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Omkar S, Shrader C, Hoskins JR, Kline JT, Mitchem MM, Nitika, Fornelli L, Wickner S, Truman AW. Acetylation of the yeast Hsp40 chaperone protein Ydj1 fine-tunes proteostasis and translational fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598777. [PMID: 38915721 PMCID: PMC11195281 DOI: 10.1101/2024.06.13.598777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Proteostasis, the maintenance of cellular protein balance, is essential for cell viability and is highly conserved across all organisms. Newly synthesized proteins, or "clients," undergo sequential processing by Hsp40, Hsp70, and Hsp90 chaperones to achieve proper folding and functionality. Despite extensive characterization of post-translational modifications (PTMs) on Hsp70 and Hsp90, the modifications on Hsp40 remain less understood. This study aims to elucidate the role of lysine acetylation on the yeast Hsp40, Ydj1. By mutating acetylation sites on Ydj1's J-domain to either abolish or mimic constitutive acetylation, we observed that preventing acetylation had no noticeable phenotypic impact, whereas acetyl-mimic mutants exhibited various defects indicative of impaired Ydj1 function. Proteomic analysis revealed several Ydj1 interactions affected by J-domain acetylation, notably with proteins involved in translation. Further investigation uncovered a novel role for Ydj1 acetylation in stabilizing ribosomal subunits and ensuring translational fidelity. Our data suggest that acetylation may facilitate the transfer of Ydj1 between Ssa1 and Hsp82. Collectively, this work highlights the critical role of Ydj1 acetylation in proteostasis and translational fidelity.
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Affiliation(s)
- Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Courtney Shrader
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Joel R. Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jake T. Kline
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019 USA
| | - Megan M. Mitchem
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Luca Fornelli
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019 USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
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2
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Dandage R, Papkov M, Greco BM, Fishman D, Friesen H, Wang K, Styles E, Kraus O, Grys B, Boone C, Andrews B, Parts L, Kuzmin E. Single-cell imaging of protein dynamics of paralogs reveals mechanisms of gene retention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568466. [PMID: 38045359 PMCID: PMC10690282 DOI: 10.1101/2023.11.23.568466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is a largely unexplored mechanism of functional divergence. We performed a systematic single-cell imaging analysis of protein dynamics and screened subcellular redistribution of proteins, capturing their localization and abundance changes, providing insight into forces determining paralog retention. Paralogs showed dependency, whereby proteins required their paralog to maintain their native abundance or localization, more often than compensation. Network feature analysis suggested the importance of functional redundancy and rewiring of protein and genetic interactions underlying redistribution response of paralogs. Translation of non-canonical protein isoform emerged as a novel compensatory mechanism. This study provides new insights into paralog retention and evolutionary forces that shape genomes.
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3
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Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
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Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
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4
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Gomar-Alba M, Pozharskaia V, Cichocki B, Schaal C, Kumar A, Jacquel B, Charvin G, Igual JC, Mendoza M. Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast. EMBO J 2022; 41:e110271. [PMID: 35735140 PMCID: PMC9340480 DOI: 10.15252/embj.2021110271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin‐associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export. Acetylation of Nup60 recruits the mRNA export factor Sac3, the scaffolding subunit of the Transcription and Export 2 (TREX‐2) complex, to the nuclear basket. The Esa1‐mediated nuclear export of mRNAs in turn promotes entry into S phase, which is inhibited by the Hos3 deacetylase in G1 daughter cells to restrain their premature commitment to a new cell division cycle. This mechanism is not only limited to G1/S‐expressed genes but also inhibits the expression of the nutrient‐regulated GAL1 gene specifically in daughter cells. Overall, these results reveal how acetylation can contribute to the functional plasticity of NPCs in mother and daughter yeast cells. In addition, our work demonstrates dual gene expression regulation by the evolutionarily conserved NuA4 complex, at the level of transcription and at the stage of mRNA export by modifying the nucleoplasmic entrance to nuclear pores.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Vasilisa Pozharskaia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Bogdan Cichocki
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Celia Schaal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Arun Kumar
- Department of Cell Biology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Basile Jacquel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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5
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Galati E, Bosio MC, Novarina D, Chiara M, Bernini GM, Mozzarelli AM, García-Rubio ML, Gómez-González B, Aguilera A, Carzaniga T, Todisco M, Bellini T, Nava GM, Frigè G, Sertic S, Horner DS, Baryshnikova A, Manzari C, D'Erchia AM, Pesole G, Brown GW, Muzi-Falconi M, Lazzaro F. VID22 counteracts G-quadruplex-induced genome instability. Nucleic Acids Res 2021; 49:12785-12804. [PMID: 34871443 PMCID: PMC8682794 DOI: 10.1093/nar/gkab1156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.
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Affiliation(s)
- Elena Galati
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Maria C Bosio
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Daniele Novarina
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Giulia M Bernini
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alessandro M Mozzarelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Maria L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Vanvitelli 32, 20129 Milan, Italy
| | - Giulia M Nava
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sarah Sertic
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - David S Horner
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Anastasia Baryshnikova
- Department of Molecular Genetics and Donnelly Centre, University of Toronto, Toronto, Canada
| | - Caterina Manzari
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Anna M D'Erchia
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari 'A. Moro', Bari, Italy
| | - Graziano Pesole
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari 'A. Moro', Bari, Italy
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Ontario M5S 3E1, Toronto, Canada
| | - Marco Muzi-Falconi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Federico Lazzaro
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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6
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Shan Y, Wang F, Wei Z, Lu Y. Synthetic lethality theory approaches to effective substance discovery and functional mechanisms elucidation of anti-cancer phytomedicine. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 91:153718. [PMID: 34531099 DOI: 10.1016/j.phymed.2021.153718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/04/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Longstanding, successful use of combinations of phytopharmaceuticals in traditional Chinese medicine (TCM) has caught the attention of several pharmacologists to natural medicines. However, the development and popularisation of TCM is mainly limited because of the unavailability of reports clarifying the mechanisms of action and pharmacologically active ingredients in such formulations. Previous studies on natural medicines have mostly focused on their dominant components using forward pharmacology which often neglects trace components. It is necessary to assess the pharmacological and therapeutic superiority of many such trace components in comparison with single constituents. PURPOSE In this study, we aimed to propose a new pharmacological research strategy for TCM. In particular, we presented the possibility that the effective mechanism of action of trace components of TCM is based on synthetic lethality. We sincerely hope to explore this theory further. METHOD We obtained retrieve published research information related to synthetic lethality, phytochemicals and Chinese medicine from PubMed and Google scholar. Based on the inclusion criteria, 71 studies were selected and discussed in this review. RESULTS As an interaction among genes, synthetic lethality can amplify co-regulatory biological effects exponentially. Synthetic strategies have been successfully applied for research and development of anti-tumour agents, including poly ADP-ribose polymerase inhibitors and clinical combination of chemotherapeutic agents for efficacy enhancement and toxicity reduction. TCM drugs contain several secondary metabolites to combat environmental stresses, providing a multi-component basis for corresponding synergistic targets. Therefore, we aimed to study whether this method could be used to identify active components present in trace amounts in TCM drugs. Based on a reverse concept of target-component-effect and identified synergistic targets, we explored the mechanisms of action of weakly active components present in trace amounts in TCM drugs to assess combinations of potential synergistic components. CONCLUSION This pattern of synthetic lethality not only elucidated the mechanisms of action of TCM drugs from a new perspective but also inspired future studies on discovering naturally occurring active components.
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Affiliation(s)
- Yunlong Shan
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Wang
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Zhonghong Wei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China.
| | - Yin Lu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China.
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7
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Bhagwat M, Nagar S, Kaur P, Mehta R, Vancurova I, Vancura A. Replication stress inhibits synthesis of histone mRNAs in yeast by removing Spt10p and Spt21p from the histone promoters. J Biol Chem 2021; 297:101246. [PMID: 34582893 PMCID: PMC8551654 DOI: 10.1016/j.jbc.2021.101246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Proliferating cells coordinate histone and DNA synthesis to maintain correct stoichiometry for chromatin assembly. Histone mRNA levels must be repressed when DNA replication is inhibited to prevent toxicity and genome instability due to free non-chromatinized histone proteins. In mammalian cells, replication stress triggers degradation of histone mRNAs, but it is unclear if this mechanism is conserved from other species. The aim of this study was to identify the histone mRNA decay pathway in the yeast Saccharomyces cerevisiae and determine the mechanism by which DNA replication stress represses histone mRNAs. Using reverse transcription-quantitative PCR and chromatin immunoprecipitation–quantitative PCR, we show here that histone mRNAs can be degraded by both 5′ → 3′ and 3′ → 5′ pathways; however, replication stress does not trigger decay of histone mRNA in yeast. Rather, replication stress inhibits transcription of histone genes by removing the histone gene–specific transcription factors Spt10p and Spt21p from histone promoters, leading to disassembly of the preinitiation complexes and eviction of RNA Pol II from histone genes by a mechanism facilitated by checkpoint kinase Rad53p and histone chaperone Asf1p. In contrast, replication stress does not remove SCB-binding factor transcription complex, another activator of histone genes, from the histone promoters, suggesting that Spt10p and Spt21p have unique roles in the transcriptional downregulation of histone genes during replication stress. Together, our data show that, unlike in mammalian cells, replication stress in yeast does not trigger decay of histone mRNAs but inhibits histone transcription.
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Affiliation(s)
- Madhura Bhagwat
- Department of Biological Sciences, St John's University, Queens, New York, USA
| | - Shreya Nagar
- Department of Biological Sciences, St John's University, Queens, New York, USA
| | - Pritpal Kaur
- Department of Biological Sciences, St John's University, Queens, New York, USA
| | - Riddhi Mehta
- Department of Biological Sciences, St John's University, Queens, New York, USA
| | - Ivana Vancurova
- Department of Biological Sciences, St John's University, Queens, New York, USA
| | - Ales Vancura
- Department of Biological Sciences, St John's University, Queens, New York, USA.
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8
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Walden EA, Fong RY, Pham TT, Knill H, Laframboise SJ, Huard S, Harper ME, Baetz K. Phenomic screen identifies a role for the yeast lysine acetyltransferase NuA4 in the control of Bcy1 subcellular localization, glycogen biosynthesis, and mitochondrial morphology. PLoS Genet 2020; 16:e1009220. [PMID: 33253187 PMCID: PMC7728387 DOI: 10.1371/journal.pgen.1009220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular metabolism is tightly regulated by many signaling pathways and processes, including lysine acetylation of proteins. While lysine acetylation of metabolic enzymes can directly influence enzyme activity, there is growing evidence that lysine acetylation can also impact protein localization. As the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 has been implicated in a variety of metabolic processes, we have explored whether NuA4 controls the localization and/or protein levels of metabolic proteins. We performed a high-throughput microscopy screen of over 360 GFP-tagged metabolic proteins and identified 23 proteins whose localization and/or abundance changed upon deletion of the NuA4 scaffolding subunit, EAF1. Within this, three proteins were required for glycogen synthesis and 14 proteins were associated with the mitochondria. We determined that in eaf1Δ cells the transcription of glycogen biosynthesis genes is upregulated resulting in increased proteins and glycogen production. Further, in the absence of EAF1, mitochondria are highly fused, increasing in volume approximately 3-fold, and are chaotically distributed but remain functional. Both the increased glycogen synthesis and mitochondrial elongation in eaf1Δ cells are dependent on Bcy1, the yeast regulatory subunit of PKA. Surprisingly, in the absence of EAF1, Bcy1 localization changes from being nuclear to cytoplasmic and PKA activity is altered. We found that NuA4-dependent localization of Bcy1 is dependent on a lysine residue at position 313 of Bcy1. However, the glycogen accumulation and mitochondrial elongation phenotypes of eaf1Δ, while dependent on Bcy1, were not fully dependent on Bcy1-K313 acetylation state and subcellular localization of Bcy1. As NuA4 is highly conserved with the human Tip60 complex, our work may inform human disease biology, revealing new avenues to investigate the role of Tip60 in metabolic diseases.
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Affiliation(s)
- Elizabeth A. Walden
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Roger Y. Fong
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Trang T. Pham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Hana Knill
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sylvain Huard
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
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9
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Kyriakou D, Constantinou M, Kirmizis A. Synthetic dosage lethal (SDL) interaction data of Hmt1 arginine methyltransferase. Data Brief 2020; 31:105885. [PMID: 32637492 PMCID: PMC7330151 DOI: 10.1016/j.dib.2020.105885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/01/2022] Open
Abstract
The introduction of methyl groups on arginine residues is catalysed by Protein Arginine Methyltransferases (PRMTs). However, the regulatory mechanisms that dictate the levels of protein arginine methylation within cells are still not completely understood. We employed Synthetic Dosage Lethality (SDL) screening in Saccharomyces cerevisiae, for the identification of putative regulators of arginine methylation mediated by Hmt1 (HnRNP methyltransferase 1), ortholog of human PRMT1. We developed an SDL array of 4548 yeast strains in which each strain contained a single non-essential gene deletion, in combination with a galactose-inducible construct overexpressing wild-type (WT) Hmt1-HZ tagged protein. We identified 129 consistent SDL interactions for WT Hmt1-HZ which represented genes whose deletion displayed significant growth reduction when combined with WT Hmt1 overexpression. To identify among the SDL interactions those that were dependent on the methyltransferase activity of Hmt1, SDL screens were repeated using an array overexpressing a catalytically inactive Hmt1(G68R)-HZ protein. Furthermore, an additional SDL control screen was performed using an array overexpressing only the protein tag HZ (His6—HA-ZZ) to eliminate false-positive SDL interactions. This analysis has led to a dataset of 50 high-confidence SDL interactions of WT Hmt1 which enrich eight Gene Ontology biological process terms. This dataset can be further exploited in biochemical and functional studies to illuminate which of the SDL interactors of Hmt1 correspond to factors implicated in the regulation of Hmt1-mediated arginine methylation and reveal the underlying molecular mechanisms.
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Affiliation(s)
- Dimitris Kyriakou
- EFEVRE TECH LTD, Larnaca, Cyprus.,Department of Biological Sciences, University of Cyprus, 1 University Ave, Nicosia, Aglantzia 2109, Cyprus
| | - Mamantia Constantinou
- Department of Biological Sciences, University of Cyprus, 1 University Ave, Nicosia, Aglantzia 2109, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, 1 University Ave, Nicosia, Aglantzia 2109, Cyprus
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10
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Singh PK, Gao W, Liao P, Li Y, Xu FC, Ma XN, Long L, Song CP. Comparative acetylome analysis of wild-type and fuzzless-lintless mutant ovules of upland cotton (Gossypium hirsutum Cv. Xu142) unveils differential protein acetylation may regulate fiber development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:56-70. [PMID: 32114400 DOI: 10.1016/j.plaphy.2020.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Protein acetylation (KAC) is a significant post-translational modification, which plays an essential role in the regulation of growth and development. Unfortunately, related studies are inadequately available in angiosperms, and to date, there is no report providing insight on the role of protein acetylation in cotton fiber development. Therefore, we first compared the lysine-acetylation proteome (acetylome) of upland cotton ovules in the early fiber development stages by using wild-type as well as its fuzzless-lintless mutant to identify the role of KAC in the fiber development. A total of 1696 proteins with 2754 acetylation sites identified with the different levels of acetylation belonging to separate subcellular compartments suggesting a large number of proteins differentially acetylated in two cotton cultivars. About 80% of the sites were predicted to localize in the cytoplasm, chloroplast, and mitochondria. Seventeen significantly enriched acetylation motifs were identified. Serine and threonine and cysteine located downstream and upstream to KAC sites. KEGG pathway enrichment analysis indicated oxidative phosphorylation, fatty acid, ribosome and protein, and folate biosynthesis pathways enriched significantly. To our knowledge, this is the first report of comparative acetylome analysis to compare the wild-type as well as its fuzzless-lintless mutant acetylome data to identify the differentially acetylated proteins, which may play a significant role in cotton fiber development.
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Affiliation(s)
- Prashant Kumar Singh
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, 7505101, Israel; State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China; Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, India.
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Peng Liao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Yang Li
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China.
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11
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Wójcikowska B, Botor M, Morończyk J, Wójcik AM, Nodzyński T, Karcz J, Gaj MD. Trichostatin A Triggers an Embryogenic Transition in Arabidopsis Explants via an Auxin-Related Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:1353. [PMID: 30271420 PMCID: PMC6146766 DOI: 10.3389/fpls.2018.01353] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/28/2018] [Indexed: 05/23/2023]
Abstract
Auxin is an important regulator of plant ontogenies including embryo development and the exogenous application of this phytohormone has been found to be necessary for the induction of the embryogenic response in plant explants that have been cultured in vitro. However, in the present study, we show that treatment of Arabidopsis explants with trichostatin A (TSA), which is a chemical inhibitor of histone deacetylases, induces somatic embryogenesis (SE) without the exogenous application of auxin. We found that the TSA-treated explants generated somatic embryos that developed efficiently on the adaxial side of the cotyledons, which are the parts of an explant that are involved in auxin-induced SE. A substantial reduction in the activity of histone deacetylase (HDAC) was observed in the TSA-treated explants, thus confirming a histone acetylation-related mechanism of the TSA-promoted embryogenic response. Unexpectedly, the embryogenic effect of TSA was lower on the auxin-supplemented media and this finding further suggests an auxin-related mechanism of TSA-induced SE. Congruently, we found a significantly increased content of indolic compounds, which is indicative of IAA and an enhanced DR5::GUS signal in the TSA-treated explants. In line with these results, two of the YUCCA genes (YUC1 and YUC10), which are involved in auxin biosynthesis, were found to be distinctly up-regulated during TSA-induced SE and their expression was colocalised with the explant sites that are involved in SE. Beside auxin, ROS were extensively accumulated in response to TSA, thereby indicating that a stress-response is involved in TSA-triggered SE. Relevantly, we showed that the genes encoding the transcription factors (TFs) that have a regulatory function in auxin biosynthesis including LEC1, LEC2, BBM, and stress responses (MYB118) were highly up-regulated in the TSA-treated explants. Collectively, the results provide several pieces of evidence about the similarities between the molecular pathways of SE induction that are triggered by TSA and 2,4-D that involve the activation of the auxin-responsive TF genes that have a regulatory function in auxin biosynthesis and stress responses. The study suggests the involvement of histone acetylation in the auxin-mediated release of the embryogenic program of development in the somatic cells of Arabidopsis.
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Affiliation(s)
| | - Malwina Botor
- Department of Molecular Biology and Genetics, Medical University of SilesiaKatowice, Poland
| | - Joanna Morończyk
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
| | - Anna Maria Wójcik
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
| | - Tomasz Nodzyński
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU – Central European Institute of Technology, Masaryk UniversityBrno, Czechia
| | - Jagna Karcz
- Scanning Electron Microscopy Laboratory, University of Silesia in KatowiceKatowice, Poland
| | - Małgorzata D. Gaj
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
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12
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Ahmed MS, Shahjaman M, Kabir E, Kamruzzaman M. Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling. Bioinformation 2018; 14:213-218. [PMID: 30108418 PMCID: PMC6077816 DOI: 10.6026/97320630014213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022] Open
Abstract
Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Features selection from protein sequences plays a significant role for acetylation sites prediction. We describe an improved feature selection approach for acetylation sites prediction based on kernel naive Bayes classifier (KNBC). We have shown that KNBC generated from selected features by a new feature selection method outperforms than the existing methods for identification of acetylation sites. The sensitivity, specificity, ACC (Accuracy), MCC (Matthews Correlation Coefficient) and AUC (Area under Curve of ROC) in our proposed method are as follows 80.71%, 93.39%, 76.73%, 41.37% and 83.0% with the optimum window size is 47. Thus the kernel naive Bayes classifier finds application in acetylation site prediction.
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Affiliation(s)
- Md. Shakil Ahmed
- Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Enamul Kabir
- School of Agricultural, Computational and Environmental Sciences, University of Southern Queensland, Australia
| | - Md. Kamruzzaman
- Data Science for Knowledge Creation Research Center, Seoul National University, Korea
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13
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G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast. Cell Syst 2018; 6:539-554.e11. [DOI: 10.1016/j.cels.2018.04.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/17/2018] [Accepted: 04/25/2018] [Indexed: 11/20/2022]
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14
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Chen Z, Luo L, Chen R, Hu H, Pan Y, Jiang H, Wan X, Jin H, Gong Y. Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. Mol Cell Proteomics 2017; 17:399-412. [PMID: 29093020 DOI: 10.1074/mcp.ra117.000339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 02/05/2023] Open
Abstract
Nε-lysine acetylation represents a highly dynamic and reversibly regulated post-translational modification widespread in almost all organisms, and plays important roles for regulation of protein function in diverse metabolic pathways. However, little is known about the role of lysine acetylation in photosynthetic eukaryotic microalgae. We integrated proteomic approaches to comprehensively characterize the lysine acetylome in the model diatom Phaeodactylum tricornutum In total, 2324 acetylation sites from 1220 acetylated proteins were identified, representing the largest data set of the lysine acetylome in plants to date. Almost all enzymes involved in fatty acid synthesis were found to be lysine acetylated. Six putative lysine acetylation sites were identified in a plastid-localized long-chain acyl-CoA synthetase. Site-directed mutagenesis and site-specific incorporation of N-acetyllysine in acyl-CoA synthetase show that acetylation at K407 and K425 increases its enzyme activity. Moreover, the nonenzymatically catalyzed overall hyperacetylation of acyl-CoA synthetase by acetyl-phosphate can be effectively deacetylated and reversed by a sirtuin-type NAD+-dependent deacetylase with subcellular localization of both the plastid and nucleus in Phaeodactylum This work indicates the regulation of acyl-CoA synthetase activity by site-specific lysine acetylation and highlights the potential regulation of fatty acid metabolism by lysine actetylation in the plastid of the diatom Phaeodactylum.
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Affiliation(s)
- Zhuo Chen
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China.,§Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Ling Luo
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Runfa Chen
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hanhua Hu
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yufang Pan
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Haibo Jiang
- ‖School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Xia Wan
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hu Jin
- ¶Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yangmin Gong
- From the ‡Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
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15
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Abstract
Nε-Lysine acetylation is now recognized as an abundant posttranslational modification (PTM) that influences many essential biological pathways. Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary to the prior notion of acetylation events being rare in bacteria. Although the mechanisms that regulate protein acetylation are still not fully defined, it is understood that this modification is finely tuned via both enzymatic and nonenzymatic mechanisms. The opposing actions of Gcn5-related N-acetyltransferases (GNATs) and deacetylases, including sirtuins, provide the enzymatic control of lysine acetylation. A nonenzymatic mechanism of acetylation has also been demonstrated and proven to be prominent in bacteria, as well as in mitochondria. The functional consequences of the vast majority of the identified acetylation sites remain unknown. From studies in mammalian systems, acetylation of critical lysine residues was shown to impact protein function by altering its structure, subcellular localization, and interactions. It is becoming apparent that the same diversity of functions can be found in bacteria. Here, we review current knowledge of the mechanisms and the functional consequences of acetylation in bacteria. Additionally, we discuss the methods available for detecting acetylation sites, including quantitative mass spectrometry-based methods, which promise to promote this field of research. We conclude with possible future directions and broader implications of the study of protein acetylation in bacteria.
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16
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Chen Z, Zhang G, Yang M, Li T, Ge F, Zhao J. Lysine Acetylome Analysis Reveals Photosystem II Manganese-stabilizing Protein Acetylation is Involved in Negative Regulation of Oxygen Evolution in Model Cyanobacterium Synechococcus sp. PCC 7002. Mol Cell Proteomics 2017; 16:1297-1311. [PMID: 28550166 PMCID: PMC5500762 DOI: 10.1074/mcp.m117.067835] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/09/2017] [Indexed: 12/11/2022] Open
Abstract
Nε-Acetylation of lysine residues represents a frequently occurring post-translational modification widespread in bacteria that plays vital roles in regulating bacterial physiology and metabolism. However, the role of lysine acetylation in cyanobacteria remains unclear, presenting a hurdle to in-depth functional study of this post-translational modification. Here, we report the lysine acetylome of Synechococcus sp. PCC 7002 (hereafter Synechococcus) using peptide prefractionation, immunoaffinity enrichment, and coupling with high-precision liquid chromatography-tandem mass spectrometry analysis. Proteomic analysis of Synechococcus identified 1653 acetylation sites on 802 acetylproteins involved in a broad range of biological processes. Interestingly, the lysine acetylated proteins were enriched for proteins involved in photosynthesis, for example. Functional studies of the photosystem II manganese-stabilizing protein were performed by site-directed mutagenesis and mutants mimicking either constitutively acetylated (K99Q, K190Q, and K219Q) or nonacetylated states (K99R, K190R, and K219R) were constructed. Mutation of the K190 acetylation site resulted in a distinguishable phenotype. Compared with the K190R mutant, the K190Q mutant exhibited a decreased oxygen evolution rate and an enhanced cyclic electron transport rate in vivo Our findings provide new insight into the molecular mechanisms of lysine acetylation that involved in the negative regulation of oxygen evolution in Synechococcus and creates opportunities for in-depth elucidation of the physiological role of protein acetylation in photosynthesis in cyanobacteria.
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Affiliation(s)
- Zhuo Chen
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
- §Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Guiying Zhang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
- ¶University of Chinese Academy of Sciences, Beijing 100094, China
| | - Mingkun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Tao Li
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China;
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China;
| | - Jindong Zhao
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
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17
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Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. G3-GENES GENOMES GENETICS 2017; 7:911-921. [PMID: 28122947 PMCID: PMC5345721 DOI: 10.1534/g3.116.038471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Kinases and transcription factors (TFs) are key modulators of important signaling pathways and their activities underlie the proper function of many basic cellular processes such as cell division, differentiation, and development. Changes in kinase and TF dosage are often associated with disease, yet a systematic assessment of the cellular phenotypes caused by the combined perturbation of kinases and TFs has not been undertaken. We used a reverse-genetics approach to study the phenotypic consequences of kinase and TF overexpression (OE) in the budding yeast, Saccharomyces cerevisiae. We constructed a collection of strains expressing stably integrated inducible alleles of kinases and TFs and used a variety of assays to characterize the phenotypes caused by TF and kinase OE. We used the Synthetic Genetic Array (SGA) method to examine dosage-dependent genetic interactions (GIs) between 239 gain-of-function (OE) alleles of TFs and six loss-of-function (LOF) and seven OE kinase alleles, the former identifying Synthetic Dosage Lethal (SDL) interactions and the latter testing a GI we call Double Dosage Lethality (DDL). We identified and confirmed 94 GIs between 65 OE alleles of TFs and 9 kinase alleles. Follow-up experiments validated regulatory relationships between genetically interacting pairs (Cdc28–Stb1 and Pho85–Pdr1), suggesting that GI studies involving OE alleles of regulatory proteins will be a rich source of new functional information.
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18
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Li X, Robbins N, O'Meara TR, Cowen LE. Extensive functional redundancy in the regulation of Candida albicans drug resistance and morphogenesis by lysine deacetylases Hos2, Hda1, Rpd3 and Rpd31. Mol Microbiol 2016; 103:635-656. [PMID: 27868254 DOI: 10.1111/mmi.13578] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2016] [Indexed: 12/22/2022]
Abstract
Current treatment efforts for fungal infections are hampered by the limited availability of antifungal drugs and by the emergence of drug resistance. A powerful strategy to enhance the efficacy of antifungal drugs is to inhibit the molecular chaperone Hsp90. Hsp90 governs drug resistance, morphogenesis and virulence in a leading fungal pathogen of humans, Candida albicans. Our previous work with Saccharomyces cerevisiae established acetylation as a novel mechanism of posttranslational control of Hsp90 function in fungi. We implicated lysine deacetylases (KDACs) as key regulators of resistance to the most widely deployed class of antifungals, the azoles, in both S. cerevisiae and C. albicans. Here, we demonstrate high levels of functional redundancy among the KDACs that are important for regulating Hsp90 function. We identify Hos2, Hda1, Rpd3 and Rpd31 as the KDACs mediating azole resistance and morphogenesis in C. albicans. Furthermore, we identify lysine 30 and 271 as critical acetylation sites on C. albicans Hsp90, and substitutions at these residues compromise Hsp90 function. Finally, we show that pharmacological inhibition of KDACs phenocopies pharmacological inhibition of Hsp90 and abrogates Hsp90-dependent azole resistance in numerous Candida species. This work illuminates new facets to the impact of KDACs on fungal drug resistance and morphogenesis, provides important insights into the divergence of the C. albicans Hsp90 regulatory network and reveals new targets for development of antifungal drugs.
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Affiliation(s)
- Xinliu Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Teresa R O'Meara
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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19
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Torres MP, Dewhurst H, Sundararaman N. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease. Mol Cell Proteomics 2016; 15:3513-3528. [PMID: 27697855 PMCID: PMC5098047 DOI: 10.1074/mcp.m116.062331] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Indexed: 01/09/2023] Open
Abstract
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health.
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Affiliation(s)
- Matthew P Torres
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Henry Dewhurst
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Niveda Sundararaman
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
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20
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Duffy S, Fam HK, Wang YK, Styles EB, Kim JH, Ang JS, Singh T, Larionov V, Shah SP, Andrews B, Boerkoel CF, Hieter P. Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. Proc Natl Acad Sci U S A 2016; 113:9967-76. [PMID: 27551064 PMCID: PMC5018746 DOI: 10.1073/pnas.1611839113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Rhabdomyosarcoma lines with elevated human Tdp1 levels also exhibit CIN that can be partially rescued by siRNA-mediated knockdown of TDP1 Overexpression of dCIN genes represents a genetic vulnerability that could be leveraged for selective killing of cancer cells through targeting of an unlinked synthetic dosage lethal (SDL) partner. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1. One gene was the histone deacetylase RPD3, for which there are known inhibitors. Both HT1080 cells overexpressing hTDP1 and rhabdomyosarcoma cells with elevated levels of hTdp1 were more sensitive to histone deacetylase inhibitors valproic acid (VPA) and trichostatin A (TSA), recapitulating the SDL interaction in human cells and suggesting VPA and TSA as potential therapeutic agents for tumors with elevated levels of hTdp1. The catalog of dCIN genes presented here provides a candidate list to identify genes that cause CIN when overexpressed in cancer, which can then be leveraged through SDL to selectively target tumors.
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Affiliation(s)
- Supipi Duffy
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Hok Khim Fam
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Yi Kan Wang
- BC Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Erin B Styles
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Jung-Hyun Kim
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - J Sidney Ang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Tejomayee Singh
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Vladimir Larionov
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | | | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Cornelius F Boerkoel
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
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Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation. Genetics 2016; 204:177-90. [PMID: 27489001 DOI: 10.1534/genetics.116.190835] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/14/2016] [Indexed: 12/18/2022] Open
Abstract
As the only catalytic member of the Sir-protein gene-silencing complex, Sir2's catalytic activity is necessary for silencing. The only known role for Sir2's catalytic activity in Saccharomyces cerevisiae silencing is to deacetylate N-terminal tails of histones H3 and H4, creating high-affinity binding sites for the Sir-protein complex, resulting in association of Sir proteins across the silenced domain. This histone deacetylation model makes the simple prediction that preemptively removing Sir2's H3 and H4 acetyl substrates, by mutating these lysines to unacetylatable arginines, or removing the acetyl transferase responsible for their acetylation, should restore silencing in the Sir2 catalytic mutant. However, this was not the case. We conducted a genetic screen to explore what aspect of Sir2's catalytic activity has not been accounted for in silencing. Mutation of a nonsirtuin histone deacetylase, Rpd3, restored Sir-protein-based silencing in the absence of Sir2's catalytic activity. Moreover, this antagonism could be mediated by either the large or the small Rpd3-containing complex. Interestingly, this restoration of silencing appeared independent of any known histone H3 or H4 substrates of Rpd3 Investigation of Sir-protein association in the Rpd3 mutant revealed that the restoration of silencing was correlated with an increased association of Sir proteins at the silencers, suggesting that Rpd3 was an antagonist of Sir2's function in nucleation of Sir proteins to the silencer. Additionally, restoration of silencing by Rpd3 was dependent on another sirtuin family member, Hst3, indicating multiple antagonistic roles for deacetylases in S. cerevisiae silencing.
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Temporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth. mSystems 2016; 1. [PMID: 27376153 PMCID: PMC4927096 DOI: 10.1128/msystems.00005-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis. To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth. Nε-Lysine acetylation has been recognized as a ubiquitous regulatory posttranslational modification that influences a variety of important biological processes in eukaryotic cells. Recently, it has been realized that acetylation is also prevalent in bacteria. Bacteria contain hundreds of acetylated proteins, with functions affecting diverse cellular pathways. Still, little is known about the regulation or biological relevance of nearly all of these modifications. Here we characterize the cellular growth-associated regulation of the Bacillus subtilis acetylome. Using acetylation enrichment and quantitative mass spectrometry, we investigate the logarithmic and stationary growth phases, identifying over 2,300 unique acetylation sites on proteins that function in essential cellular pathways. We determine an acetylation motif, EK(ac)(D/Y/E), which resembles the eukaryotic mitochondrial acetylation signature, and a distinct stationary-phase-enriched motif. By comparing the changes in acetylation with protein abundances, we discover a subset of critical acetylation events that are temporally regulated during cell growth. We functionally characterize the stationary-phase-enriched acetylation on the essential shape-determining protein MreB. Using bioinformatics, mutational analysis, and fluorescence microscopy, we define a potential role for the temporal acetylation of MreB in restricting cell wall growth and cell diameter. IMPORTANCE The past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in B. subtilis. To demonstrate that the identification of cell growth-dependent modifications can point to critical regulatory acetylation events, we further characterized MreB, the cell shape-determining protein. Our findings led us to propose a role for MreB acetylation in controlling cell width by restricting cell wall growth.
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Kuzmin E, Costanzo M, Andrews B, Boone C. Synthetic Genetic Arrays: Automation of Yeast Genetics. Cold Spring Harb Protoc 2016; 2016:pdb.top086652. [PMID: 27037078 DOI: 10.1101/pdb.top086652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype.
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Affiliation(s)
- Elena Kuzmin
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
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24
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Styles EB, Friesen H, Boone C, Andrews BJ. High-Throughput Microscopy-Based Screening in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:pdb.top087593. [PMID: 27037080 DOI: 10.1101/pdb.top087593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The budding yeastSaccharomyces cerevisiaehas served as the pioneer model organism for virtually all genome-scale methods, including genome sequencing, DNA microarrays, gene deletion collections, and a variety of proteomic platforms. Yeast has also provided a test-bed for the development of systematic fluorescence-based imaging screens to enable the analysis of protein localization and abundance in vivo. Especially important has been the integration of high-throughput microscopy with automated image-processing methods, which has allowed researchers to overcome issues associated with manual image analysis and acquire unbiased, quantitative data. Here we provide an introduction to automated imaging in budding yeast.
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Affiliation(s)
- Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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25
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Abstract
Acetylation is a dynamic post-translational modification that is attached to protein substrates by lysine acetyltransferases (KATs) and removed by lysine deacetylases (KDACs). While these enzymes are best characterized as histone modifiers and regulators of gene transcription, work in a number of systems highlights that acetylation is a pervasive modification and suggests a broad scope for KAT and KDAC functions in the cell. As we move beyond generating lists of acetylated proteins, the acetylation field is in dire need of robust tools to connect acetylation and deacetylation machineries to their respective substrates and to dissect the function of individual sites. The Saccharomyces cerevisiae model system provides such a toolkit in the context of both tried and true genetic techniques and cutting-edge proteomic and cell imaging methods. Here, we review these methods in the context of their contributions to acetylation research thus far and suggest strategies for addressing lingering questions in the field.
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26
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Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG. A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure 2015; 23:1801-1814. [PMID: 26365797 DOI: 10.1016/j.str.2015.08.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 01/09/2023]
Abstract
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.
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Affiliation(s)
- E Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oscar W Huang
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Florence Poy
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steve F Bellon
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA
| | - Yong Tang
- Department of Structural Biology, Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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27
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Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast. Proc Natl Acad Sci U S A 2015; 112:E4689-96. [PMID: 26261321 DOI: 10.1073/pnas.1506460112] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV mutagenesis. Several screening and sorting rounds resulted in the selection of eight yeast clones with significantly improved secretion of recombinant α-amylase. Efficient secretion was genetically stable in the selected clones. We performed whole-genome sequencing of the eight clones and identified 330 mutations in total. Gene ontology analysis of mutated genes revealed many biological processes, including some that have not been identified before in the context of protein secretion. Mutated genes identified in this study can be potentially used for reverse metabolic engineering, with the objective to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could broadly facilitate design of novel cell factories.
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28
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Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis. Cell 2015; 161:1413-24. [DOI: 10.1016/j.cell.2015.04.051] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/05/2015] [Accepted: 04/09/2015] [Indexed: 02/06/2023]
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Characterization of Trypanosoma cruzi Sirtuins as Possible Drug Targets for Chagas Disease. Antimicrob Agents Chemother 2015; 59:4669-79. [PMID: 26014945 DOI: 10.1128/aac.04694-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 05/18/2015] [Indexed: 12/20/2022] Open
Abstract
Acetylation of lysine is a major posttranslational modification of proteins and is catalyzed by lysine acetyltransferases, while lysine deacetylases remove acetyl groups. Among the deacetylases, the sirtuins are NAD(+)-dependent enzymes, which modulate gene silencing, DNA damage repair, and several metabolic processes. As sirtuin-specific inhibitors have been proposed as drugs for inhibiting the proliferation of tumor cells, in this study, we investigated the role of these inhibitors in the growth and differentiation of Trypanosoma cruzi, the agent of Chagas disease. We found that the use of salermide during parasite infection prevented growth and initial multiplication after mammalian cell invasion by T. cruzi at concentrations that did not affect host cell viability. In addition, in vivo infection was partially controlled upon administration of salermide. There are two sirtuins in T. cruzi, TcSir2rp1 and TcSir2rp3. By using specific antibodies and cell lines overexpressing the tagged versions of these enzymes, we found that TcSir2rp1 is localized in the cytosol and TcSir2rp3 in the mitochondrion. TcSir2rp1 overexpression acts to impair parasite growth and differentiation, whereas the wild-type version of TcSir2rp3 and not an enzyme mutated in the active site improves both. The effects observed with TcSir2rp3 were fully reverted by adding salermide, which inhibited TcSir2rp3 expressed in Escherichia coli with a 50% inhibitory concentration (IC50) ± standard error of 1 ± 0.5 μM. We concluded that sirtuin inhibitors targeting TcSir2rp3 could be used in Chagas disease chemotherapy.
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30
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The lysine acetyltransferase activator Brpf1 governs dentate gyrus development through neural stem cells and progenitors. PLoS Genet 2015; 11:e1005034. [PMID: 25757017 PMCID: PMC4355587 DOI: 10.1371/journal.pgen.1005034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 01/28/2015] [Indexed: 12/18/2022] Open
Abstract
Lysine acetylation has recently emerged as an important post-translational modification in diverse organisms, but relatively little is known about its roles in mammalian development and stem cells. Bromodomain- and PHD finger-containing protein 1 (BRPF1) is a multidomain histone binder and a master activator of three lysine acetyltransferases, MOZ, MORF and HBO1, which are also known as KAT6A, KAT6B and KAT7, respectively. While the MOZ and MORF genes are rearranged in leukemia, the MORF gene is also mutated in prostate and other cancers and in four genetic disorders with intellectual disability. Here we show that forebrain-specific inactivation of the mouse Brpf1 gene causes hypoplasia in the dentate gyrus, including underdevelopment of the suprapyramidal blade and complete loss of the infrapyramidal blade. We trace the developmental origin to compromised Sox2+ neural stem cells and Tbr2+ intermediate neuronal progenitors. We further demonstrate that Brpf1 loss deregulates neuronal migration, cell cycle progression and transcriptional control, thereby causing abnormal morphogenesis of the hippocampus. These results link histone binding and acetylation control to hippocampus development and identify an important epigenetic regulator for patterning the dentate gyrus, a brain structure critical for learning, memory and adult neurogenesis. Lysine acetylation refers to addition of the acetyl group to lysine residues after protein synthesis. Little is known about how this modification plays a role in the brain and neural stem cells. It is catalyzed by a group of enzymes known as lysine acetyltransferases. A novel epigenetic regulator called BRPF1 acts as a master activator of three different lysine acetyltransferases and also contains multiple structural domains for histone binding. In this study, we show that forebrain-specific inactivation of the mouse Brpf1 gene causes abnormal development of the dentate gyrus, a key component of the hippocampus. We trace the developmental origin to compromised neural stem cells and progenitors, and demonstrate that Brpf1 loss deregulates neuronal migration and cell cycle progression during development of the dentate gyrus. This is the first report on an epigenetic regulator whose loss has such a profound impact on the hippocampus, especially the dentate gyrus, a brain structure critical for learning, memory and adult neurogenesis.
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31
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Mo R, Yang M, Chen Z, Cheng Z, Yi X, Li C, He C, Xiong Q, Chen H, Wang Q, Ge F. Acetylome analysis reveals the involvement of lysine acetylation in photosynthesis and carbon metabolism in the model cyanobacterium Synechocystis sp. PCC 6803. J Proteome Res 2015; 14:1275-86. [PMID: 25621733 DOI: 10.1021/pr501275a] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.
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Affiliation(s)
- Ran Mo
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China
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32
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Acker J, Nguyen NTT, Vandamme M, Tavenet A, Briand-Suleau A, Conesa C. Sub1 and Maf1, two effectors of RNA polymerase III, are involved in the yeast quiescence cycle. PLoS One 2014; 9:e114587. [PMID: 25531541 PMCID: PMC4273968 DOI: 10.1371/journal.pone.0114587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/11/2014] [Indexed: 12/30/2022] Open
Abstract
Sub1 and Maf1 exert an opposite effect on RNA polymerase III transcription interfering with different steps of the transcription cycle. In this study, we present evidence that Sub1 and Maf1 also exhibit an opposite role on yeast chronological life span. First, cells lacking Sub1 need more time than wild type to exit from resting and this lag in re-proliferation is correlated with a delay in transcriptional reactivation. Second, our data show that the capacity of the cells to properly establish a quiescent state is impaired in the absence of Sub1 resulting in a premature death that is dependent on the Ras/PKA and Tor1/Sch9 signalling pathways. On the other hand, we show that maf1Δ cells are long-lived mutant suggesting a connection between Pol III transcription and yeast longevity.
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Affiliation(s)
- Joël Acker
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (CC); (JA)
| | - Ngoc-Thuy-Trinh Nguyen
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Marie Vandamme
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Arounie Tavenet
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Audrey Briand-Suleau
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Christine Conesa
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (CC); (JA)
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33
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Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Mol Cell Proteomics 2014; 14:162-76. [PMID: 25381059 DOI: 10.1074/mcp.m114.043141] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular processes related to growth and division.
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Affiliation(s)
- Michael Downey
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158;
| | - Jeffrey R Johnson
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Norman E Davey
- ¶Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Billy W Newton
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Tasha L Johnson
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - Shastyn Galaang
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
| | - Charles A Seller
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
| | - Nevan Krogan
- §Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, QB3, San Francisco, CA, 94158
| | - David P Toczyski
- From the ‡Department of Biochemistry and Biophysics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, 94158
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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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Jensen AN, Chindaudomsate W, Thitiananpakorn K, Mongkolsuk S, Jensen LT. Improper protein trafficking contributes to artemisinin sensitivity in cells lacking the KDAC Rpd3p. FEBS Lett 2014; 588:4018-25. [PMID: 25263705 DOI: 10.1016/j.febslet.2014.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 10/24/2022]
Abstract
Lysine deacetylases (KDACs) inhibitors may have therapeutic value in anti-malarial combination therapies with artemisinin. To evaluate connections between KDACs and artemisinin, Saccharomyces cerevisiae deletion mutants in KDAC genes were assayed. Deletion of RPD3, but not other KDAC genes, resulted in strong sensitivity to artemisinin, which was also observed in sit4Δ mutants with impaired endoplasmic reticulum (ER) to Golgi protein trafficking. Decreased accumulation of the transporters Pdr5p, Fur4p, and Tat2p was observed in rpd3Δ and sit4Δ cells. The unfolded protein response is induced in rpd3Δ cells consistent with retention of proteins in the ER. Disruption of protein trafficking appears to sensitize cells to artemisinin and targeting these pathways may be useful as part of artemisinin based anti-malarial therapy.
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Affiliation(s)
| | | | | | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
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36
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Abstract
Histone acetylation is a key regulatory feature for chromatin that is established by opposing enzymatic activities of lysine acetyltransferases (KATs/HATs) and deacetylases (KDACs/HDACs). Esa1, like its human homolog Tip60, is an essential MYST family enzyme that acetylates histones H4 and H2A and other nonhistone substrates. Here we report that the essential requirement for ESA1 in Saccharomyces cerevisiae can be bypassed upon loss of Sds3, a noncatalytic subunit of the Rpd3L deacetylase complex. By studying the esa1∆ sds3∆ strain, we conclude that the essential function of Esa1 is in promoting the cellular balance of acetylation. We demonstrate this by fine-tuning acetylation through modulation of HDACs and the histone tails themselves. Functional interactions between Esa1 and HDACs of class I, class II, and the Sirtuin family define specific roles of these opposing activities in cellular viability, fitness, and response to stress. The fact that both increased and decreased expression of the ESA1 homolog TIP60 has cancer associations in humans underscores just how important the balance of its activity is likely to be for human well-being.
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37
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Hou T, Zheng G, Zhang P, Jia J, Li J, Xie L, Wei C, Li Y. LAceP: lysine acetylation site prediction using logistic regression classifiers. PLoS One 2014; 9:e89575. [PMID: 24586884 PMCID: PMC3930742 DOI: 10.1371/journal.pone.0089575] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Background Lysine acetylation is a crucial type of protein post-translational modification, which is involved in many important cellular processes and serious diseases. However, identification of protein acetylated sites through traditional experiment methods is time-consuming and laborious. Those methods are not suitable to identify a large number of acetylated sites quickly. Therefore, computational methods are still very valuable to accelerate lysine acetylated site finding. Result In this study, many biological characteristics of acetylated sites have been investigated, such as the amino acid sequence around the acetylated sites, the physicochemical property of the amino acids and the transition probability of adjacent amino acids. A logistic regression method was then utilized to integrate these information for generating a novel lysine acetylation prediction system named LAceP. When compared with existing methods, LAceP overwhelms most of state-of-the-art methods. Especially, LAceP has a more balanced prediction capability for positive and negative datasets. Conclusion LAceP can integrate different biological features to predict lysine acetylation with high accuracy. An online web server is freely available at http://www.scbit.org/iPTM/.
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Affiliation(s)
- Ting Hou
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Pingyu Zhang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Chaochun Wei
- Shanghai Center for Bioinformation Technology, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Yixue Li
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
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38
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Abstract
Continuous synthesis of all cellular components requires their constant turnover in order for a cell to achieve homeostasis. To this end, eukaryotic cells are endowed with two degradation pathways - the ubiquitin-proteasome system and the lysosomal pathway. The latter pathway is partly fed by autophagy, which targets intracellular material in distinct vesicles, termed autophagosomes, to the lysosome. Central to this pathway is a set of key autophagy proteins, including the ubiquitin-like modifier Atg8, that orchestrate autophagosome initiation and biogenesis. In higher eukaryotes, the Atg8 family comprises six members known as the light chain 3 (LC3) or γ-aminobutyric acid (GABA)-receptor-associated protein (GABARAP) proteins. Considerable effort during the last 15 years to decipher the molecular mechanisms that govern autophagy has significantly advanced our understanding of the functioning of this protein family. In this Cell Science at a Glance article and the accompanying poster, we present the current LC3 protein interaction network, which has been and continues to be vital for gaining insight into the regulation of autophagy.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry II, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Yeheskely-Hayon D, Kotler A, Stark M, Hashimshony T, Sagee S, Kassir Y. The roles of the catalytic and noncatalytic activities of Rpd3L and Rpd3S in the regulation of gene transcription in yeast. PLoS One 2013; 8:e85088. [PMID: 24358376 PMCID: PMC3866184 DOI: 10.1371/journal.pone.0085088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 11/22/2013] [Indexed: 02/02/2023] Open
Abstract
In budding yeasts, the histone deacetylase Rpd3 resides in two different complexes called Rpd3L (large) and Rpd3S (small) that exert opposing effects on the transcription of meiosis-specific genes. By introducing mutations that disrupt the integrity and function of either Rpd3L or Rpd3S, we show here that Rpd3 function is determined by its association with either of these complexes. Specifically, the catalytic activity of Rpd3S activates the transcription of the two major positive regulators of meiosis, IME1 and IME2, under all growth conditions and activates the transcription of NDT80 only during vegetative growth. In contrast, the effects of Rpd3L depends on nutrients; it represses or activates transcription in the presence or absence of a nitrogen source, respectively. Further, we show that transcriptional activation does not correlate with histone H4 deacetylation, suggesting an effect on a nonhistone protein. Comparison of rpd3-null and catalytic-site point mutants revealed an inhibitory activity that is independent of either the catalytic activity of Rpd3 or the integrity of Rpd3L and Rpd3S.
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Affiliation(s)
| | - Anat Kotler
- Department of Biology, Technion, Haifa, Israel
| | | | | | - Shira Sagee
- Department of Biology, Technion, Haifa, Israel
| | - Yona Kassir
- Department of Biology, Technion, Haifa, Israel
- * E-mail:
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40
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Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast. Mol Cell Biol 2013; 34:631-42. [PMID: 24298021 DOI: 10.1128/mcb.00256-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Differentiation programs require strict spatial and temporal control of gene transcription. Genes expressed during meiotic development in Saccharomyces cerevisiae display transient induction and repression. Early meiotic gene (EMG) repression during mitosis is achieved by recruiting both histone deacetylase and chromatin remodeling complexes to their promoters by the zinc cluster DNA binding protein Ume6p. Ume6p repression is relieved by ubiquitin-mediated destruction that is stimulated by Gcn5p-induced acetylation. In this report, we demonstrate that Gcn5p acetylation of separate lysines within the zinc cluster domain negatively impacts Ume6p DNA binding. Mimicking lysine acetylation using glutamine substitution mutations decreased Ume6p binding efficiency and resulted in partial derepression of Ume6p-regulated genes. Consistent with this result, molecular modeling predicted that these lysine side chains are adjacent to the DNA phosphate backbone, suggesting that acetylation inhibits Ume6p binding by electrostatic repulsion. Preventing acetylation did not impact final EMG induction levels during meiosis. However, a delay in EMG induction was observed, which became more severe in later expression classes, ultimately resulting in delayed and reduced execution of the meiotic nuclear divisions. These results indicate that Ume6p acetylation ensures the proper timing of the transient transcription program during meiotic development.
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41
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The yeast AMPK homolog SNF1 regulates acetyl coenzyme A homeostasis and histone acetylation. Mol Cell Biol 2013; 33:4701-17. [PMID: 24081331 DOI: 10.1128/mcb.00198-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetyl coenzyme A (acetyl-CoA) is a key metabolite at the crossroads of metabolism, signaling, chromatin structure, and transcription. Concentration of acetyl-CoA affects histone acetylation and links intermediary metabolism and transcriptional regulation. Here we show that SNF1, the budding yeast ortholog of the mammalian AMP-activated protein kinase (AMPK), plays a role in the regulation of acetyl-CoA homeostasis and global histone acetylation. SNF1 phosphorylates and inhibits acetyl-CoA carboxylase, which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the first and rate-limiting reaction in the de novo synthesis of fatty acids. Inactivation of SNF1 results in a reduced pool of cellular acetyl-CoA, globally decreased histone acetylation, and reduced fitness and stress resistance. The histone acetylation and transcriptional defects can be partially suppressed and the overall fitness improved in snf1Δ mutant cells by increasing the cellular concentration of acetyl-CoA, indicating that the regulation of acetyl-CoA homeostasis represents another mechanism in the SNF1 regulatory repertoire.
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Downey M, Knight B, Vashisht AA, Seller CA, Wohlschlegel JA, Shore D, Toczyski DP. Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1. Curr Biol 2013; 23:1638-48. [PMID: 23973296 PMCID: PMC3982851 DOI: 10.1016/j.cub.2013.06.050] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/31/2013] [Accepted: 06/19/2013] [Indexed: 01/30/2023]
Abstract
BACKGROUND In eukaryotes, ribosome biosynthesis involves the coordination of ribosomal RNA and ribosomal protein (RP) production. In S. cerevisiae, the regulation of ribosome biosynthesis occurs largely at the level of transcription. The transcription factor Ifh1 binds at RP genes and promotes their transcription when growth conditions are favorable. Although Ifh1 recruitment to RP genes has been characterized, little is known about the regulation of promoter-bound Ifh1. RESULTS We used a novel whole-cell-extract screening approach to identify Spt7, a member of the SAGA transcription complex, and the RP transactivator Ifh1 as highly acetylated nonhistone species. We report that Ifh1 is modified by acetylation specifically in an N-terminal domain. These acetylations require the Gcn5 histone acetyltransferase and are reversed by the sirtuin deacetylases Hst1 and Sir2. Ifh1 acetylation is regulated by rapamycin treatment and stress and limits the ability of Ifh1 to act as a transactivator at RP genes. CONCLUSIONS Our data suggest a novel mechanism of regulation whereby Gcn5 functions to titrate the activity of Ifh1 following its recruitment to RP promoters to provide more than an all-or-nothing mode of transcriptional regulation. We provide insights into how the action of histone acetylation machineries converges with nutrient-sensing pathways to regulate important aspects of cell growth.
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Affiliation(s)
- Michael Downey
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, 1450 3 Street, San Francisco, California, 94158, U.S.A
| | - Britta Knight
- Department of Molecular Biology, University of Geneva, 30, quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Ajay A. Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Dr. South BSRB 377A, Los Angeles, California, 90095, USA
| | - Charles A. Seller
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, 1450 3 Street, San Francisco, California, 94158, U.S.A
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Dr. South BSRB 377A, Los Angeles, California, 90095, USA
| | - David Shore
- Department of Molecular Biology, University of Geneva, 30, quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - David P. Toczyski
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, 1450 3 Street, San Francisco, California, 94158, U.S.A
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43
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The transcription cofactor FgSwi6 plays a role in growth and development, carbendazim sensitivity, cellulose utilization, lithium tolerance, deoxynivalenol production and virulence in the filamentous fungus Fusarium graminearum. Fungal Genet Biol 2013; 58-59:42-52. [DOI: 10.1016/j.fgb.2013.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 01/24/2023]
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44
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Good PD, Kendall A, Ignatz-Hoover J, Miller EL, Pai DA, Rivera SR, Carrick B, Engelke DR. Silencing near tRNA genes is nucleosome-mediated and distinct from boundary element function. Gene 2013; 526:7-15. [PMID: 23707796 PMCID: PMC3745993 DOI: 10.1016/j.gene.2013.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 01/22/2023]
Abstract
Transfer RNA (tRNA) genes and other RNA polymerase III transcription units are dispersed in high copy throughout nuclear genomes, and can antagonize RNA polymerase II transcription in their immediate chromosomal locus. Previous work in Saccharomyces cerevisiae found that this local silencing required subnuclear clustering of the tRNA genes near the nucleolus. Here we show that the silencing also requires nucleosome participation, though the nature of the nucleosome interaction appears distinct from other forms of transcriptional silencing. Analysis of an extensive library of histone amino acid substitutions finds a large number of residues that affect the silencing, both in the histone N-terminal tails and on the nucleosome disk surface. The residues on the disk surfaces involved are largely distinct from those affecting other regulatory phenomena. Consistent with the large number of histone residues affecting tgm silencing, survey of chromatin modification mutations shows that several enzymes known to affect nucleosome modification and positioning are also required. The enzymes include an Rpd3 deacetylase complex, Hos1 deacetylase, Glc7 phosphatase, and the RSC nucleosome remodeling activity, but not multiple other activities required for other silencing forms or boundary element function at tRNA gene loci. Models for communication between the tRNA gene transcription complexes and local chromatin are discussed.
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Affiliation(s)
- Paul D. Good
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Ann Kendall
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | | | - Erin L. Miller
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Dave A. Pai
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Sara R. Rivera
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Brian Carrick
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - David R. Engelke
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
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45
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Stilger KL, Sullivan WJ. Elongator protein 3 (Elp3) lysine acetyltransferase is a tail-anchored mitochondrial protein in Toxoplasma gondii. J Biol Chem 2013; 288:25318-25329. [PMID: 23878194 DOI: 10.1074/jbc.m113.491373] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lysine acetylation has recently emerged as an important, widespread post-translational modification occurring on proteins that reside in multiple cellular compartments, including the mitochondria. However, no lysine acetyltransferase (KAT) has been definitively localized to this organelle to date. Here we describe the identification of an unusual homologue of Elp3 in early-branching protozoa in the phylum Apicomplexa. Elp3 is the catalytic subunit of the well-conserved transcription Elongator complex; however, Apicomplexa lack all other Elongator subunits, suggesting that the Elp3 in these organisms plays a role independent of transcription. Surprisingly, Elp3 in the parasites of this phylum, including Toxoplasma gondii (TgElp3), possesses a unique C-terminal transmembrane domain (TMD) that localizes the protein to the mitochondrion. As TgElp3 is devoid of known mitochondrial targeting signals, we used selective permeabilization studies to reveal that this KAT is oriented with its catalytic components facing the cytosol and its C-terminal TMD inserted into the outer mitochondrial membrane, consistent with a tail-anchored membrane protein. Elp3 trafficking to mitochondria is not exclusive to Toxoplasma as we also present evidence that a form of Elp3 localizes to these organelles in mammalian cells, supporting the idea that Elp3 performs novel functions across eukaryotes that are independent of transcriptional elongation. Importantly, we also present genetic studies that suggest TgElp3 is essential in Toxoplasma and must be positioned at the mitochondrial surface for parasite viability.
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Affiliation(s)
| | - William J Sullivan
- From the Departments of Pharmacology and Toxicology and; Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202.
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46
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Kim GW, Li L, Ghorbani M, You L, Yang XJ. Mice lacking α-tubulin acetyltransferase 1 are viable but display α-tubulin acetylation deficiency and dentate gyrus distortion. J Biol Chem 2013; 288:20334-50. [PMID: 23720746 DOI: 10.1074/jbc.m113.464792] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
α-Tubulin acetylation at Lys-40, located on the luminal side of microtubules, has been widely studied and used as a marker for stable microtubules in the cilia and other subcellular structures, but the functional consequences remain perplexing. Recent studies have shown that Mec-17 and its paralog are responsible for α-tubulin acetylation in Caenorhabditis elegans. There is one such protein known as Atat1 (α-tubulin acetyltransferase 1) per higher organism. Zebrafish Atat1 appears to govern embryo development, raising the intriguing possibility that Atat1 is also critical for development in mammals. In addition to Atat1, three other mammalian acetyltransferases, ARD1-NAT1, ELP3, and GCN5, have been shown to acetylate α-tubulin in vitro, so an important question is how these four enzymes contribute to the acetylation in vivo. We demonstrate here that Atat1 is a major α-tubulin acetyltransferase in mice. It is widely expressed in mouse embryos and tissues. Although Atat1-null animals display no overt phenotypes, α-tubulin acetylation is lost in sperm flagella and the dentate gyrus is slightly deformed. Furthermore, human ATAT1 colocalizes on bundled microtubules with doublecortin. These results thus suggest that mouse Atat1 may regulate advanced functions such as learning and memory, thereby shedding novel light on the physiological roles of α-tubulin acetylation in mammals.
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Affiliation(s)
- Go-Woon Kim
- Rosalind and Morris Goodman Cancer Research Center, Montréal, Québec H3A 1A3, Canada
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47
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mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases. Proc Natl Acad Sci U S A 2013; 110:E1641-50. [PMID: 23572591 DOI: 10.1073/pnas.1218515110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent global proteomic and genomic studies have determined that lysine acetylation is a highly abundant posttranslational modification. The next challenge is connecting lysine acetyltransferases (KATs) to their cellular targets. We hypothesize that proteins that physically interact with KATs may not only predict the cellular function of the KATs but may be acetylation targets. We have developed a mass spectrometry-based method that generates a KAT protein interaction network from which we simultaneously identify both in vivo acetylation sites and in vitro acetylation sites. This modified chromatin-immunopurification coupled to an in vitro KAT assay with mass spectrometry (mChIP-KAT-MS) was applied to the Saccharomyces cerevisiae KAT nucleosome acetyltransferase of histone H4 (NuA4). Using mChIP-KAT-MS, we define the NuA4 interactome and in vitro-enriched acetylome, identifying over 70 previously undescribed physical interaction partners for the complex and over 150 acetyl lysine residues, of which 108 are NuA4-specific in vitro sites. Through this method we determine NuA4 acetylation of its own subunit Epl1 is a means of self-regulation and identify a unique link between NuA4 and the spindle pole body. Our work demonstrates that this methodology may serve as a valuable tool in connecting KATs with their cellular targets.
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48
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Robbins N, Leach MD, Cowen LE. Lysine deacetylases Hda1 and Rpd3 regulate Hsp90 function thereby governing fungal drug resistance. Cell Rep 2012; 2:878-88. [PMID: 23041319 PMCID: PMC3607219 DOI: 10.1016/j.celrep.2012.08.035] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 06/26/2012] [Accepted: 08/30/2012] [Indexed: 12/03/2022] Open
Abstract
The molecular chaperone Hsp90 is a hub of protein homeostasis and regulatory circuitry. Hsp90 function is regulated by posttranslational modifications including acetylation in mammals; however, whether this regulation is conserved remains unknown. In fungi, Hsp90 governs the evolution of drug resistance by stabilizing signal transducers. Here, we establish that pharmacological inhibition of lysine deacetylases (KDACs) blocks the emergence and maintenance of Hsp90-dependent resistance to the most widely deployed antifungals, the azoles, in the human fungal pathogen Candida albicans and the model yeast Saccharomyces cerevisiae. S. cerevisiae Hsp90 is acetylated on lysine 27 and 270, and key KDACs for drug resistance are Hda1 and Rpd3. Compromising KDACs alters stability and function of Hsp90 client proteins, including the drug-resistance regulator calcineurin. Thus, we establish acetylation as a mechanism of posttranslational control of Hsp90 function in fungi, functional redundancy between KDACs Hda1 and Rpd3, as well as a mechanism governing fungal drug resistance with broad therapeutic potential.
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Affiliation(s)
- Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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49
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Functional analysis with a barcoder yeast gene overexpression system. G3-GENES GENOMES GENETICS 2012; 2:1279-89. [PMID: 23050238 PMCID: PMC3464120 DOI: 10.1534/g3.112.003400] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/22/2012] [Indexed: 01/26/2023]
Abstract
Systematic analysis of gene overexpression phenotypes provides an insight into gene function, enzyme targets, and biological pathways. Here, we describe a novel functional genomics platform that enables a highly parallel and systematic assessment of overexpression phenotypes in pooled cultures. First, we constructed a genome-level collection of ~5100 yeast barcoder strains, each of which carries a unique barcode, enabling pooled fitness assays with a barcode microarray or sequencing readout. Second, we constructed a yeast open reading frame (ORF) galactose-induced overexpression array by generating a genome-wide set of yeast transformants, each of which carries an individual plasmid-born and sequence-verified ORF derived from the Saccharomyces cerevisiae full-length EXpression-ready (FLEX) collection. We combined these collections genetically using synthetic genetic array methodology, generating ~5100 strains, each of which is barcoded and overexpresses a specific ORF, a set we termed “barFLEX.” Additional synthetic genetic array allows the barFLEX collection to be moved into different genetic backgrounds. As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions.
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