focus on yeast.
Collapse
|
35
|
Ansari SA, Morse RH. Selective role of Mediator tail module in the transcription of highly regulated genes in yeast. Transcription 2012; 3:110-4. [PMID: 22771944 DOI: 10.4161/trns.19840] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The tail module subunits of Mediator complex are targets of activators both in yeast and metazoans. Here we discuss recent evidence from studies in yeast for tail module specificity for SAGA-dependent, TATA-containing genes including highly regulated stress response genes, and for independent recruitment and function of the tail module.
Collapse
Affiliation(s)
- Suraiya A Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
| | | |
Collapse
|
36
|
Lafon A, Petty E, Pillus L. Functional antagonism between Sas3 and Gcn5 acetyltransferases and ISWI chromatin remodelers. PLoS Genet 2012; 8:e1002994. [PMID: 23055944 PMCID: PMC3464200 DOI: 10.1371/journal.pgen.1002994] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 08/13/2012] [Indexed: 12/30/2022] Open
Abstract
Chromatin-modifying enzymes and ATP-dependent remodeling complexes have been intensely studied individually, yet how these activities are coordinated to ensure essential cell functions such as transcription, replication, and repair of damage is not well understood. In this study, we show that the critical loss of Sas3 and Gcn5 acetyltransferases in yeast can be functionally rescued by inactivation of ISWI remodelers. This genetic interaction depends on the ATPase activities of Isw1 and Isw2, suggesting that it involves chromatin remodeling activities driven by the enzymes. Genetic dissection of the Isw1 complexes reveals that the antagonistic effects are mediated specifically by the Isw1a complex. Loss of Sas3 and Gcn5 correlates with defective RNA polymerase II (RNAPII) occupancy at actively transcribed genes, as well as a significant loss of H3K14 acetylation. Inactivation of the Isw1a complex in the acetyltransferase mutants restores RNAPII recruitment at active genes, indicating that transcriptional regulation may be the mechanism underlying suppression. Dosage studies and further genetic dissection reveal that the Isw1b complex may act in suppression through down-regulation of Isw1a. These studies highlight the importance of balanced chromatin modifying and remodeling activities for optimal transcription and cell growth. In eukaryotes, essential processes such as transcription, replication, and repair of damage occur in the context of chromatin. The structure of chromatin is tightly regulated during the cell cycle by chromatin-modifying enzymes, including acetyltransferases, and ATP-dependent remodeling complexes. Although there has been extensive characterization of their individual functions, little is known about how their activities are coordinated to maintain cell viability. In this study, we show that the critical loss of Sas3 and Gcn5 acetyltransferases can be functionally rescued by inactivation of ISWI remodelers. At a molecular level, the effects on cell viability tightly correlate with the recruitment of RNA polymerase II (RNAPII) at active genes, suggesting that transcriptional regulation may be the mechanism underlying cell viability rescue. Our genetic analyses reveal distinct roles for the two Isw1a and Isw1b complexes; in particular, the antagonistic effects are mediated specifically by the Isw1a complex. These studies highlight the importance of balanced chromatin modifying and remodeling activities for optimal transcription and cell growth.
Collapse
Affiliation(s)
- Anne Lafon
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- UCSD Moores Cancer Center, La Jolla, California, United States of America
| | - Emily Petty
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- UCSD Moores Cancer Center, La Jolla, California, United States of America
| | - Lorraine Pillus
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- UCSD Moores Cancer Center, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
37
|
Abstract
Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.
Collapse
|
38
|
Josling GA, Selvarajah SA, Petter M, Duffy MF. The role of bromodomain proteins in regulating gene expression. Genes (Basel) 2012; 3:320-43. [PMID: 24704920 PMCID: PMC3899951 DOI: 10.3390/genes3020320] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 05/11/2012] [Accepted: 05/17/2012] [Indexed: 11/25/2022] Open
Abstract
Histone modifications are important in regulating gene expression in eukaryotes. Of the numerous histone modifications which have been identified, acetylation is one of the best characterised and is generally associated with active genes. Histone acetylation can directly affect chromatin structure by neutralising charges on the histone tail, and can also function as a binding site for proteins which can directly or indirectly regulate transcription. Bromodomains specifically bind to acetylated lysine residues on histone tails, and bromodomain proteins play an important role in anchoring the complexes of which they are a part to acetylated chromatin. Bromodomain proteins are involved in a diverse range of functions, such as acetylating histones, remodeling chromatin, and recruiting other factors necessary for transcription. These proteins thus play a critical role in the regulation of transcription.
Collapse
Affiliation(s)
- Gabrielle A Josling
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Australia.
| | - Shamista A Selvarajah
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Australia.
| | - Michaela Petter
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Australia.
| | - Michael F Duffy
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Australia.
| |
Collapse
|
39
|
Lin Z, Yang H, Kong Q, Li J, Lee SM, Gao B, Dong H, Wei J, Song J, Zhang DD, Fang D. USP22 antagonizes p53 transcriptional activation by deubiquitinating Sirt1 to suppress cell apoptosis and is required for mouse embryonic development. Mol Cell 2012; 46:484-94. [PMID: 22542455 DOI: 10.1016/j.molcel.2012.03.024] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/17/2012] [Accepted: 03/22/2012] [Indexed: 02/07/2023]
Abstract
The NAD-dependent histone deacetylase Sirt1 antagonizes p53 transcriptional activity to regulate cell-cycle progression and apoptosis. We have identified a ubiquitin-specific peptidase, USP22, one of the 11 death-from-cancer signature genes that are critical in controlling cell growth and death, as a positive regulator of Sirt1. USP22 interacts with and stabilizes Sirt1 by removing polyubiquitin chains conjugated onto Sirt1. The USP22-mediated stabilization of Sirt1 leads to decreasing levels of p53 acetylation and suppression of p53-mediated functions. In contrast, depletion of endogenous USP22 by RNA interference destabilizes Sirt1, inhibits Sirt1-mediated deacetylation of p53 and elevates p53-dependent apoptosis. Genetic deletion of the usp22 gene results in Sirt1 instability, elevated p53 transcriptional activity and early embryonic lethality in mice. Our study elucidates a molecular mechanism in suppression of cell apoptosis by stabilizing Sirt1 in response to DNA damage and reveals a critical physiological function of USP22 in mouse embryonic development.
Collapse
Affiliation(s)
- Zhenghong Lin
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
García-Oliver E, García-Molinero V, Rodríguez-Navarro S. mRNA export and gene expression: the SAGA-TREX-2 connection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:555-65. [PMID: 22178374 DOI: 10.1016/j.bbagrm.2011.11.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 01/07/2023]
Abstract
In the gene expression field, different steps have been traditionally viewed as discrete and unconnected events. Nowadays, genetic and functional studies support the model of a coupled network of physical and functional connections to carry out mRNA biogenesis. Gene expression is a coordinated process that comprises different linked steps like transcription, RNA processing, export to the cytoplasm, translation and degradation of mRNAs. Its regulation is essential for cellular survival and can occur at many different levels. Transcription is the central function that occurs in the nucleus, and RNAPII plays an essential role in mRNA biogenesis. During transcription, nascent mRNA is associated with the mRNA-binding proteins involved in processing and export of the mRNA particle. Cells have developed a network of multi-protein complexes whose functions regulate the different factors involved both temporally and spatially. This coupling mechanism acts as a quality control to solve some of the organization problems of gene expression in vivo, where all the factors implicated ensure that mRNAs are ready to be exported and translated. In this review, we focus on the functional coupling of gene transcription and mRNA export, and place particular emphasis on the relationship between the NPC-associated complex, TREX2, and the transcription co-activator, SAGA. We have pinpointed the experimental evidence for Sus1's roles in transcription initiation, transcription elongation and mRNA export. In addition, we have reviewed other NPC-related processes such as gene gating to the nuclear envelope, the chromatin structure and the cellular context in which these processes take place. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
Collapse
Affiliation(s)
- Encar García-Oliver
- Centro de Investigación Príncipe Felipe (CIPF), Gene Expression coupled with RNA Transport Laboratory, Valencia, Spain
| | | | | |
Collapse
|
41
|
Distinct role of Mediator tail module in regulation of SAGA-dependent, TATA-containing genes in yeast. EMBO J 2011; 31:44-57. [PMID: 21971086 DOI: 10.1038/emboj.2011.362] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/07/2011] [Indexed: 11/08/2022] Open
Abstract
The evolutionarily conserved Mediator complex is required for transcription of nearly all RNA Pol II-dependent promoters, with the tail module serving to recruit Mediator to active promoters in current models. However, transcriptional dependence on tail module subunits varies in a gene-specific manner, and the generality of the tail module requirement for transcriptional activation has not been explored. Here, we show that tail module subunits function redundantly to recruit Mediator to promoters in yeast, and transcriptome analysis shows stronger effects on genome-wide expression in a double-tail subunit deletion mutant than in single-subunit deletion mutants. Unexpectedly, TATA-containing and SAGA-dependent genes were much more affected by impairment of tail module function than were TFIID-dependent genes. Consistent with this finding, Mediator and preinitiation complex association with SAGA-dependent promoters is substantially reduced in gal11/med15Δ med3Δ yeast, whereas association of TBP, Pol II, and other Mediator modules with TFIID-dependent genes is largely independent of the tail module. Thus, we have identified a connection between the Mediator tail module and the division of promoter dependence between TFIID and SAGA.
Collapse
|
42
|
Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B. Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res 2011; 39:8378-91. [PMID: 21749977 PMCID: PMC3201869 DOI: 10.1093/nar/gkr535] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a close relationship between histone acetylation and ATP-dependent chromatin remodeling that is not fully understood. We show that acetylation of histone H3 tails affects SWI/SNF (mating type switching/ sucrose non fermenting) and RSC (remodels structure of chromatin) remodeling in several distinct ways. Acetylation of the histone H3 N-terminal tail facilitated recruitment and nucleosome mobilization by the ATP-dependent chromatin remodelers SWI/SNF and RSC. Tetra-acetylated H3, but not tetra-acetylated H4 tails, increased the affinity of RSC and SWI/SNF for nucleosomes while also changing the subunits of SWI/SNF that interact with the H3 tail. The enhanced recruitment of SWI/SNF due to H3 acetylation is bromodomain dependent, but is not further enhanced by additional bromodomains found in RSC. The combined effect of H3 acetylation and transcription activators is greater than either separately which suggests they act in parallel to recruit SWI/SNF. Besides enhancing recruitment, H3 acetylation increased nucleosome mobilization and H2A/H2B displacement by RSC and SWI/SNF in a bromodomain dependent manner and to a lesser extent enhanced ATP hydrolysis independent of bromodomains. H3 and H4 acetylation did not stimulate disassembly of adjacent nucleosomes in short arrays by SWI/SNF or RSC. These data illustrate how histone acetylation modulates RSC and SWI/SNF function, and provide a mechanistic insight into their collaborative efforts to remodel chromatin.
Collapse
Affiliation(s)
- Nilanjana Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901-4413, USA
| | | | | | | | | | | |
Collapse
|
43
|
Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes. Mol Syst Biol 2011; 7:503. [PMID: 21734642 PMCID: PMC3159981 DOI: 10.1038/msb.2011.40] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 05/22/2011] [Indexed: 12/12/2022] Open
Abstract
Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.
Collapse
|
44
|
Abstract
Steroid hormone receptors regulate gene transcription in a highly tissue-specific manner. The local chromatin structure underlying promoters and hormone response elements is a major component involved in controlling these highly restricted expression patterns. Chromatin remodeling complexes, as well as histone and DNA modifying enzymes, are directed to gene-specific regions and create permissive or repressive chromatin environments. These structures further enable proper communication between transcription factors, co-regulators and basic transcription machinery. The regulatory elements active at target genes can be either constitutively accessible to receptors or subject to rapid receptor-dependent modification. The chromatin states responsible for these processes are in turn determined during development and differentiation. Thus access of regulatory factors to elements in chromatin provides a major level of cell selective regulation.
Collapse
Affiliation(s)
- Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD 20892-5055, USA
| | | | | |
Collapse
|
45
|
Abstract
The Mediator complex is required for the regulated transcription of nearly all RNA polymerase II-dependent genes. Here we demonstrate a new role for Mediator which appears to be separate from its function as a transcriptional coactivator. Mediator associates directly with heterochromatin at telomeres and influences the exact boundary between active and inactive chromatin. Loss of the Mediator Med5 subunit or mutations in Med7 cause a depletion of the complex from regions located near subtelomeric X elements, which leads to a change in the balance between the Sir2 and Sas2 proteins. These changes in turn result in increased levels of H4K16 acetylation near telomeres and in desilencing of subtelomeric genes. Increases in H4K16 acetylation have been observed at telomeres in aging cells. In agreement with this observation, we found that the loss of MED5 leads to shortening of the Saccharomyces cerevisiae (budding yeast) replicative life span.
Collapse
|
46
|
The Hog1 mitogen-activated protein kinase mediates a hypoxic response in Saccharomyces cerevisiae. Genetics 2011; 188:325-38. [PMID: 21467572 DOI: 10.1534/genetics.111.128322] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have studied hypoxic induction of transcription by studying the seripauperin (PAU) genes of Saccharomyces cerevisiae. Previous studies showed that PAU induction requires the depletion of heme and is dependent upon the transcription factor Upc2. We have now identified additional factors required for PAU induction during hypoxia, including Hog1, a mitogen-activated protein kinase (MAPK) whose signaling pathway originates at the membrane. Our results have led to a model in which heme and ergosterol depletion alters membrane fluidity, thereby activating Hog1 for hypoxic induction. Hypoxic activation of Hog1 is distinct from its previously characterized response to osmotic stress, as the two conditions cause different transcriptional consequences. Furthermore, Hog1-dependent hypoxic activation is independent of the S. cerevisiae general stress response. In addition to Hog1, specific components of the SAGA coactivator complex, including Spt20 and Sgf73, are also required for PAU induction. Interestingly, the mammalian ortholog of Spt20, p38IP, has been previously shown to interact with the mammalian ortholog of Hog1, p38. Taken together, our results have uncovered a previously unknown hypoxic-response pathway that may be conserved throughout eukaryotes.
Collapse
|
47
|
Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2. Genes Dev 2011; 24:2766-71. [PMID: 21159817 DOI: 10.1101/gad.1979710] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The positive link between the SWI/SNF and the Gcn5 histone acetyltransferase in transcriptional activation has been well described. Here we report an inhibitory role for Gcn5 in SWI/SNF targeting. We demonstrate that Gcn5-containing complexes directly acetylate the Snf2 subunit of the SWI/SNF complex in vitro, as well as in vivo. Moreover, the acetylation of Snf2 facilitates the dissociation of the SWI/SNF complex from acetylated histones, and reduces its association with promoters in vivo. These data reveal a novel mechanism by which Gcn5 modulates chromatin structure not only through the acetylation of histones, but also by directly acetylating Snf2.
Collapse
|
48
|
Lahudkar S, Shukla A, Bajwa P, Durairaj G, Stanojevic N, Bhaumik SR. The mRNA cap-binding complex stimulates the formation of pre-initiation complex at the promoter via its interaction with Mot1p in vivo. Nucleic Acids Res 2010; 39:2188-209. [PMID: 21075799 PMCID: PMC3064766 DOI: 10.1093/nar/gkq1029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The cap-binding complex (CBC) binds to the cap structure of mRNA to protect it from exonucleases as well as to regulate downstream post-transcriptional events, translational initiation and nonsense-mediated mRNA decay. However, its role in regulation of the upstream transcriptional events such as initiation or elongation remains unknown. Here, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation assay in conjunction with transcriptional, mutational and co-immunoprecipitational analyses, we show that CBC is recruited to the body of yeast gene, and then stimulates the formation of pre-initiation complex (PIC) at several yeast promoters through its interaction with Mot1p (modifier of transcription). Mot1p is recruited to these promoters, and enhances the PIC formation. We find that CBC promotes the recruitment of Mot1p which subsequently stimulates PIC formation at these promoters. Furthermore, the formation of PIC is essential for recruitment of CBC. Thus, our study presents an interesting observation that an mRNA binding factor exhibits a reciprocal synergistic effect on formation of PIC (and hence transcriptional initiation) at the promoter, revealing a new pathway of eukaryotic gene regulation in vivo.
Collapse
Affiliation(s)
| | | | | | | | | | - Sukesh R. Bhaumik
- *To whom correspondence should be addressed. Tel: +1 618 453 6479; Fax: +1 618 453 6440;
| |
Collapse
|
49
|
Bhaumik SR. Distinct regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:97-108. [PMID: 20800707 DOI: 10.1016/j.bbagrm.2010.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 08/18/2010] [Accepted: 08/19/2010] [Indexed: 01/08/2023]
Abstract
A growing number of human diseases are linked to abnormal gene expression which is largely controlled at the level of transcriptional initiation. The gene-specific activator promotes the initiation of transcription through its interaction with one or more components of the transcriptional initiation machinery, hence leading to stimulated transcriptional initiation or activation. However, all activator proteins do not target the same component(s) of the transcriptional initiation machinery. Rather, they can have different target specificities, and thus, can lead to distinct mechanisms of transcriptional activation. Two such distinct mechanisms of transcriptional activation in yeast are mediated by the SAGA (Spt-Ada-Gcn5-Acetyltransferase) and TFIID (Transcription factor IID) complexes, and are termed as "SAGA-dependent" and "TFIID-dependent" transcriptional activation, respectively. SAGA is the target of the activator in case of SAGA-dependent transcriptional activation, while the targeting of TFIID by the activator leads to TFIID-dependent transcriptional activation. Both the SAGA and TFIID complexes are highly conserved from yeast to human, and play crucial roles in gene activation among eukaryotes. The regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID are discussed here. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!
Collapse
Affiliation(s)
- Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illnois University School of Medicine, Carbondale, IL 62901, USA.
| |
Collapse
|
50
|
Cryptococcus neoformans histone acetyltransferase Gcn5 regulates fungal adaptation to the host. EUKARYOTIC CELL 2010; 9:1193-202. [PMID: 20581290 DOI: 10.1128/ec.00098-10] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cryptococcus neoformans is an environmental fungus and an opportunistic human pathogen. Previous studies have demonstrated major alterations in its transcriptional profile as this microorganism enters the hostile environment of the human host. To assess the role of chromatin remodeling in host-induced transcriptional responses, we identified the C. neoformans Gcn5 histone acetyltransferase and demonstrated its function by complementation studies of Saccharomyces cerevisiae. The C. neoformans gcn5Delta mutant strain has defects in high-temperature growth and capsule attachment to the cell surface, in addition to increased sensitivity to FK506 and oxidative stress. Treatment of wild-type cells with the histone acetyltransferase inhibitor garcinol mimics cellular effects of the gcn5Delta mutation. Gcn5 regulates the expression of many genes that are important in responding to the specific environmental conditions encountered by C. neoformans inside the host. Accordingly, the gcn5Delta mutant is avirulent in animal models of cryptococcosis. Our study demonstrates the importance of chromatin remodeling by the conserved histone acetyltransferase Gcn5 in regulating the expression of specific genes that allow C. neoformans to respond appropriately to the human host.
Collapse
|