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Malone CF, Mabe NW, Forman AB, Alexe G, Engel KL, Chen YJC, Soeung M, Salhotra S, Basanthakumar A, Liu B, Dent SYR, Stegmaier K. The KAT module of the SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma. SCIENCE ADVANCES 2024; 10:eadm9449. [PMID: 38820154 PMCID: PMC11141635 DOI: 10.1126/sciadv.adm9449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Pediatric cancers are frequently driven by genomic alterations that result in aberrant transcription factor activity. Here, we used functional genomic screens to identify multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies for MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We characterized the DNA recruitment sites of the SAGA complex in neuroblastoma and the consequences of loss of SAGA complex lysine acetyltransferase (KAT) activity on histone acetylation and gene expression. We demonstrate that loss of SAGA complex KAT activity is associated with reduced MYCN binding on chromatin, suppression of MYC/MYCN gene expression programs, and impaired cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable in vitro and in vivo with a KAT2A/KAT2B proteolysis targeting chimeric. Our findings expand our understanding of the histone-modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.
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Affiliation(s)
- Clare F. Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nathaniel W. Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Alexandra B. Forman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kathleen L. Engel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Silvi Salhotra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Allen Basanthakumar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y. R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
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Conway TP, Simonicova L, Moye-Rowley WS. Overlapping coactivator function is required for transcriptional activation by the Candida glabrata Pdr1 transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595833. [PMID: 38853834 PMCID: PMC11160619 DOI: 10.1101/2024.05.24.595833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Azole resistance in the pathogenic yeast Candida glabrata is a serious clinical complication and increasing in frequency. The majority of resistant organisms have been found to contain a substitution mutation in the Zn2Cys6 zinc cluster-containing transcription factor Pdr1. These mutations typically lead to this factor driving high, constitutive expression of target genes like the ATP-binding cassette transporter-encoding gene CDR1 . Overexpression of Cdr1 is required for the observed elevated fluconazole resistance exhibited by strains containing one of these hyperactive PDR1 alleles. While the identity of hyperactive PDR1 alleles has been extensively documented, the mechanisms underlying how these gain-of-function (GOF) forms of Pdr1 lead to elevated target gene transcription are not well understood. We have used a tandem affinity purification (TAP)-tagged form of Pdr1 to identify coactivator proteins that biochemically purify with the wild-type and two different GOF forms of Pdr1. Three coactivator proteins were found to associate with Pdr1: the SWI/SNF complex Snf2 chromatin remodeling protein and two different components of the SAGA complex, Spt7 and Ngg1. We found that deletion mutants lacking either SNF2 or SPT7 exhibited growth defects, even in the absence of fluconazole challenge. To overcome these issues, we employed a conditional degradation system to acutely deplete these coactivators and determined that loss of either coactivator complex, SWI/SNF or SAGA, caused defects in Pdr1-dependent transcription. A double degron strain that could be depleted for both SWI/SNF and SAGA exhibited a profound defect in PDR1 autoregulation, revealing that these complexes work together to ensure high level Pdr1-dependent gene transcription.
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Barbosa K, Deshpande A, Perales M, Xiang P, Murad R, Pramod AB, Minkina A, Robertson N, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, Humphries RK, Ruppin E, Shendure J, Mali P, Adams PD, Deshpande AJ. Transcriptional control of leukemogenesis by the chromatin reader SGF29. Blood 2024; 143:697-712. [PMID: 38048593 PMCID: PMC10900139 DOI: 10.1182/blood.2023021234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
ABSTRACT Aberrant expression of stem cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators coordinately controlled the transcription of several AML oncogenes. In particular, we identified a novel role for the Tudor-domain-containing chromatin reader protein SGF29 in the transcription of AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes in multiple AML subtype models. Our studies reveal a novel role for SGF29 as a nononcogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery.
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Affiliation(s)
- Karina Barbosa
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anagha Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Marlenne Perales
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Ping Xiang
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rabi Murad
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Akula Bala Pramod
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anna Minkina
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Neil Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xue Lei
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Younguk Sun
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Adam Brown
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | | | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA
| | - Peter D. Adams
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Aniruddha J. Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
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4
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Yu CK, Stephenson CJ, Villamor TC, Dyba TG, Schulz BL, Fraser JA. SAGA Complex Subunit Hfi1 Is Important in the Stress Response and Pathogenesis of Cryptococcus neoformans. J Fungi (Basel) 2023; 9:1198. [PMID: 38132798 PMCID: PMC10744473 DOI: 10.3390/jof9121198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023] Open
Abstract
The Spt-Ada-Gcn Acetyltransferase (SAGA) complex is a highly conserved co-activator found across eukaryotes. It is composed of a number of modules which can vary between species, but all contain the core module. Hfi1 (known as TADA1 in Homo sapiens) is one of the proteins that forms the core module, and has been shown to play an important role in maintaining complex structural integrity in both brewer's yeast and humans. In this study we successfully identified the gene encoding this protein in the important fungal pathogen, Cryptococcus neoformans, and named it HFI1. The hfi1Δ mutant is highly pleiotropic in vitro, influencing phenotypes, ranging from temperature sensitivity and melanin production to caffeine resistance and titan cell morphogenesis. In the absence of Hfi1, the transcription of several other SAGA genes is impacted, as is the acetylation and deubiquination of several histone residues. Importantly, loss of the gene significantly impacts virulence in a murine inhalation model of cryptococcosis. In summary, we have established that Hfi1 modulates multiple pathways that directly affect virulence and survival in C. neoformans, and provided deeper insight into the importance of the non-enzymatic components of the SAGA complex.
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Affiliation(s)
| | | | | | | | | | - James A. Fraser
- School of Chemistry & Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia; (C.K.Y.); (C.J.S.); (T.C.V.); (T.G.D.); (B.L.S.)
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5
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Barman P, Chakraborty P, Bhaumik R, Bhaumik SR. UPS writes a new saga of SAGA. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194981. [PMID: 37657588 PMCID: PMC10843445 DOI: 10.1016/j.bbagrm.2023.194981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
SAGA (Spt-Ada-Gcn5-Acetyltransferase), an evolutionarily conserved transcriptional co-activator among eukaryotes, is a large multi-subunit protein complex with two distinct enzymatic activities, namely HAT (Histone acetyltransferase) and DUB (De-ubiquitinase), and is targeted to the promoter by the gene-specific activator proteins for histone covalent modifications and PIC (Pre-initiation complex) formation in enhancing transcription (or gene activation). Targeting of SAGA to the gene promoter is further facilitated by the 19S RP (Regulatory particle) of the 26S proteasome (that is involved in targeted degradation of protein via ubiquitylation) in a proteolysis-independent manner. Moreover, SAGA is also recently found to be regulated by the 26S proteasome in a proteolysis-dependent manner via the ubiquitylation of its Sgf73/ataxin-7 component that is required for SAGA's integrity and DUB activity (and hence transcription), and is linked to various diseases including neurodegenerative disorders and cancer. Thus, SAGA itself and its targeting to the active gene are regulated by the UPS (Ubiquitin-proteasome system) with implications in diseases.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Rhea Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA.
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6
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Fu W, MacGregor DR, Comont D, Saski CA. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass ( Alopecurus myosuroides) Populations. Genes (Basel) 2023; 14:1905. [PMID: 37895254 PMCID: PMC10606437 DOI: 10.3390/genes14101905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
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Affiliation(s)
- Wangfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Dana R. MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - David Comont
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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7
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Barman P, Kaja A, Chakraborty P, Guha S, Roy A, Ferdoush J, Bhaumik SR. A novel ubiquitin-proteasome system regulation of Sgf73/ataxin-7 that maintains the integrity of the coactivator SAGA in orchestrating transcription. Genetics 2023; 224:iyad071. [PMID: 37075097 PMCID: PMC10324951 DOI: 10.1093/genetics/iyad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023] Open
Abstract
Ataxin-7 maintains the integrity of Spt-Ada-Gcn5-Acetyltransferase (SAGA), an evolutionarily conserved coactivator in stimulating preinitiation complex (PIC) formation for transcription initiation, and thus, its upregulation or downregulation is associated with various diseases. However, it remains unknown how ataxin-7 is regulated that could provide new insights into disease pathogenesis and therapeutic interventions. Here, we show that ataxin-7's yeast homologue, Sgf73, undergoes ubiquitylation and proteasomal degradation. Impairment of such regulation increases Sgf73's abundance, which enhances recruitment of TATA box-binding protein (TBP) (that nucleates PIC formation) to the promoter but impairs transcription elongation. Further, decreased Sgf73 level reduces PIC formation and transcription. Thus, Sgf73 is fine-tuned by ubiquitin-proteasome system (UPS) in orchestrating transcription. Likewise, ataxin-7 undergoes ubiquitylation and proteasomal degradation, alteration of which changes ataxin-7's abundance that is associated with altered transcription and cellular pathologies/diseases. Collectively, our results unveil a novel UPS regulation of Sgf73/ataxin-7 for normal cellular health and implicate alteration of such regulation in diseases.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Amala Kaja
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX-77030, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Arpan Roy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jannatul Ferdoush
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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8
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Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol 2022; 29:1239-1251. [PMID: 36482254 PMCID: PMC10228515 DOI: 10.1038/s41594-022-00890-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading, possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disrupting this traffic pattern, by removing CTCF, renders cells sensitive to knockout of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.
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Affiliation(s)
- Anne-Laure Valton
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Eraj Shafiq Khokhar
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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9
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Rashid S, Correia-Mesquita TO, Godoy P, Omran RP, Whiteway M. SAGA Complex Subunits in Candida albicans Differentially Regulate Filamentation, Invasiveness, and Biofilm Formation. Front Cell Infect Microbiol 2022; 12:764711. [PMID: 35350439 PMCID: PMC8957876 DOI: 10.3389/fcimb.2022.764711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Abstract
SAGA (Spt-Ada-Gcn5-acetyltransferase) is a highly conserved, multiprotein co-activator complex that consists of five distinct modules. It has two enzymatic functions, a histone acetyltransferase (HAT) and a deubiquitinase (DUB) and plays a central role in processes such as transcription initiation, elongation, protein stability, and telomere maintenance. We analyzed conditional and null mutants of the SAGA complex module components in the fungal pathogen Candida albicans; Ngg1, (the HAT module); Ubp8, (the DUB module); Tra1, (the recruitment module), Spt7, (the architecture module) and Spt8, (the TBP interaction unit), and assessed their roles in a variety of cellular processes. We observed that spt7Δ/Δ and spt8Δ/Δ strains have a filamentous phenotype, and both are highly invasive in yeast growing conditions as compared to the wild type, while ngg1Δ/Δ and ubp8Δ/Δ are in yeast-locked state and non-invasive in both YPD media and filamentous induced conditions compared to wild type. RNA-sequencing-based transcriptional profiling of SAGA mutants reveals upregulation of hyphal specific genes in spt7Δ/Δ and spt8Δ/Δ strains and downregulation of ergosterol metabolism pathway. As well, spt7Δ/Δ and spt8Δ/Δ confer susceptibility to antifungal drugs, to acidic and alkaline pH, to high temperature, and to osmotic, oxidative, cell wall, and DNA damage stresses, indicating that these proteins are important for genotoxic and cellular stress responses. Despite having similar morphological phenotypes (constitutively filamentous and invasive) spt7 and spt8 mutants displayed variation in nuclear distribution where spt7Δ/Δ cells were frequently binucleate and spt8Δ/Δ cells were consistently mononucleate. We also observed that spt7Δ/Δ and spt8Δ/Δ mutants were quickly engulfed by macrophages compared to ngg1Δ/Δ and ubp8Δ/Δ strains. All these findings suggest that the SAGA complex modules can have contrasting functions where loss of Spt7 or Spt8 enhances filamentation and invasiveness while loss of Ngg1 or Ubp8 blocks these processes.
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Affiliation(s)
| | | | | | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montreal, QC, Canada
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10
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Zuo S, Yi Y, Wang C, Li X, Zhou M, Peng Q, Zhou J, Yang Y, He Q. Extrachromosomal Circular DNA (eccDNA): From Chaos to Function. Front Cell Dev Biol 2022; 9:792555. [PMID: 35083218 PMCID: PMC8785647 DOI: 10.3389/fcell.2021.792555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/16/2021] [Indexed: 11/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a type of double-stranded circular DNA that is derived and free from chromosomes. It has a strong heterogeneity in sequence, length, and origin and has been identified in both normal and cancer cells. Although many studies suggested its potential roles in various physiological and pathological procedures including aging, telomere and rDNA maintenance, drug resistance, and tumorigenesis, the functional relevance of eccDNA remains to be elucidated. Recently, due to technological advancements, accumulated evidence highlighted that eccDNA plays an important role in cancers by regulating the expression of oncogenes, chromosome accessibility, genome replication, immune response, and cellular communications. Here, we review the features, biogenesis, physiological functions, potential functions in cancer, and research methods of eccDNAs with a focus on some open problems in the field and provide a perspective on how eccDNAs evolve specific functions out of the chaos in cells.
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Affiliation(s)
- Shanru Zuo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yihu Yi
- Department of Orthopaedics, Wuhan Union Hospital, Wuhan, China
| | - Chen Wang
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Mingqing Zhou
- Zhongshan Hospital Affiliated to Sun Yat-Sen University, Zhongshan People's Hospital, Zhongshan, China
| | - Qiyao Peng
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine and Innovation Centre for Science and Technology, Hunan University of Chinese Medicine, Changsa, China.,Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
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11
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Lu H, Shrivastava M, Whiteway M, Jiang Y. Candida albicans targets that potentially synergize with fluconazole. Crit Rev Microbiol 2021; 47:323-337. [PMID: 33587857 DOI: 10.1080/1040841x.2021.1884641] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluconazole has characteristics that make it widely used in the clinical treatment of C. albicans infections. However, fluconazole has only a fungistatic activity in C. albicans, therefore, in the long-term treatment of C. albicans infection with fluconazole, C. albicans has the potential to acquire fluconazole resistance. A promising approach to increase fluconazole's efficacy is identifying potential targets of drugs that can enhance the antifungal effect of fluconazole, or even make the drug fungicidal. In this review, we systematically provide a global overview of potential targets of drugs synergistic with fluconazole in C. albicans, identify new avenues for research on fluconazole potentiation, and highlight the promise of combinatorial strategies with fluconazole in combatting C. albicans infections.
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Affiliation(s)
- Hui Lu
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Yuanying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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12
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Goh CJH, Wong JH, El Farran C, Tan BX, Coffill CR, Loh YH, Lane D, Arumugam P. Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen. G3 (BETHESDA, MD.) 2021; 11:jkaa069. [PMID: 33604667 PMCID: PMC8022920 DOI: 10.1093/g3journal/jkaa069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Vemurafenib is a BRAF kinase inhibitor (BRAFi) that is used to treat melanoma patients harboring the constitutively active BRAF-V600E mutation. However, after a few months of treatment patients often develop resistance to vemurafenib leading to disease progression. Sequence analysis of drug-resistant tumor cells and functional genomic screens has identified several genes that regulate vemurafenib resistance. Reactivation of mitogen-activated protein kinase (MAPK) pathway is a recurrent feature of cells that develop resistance to vemurafenib. We performed a genome-scale CRISPR-based knockout screen to identify modulators of vemurafenib resistance in melanoma cells with a highly improved CRISPR sgRNA library called Brunello. We identified 33 genes that regulate resistance to vemurafenib out of which 14 genes have not been reported before. Gene ontology enrichment analysis showed that the hit genes regulate histone modification, transcription and cell cycle. We discuss how inactivation of hit genes might confer resistance to vemurafenib and provide a framework for follow-up investigations.
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Affiliation(s)
| | - Jin Huei Wong
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
| | - Chadi El Farran
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Ban Xiong Tan
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore
| | | | - Yuin-Hain Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - David Lane
- p53Lab, A*STAR, Singapore 138648, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
- Singapore Institute for Food and Biotechnology Innovation, Singapore 138632, Singapore
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13
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Vlachonasios K, Poulios S, Mougiou N. The Histone Acetyltransferase GCN5 and the Associated Coactivators ADA2: From Evolution of the SAGA Complex to the Biological Roles in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:308. [PMID: 33562796 PMCID: PMC7915528 DOI: 10.3390/plants10020308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Transcription of protein-encoding genes starts with forming a pre-initiation complex comprised of RNA polymerase II and several general transcription factors. To activate gene expression, transcription factors must overcome repressive chromatin structure, which is accomplished with multiprotein complexes. One such complex, SAGA, modifies the nucleosomal histones through acetylation and other histone modifications. A prototypical histone acetyltransferase (HAT) known as general control non-repressed protein 5 (GCN5), was defined biochemically as the first transcription-linked HAT with specificity for histone H3 lysine 14. In this review, we analyze the components of the putative plant SAGA complex during plant evolution, and current knowledge on the biological role of the key components of the HAT module, GCN5 and ADA2b in plants, will be summarized.
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Affiliation(s)
- Konstantinos Vlachonasios
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.P.); (N.M.)
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14
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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.
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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
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15
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Marsh DJ, Ma Y, Dickson KA. Histone Monoubiquitination in Chromatin Remodelling: Focus on the Histone H2B Interactome and Cancer. Cancers (Basel) 2020; 12:E3462. [PMID: 33233707 PMCID: PMC7699835 DOI: 10.3390/cancers12113462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin remodelling is a major mechanism by which cells control fundamental processes including gene expression, the DNA damage response (DDR) and ensuring the genomic plasticity required by stem cells to enable differentiation. The post-translational modification of histone H2B resulting in addition of a single ubiquitin, in humans at lysine 120 (K120; H2Bub1) and in yeast at K123, has key roles in transcriptional elongation associated with the RNA polymerase II-associated factor 1 complex (PAF1C) and in the DDR. H2Bub1 itself has been described as having tumour suppressive roles and a number of cancer-related proteins and/or complexes are recognised as part of the H2Bub1 interactome. These include the RING finger E3 ubiquitin ligases RNF20, RNF40 and BRCA1, the guardian of the genome p53, the PAF1C member CDC73, subunits of the switch/sucrose non-fermenting (SWI/SNF) chromatin remodelling complex and histone methyltransferase complexes DOT1L and COMPASS, as well as multiple deubiquitinases including USP22 and USP44. While globally depleted in many primary human malignancies, including breast, lung and colorectal cancer, H2Bub1 is selectively enriched at the coding region of certain highly expressed genes, including at p53 target genes in response to DNA damage, functioning to exercise transcriptional control of these loci. This review draws together extensive literature to cement a significant role for H2Bub1 in a range of human malignancies and discusses the interplay between key cancer-related proteins and H2Bub1-associated chromatin remodelling.
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Affiliation(s)
- Deborah J. Marsh
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
- Kolling Institute, Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Yue Ma
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
| | - Kristie-Ann Dickson
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
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16
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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17
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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18
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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19
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Pezoa SA, Artinger KB, Niswander LA. GCN5 acetylation is required for craniofacial chondrocyte maturation. Dev Biol 2020; 464:24-34. [PMID: 32446700 DOI: 10.1016/j.ydbio.2020.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
Development of the craniofacial structures requires the precise differentiation of cranial neural crest cells into osteoblasts or chondrocytes. Here, we explore the epigenetic and non-epigenetic mechanisms that are required for the development of craniofacial chondrocytes. We previously demonstrated that the acetyltransferase activity of the highly conserved acetyltransferase GCN5, or KAT2A, is required for murine craniofacial development. We show that Gcn5 is required cell autonomously in the cranial neural crest. Moreover, GCN5 is required for chondrocyte development following the arrival of the cranial neural crest within the pharyngeal arches. Using a combination of in vivo and in vitro inhibition of GCN5 acetyltransferase activity, we demonstrate that GCN5 is a potent activator of chondrocyte maturation, acting to control chondrocyte maturation and size increase during pre-hypertrophic maturation to hypertrophic chondrocytes. Rather than acting as an epigenetic regulator of histone H3K9 acetylation, our findings suggest GCN5 primarily acts as a non-histone acetyltransferase to regulate chondrocyte development. Here, we investigate the contribution of GCN5 acetylation to the activity of the mTORC1 pathway. Our findings indicate that GCN5 acetylation is required for activation of this pathway, either via direct activation of mTORC1 or through indirect mechanisms. We also investigate one possibility of how mTORC1 activity is regulated through RAPTOR acetylation, which is hypothesized to enhance mTORC1 downstream phosphorylation. This study contributes to our understanding of the specificity of acetyltransferases, and the cell type specific roles in which these enzymes function.
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Affiliation(s)
- Sofia A Pezoa
- Cell Biology, Stem Cells, and Developmental Biology Graduate Program. University of Colorado Anschutz School of Medicine, Aurora, CO, USA, 80045; Department of Molecular, Cellular, and Developmental Biology. University of Colorado Boulder, Boulder, CO, USA, 80309
| | - Kristin B Artinger
- Department of Craniofacial Biology, University of Colorado Anschutz School of Dentistry, Aurora, CO, USA, 80045
| | - Lee A Niswander
- Department of Molecular, Cellular, and Developmental Biology. University of Colorado Boulder, Boulder, CO, USA, 80309.
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20
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Ain Q, Schmeer C, Wengerodt D, Witte OW, Kretz A. Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration. Int J Mol Sci 2020; 21:E2477. [PMID: 32252492 PMCID: PMC7177960 DOI: 10.3390/ijms21072477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.
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Affiliation(s)
- Quratul Ain
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
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21
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Mustachio LM, Roszik J, Farria A, Dent SYR. Targeting the SAGA and ATAC Transcriptional Coactivator Complexes in MYC-Driven Cancers. Cancer Res 2020; 80:1905-1911. [PMID: 32094302 DOI: 10.1158/0008-5472.can-19-3652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Targeting epigenetic regulators, such as histone-modifying enzymes, provides novel strategies for cancer therapy. The GCN5 lysine acetyltransferase (KAT) functions together with MYC both during normal development and in oncogenesis. As transcription factors, MYC family members are difficult to target with small-molecule inhibitors, but the acetyltransferase domain and the bromodomain in GCN5 might provide alternative targets for disruption of MYC-driven functions. GCN5 is part of two distinct multiprotein histone-modifying complexes, SAGA and ATAC. This review summarizes key findings on the roles of SAGA and ATAC in embryo development and in cancer to better understand the functional relationships of these complexes with MYC family members, as well as their future potential as therapeutic targets.
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Affiliation(s)
- Lisa Maria Mustachio
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aimee Farria
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sharon Y R Dent
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
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22
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Mustachio LM, Roszik J, Farria AT, Guerra K, Dent SYR. Repression of GCN5 expression or activity attenuates c-MYC expression in non-small cell lung cancer. Am J Cancer Res 2019; 9:1830-1845. [PMID: 31497362 PMCID: PMC6726999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023] Open
Abstract
Lung cancer causes the highest mortality in cancer-related deaths. As these cancers often become resistant to existing therapies, definition of novel molecular targets is needed. Epigenetic modifiers may provide such targets. Recent reports suggest that the histone acetyltransferase (HAT) module within the transcriptional coactivator SAGA complex plays a role in cancer, creating a new link between epigenetic regulators and this disease. GCN5 serves as a coactivator for MYC target genes, and here we investigate links between GCN5 and c-MYC in non-small cell lung cancer (NSCLC). Our data indicate that both GCN5 and c-MYC proteins are upregulated in mouse and human NSCLC cells compared to normal lung epithelial cells. This trend is observable only at the protein level, indicating that this upregulation occurs post-transcriptionally. Human NSCLC tissue data provided by The Cancer Genome Atlas (TCGA) indicates that GCN5 and c-MYC expression are positively associated with one another and with the expression of c-MYC target genes. Depletion of GCN5 in NSCLC cells reduces c-MYC expression, cell proliferation, and increases the population of necrotic cells. Similarly, inhibition of the GCN5 catalytic site using a commercially available probe reduces c-MYC expression, cell proliferation, and increases the percentage of cells undergoing apoptosis. Our findings suggest that GCN5 might provide a novel target for inhibition of NSCLC growth and progression.
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Affiliation(s)
- Lisa Maria Mustachio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Karla Guerra
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
| | - Sharon YR Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
- Department of Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer CenterHouston, Texas 77030, USA
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23
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Saettone A, Nabeel-Shah S, Garg J, Lambert JP, Pearlman RE, Fillingham J. Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review. Genes (Basel) 2019; 10:E333. [PMID: 31052454 PMCID: PMC6562869 DOI: 10.3390/genes10050333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Identification and characterization of protein complexes and interactomes has been essential to the understanding of fundamental nuclear processes including transcription, replication, recombination, and maintenance of genome stability. Despite significant progress in elucidation of nuclear proteomes and interactomes of organisms such as yeast and mammalian systems, progress in other models has lagged. Protists, including the alveolate ciliate protozoa with Tetrahymena thermophila as one of the most studied members of this group, have a unique nuclear biology, and nuclear dimorphism, with structurally and functionally distinct nuclei in a common cytoplasm. These features have been important in providing important insights about numerous fundamental nuclear processes. Here, we review the proteomic approaches that were historically used as well as those currently employed to take advantage of the unique biology of the ciliates, focusing on Tetrahymena, to address important questions and better understand nuclear processes including chromatin biology of eukaryotes.
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Affiliation(s)
- Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| | - Jyoti Garg
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada.
- CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, QC, G1V 4G2, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
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Shih PY, Liao YT, Tseng YK, Deng FS, Lin CH. A Potential Antifungal Effect of Chitosan Against Candida albicans Is Mediated via the Inhibition of SAGA Complex Component Expression and the Subsequent Alteration of Cell Surface Integrity. Front Microbiol 2019; 10:602. [PMID: 30972050 PMCID: PMC6443709 DOI: 10.3389/fmicb.2019.00602] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022] Open
Abstract
Due to the high incidence of nosocomial Candida albicans infection, the first-line drugs for C. albicans infection have been heavily used, and the emergence of drug-resistant strains has gradually increased. Thus, a new antifungal drug or therapeutic method is needed. Chitosan, a product of chitin deacetylation, is considered to be potentially therapeutic for fungal infections because of its excellent biocompatibility, biodegradability and low toxicity. The biocidal action of chitosan against C. albicans shows great commercial potential, but the exact mechanisms underlying its antimicrobial activity are unclear. To reveal these mechanisms, mutant library screening was performed. ADA2 gene, which encodes a histone acetylation coactivator in the SAGA complex, was identified. Transmission electronic microscopy images showed that the surface of chitosan-treated ada2Δ cells was substantially disrupted and displayed an irregular morphology. Interestingly, the cell wall of ada2Δ cells was significantly thinner than that of wild-type cells, with a thickness similar to that seen in the chitosan-treated wild-type strain. Although ADA2 is required for chitosan tolerance, expression of ADA2 and several Ada2-mediated cell wall-related genes (ALS2, PGA45, and ACE2) and efflux transporter genes (MDR1 and CDR1) were significantly inhibited by chitosan. Furthermore, GCN5 encoding a SAGA complex catalytic subunit was inhibited by chitosan, and gcn5Δ cells exhibited phenotypes comparable to those of ada2Δ cells in response to chitosan and other cell surface-disrupting agents. This study demonstrated that a potential antifungal mechanism of chitosan against C. albicans operates by inhibiting SAGA complex gene expression, which decreases the protection of the cell surface against chitosan.
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Affiliation(s)
- Pei-Yu Shih
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Liao
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi-Kai Tseng
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Fu-Sheng Deng
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Hsuan Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
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25
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Wang B, Li X, Yu D, Chen X, Tabudravu J, Deng H, Pan L. Deletion of the epigenetic regulator GcnE in Aspergillus niger FGSC A1279 activates the production of multiple polyketide metabolites. Microbiol Res 2018; 217:101-107. [DOI: 10.1016/j.micres.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/22/2018] [Accepted: 10/13/2018] [Indexed: 10/28/2022]
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26
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Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Proc Natl Acad Sci U S A 2018; 115:10010-10015. [PMID: 30224453 DOI: 10.1073/pnas.1805343115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Gcn5 histone acetyltransferase (HAT) subunit of the SAGA transcriptional coactivator complex catalyzes acetylation of histone H3 and H2B N-terminal tails, posttranslational modifications associated with gene activation. Binding of the SAGA subunit partner Ada2 to Gcn5 activates Gcn5's intrinsically weak HAT activity on histone proteins, but the mechanism for this activation by the Ada2 SANT domain has remained elusive. We have employed Fab antibody fragments as crystallization chaperones to determine crystal structures of a yeast Ada2/Gcn5 complex. Our structural and biochemical results indicate that the Ada2 SANT domain does not activate Gcn5's activity by directly affecting histone peptide binding as previously proposed. Instead, the Ada2 SANT domain enhances Gcn5 binding of the enzymatic cosubstrate acetyl-CoA. This finding suggests a mechanism for regulating chromatin modification enzyme activity: controlling binding of the modification cosubstrate instead of the histone substrate.
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27
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Abstract
Chromatin packaging of DNA provides a framework for transcriptional regulation. Modifications to DNA and histone proteins in nucleosomes lead to conformational changes, alterations in the recruitment of transcriptional complexes, and ultimately modulation of gene expression. We provide a focused review of control mechanisms that help modulate the activation and deactivation of gene transcription specifically through histone acetylation writers and readers in cancer. The chemistry of these modifications is subject to clinically actionable targeting, including state-of-the-art strategies to inhibit basic oncogenic mechanisms related to histone acetylation. Although discussed in the context of acute leukemia, the concepts of acetylation writers and readers are not cell-type-specific and are generalizable to other cancers. We review the challenges and resistance mechanisms encountered to date in the development of such therapeutics and postulate how such challenges may be overcome. Because these fundamental cellular mechanisms are dysregulated in cancer biology, continued research and in-depth understanding of histone acetylation reading and writing are desired to further define optimal therapeutic strategies to affect gene activity to target cancer effectively.
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28
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Fursova NA, Nikolenko JV, Soshnikova NV, Mazina MY, Vorobyova NE, Krasnov AN. Zinc Finger Protein CG9890 - New Component of ENY2-Containing Complexes of Drosophila. Acta Naturae 2018; 10:110-114. [PMID: 30713769 PMCID: PMC6351030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In previous studies, we showed that the insulator protein Su(Hw) containing zinc finger domains interacts with the ENY2 protein and recruits the ENY2-containing complexes on Su(Hw)-dependent insulators, participating in the regulation of transcription and in the positioning of replication origins. Here, we found interaction between ENY2 and CG9890 protein, which also contains zinc finger domains. The interaction between ENY2 and CG9890 was confirmed. It was established that CG9890 protein is localized in the nucleus and interacts with the SAGA, ORC, dSWI/SNF, TFIID, and THO protein complexes.
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Affiliation(s)
- N. A. Fursova
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - J. V. Nikolenko
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - N. V. Soshnikova
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - M. Y. Mazina
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - N. E. Vorobyova
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - A. N. Krasnov
- Institute of Gene Biology Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
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29
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Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation. Stem Cell Reports 2017; 10:287-299. [PMID: 29249668 PMCID: PMC5768892 DOI: 10.1016/j.stemcr.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin-modifying enzymes affect specific developmental processes is not well defined. Here, we report that GCN5, a histone acetyltransferase essential for embryonic development, is required for proper expression of multiple genes encoding components of the fibroblast growth factor (FGF) signaling pathway in early embryoid bodies (EBs). Gcn5-/- EBs display deficient activation of ERK and p38, mislocalization of cytoskeletal components, and compromised capacity to differentiate toward mesodermal lineage. Genomic analyses identified seven genes as putative direct targets of GCN5 during early differentiation, four of which are cMYC targets. These findings established a link between GCN5 and the FGF signaling pathway and highlighted specific GCN5-MYC partnerships in gene regulation during early differentiation.
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Affiliation(s)
- Li Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Calley Hirsch
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Ryan McCarthy
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Andria Schibler
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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30
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Kassem S, Villanyi Z, Collart MA. Not5-dependent co-translational assembly of Ada2 and Spt20 is essential for functional integrity of SAGA. Nucleic Acids Res 2017; 45:1186-1199. [PMID: 28180299 PMCID: PMC5388395 DOI: 10.1093/nar/gkw1059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/04/2016] [Accepted: 10/22/2016] [Indexed: 11/13/2022] Open
Abstract
Acetylation of histones regulates gene expression in eukaryotes. In the yeast Saccharomyces cerevisiae it depends mainly upon the ADA and SAGA histone acetyltransferase complexes for which Gcn5 is the catalytic subunit. Previous screens have determined that global acetylation is reduced in cells lacking subunits of the Ccr4–Not complex, a global regulator of eukaryotic gene expression. In this study we have characterized the functional connection between the Ccr4–Not complex and SAGA. We show that SAGA mRNAs encoding a core set of SAGA subunits are tethered together for co-translational assembly of the encoded proteins. Ccr4–Not subunits bind SAGA mRNAs and promote the co-translational assembly of these subunits. This is needed for integrity of SAGA. In addition, we determine that a glycolytic enzyme, the glyceraldehyde-3-phosphate dehydrogenase Tdh3, a prototypical moonlighting protein, is tethered at this site of Ccr4–Not-dependent co-translational SAGA assembly and functions as a chaperone.
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Affiliation(s)
- Sari Kassem
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
| | - Zoltan Villanyi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics Geneva, University of Geneva, Geneva, Switzerland
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31
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SAGA complex mediates the transcriptional up-regulation of antiviral RNA silencing. Proc Natl Acad Sci U S A 2017; 114:E3499-E3506. [PMID: 28400515 DOI: 10.1073/pnas.1701196114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pathogen recognition and transcriptional activation of defense-related genes are crucial steps in cellular defense responses. RNA silencing (RNAi) functions as an antiviral defense in eukaryotic organisms. Several RNAi-related genes are known to be transcriptionally up-regulated upon virus infection in some host organisms, but little is known about their induction mechanism. A phytopathogenic ascomycete, Cryphonectria parasitica (chestnut blight fungus), provides a particularly advantageous system to study RNAi activation, because its infection by certain RNA viruses induces the transcription of dicer-like 2 (dcl2) and argonaute-like 2 (agl2), two major RNAi players. To identify cellular factors governing activation of antiviral RNAi in C. parasitica, we developed a screening protocol entailing multiple transformations of the fungus with cDNA of a hypovirus mutant lacking the RNAi suppressor (CHV1-Δp69), a reporter construct with a GFP gene driven by the dcl2 promoter, and a random mutagenic construct. Screening for GFP-negative colonies allowed the identification of sgf73, a component of the SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, a well-known transcriptional coactivator. Knockout of other SAGA components showed that the histone acetyltransferase module regulates transcriptional induction of dcl2 and agl2, whereas histone deubiquitinase mediates regulation of agl2 but not dcl2 Interestingly, full-scale induction of agl2 and dcl2 by CHV1-Δp69 required both DCL2 and AGL2, whereas that by another RNA virus, mycoreovirus 1, required only DCL2, uncovering additional roles for DCL2 and AGL2 in viral recognition and/or RNAi activation. Overall, these results provide insight into the mechanism of RNAi activation.
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32
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Wong MM, Chong GL, Verslues PE. Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA? Methods Mol Biol 2017; 1631:3-21. [PMID: 28735388 DOI: 10.1007/978-1-4939-7136-7_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There have been great research advances in epigenetics, RNA splicing, and mRNA processing over recent years. In parallel, there have been many advances in abiotic stress and Abscisic Acid (ABA) signaling. Here we overview studies that have examined stress-induced changes in the epigenome and RNA processing as well as cases where disrupting these processes changes the plant response to abiotic stress. We also highlight some examples where specific connections of stress or ABA signaling to epigenetics or RNA processing have been found. By implication, this also points out cases where such mechanistic connections are likely to exist but are yet to be characterized. In the absence of such specific connections to stress signaling, it should be kept in mind that stress sensitivity phenotypes of some epigenetic or RNA processing mutants maybe the result of indirect, pleiotropic effects and thus may perhaps not indicate a direct function in stress acclimation.
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Affiliation(s)
- Min May Wong
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, 11529, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227, Taiwan
| | - Geeng Loo Chong
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, 11529, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227, Taiwan
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Academia Road, Taipei, 11529, Taiwan. .,Biotechnology Center, National Chung-Hsing University, Taichung, 40227, Taiwan.
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33
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Rösler SM, Kramer K, Finkemeier I, Humpf HU, Tudzynski B. The SAGA complex in the rice pathogenFusarium fujikuroi: structure and functional characterization. Mol Microbiol 2016; 102:951-974. [DOI: 10.1111/mmi.13528] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah M. Rösler
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster; Corrensstraße 45 Münster 48149 Germany
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
| | - Katharina Kramer
- Max Planck Institute for Plant Breeding Research, Plant Proteomics Group; Carl-von-Linne-Weg 10 Cologne 50829 Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
- Max Planck Institute for Plant Breeding Research, Plant Proteomics Group; Carl-von-Linne-Weg 10 Cologne 50829 Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster; Corrensstraße 45 Münster 48149 Germany
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
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34
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Kamata K, Shinmyozu K, Nakayama JI, Hatashita M, Uchida H, Oki M. Four domains of Ada1 form a heterochromatin boundary through different mechanisms. Genes Cells 2016; 21:1125-1136. [PMID: 27647735 DOI: 10.1111/gtc.12421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/14/2016] [Indexed: 01/21/2023]
Abstract
In eukaryotic cells, there are two chromatin states, silenced and active, and the formation of a so-called boundary plays a critical role in demarcating these regions; however, the mechanisms underlying boundary formation are not well understood. In this study, we focused on S. cerevisiae ADA1, a gene previously shown to encode a protein with a robust boundary function. Ada1 is a component of the histone modification complex Spt-Ada-Gcn5-acetyltransferase (SAGA) and the SAGA-like (SLIK) complex, and it helps to maintain the integrity of these complexes. Domain analysis showed that four relatively small regions of Ada1 (Region I; 66-75 aa, II; 232-282 aa, III; 416-436 aa and IV; 476-488 aa) have a boundary function. Among these, Region II could form an intact SAGA complex, whereas the other regions could not. Investigation of cellular factors that interact with these small regions identified a number of proteasome-associated proteins. Interestingly, the boundary functions of Region II and Region III were affected by depletion of Ump1, a maturation and assembly factor of the 20S proteasome. These results suggest that the boundary function of Ada1 is functionally linked to proteasome processes and that the four relatively small regions in ADA1 form a boundary via different mechanisms.
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Affiliation(s)
- Kazuma Kamata
- Department of Applied Chemistry Biotechnology, Graduate School of Engineering, University of Fukui, Bunkyo, Fukui, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kaori Shinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Masanori Hatashita
- Research and Development Department, Wakasa Wan Energy Research Center, Tsuruga, Japan
| | - Hiroyuki Uchida
- Department of Applied Chemistry Biotechnology, Graduate School of Engineering, University of Fukui, Bunkyo, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry Biotechnology, Graduate School of Engineering, University of Fukui, Bunkyo, Fukui, Japan. .,Life Science Innovation Center, University of Fukui, Bunkyo, Fukui, Japan. .,PRESTO, Japan Science and Technology Agency (JST), Honcho Kawaguchi, Saitama, Japan.
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35
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Acetylation of Mammalian ADA3 Is Required for Its Functional Roles in Histone Acetylation and Cell Proliferation. Mol Cell Biol 2016; 36:2487-502. [PMID: 27402865 PMCID: PMC5021379 DOI: 10.1128/mcb.00342-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 06/30/2016] [Indexed: 12/16/2022] Open
Abstract
Alteration/deficiency in activation 3 (ADA3) is an essential component of specific histone acetyltransferase (HAT) complexes. We have previously shown that ADA3 is required for establishing global histone acetylation patterns and for normal cell cycle progression (S. Mohibi et al., J Biol Chem 287:29442-29456, 2012, http://dx.doi.org/10.1074/jbc.M112.378901). Here, we report that these functional roles of ADA3 require its acetylation. We show that ADA3 acetylation, which is dynamically regulated in a cell cycle-dependent manner, reflects a balance of coordinated actions of its associated HATs, GCN5, PCAF, and p300, and a new partner that we define, the deacetylase SIRT1. We use mass spectrometry and site-directed mutagenesis to identify major sites of ADA3 acetylated by GCN5 and p300. Acetylation-defective mutants are capable of interacting with HATs and other components of HAT complexes but are deficient in their ability to restore ADA3-dependent global or locus-specific histone acetylation marks and cell proliferation in Ada3-deleted murine embryonic fibroblasts (MEFs). Given the key importance of ADA3-containing HAT complexes in the regulation of various biological processes, including the cell cycle, our study presents a novel mechanism to regulate the function of these complexes through dynamic ADA3 acetylation.
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36
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Randise-Hinchliff C, Brickner JH. Transcription factors dynamically control the spatial organization of the yeast genome. Nucleus 2016; 7:369-74. [PMID: 27442220 PMCID: PMC5039007 DOI: 10.1080/19491034.2016.1212797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In yeast, inducible genes such as INO1, PRM1 and HIS4 reposition from the nucleoplasm to nuclear periphery upon activation. This leads to a physical interaction with nuclear pore complex (NPC), interchromosomal clustering, and stronger transcription. Repositioning to the nuclear periphery is controlled by cis-acting transcription factor (TF) binding sites located within the promoters of these genes and the TFs that bind to them. Such elements are both necessary and sufficient to control positioning of genes to the nuclear periphery. We have identified 4 TFs capable of controlling the regulated positioning of genes to the nuclear periphery in budding yeast under different conditions: Put3, Cbf1, Gcn4 and Ste12. In each case, we have defined the molecular basis of regulated relocalization to the nuclear periphery. Put3- and Cbf1-mediated targeting to nuclear periphery is regulated through local recruitment of Rpd3(L) histone deacetylase complex by transcriptional repressors. Rpd3(L), through its histone deacetylase activity, prevents TF-mediated gene positioning by blocking TF binding. Many yeast transcriptional repressors were capable of blocking Put3-mediated recruitment; 11 of these required Rpd3. Thus, it is a general function of transcription repressors to regulate TF-mediated recruitment. However, Ste12 and Gcn4-mediated recruitment is regulated independently of Rpd3(L) and transcriptional repressors. Ste12-mediated recruitment is regulated by phosphorylation of an inhibitor called Dig2, and Gcn4-mediated gene targeting is up-regulated by increasing Gcn4 protein levels. The ability to control spatial position of genes in yeast represents a novel function for TFs and different regulatory strategies provide dynamic control of the yeast genome through different time scales.
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Affiliation(s)
| | - Jason H Brickner
- a Department of Molecular Biosciences , Northwestern University , Evanston , IL , USA
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37
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Abstract
With the impressive advancement in high-throughput 'omics' technologies over the past two decades, epigenetic mechanisms have emerged as the regulatory interface between the genome and environmental factors. These mechanisms include DNA methylation, histone modifications, ATP-dependent chromatin remodeling and RNA-based mechanisms. Their highly interdependent and coordinated action modulates the chromatin structure controlling access of the transcription machinery and thereby regulating expression of target genes. Given the rather limited proliferative capability of human cardiomyocytes, epigenetic regulation appears to play a particularly important role in the myocardium. The highly dynamic nature of the epigenome allows the heart to adapt to environmental challenges and to respond quickly and properly to cardiac stress. It is now becoming evident that histone-modifying and chromatin-remodeling enzymes as well as numerous non-coding RNAs play critical roles in cardiac development and function, while their dysregulation contributes to the onset and development of pathological cardiac remodeling culminating in HF. This review focuses on up-to-date knowledge about the epigenetic mechanisms and highlights their emerging role in the healthy and failing heart. Uncovering the determinants of epigenetic regulation holds great promise to accelerate the development of successful new diagnostic and therapeutic strategies in human cardiac disease.
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Affiliation(s)
- José Marín-García
- The Molecular Cardiology and Neuromuscular Institute, 75 Raritan Ave., Highland Park, NJ, 08904, USA,
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38
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Yamamuro C, Zhu JK, Yang Z. Epigenetic Modifications and Plant Hormone Action. MOLECULAR PLANT 2016; 9:57-70. [PMID: 26520015 PMCID: PMC5575749 DOI: 10.1016/j.molp.2015.10.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/27/2015] [Accepted: 10/22/2015] [Indexed: 05/18/2023]
Abstract
The action of phytohormones in plants requires the spatiotemporal regulation of their accumulation and responses at various levels. Recent studies reveal an emerging relationship between the function of phytohormones and epigenetic modifications. In particular, evidence suggests that auxin biosynthesis, transport, and signal transduction is modulated by microRNAs and epigenetic factors such as histone modification, chromatin remodeling, and DNA methylation. Furthermore, some phytohormones have been shown to affect epigenetic modifications. These findings are shedding light on the mode of action of phytohormones and are opening up a new avenue of research on phytohormones as well as on the mechanisms regulating epigenetic modifications.
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Affiliation(s)
- Chizuko Yamamuro
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Horticultural Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, PRC.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Zhenbiao Yang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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39
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40
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Giri S, Chakraborty A, Sathyan KM, Prasanth KV, Prasanth SG. Orc5 induces large-scale chromatin decondensation in a GCN5-dependent manner. J Cell Sci 2015; 129:417-29. [PMID: 26644179 DOI: 10.1242/jcs.178889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022] Open
Abstract
In eukaryotes, origin recognition complex (ORC) proteins establish the pre-replicative complex (preRC) at the origins, and this is essential for the initiation of DNA replication. Open chromatin structures regulate the efficiency of preRC formation and replication initiation. However, the molecular mechanisms that control chromatin structure, and how the preRC components establish themselves on the chromatin remain to be understood. In human cells, the ORC is a highly dynamic complex with many separate functions attributed to sub-complexes or individual subunits of the ORC, including heterochromatin organization, telomere and centromere function, centrosome duplication and cytokinesis. We demonstrate that human Orc5, unlike other ORC subunits, when ectopically tethered to a chromatin locus, induces large-scale chromatin decondensation, predominantly during G1 phase of the cell cycle. Orc5 associates with the H3 histone acetyl transferase GCN5 (also known as KAT2A), and this association enhances the chromatin-opening function of Orc5. In the absence of Orc5, histone H3 acetylation is decreased at the origins. We propose that the ability of Orc5 to induce chromatin unfolding during G1 allows the establishment of the preRC at the origins.
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Affiliation(s)
- Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kizhakke M Sathyan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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Zhao W, Wang T, Liu S, Chen Q, Qi R. The histone acetyltransferase PsGcn5 mediates oxidative stress responses and is required for full virulence of Phytophthora sojae. Microb Pathog 2015; 87:51-8. [PMID: 26209751 DOI: 10.1016/j.micpath.2015.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/05/2015] [Accepted: 07/20/2015] [Indexed: 12/13/2022]
Abstract
In eukaryotic organisms, histone acetyltransferase complexes are coactivators that are important for transcriptional activation by modifying chromatin. In this study, a gene (PsGcn5) from Phytophthora sojae encoding a histone acetyltransferase was identified as a homolog of one component of the histone acetyltransferase complex from yeasts to mammals. PsGcn5 was constitutively expressed in each stage tested, but had a slightly higher expression in sporulating hyphae and 3 h after infection. PsGcn5-silenced mutants were generated using polyethylene glycol-mediated protoplast stable transformation. These mutants had normal development, but compared to wild type strains they had higher sensitivity to hydrogen peroxide (H2O2) and significantly reduced virulence in soybean. Diaminobenzidine staining revealed an accumulation of H2O2 around the infection sites of PsGcn5-silenced mutants but not for wild type strains. Inhibition of the plant NADPH oxidase by diphenyleneiodonium prevented host-derived H2O2 accumulation in soybean cells and restored infectious hyphal growth of the mutants. Thus, we concluded that PsGcn5 is important for growth under conditions of oxidative stress and contributes to the full virulence of P. sojae by suppressing the host-derived reactive oxygen species.
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Affiliation(s)
- Wei Zhao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, Hefei, Anhui, China
| | - Tao Wang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, Hefei, Anhui, China
| | - Shusen Liu
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Qingqing Chen
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Rende Qi
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, Hefei, Anhui, China.
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Kurabe N, Murakami S, Tashiro F. SGF29 and Sry pathway in hepatocarcinogenesis. World J Biol Chem 2015; 6:139-147. [PMID: 26322172 PMCID: PMC4549758 DOI: 10.4331/wjbc.v6.i3.139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/31/2015] [Accepted: 07/02/2015] [Indexed: 02/05/2023] Open
Abstract
Deregulated c-Myc expression is a hallmark of many human cancers. We have recently identified a role of mammalian homolog of yeast SPT-ADA-GCN5-acetyltransferas (SAGA) complex component, SAGA-associated factor 29 (SGF29), in regulating the c-Myc overexpression. Here, we discuss the molecular nature of SFG29 in SPT3-TAF9-GCN5-acetyltransferase complex, a counterpart of yeast SAGA complex, and the mechanism through which the elevated SGF29 expression contribute to oncogenic potential of c-Myc in hepatocellularcarcinoma (HCC). We propose that the upstream regulation of SGF29 elicited by sex-determining region Y (Sry) is also augmented in HCC. We hypothesize that c-Myc elevation driven by the deregulated Sry and SGF29 pathway is implicated in the male specific acquisition of human HCCs.
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Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination. PLoS One 2015; 10:e0134709. [PMID: 26263547 PMCID: PMC4532415 DOI: 10.1371/journal.pone.0134709] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023] Open
Abstract
The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.
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Yang H, Liu S, He WT, Zhao J, Jiang LL, Hu HY. Aggregation of Polyglutamine-expanded Ataxin 7 Protein Specifically Sequesters Ubiquitin-specific Protease 22 and Deteriorates Its Deubiquitinating Function in the Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex. J Biol Chem 2015. [PMID: 26195632 DOI: 10.1074/jbc.m114.631663] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human ataxin 7 (Atx7) is a component of the deubiquitination module (DUBm) in the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex for transcriptional regulation, and expansion of its polyglutamine (polyQ) tract leads to spinocerebellar ataxia type 7. However, how polyQ expansion of Atx7 affects DUBm function remains elusive. We investigated the effects of polyQ-expanded Atx7 on ubiquitin-specific protease (USP22), an interacting partner of Atx7 functioning in deubiquitination of histone H2B. The results showed that the inclusions or aggregates formed by polyQ-expanded Atx7 specifically sequester USP22 through their interactions mediated by the N-terminal zinc finger domain of Atx7. The mutation of the zinc finger domain in Atx7 that disrupts its interaction with USP22 dramatically abolishes sequestration of USP22. Moreover, polyQ expansion of Atx7 decreases the deubiquitinating activity of USP22 and, consequently, increases the level of monoubiquitinated H2B. Therefore, we propose that polyQ-expanded Atx7 forms insoluble aggregates that sequester USP22 into a catalytically inactive state, and then the impaired DUBm loses the function to deubiquitinate monoubiquitinated histone H2B or H2A. This may result in dysfunction of the SAGA complex and transcriptional dysregulation in spinocerebellar ataxia type 7 disease.
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Affiliation(s)
- Hui Yang
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
| | - Shuai Liu
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
| | - Wen-Tian He
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
| | - Jian Zhao
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
| | - Lei-Lei Jiang
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
| | - Hong-Yu Hu
- From the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
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Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 2015; 6:299. [PMID: 25941517 PMCID: PMC4403501 DOI: 10.3389/fmicb.2015.00299] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/26/2015] [Indexed: 11/22/2022] Open
Abstract
Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.
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Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Claudia C König
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
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Hong A, Lee JE, Chung KWANGCHUL. Ubiquitin-specific protease 22 (USP22) positively regulates RCAN1 protein levels through RCAN1 de-ubiquitination. J Cell Physiol 2015; 230:1651-60. [DOI: 10.1002/jcp.24917] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 12/18/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Ahyoung Hong
- Department of Systems Biology; College of Life Science and Biotechnology; Yonsei University; Seoul Republic of Korea
| | - Ji Eun Lee
- Department of Systems Biology; College of Life Science and Biotechnology; Yonsei University; Seoul Republic of Korea
| | - KWANG CHUL Chung
- Department of Systems Biology; College of Life Science and Biotechnology; Yonsei University; Seoul Republic of Korea
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47
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Epigenetics of Fungal Secondary Metabolism Related Genes. Fungal Biol 2015. [DOI: 10.1007/978-1-4939-2531-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Protein acetylation and acetyl coenzyme a metabolism in budding yeast. EUKARYOTIC CELL 2014; 13:1472-83. [PMID: 25326522 DOI: 10.1128/ec.00189-14] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells sense and appropriately respond to the physical conditions and availability of nutrients in their environment. This sensing of the environment and consequent cellular responses are orchestrated by a multitude of signaling pathways and typically involve changes in transcription and metabolism. Recent discoveries suggest that the signaling and transcription machineries are regulated by signals which are derived from metabolism and reflect the metabolic state of the cell. Acetyl coenzyme A (CoA) is a key metabolite that links metabolism with signaling, chromatin structure, and transcription. Acetyl-CoA is produced by glycolysis as well as other catabolic pathways and used as a substrate for the citric acid cycle and as a precursor in synthesis of fatty acids and steroids and in other anabolic pathways. This central position in metabolism endows acetyl-CoA with an important regulatory role. Acetyl-CoA serves as a substrate for lysine acetyltransferases (KATs), which catalyze the transfer of acetyl groups to the epsilon-amino groups of lysines in histones and many other proteins. Fluctuations in the concentration of acetyl-CoA, reflecting the metabolic state of the cell, are translated into dynamic protein acetylations that regulate a variety of cell functions, including transcription, replication, DNA repair, cell cycle progression, and aging. This review highlights the synthesis and homeostasis of acetyl-CoA and the regulation of transcriptional and signaling machineries in yeast by acetylation.
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Howe FS, Boubriak I, Sale MJ, Nair A, Clynes D, Grijzenhout A, Murray SC, Woloszczuk R, Mellor J. Lysine acetylation controls local protein conformation by influencing proline isomerization. Mol Cell 2014; 55:733-44. [PMID: 25127513 PMCID: PMC4157579 DOI: 10.1016/j.molcel.2014.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 05/15/2014] [Accepted: 07/02/2014] [Indexed: 11/09/2022]
Abstract
Gene transcription responds to stress and metabolic signals to optimize growth and survival. Histone H3 (H3) lysine 4 trimethylation (K4me3) facilitates state changes, but how levels are coordinated with the environment is unclear. Here, we show that isomerization of H3 at the alanine 15-proline 16 (A15-P16) peptide bond is influenced by lysine 14 (K14) and controls gene-specific K4me3 by balancing the actions of Jhd2, the K4me3 demethylase, and Spp1, a subunit of the Set1 K4 methyltransferase complex. Acetylation at K14 favors the A15-P16trans conformation and reduces K4me3. Environmental stress-induced genes are most sensitive to the changes at K14 influencing H3 tail conformation and K4me3. By contrast, ribosomal protein genes maintain K4me3, required for their repression during stress, independently of Spp1, K14, and P16. Thus, the plasticity in control of K4me3, via signaling to K14 and isomerization at P16, informs distinct gene regulatory mechanisms and processes involving K4me3. H3K14 acetylation influences cis-trans isomerization at the H3A15-P16 peptide bond H3A15-P16trans is associated with H3K14ac and reduced global H3K4me3 A15-P16cis-trans isomerization balances K4me3 (Set1/Spp1) and demethylation (Jhd2) K4me3 on RPGs is largely Spp1- and K14/P16-insensitive while ESR genes are dependent
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Affiliation(s)
- Françoise S Howe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ivan Boubriak
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthew J Sale
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anitha Nair
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - David Clynes
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anne Grijzenhout
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Struan C Murray
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ronja Woloszczuk
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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The histone acetyltransferase GcnE (GCN5) plays a central role in the regulation of Aspergillus asexual development. Genetics 2014; 197:1175-89. [PMID: 24907261 DOI: 10.1534/genetics.114.165688] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Acetylation of histones is a key regulatory mechanism of gene expression in eukaryotes. GcnE is an acetyltransferase of Aspergillus nidulans involved in the acetylation of histone H3 at lysine 9 and lysine 14. Previous works have demonstrated that deletion of gcnE results in defects in primary and secondary metabolism. Here we unveil the role of GcnE in development and show that a ∆gcnE mutant strain has minor growth defects but is impaired in normal conidiophore development. No signs of conidiation were found after 3 days of incubation, and immature and aberrant conidiophores were found after 1 week of incubation. Centroid linkage clustering and principal component (PC) analysis of transcriptomic data suggest that GcnE occupies a central position in Aspergillus developmental regulation and that it is essential for inducing conidiation genes. GcnE function was found to be required for the acetylation of histone H3K9/K14 at the promoter of the master regulator of conidiation, brlA, as well as at the promoters of the upstream developmental regulators of conidiation flbA, flbB, flbC, and flbD (fluffy genes). However, analysis of the gene expression of brlA and the fluffy genes revealed that the lack of conidiation originated in a complete absence of brlA expression in the ∆gcnE strain. Ectopic induction of brlA from a heterologous alcA promoter did not remediate the conidiation defects in the ∆gcnE strain, suggesting that additional GcnE-mediated mechanisms must operate. Therefore, we conclude that GcnE is the only nonessential histone modifier with a strong role in fungal development found so far.
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