1
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Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell 2024; 35:ar60. [PMID: 38446618 PMCID: PMC11064662 DOI: 10.1091/mbc.e23-02-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 02/13/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
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Affiliation(s)
- Michael Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Nicole Carmiol
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Bassam Mitri
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | | | - Paul R. Langlais
- The Department of Medicine, University of Arizona, Tucson, AZ 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
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2
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Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
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Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
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3
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Cecil JH, Padilla CM, Lipinski AA, Langlais PR, Luo X, Capaldi AP. The Molecular Logic of Gtr1/2 and Pib2 Dependent TORC1 Regulation in Budding Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570342. [PMID: 38106135 PMCID: PMC10723367 DOI: 10.1101/2023.12.06.570342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The Target of Rapamycin kinase Complex I (TORC1) regulates cell growth and metabolism in eukaryotes. Previous studies have shown that, in Saccharomyces cerevisiae, nitrogen and amino acid signals activate TORC1 via the highly conserved small GTPases, Gtr1/2, and the phosphatidylinositol 3-phosphate binding protein, Pib2. However, it was unclear if/how Gtr1/2 and Pib2 cooperate to control TORC1. Here we report that this dual regulator system pushes TORC1 into three distinct signaling states: (i) a Gtr1/2 on, Pib2 on, rapid growth state in nutrient replete conditions; (ii) a Gtr1/2 off, Pib2 on, adaptive/slow growth state in poor-quality growth medium; and (iii) a Gtr1/2 off, Pib2 off, quiescent state in starvation conditions. We suggest that other signaling pathways work in a similar way, to drive a multi-level response via a single kinase, but the behavior has been overlooked since most studies follow signaling to a single reporter protein.
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Affiliation(s)
- Jacob H. Cecil
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | - Cristina M. Padilla
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | | | - Paul R. Langlais
- Department of Medicine, University of Arizona, Tucson, AZ, 85721
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721
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4
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Hirai H, Sen Y, Tamura M, Ohta K. TOR inactivation triggers heterochromatin formation in rDNA during glucose starvation. Cell Rep 2023; 42:113320. [PMID: 37913773 DOI: 10.1016/j.celrep.2023.113320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
In response to environmental cues, such as nutrient starvation, living organisms modulate gene expression through mechanisms involving histone modifications. Specifically, nutrient depletion inactivates the TOR (target of rapamycin) pathway, leading to reduced expression of ribosomal genes. While these regulatory mechanisms are well elucidated in budding yeast Saccharomyces cerevisiae, their conservation across diverse organisms remains unclear. In this study, we demonstrate that fission yeast Schizosaccharomyces pombe cells repress ribosomal gene transcription through a different mechanism. TORC1, which accumulates in the rDNA region, dissociates upon starvation, resulting in enhanced methylation of H3K9 and heterochromatin formation, facilitated by dissociation of the stress-responsive transcription factor Atf1 and accumulation of the histone chaperone FACT. We propose that this mechanism might be adapted in mammals that possess Suv39H1 and HP1, which are absent in budding yeast.
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Affiliation(s)
- Hayato Hirai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.
| | - Yuki Sen
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
| | - Miki Tamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan; Universal Biology Institute, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Foltman M, Sanchez-Diaz A. TOR Complex 1: Orchestrating Nutrient Signaling and Cell Cycle Progression. Int J Mol Sci 2023; 24:15745. [PMID: 37958727 PMCID: PMC10647266 DOI: 10.3390/ijms242115745] [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: 09/01/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy their chromosomes, segregate them in mitosis, divide all their components during cytokinesis, and finally physically separate mother and daughter cells to start a new cell cycle apart from each other. To maintain cell size homeostasis and chromosome stability, it is crucial that mechanisms that control growth are connected and coordinated with the cell cycle. Successive periods of high and low TORC1 activity would participate in the adequate cell cycle progression. Here, we review the known molecular mechanisms through which TORC1 regulates the cell cycle in the budding yeast Saccharomyces cerevisiae that have been extensively used as a model organism to understand the role of its mammalian ortholog, mTORC1.
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Affiliation(s)
- Magdalena Foltman
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
| | - Alberto Sanchez-Diaz
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
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6
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Caligaris M, Sampaio-Marques B, Hatakeyama R, Pillet B, Ludovico P, De Virgilio C, Winderickx J, Nicastro R. The Yeast Protein Kinase Sch9 Functions as a Central Nutrient-Responsive Hub That Calibrates Metabolic and Stress-Related Responses. J Fungi (Basel) 2023; 9:787. [PMID: 37623558 PMCID: PMC10455444 DOI: 10.3390/jof9080787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Yeast cells are equipped with different nutrient signaling pathways that enable them to sense the availability of various nutrients and adjust metabolism and growth accordingly. These pathways are part of an intricate network since most of them are cross-regulated and subject to feedback regulation at different levels. In yeast, a central role is played by Sch9, a protein kinase that functions as a proximal effector of the conserved growth-regulatory TORC1 complex to mediate information on the availability of free amino acids. However, recent studies established that Sch9 is more than a TORC1-effector as its activity is tuned by several other kinases. This allows Sch9 to function as an integrator that aligns different input signals to achieve accuracy in metabolic responses and stress-related molecular adaptations. In this review, we highlight the latest findings on the structure and regulation of Sch9, as well as its role as a nutrient-responsive hub that impacts on growth and longevity of yeast cells. Given that most key players impinging on Sch9 are well-conserved, we also discuss how studies on Sch9 can be instrumental to further elucidate mechanisms underpinning healthy aging in mammalians.
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Affiliation(s)
- Marco Caligaris
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Riko Hatakeyama
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Benjamin Pillet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, B-3001 Heverlee, Belgium;
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
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7
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Minden S, Aniolek M, Noorman H, Takors R. Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts. Genes (Basel) 2023; 14:genes14050997. [PMID: 37239357 DOI: 10.3390/genes14050997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
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8
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Schofield JA, Hahn S. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. Cell Rep 2023; 42:112387. [PMID: 37058407 PMCID: PMC10567116 DOI: 10.1016/j.celrep.2023.112387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Three classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA, and Mediator (MED) Tail, but whether this dependence is determined by the core promoter, upstream activating sequences (UASs), or other gene features is unclear. Also unclear is whether UASs can broadly activate transcription from the different promoter classes. Here, we measure transcription and cofactor specificity for thousands of UAS-core promoter combinations and find that most UASs broadly activate promoters regardless of regulatory class, while few display strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. We find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and core promoter, while dependence on TFIID localizes to only the promoter. Finally, our results suggest the role of TATA and TATA-like promoter sequences in MED Tail function.
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Affiliation(s)
- Jeremy A Schofield
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA.
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9
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Nishio K, Kawarasaki T, Sugiura Y, Matsumoto S, Konoshima A, Takano Y, Hayashi M, Okumura F, Kamura T, Mizushima T, Nakatsukasa K. Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. SCIENCE ADVANCES 2023; 9:eadf1956. [PMID: 37058555 PMCID: PMC10104474 DOI: 10.1126/sciadv.adf1956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Deficiencies in mitochondrial protein import are associated with a number of diseases. However, although nonimported mitochondrial proteins are at great risk of aggregation, it remains largely unclear how their accumulation causes cell dysfunction. Here, we show that nonimported citrate synthase is targeted for proteasomal degradation by the ubiquitin ligase SCFUcc1. Unexpectedly, our structural and genetic analyses revealed that nonimported citrate synthase appears to form an enzymatically active conformation in the cytosol. Its excess accumulation caused ectopic citrate synthesis, which, in turn, led to an imbalance in carbon flux of sugar, a reduction of the pool of amino acids and nucleotides, and a growth defect. Under these conditions, translation repression is induced and acts as a protective mechanism that mitigates the growth defect. We propose that the consequence of mitochondrial import failure is not limited to proteotoxic insults, but that the accumulation of a nonimported metabolic enzyme elicits ectopic metabolic stress.
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Affiliation(s)
- Kazuya Nishio
- Department of Life Science, Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
| | - Tomoyuki Kawarasaki
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Yuki Sugiura
- Department of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Multiomics Platform, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Shunsuke Matsumoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ayano Konoshima
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Yuki Takano
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Mayuko Hayashi
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women’s University, Fukuoka 813-8582, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Tsunehiro Mizushima
- Department of Life Science, Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
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10
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Gutiérrez-Santiago F, Navarro F. Transcription by the Three RNA Polymerases under the Control of the TOR Signaling Pathway in Saccharomyces cerevisiae. Biomolecules 2023; 13:biom13040642. [PMID: 37189389 DOI: 10.3390/biom13040642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Ribosomes are the basis for protein production, whose biogenesis is essential for cells to drive growth and proliferation. Ribosome biogenesis is highly regulated in accordance with cellular energy status and stress signals. In eukaryotic cells, response to stress signals and the production of newly-synthesized ribosomes require elements to be transcribed by the three RNA polymerases (RNA pols). Thus, cells need the tight coordination of RNA pols to adjust adequate components production for ribosome biogenesis which depends on environmental cues. This complex coordination probably occurs through a signaling pathway that links nutrient availability with transcription. Several pieces of evidence strongly support that the Target of Rapamycin (TOR) pathway, conserved among eukaryotes, influences the transcription of RNA pols through different mechanisms to ensure proper ribosome components production. This review summarizes the connection between TOR and regulatory elements for the transcription of each RNA pol in the budding yeast Saccharomyces cerevisiae. It also focuses on how TOR regulates transcription depending on external cues. Finally, it discusses the simultaneous coordination of the three RNA pols through common factors regulated by TOR and summarizes the most important similarities and differences between S. cerevisiae and mammals.
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Affiliation(s)
- Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
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11
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Mierke F, Brink DP, Norbeck J, Siewers V, Andlid T. Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates. Fungal Genet Biol 2023; 166:103783. [PMID: 36870442 DOI: 10.1016/j.fgb.2023.103783] [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: 05/06/2022] [Revised: 02/10/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.
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Affiliation(s)
- Friederike Mierke
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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12
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Comparative Research: Regulatory Mechanisms of Ribosomal Gene Transcription in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Biomolecules 2023; 13:biom13020288. [PMID: 36830657 PMCID: PMC9952952 DOI: 10.3390/biom13020288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Restricting ribosome biosynthesis and assembly in response to nutrient starvation is a universal phenomenon that enables cells to survive with limited intracellular resources. When cells experience starvation, nutrient signaling pathways, such as the target of rapamycin (TOR) and protein kinase A (PKA), become quiescent, leading to several transcription factors and histone modification enzymes cooperatively and rapidly repressing ribosomal genes. Fission yeast has factors for heterochromatin formation similar to mammalian cells, such as H3K9 methyltransferase and HP1 protein, which are absent in budding yeast. However, limited studies on heterochromatinization in ribosomal genes have been conducted on fission yeast. Herein, we shed light on and compare the regulatory mechanisms of ribosomal gene transcription in two species with the latest insights.
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13
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TORC1 Signaling in Fungi: From Yeasts to Filamentous Fungi. Microorganisms 2023; 11:microorganisms11010218. [PMID: 36677510 PMCID: PMC9864104 DOI: 10.3390/microorganisms11010218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been reported that TORC1 is of great significance in regulating cytotoxicity, morphology, protein synthesis and degradation, nutrient absorption, and metabolism. In this review, we mainly discuss the upstream and downstream signaling pathways of TORC1 to reveal its role in fungi.
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14
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Minden S, Aniolek M, Noorman H, Takors R. Performing in spite of starvation: How Saccharomyces cerevisiae maintains robust growth when facing famine zones in industrial bioreactors. Microb Biotechnol 2022; 16:148-168. [PMID: 36479922 PMCID: PMC9803336 DOI: 10.1111/1751-7915.14188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022] Open
Abstract
In fed-batch operated industrial bioreactors, glucose-limited feeding is commonly applied for optimal control of cell growth and product formation. Still, microbial cells such as yeasts and bacteria are frequently exposed to glucose starvation conditions in poorly mixed zones or far away from the feedstock inlet point. Despite its commonness, studies mimicking related stimuli are still underrepresented in scale-up/scale-down considerations. This may surprise as the transition from glucose limitation to starvation has the potential to provoke regulatory responses with negative consequences for production performance. In order to shed more light, we performed gene-expression analysis of Saccharomyces cerevisiae grown in intermittently fed chemostat cultures to study the effect of limitation-starvation transitions. The resulting glucose concentration gradient was representative for the commercial scale and compelled cells to tolerate about 76 s with sub-optimal substrate supply. Special attention was paid to the adaptation status of the population by discriminating between first time and repeated entry into the starvation regime. Unprepared cells reacted with a transiently reduced growth rate governed by the general stress response. Yeasts adapted to the dynamic environment by increasing internal growth capacities at the cost of rising maintenance demands by 2.7%. Evidence was found that multiple protein kinase A (PKA) and Snf1-mediated regulatory circuits were initiated and ramped down still keeping the cells in an adapted trade-off between growth optimization and down-regulation of stress response. From this finding, primary engineering guidelines are deduced to optimize both the production host's genetic background and the design of scale-down experiments.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Maria Aniolek
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Henk Noorman
- Royal DSMDelftThe Netherlands,Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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15
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Yahya G, Menges P, Amponsah PS, Ngandiri DA, Schulz D, Wallek A, Kulak N, Mann M, Cramer P, Savage V, Räschle M, Storchova Z. Sublinear scaling of the cellular proteome with ploidy. Nat Commun 2022; 13:6182. [PMID: 36261409 PMCID: PMC9581932 DOI: 10.1038/s41467-022-33904-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation, metabolic changes, lower fitness, and increased genomic instability, but the underlying mechanisms remain poorly understood. To investigate how gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in protein abundance compared to haploids. This ploidy-dependent sublinear scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the activity of Tor1 is reduced with increasing ploidy, which leads to diminished rRNA gene repression via a Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results suggest that the mTORC1-Sch9/S6K-Tup1/TLE1 pathway ensures proteome remodeling in response to increased ploidy.
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Affiliation(s)
- G. Yahya
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany ,grid.31451.320000 0001 2158 2757Department of Microbiology and Immunology, School of Pharmacy, Zagazig University, Zagazig, Egypt
| | - P. Menges
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - P. S. Amponsah
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - D. A. Ngandiri
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - D. Schulz
- grid.7400.30000 0004 1937 0650Institute of Molecular Biology, University of Zurich, Zurich, Switzerland
| | - A. Wallek
- grid.418615.f0000 0004 0491 845XMax Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - N. Kulak
- grid.418615.f0000 0004 0491 845XMax Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - M. Mann
- grid.418615.f0000 0004 0491 845XMax Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - P. Cramer
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - V. Savage
- grid.19006.3e0000 0000 9632 6718Department of Biomathematics, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - M. Räschle
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - Z. Storchova
- grid.7645.00000 0001 2155 0333Department of Molecular Genetics, TU Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
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16
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Guerra P, Vuillemenot LAPE, van Oppen YB, Been M, Milias-Argeitis A. TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle. J Cell Sci 2022; 135:276358. [PMID: 35975715 DOI: 10.1242/jcs.260378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 10/15/2022] Open
Abstract
Recent studies have revealed that the growth rate of budding yeast and mammalian cells varies during the cell cycle. By linking a multitude of signals to cell growth, the highly conserved Target of Rapamycin Complex 1 (TORC1) and Protein Kinase A (PKA) pathways are prime candidates for mediating the dynamic coupling between growth and division. However, measurements of TORC1 and PKA activity during the cell cycle are still lacking. Following the localization dynamics of two TORC1 and PKA targets via time-lapse microscopy in hundreds of yeast cells, we found that the activity of these pathways towards ribosome biogenesis fluctuates in synchrony with the cell cycle even under constant external conditions. Mutations of upstream TORC1 and PKA regulators suggested that internal metabolic signals partially mediate these activity changes. Our study reveals a new aspect of TORC1 and PKA signaling, which will be important for understanding growth regulation during the cell cycle.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Luc-Alban P E Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Yulan B van Oppen
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Marije Been
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
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17
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Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription. Nat Commun 2022; 13:3726. [PMID: 35768402 PMCID: PMC9242984 DOI: 10.1038/s41467-022-30350-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/21/2022] [Indexed: 11/10/2022] Open
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18
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Casamayor A, Ariño J. When Phosphatases Go Mad: The Molecular Basis for Toxicity of Yeast Ppz1. Int J Mol Sci 2022; 23:ijms23084304. [PMID: 35457140 PMCID: PMC9029398 DOI: 10.3390/ijms23084304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
The fact that overexpression of the yeast Ser/Thr protein phosphatase Ppz1 induces a dramatic halt in cell proliferation was known long ago, but only work in the last few years has provided insight into the molecular basis for this toxicity. Overexpression of Ppz1 causes abundant changes in gene expression and modifies the phosphorylation state of more than 150 proteins, including key signaling protein kinases such as Hog1 or Snf1. Diverse cellular processes are altered: halt in translation, failure to properly adapt to low glucose supply, acidification of the cytosol, or depletion of intracellular potassium content are a few examples. Therefore, the toxicity derived from an excess of Ppz1 appears to be multifactorial, the characteristic cell growth blockage thus arising from the combination of various altered processes. Notably, overexpression of the Ppz1 regulatory subunit Hal3 fully counteracts the toxic effects of the phosphatase, and this process involves intracellular relocation of the phosphatase to internal membranes.
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19
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Harmon TS, Jülicher F. Molecular Assembly Lines in Active Droplets. PHYSICAL REVIEW LETTERS 2022; 128:108102. [PMID: 35333067 DOI: 10.1103/physrevlett.128.108102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/30/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. Using droplet interfaces to position compartment boundaries, we show that an assembly line can be self-organized by active droplets. As a consequence, assembly steps can be arranged spatially so that a specific order of assembly is achieved and incorrect assembly is strongly suppressed.
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Affiliation(s)
- Tyler S Harmon
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohestraße 6, 01069 Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
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20
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Kusama K, Suzuki Y, Kurita E, Kawarasaki T, Obara K, Okumura F, Kamura T, Nakatsukasa K. Dot6/Tod6 degradation fine-tunes the repression of ribosome biogenesis under nutrient-limited conditions. iScience 2022; 25:103986. [PMID: 35310337 PMCID: PMC8924686 DOI: 10.1016/j.isci.2022.103986] [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: 06/25/2021] [Revised: 01/31/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis (Ribi) is a complex and energy-consuming process, and should therefore be repressed under nutrient-limited conditions to minimize unnecessary cellular energy consumption. In yeast, the transcriptional repressors Dot6 and Tod6 are phosphorylated and inactivated by the TORC1 pathway under nutrient-rich conditions, but are activated and repress ∼200 Ribi genes under nutrient-limited conditions. However, we show that in the presence of rapamycin or under nitrogen starvation conditions, Dot6 and Tod6 were readily degraded by the proteasome in a SCFGrr1 and Tom1 ubiquitin ligase-dependent manner, respectively. Moreover, promiscuous accumulation of Dot6 and Tod6 excessively repressed Ribi gene expression as well as translation activity and caused a growth defect in the presence of rapamycin. Thus, we propose that degradation of Dot6 and Tod6 is a novel mechanism to ensure an appropriate level of Ribi gene expression and thereby fine-tune the repression of Ribi and translation activity for cell survival under nutrient-limited conditions. Dot6 and Tod6 repress Ribi gene expression under nutrient-limited conditions Dot6 and Tod6 are degraded by the proteasome Excess repression of Ribi causes a growth defect in the presence of rapamycin Dot6 and Tod6 degradation fine-tunes the repression of Ribi and translation activity
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21
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Interaction of TOR and PKA Signaling in S. cerevisiae. Biomolecules 2022; 12:biom12020210. [PMID: 35204711 PMCID: PMC8961621 DOI: 10.3390/biom12020210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/13/2023] Open
Abstract
TOR and PKA signaling are the major growth-regulatory nutrient-sensing pathways in S. cerevisiae. A number of experimental findings demonstrated a close relationship between these pathways: Both are responsive to glucose availability. Both regulate ribosome production on the transcriptional level and repress autophagy and the cellular stress response. Sch9, a major downstream effector of TORC1 presumably shares its kinase consensus motif with PKA, and genetic rescue and synthetic defects between PKA and Sch9 have been known for a long time. Further, studies in the first decade of this century have suggested direct regulation of PKA by TORC1. Nonetheless, the contribution of a potential direct cross-talk vs. potential sharing of targets between the pathways has still not been completely resolved. What is more, other findings have in contrast highlighted an antagonistic relationship between the two pathways. In this review, I explore the association between TOR and PKA signaling, mainly by focusing on proteins that are commonly referred to as shared TOR and PKA targets. Most of these proteins are transcription factors which to a large part explain the major transcriptional responses elicited by TOR and PKA upon nutrient shifts. I examine the evidence that these proteins are indeed direct targets of both pathways and which aspects of their regulation are targeted by TOR and PKA. I further explore if they are phosphorylated on shared sites by PKA and Sch9 or when experimental findings point towards regulation via the PP2ASit4/PP2A branch downstream of TORC1. Finally, I critically review data suggesting direct cross-talk between the pathways and its potential mechanism.
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22
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Kumar S, Mashkoor M, Grove A. Yeast Crf1p: An activator in need is an activator indeed. Comput Struct Biotechnol J 2022; 20:107-116. [PMID: 34976315 PMCID: PMC8688861 DOI: 10.1016/j.csbj.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/15/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
Ribosome biogenesis is an energetically costly process, and tight regulation is required for stoichiometric balance between components. This requires coordination of RNA polymerases I, II, and III. Lack of nutrients or the presence of stress leads to downregulation of ribosome biogenesis, a process for which mechanistic target of rapamycin complex I (mTORC1) is key. mTORC1 activity is communicated by means of specific transcription factors, and in yeast, which is a primary model system in which transcriptional coordination has been delineated, transcription factors involved in regulation of ribosomal protein genes include Fhl1p and its cofactors, Ifh1p and Crf1p. Ifh1p is an activator, whereas Crf1p has been implicated in maintaining the repressed state upon mTORC1 inhibition. Computational analyses of evolutionary relationships have indicated that Ifh1p and Crf1p descend from a common ancestor. Here, we discuss recent evidence, which suggests that Crf1p also functions as an activator. We propose a model that consolidates available experimental evidence, which posits that Crf1p functions as an alternate activator to prevent the stronger activator Ifh1p from re-binding gene promoters upon mTORC1 inhibition. The correlation between retention of Crf1p in related yeast strains and duplication of ribosomal protein genes suggests that this backup activation may be important to ensure gene expression when Ifh1p is limiting. With ribosome biogenesis as a hallmark of cell growth, failure to control assembly of ribosomal components leads to several human pathologies. A comprehensive understanding of mechanisms underlying this process is therefore of the essence.
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Key Words
- CK2, casein kinase 2
- Crf1, corepressor with forkhead like
- Crf1p
- FHA, forkhead-associated
- FHB, forkhead-binding
- FKBP, FK506 binding protein
- Fhl1, forkhead like
- Fpr1, FK506-sensitive proline rotamase
- Gene regulation
- Hmo1, high mobility group
- Ifh1, interacts with forkhead like
- Ifh1p
- RASTR, ribosome assembly stress response
- RP, ribosomal protein
- Rap1, repressor/activator protein
- RiBi, ribosome biogenesis
- Ribosomal protein
- Ribosome biogenesis
- Sfp1, split finger protein
- WGD, whole genome duplication
- mTORC1
- mTORC1, mechanistic target of rapamycin complex 1
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Affiliation(s)
- Sanjay Kumar
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Muneera Mashkoor
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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23
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Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep 2021; 37:110149. [PMID: 34965436 DOI: 10.1016/j.celrep.2021.110149] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/19/2021] [Accepted: 11/30/2021] [Indexed: 01/18/2023] Open
Abstract
The eukaryotic TORC1 kinase assimilates diverse environmental cues, including growth factors and nutrients, to control growth by tuning anabolic and catabolic processes. In yeast, TORC1 stimulates protein synthesis in response to abundant nutrients primarily through its proximal effector kinase Sch9. Conversely, TORC1 inhibition following nutrient limitation unlocks various distally controlled kinases (e.g., Atg1, Gcn2, Npr1, Rim15, Slt2/Mpk1, and Yak1), which cooperate through poorly defined circuits to orchestrate the quiescence program. To better define the signaling landscape of the latter kinases, we use in vivo quantitative phosphoproteomics. Through pinpointing known and uncharted Npr1, Rim15, Slt2/Mpk1, and Yak1 effectors, our study examines the architecture of the distally controlled TORC1 kinase network. Accordingly, this is built on a combination of discrete, convergent, and multilayered feedback regulatory mechanisms, which likely ensure homeostatic control of and/or robust responses by TORC1 and its effector kinases under fluctuating nutritional conditions.
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24
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Mo C, Xie C, Wang G, Tian T, Liu J, Zhu C, Xiao X, Xiao Y. Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi. Nucleic Acids Res 2021; 49:12358-12376. [PMID: 34792171 PMCID: PMC8643696 DOI: 10.1093/nar/gkab1102] [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: 07/11/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/14/2022] Open
Abstract
The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
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Affiliation(s)
- Chenmi Mo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chong Xie
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Gaofeng Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tian Tian
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Juan Liu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chunxiao Zhu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yannong Xiao
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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25
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Mawer JSP, Massen J, Reichert C, Grabenhorst N, Mylonas C, Tessarz P. Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis. EMBO Rep 2021; 22:e52435. [PMID: 34409714 PMCID: PMC8490984 DOI: 10.15252/embr.202152435] [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: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023] Open
Abstract
Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post‐transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.
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Affiliation(s)
- Julia S P Mawer
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christina Reichert
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Grabenhorst
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Constantine Mylonas
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
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26
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Diphthamide promotes TOR signaling by increasing the translation of proteins in the TORC1 pathway. Proc Natl Acad Sci U S A 2021; 118:2104577118. [PMID: 34507998 PMCID: PMC8449394 DOI: 10.1073/pnas.2104577118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 01/31/2023] Open
Abstract
Diphthamide, a modification found only on translation elongation factor 2 (EF2), was proposed to suppress -1 frameshifting in translation. Although diphthamide is conserved among all eukaryotes, exactly what proteins are affected by diphthamide deletion is not clear in cells. Through genome-wide profiling for a potential -1 frameshifting site, we identified that the target of rapamycin complex 1 (TORC1)/mammalian TORC1 (mTORC1) signaling pathway is affected by deletion of diphthamide. Diphthamide deficiency in yeast suppresses the translation of TORC1-activating proteins Vam6 and Rtc1. Interestingly, TORC1 signaling also promotes diphthamide biosynthesis, suggesting that diphthamide forms a positive feedback loop to promote translation under nutrient-rich conditions. Our results provide an explanation for why diphthamide is evolutionarily conserved and why diphthamide deletion can cause severe developmental defects.
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27
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Kumar A. The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth. Annu Rev Genet 2021; 55:1-21. [PMID: 34280314 DOI: 10.1146/annurev-genet-071719-020249] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic cells are exquisitely responsive to external and internal cues, achieving precise control of seemingly diverse growth processes through a complex interplay of regulatory mechanisms. The budding yeast Saccharomyces cerevisiae provides a fascinating model of cell growth in its stress-responsive transition from planktonic single cells to a filamentous pseudohyphal growth form. During pseudohyphal growth, yeast cells undergo changes in morphology, polarity, and adhesion to form extended and invasive multicellular filaments. This pseudohyphal transition has been studied extensively as a model of conserved signaling pathways regulating cell growth and for its relevance in understanding the pathogenicity of the related opportunistic fungus Candida albicans, wherein filamentous growth is required for virulence. This review highlights the broad gene set enabling yeast pseudohyphal growth, signaling pathways that regulate this process, the role and regulation of proteins conferring cell adhesion, and interesting regulatory mechanisms enabling the pseudohyphal transition. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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28
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Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals. Biochem Soc Trans 2021; 49:1589-1599. [PMID: 34240738 PMCID: PMC8421047 DOI: 10.1042/bst20201136] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022]
Abstract
Ribosome biogenesis requires prodigious transcriptional output in rapidly growing yeast cells and is highly regulated in response to both growth and stress signals. This minireview focuses on recent developments in our understanding of this regulatory process, with an emphasis on the 138 ribosomal protein genes (RPGs) themselves and a group of >200 ribosome biogenesis (RiBi) genes whose products contribute to assembly but are not part of the ribosome. Expression of most RPGs depends upon Rap1, a pioneer transcription factor (TF) required for the binding of a pair of RPG-specific TFs called Fhl1 and Ifh1. RPG expression is correlated with Ifh1 promoter binding, whereas Rap1 and Fhl1 remain promoter-associated upon stress-induced down regulation. A TF called Sfp1 has also been implicated in RPG regulation, though recent work reveals that its primary function is in activation of RiBi and other growth-related genes. Sfp1 plays an important regulatory role at a small number of RPGs where Rap1–Fhl1–Ifh1 action is subsidiary or non-existent. In addition, nearly half of all RPGs are bound by Hmo1, which either stabilizes or re-configures Fhl1–Ifh1 binding. Recent studies identified the proline rotamase Fpr1, known primarily for its role in rapamycin-mediated inhibition of the TORC1 kinase, as an additional TF at RPG promoters. Fpr1 also affects Fhl1–Ifh1 binding, either independently or in cooperation with Hmo1. Finally, a major recent development was the discovery of a protein homeostasis mechanism driven by unassembled ribosomal proteins, referred to as the Ribosome Assembly Stress Response (RASTR), that controls RPG transcription through the reversible condensation of Ifh1.
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29
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Peterson PP, Liu Z. Identification and Characterization of Rapidly Accumulating sch9Δ Suppressor Mutations in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6254187. [PMID: 33901283 DOI: 10.1093/g3journal/jkab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/14/2021] [Indexed: 01/30/2023]
Abstract
Nutrient sensing is important for cell growth, aging, and longevity. In Saccharomyces cerevisiae, Sch9, an AGC-family protein kinase, is a major nutrient sensing kinase homologous to mammalian Akt and S6 kinase. Sch9 integrates environmental cues with cell growth by functioning downstream of TORC1 and in parallel with the Ras/PKA pathway. Mutations in SCH9 lead to reduced cell growth in dextrose medium; however, reports on the ability of sch9Δ mutants to utilize non-fermentable carbon sources are inconsistent. Here we show that sch9Δ mutant strains cannot grow on non-fermentable carbon sources and rapidly accumulate suppressor mutations, which reverse growth defects of sch9Δ mutants. sch9Δ induces gene expression of three transcription factors required for utilization of non-fermentable carbon sources, Cat8, Adr1, and Hap4, while sch9Δ suppressor mutations, termed sns1 and sns2, strongly decrease the gene expression of those transcription factors. Despite the genetic suppression interactions, both sch9Δ and sns1 (or sns2) homozygous mutants have severe defects in meiosis. By screening mutants defective in sporulation, we identified additional sch9Δ suppressor mutants with mutations in GPB1, GPB2, and MCK1. Using library complementation and genetic analysis, we identified SNS1 and SNS2 to be IRA2 and IRA1, respectively. Furthermore, we discovered that lifespan extension in sch9Δ mutants is dependent on IRA2 and that PKA inactivation greatly increases basal expression of CAT8, ADR1, and HAP4. Our results demonstrate that sch9Δ leads to complete loss of growth on non-fermentable carbon sources and mutations in MCK1 or genes encoding negative regulators of the Ras/PKA pathway reverse sch9Δ mutant phenotypes.
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Affiliation(s)
- Patricia P Peterson
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
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30
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Eiyama A, Aaltonen MJ, Nolte H, Tatsuta T, Langer T. Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling. J Biol Chem 2021; 296:100335. [PMID: 33497623 PMCID: PMC7949116 DOI: 10.1016/j.jbc.2021.100335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 01/18/2023] Open
Abstract
Lipid transfer proteins of the Ups1/PRELID1 family facilitate the transport of phospholipids across the intermembrane space of mitochondria in a lipid-specific manner. Heterodimeric complexes of yeast Ups1/Mdm35 or human PRELID1/TRIAP1 shuttle phosphatidic acid (PA) mainly synthesized in the endoplasmic reticulum (ER) to the inner membrane, where it is converted to cardiolipin (CL), the signature phospholipid of mitochondria. Loss of Ups1/PRELID1 proteins impairs the accumulation of CL and broadly affects mitochondrial structure and function. Unexpectedly and unlike yeast cells lacking the CL synthase Crd1, Ups1-deficient yeast cells exhibit glycolytic growth defects, pointing to functions of Ups1-mediated PA transfer beyond CL synthesis. Here, we show that the disturbed intramitochondrial transport of PA in ups1Δ cells leads to altered unfolded protein response (UPR) and mTORC1 signaling, independent of disturbances in CL synthesis. The impaired flux of PA into mitochondria is associated with the increased synthesis of phosphatidylcholine and a reduced phosphatidylethanolamine/phosphatidylcholine ratio in the ER of ups1Δ cells which suppresses the UPR. Moreover, we observed inhibition of target of rapamycin complex 1 (TORC1) signaling in these cells. Activation of either UPR by ER protein stress or of TORC1 signaling by disruption of its negative regulator, the Seh1-associated complex inhibiting TORC1 complex, increased cytosolic protein synthesis, and restored glycolytic growth of ups1Δ cells. These results demonstrate that PA influx into mitochondria is required to preserve ER membrane homeostasis and that its disturbance is associated with impaired glycolytic growth and cellular stress signaling.
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Affiliation(s)
- Akinori Eiyama
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Mari J Aaltonen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Hendrik Nolte
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Takashi Tatsuta
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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31
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Miles S, Bradley GT, Breeden LL. The budding yeast transition to quiescence. Yeast 2021; 38:30-38. [PMID: 33350501 DOI: 10.1002/yea.3546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/06/2022] Open
Abstract
A subset of Saccharomyces cerevisiae cells in a stationary phase culture achieve a unique quiescent state characterized by increased cell density, stress tolerance, and longevity. Trehalose accumulation is necessary but not sufficient for conferring this state, and it is not recapitulated by abrupt starvation. The fraction of cells that achieve this state varies widely in haploids and diploids and can approach 100%, indicating that both mother and daughter cells can enter quiescence. The transition begins when about half the glucose has been taken up from the medium. The high affinity glucose transporters are turned on, glycogen storage begins, the Rim15 kinase enters the nucleus and the accumulation of cells in G1 is initiated. After the diauxic shift (DS), when glucose is exhausted from the medium, growth promoting genes are repressed by the recruitment of the histone deacetylase Rpd3 by quiescence-specific repressors. The final division that takes place post-DS is highly asymmetrical and G1 arrest is complete after 48 h. The timing of these events can vary considerably, but they are tightly correlated with total biomass of the culture, suggesting that the transition to quiescence is tightly linked to changes in external glucose levels. After 7 days in culture, there are massive morphological changes at the protein and organelle level. There are global changes in histone modification. An extensive array of condensin-dependent, long-range chromatin interactions lead to genome-wide chromatin compaction that is conserved in yeast and human cells. These interactions are required for the global transcriptional repression that occurs in quiescent yeast.
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Affiliation(s)
- Shawna Miles
- Fred Hutchinson Cancer Research Center, Basic Science Division, Seattle, Washington, USA
| | | | - Linda L Breeden
- Fred Hutchinson Cancer Research Center, Basic Science Division, Seattle, Washington, USA
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32
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Hu Z, Raucci S, Jaquenoud M, Hatakeyama R, Stumpe M, Rohr R, Reggiori F, De Virgilio C, Dengjel J. Multilayered Control of Protein Turnover by TORC1 and Atg1. Cell Rep 2020; 28:3486-3496.e6. [PMID: 31553916 DOI: 10.1016/j.celrep.2019.08.069] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/19/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
The target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, which promotes anabolic reactions and synchronously inhibits catabolic processes such as autophagy-mediated protein degradation. Its prime autophagy target is Atg13, a subunit of the Atg1 kinase complex that acts as the gatekeeper of canonical autophagy. To study whether the activities of TORC1 and Atg1 are coupled through additional, more intricate control mechanisms than simply this linear pathway, we analyzed the epistatic relationship between TORC1 and Atg1 by using quantitative phosphoproteomics. Our in vivo data, combined with targeted in vitro TORC1 and Atg1 kinase assays, not only uncover numerous TORC1 and Atg1 effectors, but also suggest distinct bi-directional regulatory feedback loops and characterize Atg29 as a commonly regulated downstream target of both TORC1 and Atg1. Thus, an exquisitely multilayered regulatory network appears to coordinate TORC1 and Atg1 activities to robustly tune autophagy in response to nutritional cues.
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Affiliation(s)
- Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Serena Raucci
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Malika Jaquenoud
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Rudolf Rohr
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | | | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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33
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Morrissette VA, Rolfes RJ. The intersection between stress responses and inositol pyrophosphates in Saccharomyces cerevisiae. Curr Genet 2020; 66:901-910. [PMID: 32322930 DOI: 10.1007/s00294-020-01078-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 01/08/2023]
Abstract
Saccharomyces cerevisiae adapts to oxidative, osmotic stress and nutrient deprivation through transcriptional changes, decreased proliferation, and entry into other developmental pathways such as pseudohyphal formation and sporulation. Inositol pyrophosphates are necessary for these cellular responses. Inositol pyrophosphates are molecules composed of the phosphorylated myo-inositol ring that carries one or more diphosphates. Mutations in the enzymes that metabolize these molecules lead to altered patterns of stress resistance, altered morphology, and defective sporulation. Mechanisms to alter the synthesis of inositol pyrophosphates have been recently described, including inhibition of enzyme activity by oxidation and by phosphorylation. Cells with increased levels of 5-diphosphoinositol pentakisphosphate have increased nuclear localization of Msn2 and Gln3. The altered localization of these factors is consistent with the partially induced environmental stress response and increased expression of genes under the control of Msn2/4 and Gln3. Other transcription factors may also exhibit increased nuclear localization based on increased expression of their target genes. These transcription factors are each regulated by TORC1, suggesting that TORC1 may be inhibited by inositol pyrophosphates. Inositol pyrophosphates affect stress responses in other fungi (Aspergillus nidulans, Ustilago maydis, Schizosaccharomyces pombe, and Cryptococcus neoformans), in human and mouse, and in plants, suggesting common mechanisms and possible novel drug development targets.
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Affiliation(s)
- Victoria A Morrissette
- Department of Biology, Georgetown University, Reiss Science Building 406, Washington, DC, 20057, USA
| | - Ronda J Rolfes
- Department of Biology, Georgetown University, Reiss Science Building 406, Washington, DC, 20057, USA.
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34
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Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. Mol Cell Proteomics 2020; 19:655-671. [PMID: 32102971 PMCID: PMC7124472 DOI: 10.1074/mcp.ra120.001955] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in S. cerevisiae To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs suggesting that many are directly phosphorylated by these enzymes. Interestingly, when inhibiting Ypk1 we not only detected several hypo-phosphorylated sites in the previously reported RxRxxS/T-, but also in an RRxS/T-motif. Validation experiments revealed that neutral trehalase Nth1, a known PKA target, is additionally phosphorylated and activated downstream of Ypk1. Signaling through Ypk1 is therefore more closely related to PKA- and Sch9-signaling than previously appreciated and may perform functions previously only attributed to the latter kinases.
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Affiliation(s)
- Michael Plank
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
| | - Mariya Perepelkina
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Markus Müller
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Xiaoming Zou
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Marina Berti
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Jacques Saarbach
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Steven Haesendonckx
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland; Faculty of Science, University of Zurich, CH-8006, Zurich, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
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35
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Morrison AJ. Chromatin-remodeling links metabolic signaling to gene expression. Mol Metab 2020; 38:100973. [PMID: 32251664 PMCID: PMC7300377 DOI: 10.1016/j.molmet.2020.100973] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND ATP-dependent chromatin remodelers are evolutionarily conserved complexes that alter nucleosome positioning to influence many DNA-templated processes, such as replication, repair, and transcription. In particular, chromatin remodeling can dynamically regulate gene expression by altering accessibility of chromatin to transcription factors. SCOPE OF REVIEW This review provides an overview of the importance of chromatin remodelers in the regulation of metabolic gene expression. Particular emphasis is placed on the INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers in both yeast and mammals. This review details discoveries from the initial identification of chromatin remodelers in Saccharomyces cerevisiae to recent discoveries in the metabolic requirements of developing embryonic tissues in mammals. MAJOR CONCLUSIONS INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers regulate the expression of energy metabolism pathways in S. cerevisiae and mammals in response to diverse nutrient environments. In particular, the INO80 complex organizes the temporal expression of gene expression in the metabolically synchronized S. cerevisiae system. INO80-mediated chromatin remodeling is also needed to constrain cell division during metabolically favorable conditions. Conversely, the BAF/PBAF remodeler regulates tissue-specific glycolytic metabolism and is disrupted in cancers that are dependent on glycolysis for proliferation. The role of chromatin remodeling in metabolic gene expression is downstream of the metabolic signaling pathways, such as the TOR pathway, a critical regulator of metabolic homeostasis. Furthermore, the INO80 and BAF/PBAF chromatin remodelers have both been shown to regulate heart development, the tissues of which have unique requirements for energy metabolism during development. Collectively, these results demonstrate that chromatin remodelers communicate metabolic status to chromatin and are a central component of homeostasis pathways that optimize cell fitness, organismal development, and prevent disease.
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Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, Stanford CA 94305, USA.
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36
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Multi-kinase control of environmental stress responsive transcription. PLoS One 2020; 15:e0230246. [PMID: 32160258 PMCID: PMC7065805 DOI: 10.1371/journal.pone.0230246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/26/2020] [Indexed: 11/19/2022] Open
Abstract
Cells respond to changes in environmental conditions by activating signal transduction pathways and gene expression programs. Here we present a dataset to explore the relationship between environmental stresses, kinases, and global gene expression in yeast. We subjected 28 drug-sensitive kinase mutants to 10 environmental conditions in the presence of inhibitor and performed mRNA deep sequencing. With these data, we reconstructed canonical stress pathways and identified examples of crosstalk among pathways. The data also implicated numerous kinases in novel environment-specific roles. However, rather than regulating dedicated sets of target genes, individual kinases tuned the magnitude of induction of the environmental stress response (ESR)–a gene expression signature shared across the set of perturbations–in environment-specific ways. This suggests that the ESR integrates inputs from multiple sensory kinases to modulate gene expression and growth control. As an example, we provide experimental evidence that the high osmolarity glycerol pathway is an upstream negative regulator of protein kinase A, a known inhibitor of the ESR. These results elaborate the central axis of cellular stress response signaling.
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37
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Eshleman N, Luo X, Capaldi A, Buchan JR. Alterations of signaling pathways in response to chemical perturbations used to measure mRNA decay rates in yeast. RNA (NEW YORK, N.Y.) 2020; 26:10-18. [PMID: 31601735 PMCID: PMC6913126 DOI: 10.1261/rna.072892.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Assessing variations in mRNA stability typically involves inhibiting transcription either globally or in a gene-specific manner. Alternatively, mRNA pulse-labeling strategies offer a means to calculate mRNA stability without inhibiting transcription. However, key stress-responsive cell signaling pathways, which affect mRNA stability, may themselves be perturbed by the approaches used to measure mRNA stability, leading to artifactual results. Here, we have focused on common strategies to measure mRNA half-lives in yeast and determined that commonly used transcription inhibitors thiolutin and 1,10 phenanthroline inhibit TORC1 signaling, PKC signaling, and partially activate HOG signaling. Additionally, 4-thiouracil (4tU), a uracil analog used in mRNA pulse-labeling approaches, modestly induces P-bodies, mRNA-protein granules implicated in storage and decay of nontranslating mRNA. Thiolutin also induces P-bodies, whereas phenanthroline has no effect. Doxycycline, which controls "Tet On/Tet Off" regulatable promoters, shows no impact on the above signaling pathways or P-bodies. In summary, our data argues that broad-acting transcriptional inhibitors are problematic for determining mRNA half-life, particularly if studying the impacts of the TORC1, HOG, or PKC pathway on mRNA stability. Regulatable promoter systems are a preferred approach for individual mRNA half-life studies, with 4tU labeling representing a good approach to global mRNA half-life analysis, despite modestly inducing P-bodies.
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Affiliation(s)
- Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Andrew Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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38
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Leutert M, Rodríguez‐Mias RA, Fukuda NK, Villén J. R2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies. Mol Syst Biol 2019; 15:e9021. [PMID: 31885202 PMCID: PMC6920700 DOI: 10.15252/msb.20199021] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
Recent developments in proteomics have enabled signaling studies where > 10,000 phosphosites can be routinely identified and quantified. Yet, current analyses are limited in throughput, reproducibility, and robustness, hampering experiments that involve multiple perturbations, such as those needed to map kinase-substrate relationships, capture pathway crosstalks, and network inference analysis. To address these challenges, we introduce rapid-robotic phosphoproteomics (R2-P2), an end-to-end automated method that uses magnetic particles to process protein extracts to deliver mass spectrometry-ready phosphopeptides. R2-P2 is rapid, robust, versatile, and high-throughput. To showcase the method, we applied it, in combination with data-independent acquisition mass spectrometry, to study signaling dynamics in the mitogen-activated protein kinase (MAPK) pathway in yeast. Our results reveal broad and specific signaling events along the mating, the high-osmolarity glycerol, and the invasive growth branches of the MAPK pathway, with robust phosphorylation of downstream regulatory proteins and transcription factors. Our method facilitates large-scale signaling studies involving hundreds of perturbations opening the door to systems-level studies aiming to capture signaling complexity.
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Affiliation(s)
- Mario Leutert
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Noelle K Fukuda
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Judit Villén
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
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39
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Santos DA, Shi L, Tu BP, Weissman JS. Cycloheximide can distort measurements of mRNA levels and translation efficiency. Nucleic Acids Res 2019; 47:4974-4985. [PMID: 30916348 PMCID: PMC6547433 DOI: 10.1093/nar/gkz205] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/01/2019] [Accepted: 03/16/2019] [Indexed: 01/26/2023] Open
Abstract
Regulation of the efficiency with which an mRNA is translated into proteins represents a key mechanism for controlling gene expression. Such regulation impacts the number of actively translating ribosomes per mRNA molecule, referred to as translation efficiency (TE), which can be monitored using ribosome profiling and RNA-seq, or by evaluating the position of an mRNA in a polysome gradient. Here we show that in budding yeast, under nutrient limiting conditions, the commonly used translation inhibitor cycloheximide induces rapid transcriptional upregulation of hundreds of genes involved in ribosome biogenesis. Cycloheximide also prevents translation of these newly transcribed messages, leading to an apparent drop in TE of these genes under conditions that include key transitions during the yeast metabolic cycle, meiosis, and amino acid starvation; however, this effect is abolished when cycloheximide pretreatment is omitted. This response requires TORC1 signaling, and is modulated by the genetic background as well as the vehicle used to deliver the drug. The present work highlights an important caveat to the use of translation inhibitors when measuring TE or mRNA levels, and will hopefully aid in future experimental design as well as interpretation of prior results.
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Affiliation(s)
- Daniel A Santos
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lei Shi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
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40
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Gowans GJ, Bridgers JB, Zhang J, Dronamraju R, Burnetti A, King DA, Thiengmany AV, Shinsky SA, Bhanu NV, Garcia BA, Buchler NE, Strahl BD, Morrison AJ. Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression. Mol Cell 2019; 76:909-921.e3. [PMID: 31676231 DOI: 10.1016/j.molcel.2019.09.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 09/07/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid β-oxidation genes are periodically expressed coincident with the β-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.
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Affiliation(s)
- Graeme J Gowans
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Bridgers
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jibo Zhang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Raghuvar Dronamraju
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anthony Burnetti
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Stephen A Shinsky
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicolas E Buchler
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Ashby J Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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41
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Lee BB, Choi A, Kim JH, Jun Y, Woo H, Ha SD, Yoon CY, Hwang JT, Steinmetz L, Buratowski S, Lee S, Kim HY, Kim T. Rpd3L HDAC links H3K4me3 to transcriptional repression memory. Nucleic Acids Res 2019; 46:8261-8274. [PMID: 29982589 PMCID: PMC6144869 DOI: 10.1093/nar/gky573] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/14/2018] [Indexed: 11/13/2022] Open
Abstract
Transcriptional memory is critical for the faster reactivation of necessary genes upon environmental changes and requires that the genes were previously in an active state. However, whether transcriptional repression also displays ‘memory’ of the prior transcriptionally inactive state remains unknown. In this study, we show that transcriptional repression of ∼540 genes in yeast occurs much more rapidly if the genes have been previously repressed during carbon source shifts. This novel transcriptional response has been termed transcriptional repression memory (TREM). Interestingly, Rpd3L histone deacetylase (HDAC), targeted to active promoters induces TREM. Mutants for Rpd3L exhibit increased acetylation at active promoters and delay TREM significantly. Surprisingly, the interaction between H3K4me3 and Rpd3L via the Pho23 PHD finger is critical to promote histone deacetylation and TREM by Rpd3L. Therefore, we propose that an active mark, H3K4me3 enriched at active promoters, instructs Rpd3L HDAC to induce histone deacetylation and TREM.
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Affiliation(s)
- Bo Bae Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ahyoung Choi
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Hyun Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Yukyung Jun
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hyeonju Woo
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - So Dam Ha
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Chae Young Yoon
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | | | - Lars Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, and Stanford Genome Technology Center and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanghyuk Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hye Young Kim
- Department of Biomedical Sciences and Medical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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42
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Kunkel J, Luo X, Capaldi AP. Integrated TORC1 and PKA signaling control the temporal activation of glucose-induced gene expression in yeast. Nat Commun 2019; 10:3558. [PMID: 31395866 PMCID: PMC6687784 DOI: 10.1038/s41467-019-11540-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/19/2019] [Indexed: 01/04/2023] Open
Abstract
The growth rate of a yeast cell is controlled by the target of rapamycin kinase complex I (TORC1) and cAMP-dependent protein kinase (PKA) pathways. To determine how TORC1 and PKA cooperate to regulate cell growth, we performed temporal analysis of gene expression in yeast switched from a non-fermentable substrate, to glucose, in the presence and absence of TORC1 and PKA inhibitors. Quantitative analysis of these data reveals that PKA drives the expression of key cell growth genes during transitions into, and out of, the rapid growth state in glucose, while TORC1 is important for the steady-state expression of the same genes. This circuit design may enable yeast to set an exact growth rate based on the abundance of internal metabolites such as amino acids, via TORC1, but also adapt rapidly to changes in external nutrients, such as glucose, via PKA.
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Affiliation(s)
- Joseph Kunkel
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721-0206, USA
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721-0206, USA
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721-0206, USA.
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43
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Romero AM, Ramos-Alonso L, Montellá-Manuel S, García-Martínez J, de la Torre-Ruiz MÁ, Pérez-Ortín JE, Martínez-Pastor MT, Puig S. A genome-wide transcriptional study reveals that iron deficiency inhibits the yeast TORC1 pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194414. [PMID: 31394264 DOI: 10.1016/j.bbagrm.2019.194414] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Iron is an essential micronutrient that participates as a cofactor in a broad range of metabolic processes including mitochondrial respiration, DNA replication, protein translation and lipid biosynthesis. Adaptation to iron deficiency requires the global reorganization of cellular metabolism directed to optimize iron utilization. The budding yeast Saccharomyces cerevisiae has been widely used to characterize the responses of eukaryotic microorganisms to iron depletion. In this report, we used a genomic approach to investigate the contribution of transcription rates to the modulation of mRNA levels during adaptation of yeast cells to iron starvation. We reveal that a decrease in the activity of all RNA polymerases contributes to the down-regulation of many mRNAs, tRNAs and rRNAs. Opposite to the general expression pattern, many genes including components of the iron deficiency response, the mitochondrial retrograde pathway and the general stress response display a remarkable increase in both transcription rates and mRNA levels upon iron limitation, whereas genes encoding ribosomal proteins or implicated in ribosome biogenesis exhibit a pronounced fall. This expression profile is consistent with an activation of the environmental stress response. The phosphorylation stage of multiple regulatory factors strongly suggests that the conserved nutrient signaling pathway TORC1 is inhibited during the progress of iron deficiency. These results suggest an intricate crosstalk between iron metabolism and the TORC1 pathway that should be considered in many disorders.
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Affiliation(s)
- Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain
| | - Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain
| | - Sandra Montellá-Manuel
- Department of Basic Medical Sciences, IRB-Lleida, University of Lleida, E-25198 Lleida, Spain
| | - José García-Martínez
- Departamento de Genética, Universitat de València, E-46100 Burjassot, Valencia, Spain; ERI Biotecmed, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | | | - José Enrique Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, E-46100 Burjassot, Valencia, Spain; ERI Biotecmed, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | | | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), E-46980 Paterna, Valencia, Spain.
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44
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Parnell EJ, Stillman DJ. Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to the HO Promoter in Saccharomyces cerevisiae. Genetics 2019; 212:1181-1204. [PMID: 31167839 PMCID: PMC6707452 DOI: 10.1534/genetics.119.302359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/30/2019] [Indexed: 01/22/2023] Open
Abstract
Activation of the Saccharomyces cerevisiae HO promoter is highly regulated, requiring the ordered recruitment of activators and coactivators and allowing production of only a few transcripts in mother cells within a short cell cycle window. We conducted genetic screens to identify the negative regulators of HO expression necessary to limit HO transcription. Known repressors of HO (Ash1 and Rpd3) were identified, as well as several additional chromatin-associated factors including the Hda1 histone deacetylase, the Isw2 chromatin remodeler, and the corepressor Tup1 We also identified clusters of HO promoter mutations that suggested roles for the Dot6/Tod6 (PAC site) and Ume6 repression pathways. We used ChIP assays with synchronized cells to validate the involvement of these factors and map the association of Ash1, Dot6, and Ume6 with the HO promoter to a brief window in the cell cycle between binding of the initial activating transcription factor and initiation of transcription. We found that Ash1 and Ume6 each recruit the Rpd3 histone deacetylase to HO, and their effects are additive. In contrast, Rpd3 was not recruited significantly to the PAC site, suggesting this site has a distinct mechanism for repression. Increases in HO expression and SWI/SNF recruitment were all additive upon loss of Ash1, Ume6, and PAC site factors, indicating the convergence of independent pathways for repression. Our results demonstrate that multiple protein complexes are important for limiting the spread of SWI/SNF-mediated nucleosome eviction across the HO promoter, suggesting that regulation requires a delicate balance of activities that promote and repress transcription.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
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45
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INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. Cell Rep 2019; 22:611-623. [PMID: 29346761 PMCID: PMC5949282 DOI: 10.1016/j.celrep.2017.12.079] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.
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46
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Kuang Z, Ji Z, Boeke JD, Ji H. Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. Nucleic Acids Res 2019; 46:e2. [PMID: 29325176 PMCID: PMC5758894 DOI: 10.1093/nar/gkx905] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 09/26/2017] [Indexed: 01/02/2023] Open
Abstract
Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data. In the first step, DynaMO predicts TF binding sites with a random forests approach. Next and uniquely, DynaMO infers dynamic TF binding activities at predicted binding sites using their local chromatin profiles from multiple biological conditions. Another landmark of DynaMO is to identify key TFs in a dynamic process using a clustering and enrichment analysis of dynamic TF binding patterns. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes.
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Affiliation(s)
- Zheng Kuang
- Institute for Systems Genetics, NYU Langone Medical Center, New York City, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York City, NY 10016, USA.,Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Medical Center, New York City, NY 10016, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York City, NY 10016, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
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47
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Cheng Z, Brar GA. Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs. Nucleic Acids Res 2019; 47:5061-5073. [PMID: 30937450 PMCID: PMC6547411 DOI: 10.1093/nar/gkz231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 11/15/2022] Open
Abstract
Ribosome biogenesis (RiBi) is an extremely energy intensive process that is critical for gene expression. It is thus highly regulated, including through the tightly coordinated expression of over 200 RiBi genes by positive and negative transcriptional regulators. We investigated RiBi regulation as cells initiated meiosis in budding yeast and noted early transcriptional activation of RiBi genes, followed by their apparent translational repression 1 hour (h) after stimulation to enter meiosis. Surprisingly, in the representative genes examined, measured translational repression depended on their promoters rather than mRNA regions. Further investigation revealed that the signature of this regulation in our data depended on pre-treating cells with the translation inhibitor, cycloheximide (CHX). This treatment, at 1 h in meiosis, but not earlier, rapidly resulted in accumulation of RiBi mRNAs that were not translated. This effect was also seen in with CHX pre-treatment of cells grown in media lacking amino acids. For NSR1, this effect depended on the -150 to -101 region of the promoter, as well as the RiBi transcriptional repressors Dot6 and Tod6. Condition-specific RiBi mRNA accumulation was also seen with translation inhibitors that are dissimilar from CHX, suggesting that this phenomenon might represent a feedback response to global translation inhibition.
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Affiliation(s)
- Ze Cheng
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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48
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Deprez MA, Eskes E, Winderickx J, Wilms T. The TORC1-Sch9 pathway as a crucial mediator of chronological lifespan in the yeast Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:4980911. [PMID: 29788208 DOI: 10.1093/femsyr/foy048] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 12/18/2022] Open
Abstract
The concept of ageing is one that has intrigued mankind since the beginning of time and is now more important than ever as the incidence of age-related disorders is increasing in our ageing population. Over the past decades, extensive research has been performed using various model organisms. As such, it has become apparent that many fundamental aspects of biological ageing are highly conserved across large evolutionary distances. In this review, we illustrate that the unicellular eukaryotic organism Saccharomyces cerevisiae has proven to be a valuable tool to gain fundamental insights into the molecular mechanisms of cellular ageing in multicellular eukaryotes. In addition, we outline the current knowledge on how downregulation of nutrient signaling through the target of rapamycin (TOR)-Sch9 pathway or reducing calorie intake attenuates many detrimental effects associated with ageing and leads to the extension of yeast chronological lifespan. Given that both TOR Complex 1 (TORC1) and Sch9 have mammalian orthologues that have been implicated in various age-related disorders, unraveling the connections of TORC1 and Sch9 with yeast ageing may provide additional clues on how their mammalian orthologues contribute to the mechanisms underpinning human ageing and health.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Tobias Wilms
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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49
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Sellam A, Chaillot J, Mallick J, Tebbji F, Richard Albert J, Cook MA, Tyers M. The p38/HOG stress-activated protein kinase network couples growth to division in Candida albicans. PLoS Genet 2019; 15:e1008052. [PMID: 30921326 PMCID: PMC6456229 DOI: 10.1371/journal.pgen.1008052] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/09/2019] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
Cell size is a complex trait that responds to developmental and environmental cues. Quantitative size analysis of mutant strain collections disrupted for protein kinases and transcriptional regulators in the pathogenic yeast Candida albicans uncovered 66 genes that altered cell size, few of which overlapped with known size genes in the budding yeast Saccharomyces cerevisiae. A potent size regulator specific to C. albicans was the conserved p38/HOG MAPK module that mediates the osmostress response. Basal HOG activity inhibited the SBF G1/S transcription factor complex in a stress-independent fashion to delay the G1/S transition. The HOG network also governed ribosome biogenesis through the master transcriptional regulator Sfp1. Hog1 bound to the promoters and cognate transcription factors for ribosome biogenesis regulons and interacted genetically with the SBF G1/S machinery, and thereby directly linked cell growth and division. These results illuminate the evolutionary plasticity of size control and identify the HOG module as a nexus of cell cycle and growth regulation.
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Affiliation(s)
- Adnane Sellam
- Infectious Diseases Research Centre (CRI), CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Julien Chaillot
- Infectious Diseases Research Centre (CRI), CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Jaideep Mallick
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Faiza Tebbji
- Infectious Diseases Research Centre (CRI), CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, QC, Canada
| | - Julien Richard Albert
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael A. Cook
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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50
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Albert B, Tomassetti S, Gloor Y, Dilg D, Mattarocci S, Kubik S, Hafner L, Shore D. Sfp1 regulates transcriptional networks driving cell growth and division through multiple promoter-binding modes. Genes Dev 2019; 33:288-293. [PMID: 30804227 PMCID: PMC6411004 DOI: 10.1101/gad.322040.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
In this study, Albert et al. investigated the mechanisms by which the yeast Sfp1 protein coordinates both cell division and growth. They demonstrate that Sfp1 directly controls genes required for ribosome production and many other growth-promoting processes. The yeast Sfp1 protein regulates both cell division and growth but how it coordinates these processes is poorly understood. We demonstrate that Sfp1 directly controls genes required for ribosome production and many other growth-promoting processes. Remarkably, the complete set of Sfp1 target genes is revealed only by a combination of ChIP (chromatin immunoprecipitation) and ChEC (chromatin endogenous cleavage) methods, which uncover two promoter binding modes, one requiring a cofactor and the other a DNA-recognition motif. Glucose-regulated Sfp1 binding at cell cycle “START” genes suggests that Sfp1 controls cell size by coordinating expression of genes implicated in mass accumulation and cell division.
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Affiliation(s)
- Benjamin Albert
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Susanna Tomassetti
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Yvonne Gloor
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Daniel Dilg
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Lukas Hafner
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
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