1
|
Cohen A, Lubenski L, Mouzon A, Kupiec M, Weisman R. TORC2 is required for accumulation of γH2A in response to DNA damage. J Biol Chem 2024:107531. [PMID: 38971312 DOI: 10.1016/j.jbc.2024.107531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/08/2024] Open
Abstract
TOR protein kinases serve as the catalytic subunit of the TORC1 and TORC2 complexes, which regulate cellular growth, proliferation and survival. In the fission yeast, Schizosaccharomyces pombe, cells lacking TORC2 or its downstream kinase Gad8 (AKT or SGK1 in human cells) exhibit sensitivity to a wide range of stress conditions, including DNA damage stress. One of the first responses to DNA damage is the phosphorylation of C-terminal serine residues within histone H2AX in human cells (γH2AX), or histone H2A in yeast cells (γH2A). The kinases responsible for γH2A in S. pombe are the two DNA damage checkpoint kinases Rad3 and Tel1 (ATR and ATM, respectively, in human cells). Here we report that TORC2-Gad8 signaling is required for accumulation of γH2A in response to DNA damage and during quiescence. Using the TOR specific inhibitor, Torin1, we demonstrate that the effect of TORC2 on γH2A in response to DNA damage is immediate, rather than adaptive. The lack of γH2A is restored by deletion mutations of transcription and chromatin modification factors, including loss of components of Paf1C, SAGA, Mediator and the bromo-domain proteins Bdf1/Bdf2. Thus, we suggest that TORC2-Gad8 may affect the accumulation of γH2A by regulating chromatin structure and function.
Collapse
Affiliation(s)
- Adiel Cohen
- Department of Natural Sciences, The Open University of Israel, University Road 1, 4353701, Ranana, Israel
| | - Lea Lubenski
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ava Mouzon
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ronit Weisman
- Department of Natural Sciences, The Open University of Israel, University Road 1, 4353701, Ranana, Israel.
| |
Collapse
|
2
|
Kawamukai M. Regulation of sexual differentiation initiation in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 2024; 88:475-492. [PMID: 38449372 DOI: 10.1093/bbb/zbae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism to explore cellular events owing to rich tools in genetics, molecular biology, cellular biology, and biochemistry. Schizosaccharomyces pombe proliferates continuously when nutrients are abundant but arrests in G1 phase upon depletion of nutrients such as nitrogen and glucose. When cells of opposite mating types are present, cells conjugate, fuse, undergo meiosis, and finally form 4 spores. This sexual differentiation process in S. pombe has been studied extensively. To execute sexual differentiation, the glucose-sensing cAMP-PKA (cyclic adenosine monophosphate-protein kinase A) pathway, nitrogen-sensing TOR (target of rapamycin) pathway, and SAPK (stress-activating protein kinase) pathway are crucial, and the MAPK (mitogen-activating protein kinase) cascade is essential for pheromone sensing. These signals regulate ste11 at the transcriptional and translational levels, and Ste11 is modified in multiple ways. This review summarizes the initiation of sexual differentiation in S. pombe based on results I have helped to obtain, including the work of many excellent researchers.
Collapse
Affiliation(s)
- Makoto Kawamukai
- D epartment of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Nishikawatsu, Matsue, Japan
| |
Collapse
|
3
|
Fierling N, Billard P, Bauda P, Blaudez D. Global deletome profile of Saccharomyces cerevisiae exposed to lithium. Metallomics 2024; 16:mfad073. [PMID: 38142127 DOI: 10.1093/mtomcs/mfad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023]
Abstract
The increasing use of lithium (Li) in new technologies raises the question of its impact on living microorganisms. In the present study, we aimed to identify putative Li targets and resistance mechanisms in the yeast model Saccharomyces cerevisiae using a deletomic approach based on the screening of a collection of 4733 knockout mutants under Li exposure. This screening highlighted 60 mutants resistant to Li and 124 mutants sensitive to Li. Through functional enrichment analyses, transport systems were identified as playing a central role in cell resistance to toxic concentrations of Li. In contrast, the AKT/protein kinase B family, signal transduction or cell communication were identified as potential toxic targets of Li. The majority of the mutants with a Li-sensitive phenotype were also sensitive to other alkali and alkaline earth metals, whereas the Li-resistance phenotype was mostly resistant to Na but poorly resistant to other metals. A comparison with the results of deletomics studies carried out in the presence of other metals highlighted Li-specific phenotypes. Three genes (NAM7, NMD2, UPF3) of the nonsense-mediated decay pathway were specifically involved in resistance to Li. In contrast, mutants with the NCA2, SPT20, GCN5, YOR376W, YPK3, and DCW1 genes deleted were specifically resistant to Li. These genes encode various functions from putative mannosidase to constitution of the Spt-Ada-Gcn5 acetyltransferase complex. This work provides a better understanding of potential specific resistance mechanisms and cellular targets of Li in yeast.
Collapse
|
4
|
del Dedo JE, Segundo RLS, Vázquez-Bolado A, Sun J, García-Blanco N, Suárez MB, García P, Tricquet P, Chen JS, Dedon PC, Gould KL, Hidalgo E, Hermand D, Moreno S. The Greatwall-Endosulfine-PP2A/B55 pathway controls entry into quiescence by promoting translation of Elongator-tuneable transcripts. RESEARCH SQUARE 2023:rs.3.rs-3616701. [PMID: 38105947 PMCID: PMC10723533 DOI: 10.21203/rs.3.rs-3616701/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Quiescent cells require a continuous supply of proteins to maintain protein homeostasis. In fission yeast, entry into quiescence is triggered by nitrogen stress, leading to the inactivation of TORC1 and the activation of TORC2. Here, we report that the Greatwall-Endosulfine-PPA/B55 pathway connects the downregulation of TORC1 with the upregulation of TORC2, resulting in the activation of Elongator-dependent tRNA modifications essential for sustaining the translation programme during entry into quiescence. This process promotes U34 and A37 tRNA modifications at the anticodon stem loop, enhancing translation efficiency and fidelity of mRNAs enriched for AAA versus AAG lysine codons. Notably, some of these mRNAs encode inhibitors of TORC1, activators of TORC2, tRNA modifiers, and proteins necessary for telomeric and subtelomeric functions. Therefore, we propose a novel mechanism by which cells respond to nitrogen stress at the level of translation, involving a coordinated interplay between the tRNA epitranscriptome and biased codon usage.
Collapse
Affiliation(s)
- Javier Encinar del Dedo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Rafael López-San Segundo
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Alicia Vázquez-Bolado
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - Jingjing Sun
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Natalia García-Blanco
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
| | - M. Belén Suárez
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Patricia García
- Instituto de Biología Funcional y Genómica, University of Salamanca, CSIC, 37007 Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, 37007 Salamanca, Spain
| | - Pauline Tricquet
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Peter C. Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Damien Hermand
- URPHYM-GEMO, University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica, CSIC, University of Salamanca, 37007 Salamanca, Spain
- Lead contact
| |
Collapse
|
5
|
Barman P, Chakraborty P, Bhaumik R, Bhaumik SR. UPS writes a new saga of SAGA. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194981. [PMID: 37657588 PMCID: PMC10843445 DOI: 10.1016/j.bbagrm.2023.194981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
SAGA (Spt-Ada-Gcn5-Acetyltransferase), an evolutionarily conserved transcriptional co-activator among eukaryotes, is a large multi-subunit protein complex with two distinct enzymatic activities, namely HAT (Histone acetyltransferase) and DUB (De-ubiquitinase), and is targeted to the promoter by the gene-specific activator proteins for histone covalent modifications and PIC (Pre-initiation complex) formation in enhancing transcription (or gene activation). Targeting of SAGA to the gene promoter is further facilitated by the 19S RP (Regulatory particle) of the 26S proteasome (that is involved in targeted degradation of protein via ubiquitylation) in a proteolysis-independent manner. Moreover, SAGA is also recently found to be regulated by the 26S proteasome in a proteolysis-dependent manner via the ubiquitylation of its Sgf73/ataxin-7 component that is required for SAGA's integrity and DUB activity (and hence transcription), and is linked to various diseases including neurodegenerative disorders and cancer. Thus, SAGA itself and its targeting to the active gene are regulated by the UPS (Ubiquitin-proteasome system) with implications in diseases.
Collapse
Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Rhea Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA.
| |
Collapse
|
6
|
Vázquez-Bolado A, López-San Segundo R, García-Blanco N, Rozalén AE, González-Álvarez D, Suárez MB, Pérez-Hidalgo L, Moreno S. The Greatwall-Endosulfine Switch Accelerates Autophagic Flux during the Cell Divisions Leading to G1 Arrest and Entry into Quiescence in Fission Yeast. Int J Mol Sci 2022; 24:ijms24010148. [PMID: 36613592 PMCID: PMC9820488 DOI: 10.3390/ijms24010148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Entry into quiescence in the fission yeast Schizosaccharomyces pombe is induced by nitrogen starvation. In the absence of nitrogen, proliferating fission yeast cells divide twice without cell growth and undergo cell cycle arrest in G1 before becoming G0 quiescent cells. Under these conditions, autophagy is induced to produce enough nitrogen for the two successive cell divisions that take place before the G1 arrest. In parallel to the induction of autophagy, the Greatwall-Endosulfine switch is activated upon nitrogen starvation to down-regulate protein phosphatase PP2A/B55 activity, which is essential for cell cycle arrest in G1 and implementation of the quiescent program. Here we show that, although inactivation of PP2A/B55 by the Greatwall-Endosulfine switch is not required to promote autophagy initiation, it increases autophagic flux at least in part by upregulating the expression of a number of autophagy-related genes.
Collapse
Affiliation(s)
- Alicia Vázquez-Bolado
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - Rafael López-San Segundo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - Natalia García-Blanco
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - Ana Elisa Rozalén
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - Daniel González-Álvarez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - M. Belén Suárez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
- Department of Microbiology and Genetics, Salamanca University, 37007 Salamanca, Spain
| | - Livia Pérez-Hidalgo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
| | - Sergio Moreno
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Salamanca University, Zacarías González 2, 37007 Salamanca, Spain
- Correspondence:
| |
Collapse
|
7
|
Ohtsuka H, Shimasaki T, Aiba H. Response to leucine in Schizosaccharomyces pombe (fission yeast). FEMS Yeast Res 2022; 22:6553821. [PMID: 35325114 PMCID: PMC9041340 DOI: 10.1093/femsyr/foac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
Collapse
Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| |
Collapse
|
8
|
Kleijn IT, Martínez-Segura A, Bertaux F, Saint M, Kramer H, Shahrezaei V, Marguerat S. Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. Life Sci Alliance 2022; 5:5/5/e202101223. [PMID: 35228260 PMCID: PMC8886410 DOI: 10.26508/lsa.202101223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/20/2022] Open
Abstract
Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Here, we determined the importance of the growth rate in explaining relative changes in protein and mRNA levels in the simple eukaryote Schizosaccharomyces pombe grown on non-limiting nitrogen sources. Although expression of half of fission yeast genes was significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production apart from RNA polymerase II-dependent transcription. Negatively correlated genes belonged mainly to the environmental stress response programme. Critically, metabolic enzymes, which represent ∼55-70% of the proteome by mass, showed mostly condition-specific regulation. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate-dependent and nutrient-specific gene expression.
Collapse
Affiliation(s)
- Istvan T Kleijn
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK,Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Amalia Martínez-Segura
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - François Bertaux
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK,Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Malika Saint
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Holger Kramer
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Marguerat
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK .,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
9
|
Cohen A, Pataki E, Kupiec M, Weisman R. TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes. PLoS Genet 2022; 18:e1010061. [PMID: 35157728 PMCID: PMC8880919 DOI: 10.1371/journal.pgen.1010061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/25/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
The fission yeast TOR complex 2 (TORC2) is required for gene silencing at subtelomeric regions and for the induction of gene transcription in response to DNA replication stress. Thus, TORC2 affects transcription regulation both negatively and positively. Whether these two TORC2-dependent functions share a common molecular mechanism is currently unknown. Here, we show that Gad8 physically interacts with proteins that regulate transcription, including subunits of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and the BET bromodomain protein Bdf2. We demonstrate that in the absence of TORC2, Gcn5, the histone acetyltransferase subunit of SAGA, accumulates at subtelomeric genes and at non-induced promoters of DNA replication genes. Remarkably, the loss of Gcn5 in TORC2 mutant cells restores gene silencing as well as transcriptional induction in response to DNA replication stress. Loss of Bdf2 alleviates excess of Gcn5 binding in TORC2 mutant cells and also rescues the aberrant regulation of transcription in these cells. Furthermore, the loss of either SAGA or Bdf2 suppresses the sensitivity of TORC2 mutant cells to a variety of stresses, including DNA replication, DNA damage, temperature and nutrient stresses. We suggest a role of TORC2 in transcriptional regulation that is critical for gene silencing and gene induction in response to stress and involves the binding of Gcn5 to the chromatin. A fundamental characteristic of signaling pathways is their role in the regulation of gene expression. Target of rapamycin (TOR), an atypical protein kinase, is a component of two highly conserved TOR complexes: TORC1 and TORC2. These complexes affect nuclear functions through their activity in the cytoplasm as well as directly, through nuclear TOR pools. We previously showed that in fission yeast, TORC2 and its downstream substrate Gad8 associate with the chromatin fraction. We have also demonstrated that TORC2-Gad8 is required for gene silencing and transcriptional induction in response to stresses. Here, we demonstrate that Gad8 physically associates with proteins of the transcriptional machinery. We found that the loss of two positive transcriptional regulators, the SAGA complex and the bromodomain protein Bdf2, restored gene silencing as well as stress-induced transcriptional induction in TORC2 mutant cells. Our data suggests that TORC2-Gad8 contributes to gene regulation through a mechanism involving the inhibition of the accumulation of Gcn5 at the chromatin. These findings suggest a novel and possibly conserved functional relationship between TORC2, Gcn5 and Bdf2. These proteins and protein complexes are key targets in cancer therapies, thus, deciphering their functional relationship may be valuable for combination therapy in personalized medicine.
Collapse
Affiliation(s)
- Adiel Cohen
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Emese Pataki
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
- * E-mail:
| |
Collapse
|
10
|
Wang T, Woodman P, Humphrey SJ, Petersen J. Environmental control of Pub1 (NEDD4 family E3 ligase) in Schizosaccharomyces pombe is regulated by TORC2 and Gsk3. Life Sci Alliance 2022; 5:5/5/e202101082. [PMID: 35121625 PMCID: PMC8817228 DOI: 10.26508/lsa.202101082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
The NEDD4 family E3 ligase Pub1 is regulated by the nutrient environment, TORC2, and Gsk3 signalling pathway to control the level of amino acid transporters on the plasma membrane and thus nutrient uptake. Cells respond to changing nutrient environments by adjusting the abundance of surface nutrient transporters and receptors. This can be achieved by modulating ubiquitin-dependent endocytosis, which in part is regulated by the NEDD4 family of E3 ligases. Here we report novel regulation of Pub1, a fission yeast Schizosaccharomyces pombe member of the NEDD4-family of E3 ligases. We show that nitrogen stress inhibits Pub1 function, thereby increasing the abundance of the amino acid transporter Aat1 at the plasma membrane and enhancing sensitivity to the toxic arginine analogue canavanine. We show that TOR complex 2 (TORC2) signalling negatively regulates Pub1, thus TORC2 mutants under nutrient stress have decreased Aat1 at the plasma membrane and are resistant to canavanine. Inhibition of TORC2 signalling increases Pub1 phosphorylation, and this is dependent on Gsk3 activity. Addition of the Tor inhibitor Torin1 increases phosphorylation of Pub1 at serine 199 (S199) by 2.5-fold, and Pub1 protein levels in S199A phospho-ablated mutants are reduced. S199 is conserved in NEDD4 and is located immediately upstream of a WW domain required for protein interaction. Together, we describe how the major TORC2 nutrient-sensing signalling network regulates environmental control of Pub1 to modulate the abundance of nutrient transporters.
Collapse
Affiliation(s)
- Tingting Wang
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, Australia
| | - Philip Woodman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, Australia
| | - Janni Petersen
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, Australia
| |
Collapse
|
11
|
Abstract
Autophagy is an intracellular catabolic degradative process in which damaged cellular organelles, unwanted proteins and different cytoplasmic components get recycled to maintain cellular homeostasis or metabolic balance. During autophagy, a double membrane vesicle is formed to engulf these cytosolic materials and fuse to lysosomes wherein the entire cargo degrades to be used again. Because of this unique recycling ability of cells, autophagy is a universal stress response mechanism. Dysregulation of autophagy leads to several diseases, including cancer, neurodegeneration and microbial infection. Thus, autophagy machineries have become targets for therapeutics. This chapter provides an overview of the paradoxical role of autophagy in tumorigenesis in the perspective of metabolism.
Collapse
Affiliation(s)
- Sweta Sikder
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, India.
| |
Collapse
|
12
|
Toullec D, Elías-Villalobos A, Faux C, Noly A, Lledo G, Séveno M, Helmlinger D. The Hsp90 cochaperone TTT promotes cotranslational maturation of PIKKs prior to complex assembly. Cell Rep 2021; 37:109867. [PMID: 34686329 DOI: 10.1016/j.celrep.2021.109867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/30/2021] [Accepted: 09/30/2021] [Indexed: 01/28/2023] Open
Abstract
Phosphatidylinositol 3-kinase-related kinases (PIKKs) are a family of kinases that control fundamental processes, including cell growth, DNA damage repair, and gene expression. Although their regulation and activities are well characterized, little is known about how PIKKs fold and assemble into active complexes. Previous work has identified a heat shock protein 90 (Hsp90) cochaperone, the TTT complex, that specifically stabilizes PIKKs. Here, we describe a mechanism by which TTT promotes their de novo maturation in fission yeast. We show that TTT recognizes newly synthesized PIKKs during translation. Although PIKKs form multimeric complexes, we find that they do not engage in cotranslational assembly with their partners. Rather, our findings suggest a model by which TTT protects nascent PIKK polypeptides from misfolding and degradation because PIKKs acquire their native state after translation is terminated. Thus, PIKK maturation and assembly are temporally segregated, suggesting that the biogenesis of large complexes requires both dedicated chaperones and cotranslational interactions between subunits.
Collapse
Affiliation(s)
- Damien Toullec
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Céline Faux
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | - Ambre Noly
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Martial Séveno
- BioCampus Montpellier, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | |
Collapse
|
13
|
Tarhan Ç, Çakır Ö. Transcriptome sequencing and screening of genes related to glucose availability in Schizosaccharomyces pombe by RNA-seq analysis. Genet Mol Biol 2021; 44:e20200245. [PMID: 34460892 PMCID: PMC8404550 DOI: 10.1590/1678-4685-gmb-2020-0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
While calorie restriction is the most used experimental intervention to increase lifespan in numerous model organisms, increasing evidence suggests that excess glucose leads to decreased lifespan in various organisms. To fully understand the molecular basis of the pro-aging effect of glucose, it is still important to discover genetic interactions, gene expression patterns, and molecular responses depending on glucose availability. Here, we compared the gene expression profiles in Schizosaccharomyces pombe mid-log-phase cells grown in three different Synthetic Dextrose media with 3%, 5%, and 8% glucose, using the RNA sequencing method. Expression patterns of genes that function in carbohydrate metabolism were downregulated as expected, and these genes were downregulated in line with the increase in glucose content. Significant and consistent changes in the expression were observed such as genes that encoding retrotransposable elements, heat shock proteins, glutathione S-transferase, cell agglutination protein, and conserved fungal proteins. We group some genes that function together in the transcription process and mitotic regulation, which have recently been associated with glucose availability. Our results shed light on the relationship between excess glucose, diverse cellular processes, and aging.
Collapse
Affiliation(s)
- Çağatay Tarhan
- Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Özgür Çakır
- Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul, Turkey
| |
Collapse
|
14
|
The GCN5: its biological functions and therapeutic potentials. Clin Sci (Lond) 2021; 135:231-257. [PMID: 33443284 DOI: 10.1042/cs20200986] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
General control non-depressible 5 (GCN5) or lysine acetyltransferase 2A (KAT2A) is one of the most highly studied histone acetyltransferases. It acts as both histone acetyltransferase (HAT) and lysine acetyltransferase (KAT). As an HAT it plays a pivotal role in the epigenetic landscape and chromatin modification. Besides, GCN5 regulates a wide range of biological events such as gene regulation, cellular proliferation, metabolism and inflammation. Imbalance in the GCN5 activity has been reported in many disorders such as cancer, metabolic disorders, autoimmune disorders and neurological disorders. Therefore, unravelling the role of GCN5 in different diseases progression is a prerequisite for both understanding and developing novel therapeutic agents of these diseases. In this review, we have discussed the structural features, the biological function of GCN5 and the mechanical link with the diseases associated with its imbalance. Moreover, the present GCN5 modulators and their limitations will be presented in a medicinal chemistry perspective.
Collapse
|
15
|
Shi Y, Shen HM, Gopalakrishnan V, Gordon N. Epigenetic Regulation of Autophagy Beyond the Cytoplasm: A Review. Front Cell Dev Biol 2021; 9:675599. [PMID: 34195194 PMCID: PMC8237754 DOI: 10.3389/fcell.2021.675599] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a highly conserved catabolic process induced under various stress conditions to protect the cell from harm and allow survival in the face of nutrient- or energy-deficient states. Regulation of autophagy is complex, as cells need to adapt to a continuously changing microenvironment. It is well recognized that the AMPK and mTOR signaling pathways are the main regulators of autophagy. However, various other signaling pathways have also been described to regulate the autophagic process. A better understanding of these complex autophagy regulatory mechanisms will allow the discovery of new potential therapeutic targets. Here, we present a brief overview of autophagy and its regulatory pathways with emphasis on the epigenetic control mechanisms.
Collapse
Affiliation(s)
- Yin Shi
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, China
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Vidya Gopalakrishnan
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nancy Gordon
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| |
Collapse
|
16
|
Halova L, Cobley D, Franz-Wachtel M, Wang T, Morrison KR, Krug K, Nalpas N, Maček B, Hagan IM, Humphrey SJ, Petersen J. A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans. Open Biol 2021; 11:200405. [PMID: 33823663 PMCID: PMC8025308 DOI: 10.1098/rsob.200405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Fluctuations in TOR, AMPK and MAP-kinase signalling maintain cellular homeostasis and coordinate growth and division with environmental context. We have applied quantitative, SILAC mass spectrometry to map TOR and nutrient-controlled signalling in the fission yeast Schizosaccharomyces pombe. Phosphorylation levels at more than 1000 sites were altered following nitrogen stress or Torin1 inhibition of the TORC1 and TORC2 networks that comprise TOR signalling. One hundred and thirty of these sites were regulated by both perturbations, and the majority of these (119) new targets have not previously been linked to either nutritional or TOR control in either yeasts or humans. Elimination of AMPK inhibition of TORC1, by removal of AMPKα (ssp2::ura4+), identified phosphosites where nitrogen stress-induced changes were independent of TOR control. Using a yeast strain with an ATP analogue-sensitized Cdc2 kinase, we excluded sites that were changed as an indirect consequence of mitotic control modulation by nitrogen stress or TOR signalling. Nutritional control of gene expression was reflected in multiple targets in RNA metabolism, while significant modulation of actin cytoskeletal components points to adaptations in morphogenesis and cell integrity networks. Reduced phosphorylation of the MAPKK Byr1, at a site whose human equivalent controls docking between MEK and ERK, prevented sexual differentiation when resources were sparse but not eliminated.
Collapse
Affiliation(s)
- Lenka Halova
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, UK
| | - David Cobley
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Mirita Franz-Wachtel
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Tingting Wang
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
| | - Kaitlin R. Morrison
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
| | - Karsten Krug
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Boris Maček
- Proteome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Iain M. Hagan
- Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, UK
| | - Sean J. Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Janni Petersen
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Flinders Health and Medical Research Institute, Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5042, Australia
- Nutrition and Metabolism, South Australia Health and Medical Research Institute, North Terrace, Adelaide, South Australia 5000, Australia
| |
Collapse
|
17
|
Mutlu B, Puigserver P. GCN5 acetyltransferase in cellular energetic and metabolic processes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194626. [PMID: 32827753 PMCID: PMC7854474 DOI: 10.1016/j.bbagrm.2020.194626] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 12/23/2022]
Abstract
General Control Non-repressed 5 protein (GCN5), encoded by the mammalian gene Kat2a, is the first histone acetyltransferase discovered to link histone acetylation to transcriptional activation [1]. The enzymatic activity of GCN5 is linked to cellular metabolic and energetic states regulating gene expression programs. GCN5 has a major impact on energy metabolism by i) sensing acetyl-CoA, a central metabolite and substrate of the GCN5 catalytic reaction, and ii) acetylating proteins such as PGC-1α, a transcriptional coactivator that controls genes linked to energy metabolism and mitochondrial biogenesis. PGC-1α is biochemically associated with the GCN5 protein complex during active metabolic reprogramming. In the first part of the review, we examine how metabolism can change GCN5-dependent histone acetylation to regulate gene expression to adapt cells. In the second part, we summarize the GCN5 function as a nutrient sensor, focusing on non-histone protein acetylation, mainly the metabolic role of PGC-1α acetylation across different tissues.
Collapse
Affiliation(s)
- Beste Mutlu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Pere Puigserver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
18
|
Ohtsuka H, Shimasaki T, Aiba H. Genes affecting the extension of chronological lifespan in Schizosaccharomyces pombe (fission yeast). Mol Microbiol 2020; 115:623-642. [PMID: 33064911 PMCID: PMC8246873 DOI: 10.1111/mmi.14627] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
So far, more than 70 genes involved in the chronological lifespan (CLS) of Schizosaccharomyces pombe (fission yeast) have been reported. In this mini‐review, we arrange and summarize these genes based on the reported genetic interactions between them and the physical interactions between their products. We describe the signal transduction pathways that affect CLS in S. pombe: target of rapamycin complex 1, cAMP‐dependent protein kinase, Sty1, and Pmk1 pathways have important functions in the regulation of CLS extension. Furthermore, the Php transcription complex, Ecl1 family proteins, cyclin Clg1, and the cyclin‐dependent kinase Pef1 are important for the regulation of CLS extension in S. pombe. Most of the known genes involved in CLS extension are related to these pathways and genes. In this review, we focus on the individual genes regulating CLS extension in S. pombe and discuss the interactions among them.
Collapse
Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
19
|
Pataki E, Simhaev L, Engel H, Cohen A, Kupiec M, Weisman R. TOR Complex 2- independent mutations in the regulatory PIF pocket of Gad8AKT1/SGK1 define separate branches of the stress response mechanisms in fission yeast. PLoS Genet 2020; 16:e1009196. [PMID: 33137119 PMCID: PMC7660925 DOI: 10.1371/journal.pgen.1009196] [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: 07/24/2020] [Revised: 11/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
The Target of rapamycin (TOR) protein kinase forms part of TOR complex 1 (TORC1) and TOR complex 2 (TORC2), two multi-subunit protein complexes that regulate growth, proliferation, survival and developmental processes by phosphorylation and activation of AGC-family kinases. In the fission yeast, Schizosaccharomyces pombe, TORC2 and its target, the AGC kinase Gad8 (an orthologue of human AKT or SGK1) are required for viability under stress conditions and for developmental processes in response to starvation cues. In this study, we describe the isolation of gad8 mutant alleles that bypass the requirement for TORC2 and reveal a separation of function of TORC2 and Gad8 under stress conditions. In particular, osmotic and nutritional stress responses appear to form a separate branch from genotoxic stress responses downstream of TORC2-Gad8. Interestingly, TORC2-independent mutations map into the regulatory PIF pocket of Gad8, a highly conserved motif in AGC kinases that regulates substrate binding in PDK1 (phosphoinositide dependent kinase-1) and kinase activity in several AGC kinases. Gad8 activation is thought to require a two-step mechanism, in which phosphorylation by TORC2 allows further phosphorylation and activation by Ksg1 (an orthologue of PDK1). We focus on the Gad8-K263C mutation and demonstrate that it renders the Gad8 kinase activity independent of TORC2 in vitro and independent of the phosphorylation sites of TORC2 in vivo. Molecular dynamics simulations of Gad8-K263C revealed abnormal high flexibility at T387, the phosphorylation site for Ksg1, suggesting a mechanism for the TORC2-independent Gad8 activity. Significantly, the K263 residue is highly conserved in the family of AGC-kinases, which may suggest a general way of keeping their activity in check when acting downstream of TOR complexes. Protein kinases catalyze the transfer of phosphate from high-energy, phosphate-donating molecules, such as ATP, to their substrates. This process is pivotal for regulation of almost any aspect of cellular biology. Many human diseases are associated with aberrant functions of protein kinases due to mutations. Accordingly, there is a growing number of kinase inhibitors that have been approved for clinical use. A better understanding of how protein kinases become active and how their activity is relayed to regulate their cellular functions is much needed for rational design of kinase inhibitors and for their optimal use in the clinic. The AGC-family of protein kinases play key roles in regulating cellular growth, proliferation and survival. In human cells, as well as in the fission yeast, our cellular model system, a subgroup of the AGC kinases is activated by the TOR protein kinases. Here we report the isolation of mutations in the AGC kinase Gad8 (AKT or SGK1 in human) that bypass the requirement for activation by TOR. Analyses of how these mutations affect cellular growth revealed separate branches of stress response mechanisms downstream of Gad8, while computer simulation methods suggested a molecular mechanism that keeps the activity of Gad8 in check.
Collapse
Affiliation(s)
- Emese Pataki
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Luba Simhaev
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, Israel
| | - Hamutal Engel
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, Israel
| | - Adiel Cohen
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
- * E-mail:
| |
Collapse
|
20
|
Laribee RN, Weisman R. Nuclear Functions of TOR: Impact on Transcription and the Epigenome. Genes (Basel) 2020; 11:E641. [PMID: 32532005 PMCID: PMC7349558 DOI: 10.3390/genes11060641] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
The target of rapamycin (TOR) protein kinase is at the core of growth factor- and nutrient-dependent signaling pathways that are well-known for their regulation of metabolism, growth, and proliferation. However, TOR is also involved in the regulation of gene expression, genomic and epigenomic stability. TOR affects nuclear functions indirectly through its activity in the cytoplasm, but also directly through active nuclear TOR pools. The mechanisms by which TOR regulates its nuclear functions are less well-understood compared with its cytoplasmic activities. TOR is an important pharmacological target for several diseases, including cancer, metabolic and neurological disorders. Thus, studies of the nuclear functions of TOR are important for our understanding of basic biological processes, as well as for clinical implications.
Collapse
Affiliation(s)
- R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, University Road 1, Ra’anana 4353701, Israel
| |
Collapse
|
21
|
García-Blanco N, Vázquez-Bolado A, Moreno S. Greatwall-Endosulfine: A Molecular Switch that Regulates PP2A/B55 Protein Phosphatase Activity in Dividing and Quiescent Cells. Int J Mol Sci 2019; 20:ijms20246228. [PMID: 31835586 PMCID: PMC6941129 DOI: 10.3390/ijms20246228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022] Open
Abstract
During the cell cycle, hundreds of proteins become phosphorylated and dephosphorylated, indicating that protein kinases and protein phosphatases play a central role in its regulation. It has been widely recognized that oscillation in cyclin-dependent kinase (CDK) activity promotes DNA replication, during S-phase, and chromosome segregation, during mitosis. Each CDK substrate phosphorylation status is defined by the balance between CDKs and CDK-counteracting phosphatases. In fission yeast and animal cells, PP2A/B55 is the main protein phosphatase that counteracts CDK activity. PP2A/B55 plays a key role in mitotic entry and mitotic exit, and it is regulated by the Greatwall-Endosulfine (ENSA) molecular switch that inactivates PP2A/B55 at the onset of mitosis, allowing maximal CDK activity at metaphase. The Greatwall-ENSA-PP2A/B55 pathway is highly conserved from yeast to animal cells. In yeasts, Greatwall is negatively regulated by nutrients through TORC1 and S6 kinase, and couples cell growth, regulated by TORC1, to cell cycle progression, driven by CDK activity. In animal cells, Greatwall is phosphorylated and activated by Cdk1 at G2/M, generating a bistable molecular switch that results in full activation of Cdk1/CyclinB. Here we review the current knowledge of the Greatwall-ENSA-PP2A/B55 pathway and discuss its role in cell cycle progression and as an integrator of nutritional cues.
Collapse
|
22
|
Targeted Forward Genetics: Population-Scale Analyses of Allele Replacements Spanning Thousands of Base Pairs in Fission Yeast. G3-GENES GENOMES GENETICS 2019; 9:4097-4106. [PMID: 31597677 PMCID: PMC6893178 DOI: 10.1534/g3.119.400805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Precise allele replacement (genome editing), without unwanted changes to the genome, provides a powerful tool to define the functions of DNA elements and encoded factors in their normal biological context. While CRISPR is now used extensively for gene targeting, its utility for precise allele replacement at population scale is limited because: (A) there is a strict requirement for a correctly positioned PAM motif to introduce recombinogenic dsDNA breaks (DSBs); (B) efficient replacements only occur very close to the DSBs; and (C) indels and off-target changes are frequently generated. Here we show, using a saturated mutation library with about 15,000 alleles of the ade6 gene of Schizosaccharomyces pombe, that pop-in, pop-out allele replacement circumvents these problems. Two rounds of selection ensure that clones arise by homologous recombination with the target locus. Moreover, the exceptionally high efficiency allows one to carry out the process in bulk, then screen individual clones for phenotypes and genotypes. Alleles were introduced successfully throughout the region targeted, up to 1,956 base pairs from the DSB. About 11% of mutant alleles were hypomorphic, demonstrating utility for analyses of essential genes and genetic elements. This process of “targeted forward genetics” can be used to analyze comprehensively, across thousands of base pairs within a specific target region, a variety of allelic changes, such as scanning amino acid substitutions, deletions, and epitope tags. The overall approach and optimized workflow are extensible to other organisms that support gene targeting.
Collapse
|
23
|
Elías-Villalobos A, Toullec D, Faux C, Séveno M, Helmlinger D. Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast. Nat Commun 2019; 10:5237. [PMID: 31748520 PMCID: PMC6868236 DOI: 10.1038/s41467-019-13243-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Transcription initiation involves the coordinated activities of large multimeric complexes, but little is known about their biogenesis. Here we report several principles underlying the assembly and topological organization of the highly conserved SAGA and NuA4 co-activator complexes, which share the Tra1 subunit. We show that Tra1 contributes to the overall integrity of NuA4, whereas, within SAGA, it specifically controls the incorporation of the de-ubiquitination module (DUB), as part of an ordered assembly pathway. Biochemical and functional analyses reveal the mechanism by which Tra1 specifically interacts with either SAGA or NuA4. Finally, we demonstrate that Hsp90 and its cochaperone TTT promote Tra1 de novo incorporation into both complexes, indicating that Tra1, the sole pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the assembly of transcriptional complexes and reveals the contribution of dedicated chaperones to this process. Transcription initiation involves the coordinated assembly and activity of large multimeric complexes. Here the authors report on the chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in fission yeast, providing insight into the de novo assembly of transcriptional complexes and the contribution of dedicated chaperones to this process.
Collapse
Affiliation(s)
| | - Damien Toullec
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Céline Faux
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | |
Collapse
|
24
|
Torok MS, Pray-Grant MG, Grant BM, Josephs ME, Grant PA. The Novel ReNu Region of TAF12 Regulates Gcn5 Nucleosomal Acetylation. JOURNAL OF MOLECULAR GENETICS (ISLEWORTH, LONDON, ENGLAND) 2019; 2:https://researchopenworld.com/wp-content/uploads/2019/07/JMG-2019-105-Patrick-Grant-USA.pdf. [PMID: 32832935 PMCID: PMC7437354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The post-translational acetylation of the histone components of chromatin mediates numerous DNA-templated events, including transcriptional activation, DNA repair, and genomic replication. The conserved SAGA (Spt-Ada-Gcn5 Acetyltranferase) and SLIK (SAGA-Like) Histone Acetyltransferase (HAT) complexes are required for transcriptional activation of a subset of yeast genes and contain multiple subunits including the histone fold-containing TBP- Associated Factors (TAFs): 6, 9, 10, and 12. These TAFs are also components of the TFIID complex and are consequently involved in most RNA polymerase II-transcription in yeast. Here we identify a novel conserved region of TAF12, termed ReNu, outside of its histone fold, which is required for SAGA and SLIK-directed nucleosomal acetylation. We demonstrate that this region is not required for chromatin association, but show that this region plays an important role for histone H3 acetylation at specific SAGA and SLIK-regulated promoters. Our data suggests that the ReNu region of TAF12 regulates Gcn5 acetylation of specific substrates within the SAGA super-family of HAT complexes.
Collapse
Affiliation(s)
| | | | | | | | - Patrick A. Grant
- Corresponding author: Patrick A. Grant, University of Virginia School of Medicine, Box 800733, Charlottesville, VA 22908, USA; Tel: (434) 243-5766; Fax: (434) 924-5069;
| |
Collapse
|
25
|
Reidman S, Cohen A, Kupiec M, Weisman R. The cytosolic form of aspartate aminotransferase is required for full activation of TOR complex 1 in fission yeast. J Biol Chem 2019; 294:18244-18255. [PMID: 31641022 DOI: 10.1074/jbc.ra119.010101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/18/2019] [Indexed: 12/17/2022] Open
Abstract
The evolutionarily conserved TOR complex 1 (TORC1) activates cell growth and proliferation in response to nutritional signals. In the fission yeast Schizosaccharomyces pombe, TORC1 is essential for vegetative growth, and its activity is regulated in response to nitrogen quantity and quality. Yet, how TORC1 senses nitrogen is poorly understood. Rapamycin, a specific TOR inhibitor, inhibits growth in S. pombe only under conditions in which the activity of TORC1 is compromised. In a genetic screen for rapamycin-sensitive mutations, we isolated caa1-1, a loss-of-function mutation of the cytosolic form of aspartate aminotransferase (Caa1). We demonstrate that loss of caa1 + partially mimics loss of TORC1 activity and that Caa1 is required for full TORC1 activity. Disruption of caa1 + resulted in aspartate auxotrophy, a finding that prompted us to assess the role of aspartate in TORC1 activation. We found that the amino acids glutamine, asparagine, arginine, aspartate, and serine activate TORC1 most efficiently following nitrogen starvation. The glutamine synthetase inhibitor l-methionine sulfoximine abolished the ability of asparagine, arginine, aspartate, or serine, but not that of glutamine, to induce TORC1 activity, consistent with a central role for glutamine in activating TORC1. Neither addition of aspartate nor addition of glutamine restored TORC1 activity in caa1-deleted cells or in cells carrying a Caa1 variant with a catalytic site substitution, suggesting that the catalytic activity of Caa1 is required for TORC1 activation. Taken together, our results reveal the contribution of the key metabolic enzyme Caa1 to TORC1 activity in S. pombe.
Collapse
Affiliation(s)
- Sophie Reidman
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Adiel Cohen
- Department of Natural and Life Sciences, the Open University of Israel, University Road 1, 4353701 Ra'anana, Israel
| | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, the Open University of Israel, University Road 1, 4353701 Ra'anana, Israel.
| |
Collapse
|
26
|
Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication Interferes with mTORC1 Regulation of Autophagy and Viral Protein Synthesis. J Virol 2019; 93:JVI.00854-19. [PMID: 31375594 PMCID: PMC6803247 DOI: 10.1128/jvi.00854-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
All viruses require host cell machinery to synthesize viral proteins. A host cell protein complex known as mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of protein synthesis. Under nutrient-rich conditions, mTORC1 is active and promotes protein synthesis to meet cellular anabolic demands. Under nutrient-poor conditions or under stress, mTORC1 is rapidly inhibited, global protein synthesis is arrested, and a cellular catabolic process known as autophagy is activated. Kaposi’s sarcoma-associated herpesvirus (KSHV) stimulates mTORC1 activity and utilizes host machinery to synthesize viral proteins. However, we discovered that mTORC1 activity was largely dispensable for viral protein synthesis, genome replication, and the release of infectious progeny. Likewise, during lytic replication, mTORC1 was no longer able to control autophagy. These findings suggest that KSHV undermines mTORC1-dependent cellular processes during the lytic cycle to ensure efficient viral replication. Mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cellular metabolism. In nutrient-rich environments, mTORC1 kinase activity stimulates protein synthesis to meet cellular anabolic demands. Under nutrient-poor conditions or under stress, mTORC1 is rapidly inhibited, global protein synthesis is arrested, and a cellular catabolic process known as autophagy is activated. Kaposi’s sarcoma-associated herpesvirus (KSHV) encodes multiple proteins that stimulate mTORC1 activity or subvert autophagy, but precise roles for mTORC1 in different stages of KSHV infection remain incompletely understood. Here, we report that during latent and lytic stages of KSHV infection, chemical inhibition of mTORC1 caused eukaryotic initiation factor 4F (eIF4F) disassembly and diminished global protein synthesis, which indicated that mTORC1-mediated control of translation initiation was largely intact. We observed that mTORC1 was required for synthesis of the replication and transcription activator (RTA) lytic switch protein and reactivation from latency, but once early lytic gene expression had begun, mTORC1 was not required for genome replication, late gene expression, or the release of infectious progeny. Moreover, mTORC1 control of autophagy was dysregulated during lytic replication, whereby chemical inhibition of mTORC1 prevented ULK1 phosphorylation but did not affect autophagosome formation or rates of autophagic flux. Together, these findings suggest that mTORC1 is dispensable for viral protein synthesis and viral control of autophagy during lytic infection and that KSHV undermines mTORC1-dependent cellular processes during the lytic cycle to ensure efficient viral replication. IMPORTANCE All viruses require host cell machinery to synthesize viral proteins. A host cell protein complex known as mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of protein synthesis. Under nutrient-rich conditions, mTORC1 is active and promotes protein synthesis to meet cellular anabolic demands. Under nutrient-poor conditions or under stress, mTORC1 is rapidly inhibited, global protein synthesis is arrested, and a cellular catabolic process known as autophagy is activated. Kaposi’s sarcoma-associated herpesvirus (KSHV) stimulates mTORC1 activity and utilizes host machinery to synthesize viral proteins. However, we discovered that mTORC1 activity was largely dispensable for viral protein synthesis, genome replication, and the release of infectious progeny. Likewise, during lytic replication, mTORC1 was no longer able to control autophagy. These findings suggest that KSHV undermines mTORC1-dependent cellular processes during the lytic cycle to ensure efficient viral replication.
Collapse
|
27
|
Baker K, Gyamfi IA, Mashanov GI, Molloy JE, Geeves MA, Mulvihill DP. TORC2-Gad8-dependent myosin phosphorylation modulates regulation by calcium. eLife 2019; 8:e51150. [PMID: 31566560 PMCID: PMC6802964 DOI: 10.7554/elife.51150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/26/2019] [Indexed: 01/22/2023] Open
Abstract
Cells respond to changes in their environment through signaling networks that modulate cytoskeleton and membrane organization to coordinate cell-cycle progression, polarized cell growth and multicellular development. Here, we define a novel regulatory mechanism by which the motor activity and function of the fission yeast type one myosin, Myo1, is modulated by TORC2-signalling-dependent phosphorylation. Phosphorylation of the conserved serine at position 742 (S742) within the neck region changes both the conformation of the neck region and the interactions between Myo1 and its associating calmodulin light chains. S742 phosphorylation thereby couples the calcium and TOR signaling networks that are involved in the modulation of myosin-1 dynamics to co-ordinate actin polymerization and membrane reorganization at sites of endocytosis and polarised cell growth in response to environmental and cell-cycle cues.
Collapse
Affiliation(s)
- Karen Baker
- School of BiosciencesUniversity of KentCanterburyUnited Kingdom
| | - Irene A Gyamfi
- School of BiosciencesUniversity of KentCanterburyUnited Kingdom
| | | | | | | | | |
Collapse
|
28
|
Ahmed K, Carter DE, Lajoie P. Hyperactive
TORC
1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity. FEBS Lett 2019; 593:1957-1973. [DOI: 10.1002/1873-3468.13463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Khadija Ahmed
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
| | - David E. Carter
- Robarts Research Institute The University of Western Ontario London Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology The University of Western Ontario London Canada
| |
Collapse
|
29
|
Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics 2019; 212:667-690. [PMID: 31053593 DOI: 10.1534/genetics.119.302004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/18/2019] [Indexed: 01/07/2023] Open
Abstract
Signaling pathways can regulate biological responses by the transcriptional regulation of target genes. In yeast, multiple signaling pathways control filamentous growth, a morphogenetic response that occurs in many species including fungal pathogens. Here, we examine the role of signaling pathways that control filamentous growth in regulating adhesion-dependent surface responses, including mat formation and colony patterning. Expression profiling and mutant phenotype analysis showed that the major pathways that regulate filamentous growth [filamentous growth MAPK (fMAPK), RAS, retrograde (RTG), RIM101, RPD3, ELP, SNF1, and PHO85] also regulated mat formation and colony patterning. The chromatin remodeling complex, SAGA, also regulated these responses. We also show that the RAS and RTG pathways coregulated a common set of target genes, and that SAGA regulated target genes known to be controlled by the fMAPK, RAS, and RTG pathways. Analysis of surface growth-specific targets identified genes that respond to low oxygen, high temperature, and desiccation stresses. We also explore the question of why cells make adhesive contacts in colonies. Cell adhesion contacts mediated by the coregulated target and adhesion molecule, Flo11p, deterred entry into colonies by macroscopic predators and impacted colony temperature regulation. The identification of new regulators (e.g., SAGA), and targets of surface growth in yeast may provide insights into fungal pathogenesis in settings where surface growth and adhesion contributes to virulence.
Collapse
|
30
|
Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
Collapse
Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| |
Collapse
|
31
|
Elías-Villalobos A, Barrales RR, Ibeas JI. Chromatin modification factors in plant pathogenic fungi: Insights from Ustilago maydis. Fungal Genet Biol 2019; 129:52-64. [PMID: 30980908 DOI: 10.1016/j.fgb.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 01/10/2023]
Abstract
Adaptation to the environment is a requirement for the survival of every organism. For pathogenic fungi this also implies coping with the different conditions that occur during the infection cycle. After detecting changes to external media, organisms must modify their gene expression patterns in order to accommodate the new circumstances. Control of gene expression is a complex process that involves the coordinated action of multiple regulatory elements. Chromatin modification is a well-known mechanism for controlling gene expression in response to environmental changes in all eukaryotes. In pathogenic fungi, chromatin modifications are known to play crucial roles in controlling host interactions and their virulence capacity, yet little is known about the specific genes they directly target and to which signals they respond. The smut fungus Ustilago maydis is an excellent model system in which multiple molecular and cellular approaches are available to study biotrophic interactions. Many target genes regulated during the infection process have been well studied, however, how they are controlled and specifically how chromatin modifications affect gene regulation in the context of infection is not well known in this organism. Here, we analyse the presence of chromatin modifying enzymes and complexes in U. maydis and discuss their putative roles in this plant pathogen in the context of findings from other organisms, including other plant pathogens such as Magnaporthe oryzae and Fusarium graminearum. We propose U. maydis as a remarkable organism with interesting chromatin features, which would allow finding new functions of chromatin modifications during plant pathogenesis.
Collapse
Affiliation(s)
- Alberto Elías-Villalobos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR5237-Centre National de la Recherche Scientifique-Université de Montpellier, Montpellier, France.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain.
| | - José I Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
| |
Collapse
|
32
|
Jiang Y, Berg MD, Genereaux J, Ahmed K, Duennwald ML, Brandl CJ, Lajoie P. Sfp1 links TORC1 and cell growth regulation to the yeast SAGA‐complex component Tra1 in response to polyQ proteotoxicity. Traffic 2019; 20:267-283. [DOI: 10.1111/tra.12637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Yuwei Jiang
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Matthew D. Berg
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Julie Genereaux
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Khadija Ahmed
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Martin L. Duennwald
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of Pathology and Laboratory MedicineThe University of Western Ontario London Ontario Canada
| | | | - Patrick Lajoie
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| |
Collapse
|
33
|
Lie S, Banks P, Lawless C, Lydall D, Petersen J. The contribution of non-essential Schizosaccharomyces pombe genes to fitness in response to altered nutrient supply and target of rapamycin activity. Open Biol 2019; 8:rsob.180015. [PMID: 29720420 PMCID: PMC5990653 DOI: 10.1098/rsob.180015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022] Open
Abstract
Nutrient fluctuations in the cellular environment promote changes in cell metabolism and growth to adapt cell proliferation accordingly. The target of rapamycin (TOR) signalling network plays a key role in the coordination of growth and cell proliferation with the nutrient environment and, importantly, nutrient limitation reduces TOR complex 1 (TORC1) signalling. We have performed global quantitative fitness profiling of the collection of Schizosaccharomyces pombe strains from which non-essential genes have been deleted. We identified genes that regulate fitness when cells are grown in a nutrient-rich environment compared with minimal environments, with varying nitrogen sources including ammonium, glutamate and proline. In addition, we have performed the first global screen for genes that regulate fitness when both TORC1 and TORC2 signalling is reduced by Torin1. Analysis of genes whose deletions altered fitness when nutrients were limited, or when TOR signalling was compromised, identified a large number of genes that regulate transmembrane transport, transcription and chromatin organization/regulation and vesicle-mediated transport. The ability to tolerate reduced TOR signalling placed demands upon a large number of biological processes including autophagy, mRNA metabolic processing and nucleocytoplasmic transport. Importantly, novel biological processes and all processes known to be regulated by TOR were identified in our screens. In addition, deletion of 62 genes conserved in humans gave rise to strong sensitivity or resistance to Torin1, and 29 of these 62 genes have novel links to TOR signalling. The identification of chromatin and transcriptional regulation, nutritional uptake and transport pathways in this powerful genetic model now paves the way for a molecular understanding of how cells adapt to the chronic and acute fluctuations in nutrient supply that all eukaryotes experience at some stage, and which is a key feature of cancer cells within solid tumours.
Collapse
Affiliation(s)
- Shervi Lie
- Flinders Centre for Innovation in Cancer, College of Medicine & Public Health, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia
| | - Peter Banks
- High Throughput Screening Facility, Newcastle Biomedicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Conor Lawless
- Institute for Cell & Molecular Biosciences, Newcastle University Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - David Lydall
- Institute for Cell & Molecular Biosciences, Newcastle University Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Janni Petersen
- Flinders Centre for Innovation in Cancer, College of Medicine & Public Health, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia .,South Australia Health and Medical Research Institute, North Terrace, PO Box 11060, Adelaide, South Australia 5000, Australia
| |
Collapse
|
34
|
Laribee RN. Transcriptional and Epigenetic Regulation by the Mechanistic Target of Rapamycin Complex 1 Pathway. J Mol Biol 2018; 430:4874-4890. [PMID: 30359581 DOI: 10.1016/j.jmb.2018.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 11/28/2022]
Abstract
Nutrient availability impacts health such that nutrient excess states can dysregulate epigenetic and transcriptional pathways to cause many diseases. Increasing evidence implicates aberrant regulation of nutrient signaling cascades as one means of communicating nutrient information to the epigenetic and transcriptional regulatory machinery. One such signaling cascade, the mechanistic target of rapamycin complex 1 (mTORC1), is conserved from yeast to man, and it is deregulated in diverse disease states. The catalytic subunit of the mTORC1 kinase complex (Tor1 or Tor2 in budding yeast and mTor in mammals) phosphorylates several downstream effectors regulating transcriptional and translational responses controlling growth and proliferation. Delineating mechanisms of cytoplasmic nutrient mTORC1 activation continues to be a major research focus. However, Tor kinases not only localize to the cytoplasm but also are found in the nucleus where they selectively bind and regulate genes controlling cellular metabolism and anabolism. The nuclear mTORC1 functions are now beginning to be defined, and they suggest that mTORC1 has a critical role in regulating the complex transcriptional activities required for ribosomal biogenesis. The mTORC1 pathway also interacts with epigenetic regulators required for modifying chromatin structure and function to control gene expression. Because altered nutrient states exert both individual and transgenerational phenotypic changes, mTORC1 signaling to chromatin effectors may have a significant role in mediating the effects of diet and nutrients on the epigenome. This article will discuss the recent inroads into the function of nuclear mTORC1 and its role in epigenetic and transcriptional regulation.
Collapse
Affiliation(s)
- R Nicholas Laribee
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA.
| |
Collapse
|
35
|
Cohen A, Habib A, Laor D, Yadav S, Kupiec M, Weisman R. TOR complex 2 in fission yeast is required for chromatin-mediated gene silencing and assembly of heterochromatic domains at subtelomeres. J Biol Chem 2018; 293:8138-8150. [PMID: 29632066 DOI: 10.1074/jbc.ra118.002270] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/14/2018] [Indexed: 12/21/2022] Open
Abstract
The conserved serine/threonine protein kinase target of rapamycin (TOR) is a major regulator of eukaryotic cellular and organismal growth and a valuable target for drug therapy. TOR forms the core of two evolutionary conserved complexes, TOR complex 1 (TORC1) and TORC2. In the fission yeast Schizosaccharomyces pombe, TORC2 responds to glucose levels and, by activating the protein kinase Gad8 (an orthologue of human AKT), is required for well-regulated cell cycle progression, starvation responses, and cell survival. Here, we report that TORC2-Gad8 is also required for gene silencing and the formation of heterochromatin at the S. pombe mating-type locus and at subtelomeric regions. Deletion of TORC2-Gad8 resulted in loss of the heterochromatic modification of histone 3 lysine 9 dimethylation (H3K9me2) and an increase in euchromatic modifications, including histone 3 lysine 4 trimethylation (H3K4me3) and histone 4 lysine 16 acetylation (H4K16Ac). Accumulation of RNA polymerase II (Pol II) at subtelomeric genes in TORC2-Gad8 mutant cells indicated a defect in silencing at the transcriptional level. Moreover, a concurrent decrease in histone 4 lysine 20 dimethylation (H4K20me2) suggested elevated histone turnover. Loss of gene silencing in cells lacking TORC2-Gad8 is partially suppressed by loss of the anti-silencer Epe1 and fully suppressed by loss of the Pol II-associated Paf1 complex, two chromatin regulators that have been implicated in heterochromatin stability and spreading. Taken together, our findings suggest that TORC2-Gad8 signaling contributes to epigenetic stability at subtelomeric regions and the mating-type locus in S. pombe.
Collapse
Affiliation(s)
- Adiel Cohen
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel
| | - Aline Habib
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Dana Laor
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Sudhanshu Yadav
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana, Israel.
| |
Collapse
|
36
|
Laboucarié T, Detilleux D, Rodriguez-Mias RA, Faux C, Romeo Y, Franz-Wachtel M, Krug K, Maček B, Villén J, Petersen J, Helmlinger D. TORC1 and TORC2 converge to regulate the SAGA co-activator in response to nutrient availability. EMBO Rep 2017; 18:2197-2218. [PMID: 29079657 DOI: 10.15252/embr.201744942] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 12/19/2022] Open
Abstract
Gene expression regulation is essential for cells to adapt to changes in their environment. Co-activator complexes have well-established roles in transcriptional regulation, but less is known about how they sense and respond to signaling cues. We have previously shown that, in fission yeast, one such co-activator, the SAGA complex, controls gene expression and the switch from proliferation to differentiation in response to nutrient availability. Here, using a combination of genetic, biochemical, and proteomic approaches, we show that SAGA responds to nutrients through the differential phosphorylation of its Taf12 component, downstream of both the TORC1 and TORC2 pathways. Taf12 phosphorylation increases early upon starvation and is controlled by the opposing activities of the PP2A phosphatase, which is activated by TORC1, and the TORC2-activated Gad8AKT kinase. Mutational analyses suggest that Taf12 phosphorylation prevents cells from committing to differentiation until starvation reaches a critical level. Overall, our work reveals that SAGA is a direct target of nutrient-sensing pathways and has uncovered a mechanism by which TORC1 and TORC2 converge to control gene expression and cell fate decisions.
Collapse
Affiliation(s)
| | | | | | - Céline Faux
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Yves Romeo
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | | | | | - Boris Maček
- Proteome Center Tübingen, Tuebingen, Germany
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Janni Petersen
- Flinders Centre for Innovation in Cancer, School of Medicine, Faculty of Health Science, Flinders University, Adelaide, SA, Australia
| | | |
Collapse
|