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Gutiérrez-Santiago F, Martínez-Fernández V, Garrido-Godino AI, Colino-Palomino C, Clemente-Blanco A, Conesa C, Acker J, Navarro F. Maf1 phosphorylation is regulated through the action of prefoldin-like Bud27 on PP4 phosphatase in Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:7081-7095. [PMID: 38864693 PMCID: PMC11229332 DOI: 10.1093/nar/gkae414] [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: 12/20/2023] [Revised: 04/12/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Bud27 is a prefoldin-like protein that participates in transcriptional regulation mediated by the three RNA polymerases in Saccharomyces cerevisiae. Lack of Bud27 significantly affects RNA pol III transcription, although the involved mechanisms have not been characterized. Here, we show that Bud27 regulates the phosphorylation state of the RNA pol III transcriptional repressor, Maf1, influences its nuclear localization, and likely its activity. We demonstrate that Bud27 is associated with the Maf1 main phosphatase PP4 in vivo, and that this interaction is required for proper Maf1 dephosphorylation. Lack of Bud27 decreases the interaction among PP4 and Maf1, Maf1 dephosphorylation, and its nuclear entry. Our data uncover a new nuclear function of Bud27, identify PP4 as a novel Bud27 interactor and demonstrate the effect of this prefoldin-like protein on the posttranslational regulation of Maf1. Finally, our data reveal a broader effect of Bud27 on PP4 activity by influencing, at least, the phosphorylation of Rad53.
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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
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | - Ana Isabel Garrido-Godino
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | - Cristina Colino-Palomino
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
| | | | - Christine Conesa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Joël Acker
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética; Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO). Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071. Jaén, Spain
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2
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Chatterjee S, Ganguly A, Bhattacharyya D. Reprogramming nucleolar size by genetic perturbation of the extranuclear Rab GTPases Ypt6 and Ypt32. FEBS Lett 2024; 598:283-301. [PMID: 37994551 DOI: 10.1002/1873-3468.14776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/24/2023]
Abstract
Reprogramming organelle size has been proposed as a potential therapeutic approach. However, there have been few reports of nucleolar size reprogramming. We addressed this question in Saccharomyces cerevisiae by studying mutants having opposite effects on the nucleolar size. Mutations in genes involved in nuclear functions (KAR3, CIN8, and PRP45) led to enlarged nuclei/nucleoli, whereas mutations in secretory pathway family genes, namely the Rab-GTPases YPT6 and YPT32, reduced nucleolar size. When combined with mutations leading to enlarged nuclei/nucleoli, the YPT6 or YPT32 mutants can effectively reprogram the nuclear/nucleolar size almost back to normal. Our results further indicate that null mutation of YPT6 causes secretory stress that indirectly influences nuclear localization of Maf1, the negative regulator of RNA Polymerase III, which might reduce the nucleolar size by inhibiting nucleolar transcript enrichment.
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Affiliation(s)
- Shreosi Chatterjee
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, Maharashtra, India
| | - Abira Ganguly
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, Maharashtra, India
| | - Dibyendu Bhattacharyya
- Department of Cell and Tumor Biology, Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, Maharashtra, India
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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3
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Sun Q, Xu G, Li X, Li S, Jia Z, Yan M, Chen W, Shi Z, Li Z, Chen M. Functional Study of cAMP-Dependent Protein Kinase A in Penicillium oxalicum. J Fungi (Basel) 2023; 9:1203. [PMID: 38132803 PMCID: PMC10745023 DOI: 10.3390/jof9121203] [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: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Signaling pathways play a crucial role in regulating cellulase production. The pathway mediated by signaling proteins plays a crucial role in understanding how cellulase expression is regulated. In this study, using affinity purification of ClrB, we have identified sixteen proteins that potentially interact with ClrB. One of the proteins, the catalytic subunit of cAMP-dependent protein kinase A (PoPKA-C), is an important component of the cAMP/PKA signaling pathway. Knocking out PoPKA-C resulted in significant decreases in the growth, glucose utilization, and cellulose hydrolysis ability of the mutant strain. Furthermore, the cellulase activity and gene transcription levels were significantly reduced in the ΔPoPKA-C mutant, while the expression activity of CreA, a transcriptional regulator of carbon metabolism repression, was notably increased. Additionally, deletion of PoPKA-C also led to earlier timing of conidia production. The expression levels of key transcription factor genes stuA and brlA, which are involved in the production of the conidia, showed significant enhancement in the ΔPoPKA-C mutant. These findings highlight the involvement of PoPKA-C in mycelial development, conidiation, and the regulation of cellulase expression. The functional analysis of PoPKA-C provides insights into the mechanism of the cAMP/PKA signaling pathway in cellulase expression in filamentous fungi and has significant implications for the development of high-yielding cellulase strains.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; (Q.S.); (G.X.); (X.L.); (S.L.); (Z.J.); (M.Y.); (W.C.); (Z.S.)
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; (Q.S.); (G.X.); (X.L.); (S.L.); (Z.J.); (M.Y.); (W.C.); (Z.S.)
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4
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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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5
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MoMaf1 Mediates Vegetative Growth, Conidiogenesis, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae. J Fungi (Basel) 2023; 9:jof9010106. [PMID: 36675927 PMCID: PMC9861366 DOI: 10.3390/jof9010106] [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: 12/07/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
In eukaryotes, Maf1 is an essential and specific negative regulator of RNA polymerase (Pol) III. Pol III, which synthesizes 5S RNA and transfer RNAs (tRNAs), is suppressed by Maf1 under the conditions of nutrient starvation or environmental stress. Here, we identified M. oryzae MoMaf1, a homolog of ScMaf1 in budding yeast. A heterogeneous complementation assay revealed that MoMaf1 restored growth defects in the ΔScmaf1 mutant under SDS stress. Destruction of MoMAF1 elevated 5S rRNA content and increased sensitivity to cell wall agents. Moreover, the ΔMomaf1 mutant exhibited reduced vegetative growth, conidiogenesis, and pathogenicity. Interestingly, we found that MoMaf1 underwent nuclear-cytoplasmic shuffling, through which MoMaf1 accumulated in nuclei under nutrient deficiency or upon the interaction of M. oryzae with rice. Therefore, this study can help to elucidate the pathogenic molecular mechanism of M. oryzae.
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6
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Wang Q, Daiß JL, Xu Y, Engel C. Snapshots of RNA polymerase III in action - A mini review. Gene 2022; 821:146282. [PMID: 35149153 DOI: 10.1016/j.gene.2022.146282] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/20/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022]
Abstract
RNA polymerase (Pol) III is responsible for the transcription of tRNAs, 5S rRNA, U6 snRNA, and other non-coding RNAs. Transcription factors such as TFIIIA, -B, -C, SNAPc, and Maf1 are required for promoter recognition, promoter opening, and Pol III activity regulation. Recent developments in cryo-electron microscopy and advanced purification approaches for endogenous multi-subunit complexes accelerated structural studies resulting in detailed structural insights which allowed an in-depth understanding of the molecular mechanisms underlying Pol III transcription. Here, we summarize structural data on Pol III and its regulating factors providing a three-dimensional framework to guide further analysis of RNA polymerase III.
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Affiliation(s)
- Qianmin Wang
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; Present address: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Youwei Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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7
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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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8
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Enserink JM, Chymkowitch P. Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries. Int J Mol Sci 2022; 23:ijms23031293. [PMID: 35163213 PMCID: PMC8835803 DOI: 10.3390/ijms23031293] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle.
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Affiliation(s)
- Jorrit M. Enserink
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
| | - Pierre Chymkowitch
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
- Correspondence: (J.M.E.); (P.C.)
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9
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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10
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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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11
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Kritsiligkou P, Nowicki-Osuch K, Carter Z, Kershaw CJ, Creamer DR, Weids AJ, Grant CM. Tolerance to nascent protein misfolding stress requires fine-tuning of the cAMP/PKA pathway. J Biol Chem 2021; 296:100690. [PMID: 33894203 PMCID: PMC8164027 DOI: 10.1016/j.jbc.2021.100690] [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: 11/12/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/08/2023] Open
Abstract
Protein aggregation is the abnormal association of misfolded proteins into larger, often insoluble structures that can be toxic during aging and in protein aggregation-associated diseases. Previous research has established a role for the cytosolic Tsa1 peroxiredoxin in responding to protein misfolding stress. Tsa1 is also known to downregulate the cAMP/protein kinase A (PKA) pathway as part of the response to hydrogen peroxide stress. However, whether the cAMP/PKA pathway is involved in protein misfolding stress is not known. Using transcriptomics, we examined the response to protein misfolding stress and found upregulation of numerous stress gene functions and downregulation of many genes related to protein synthesis and other growth-related processes consistent with the well-characterized environmental stress response. The scope of the transcriptional response is largely similar in wild-type and tsa1 mutant strains, but the magnitude is dampened in the strain lacking Tsa1. We identified a direct protein interaction between Tsa1 and the Bcy1 regulatory subunit of PKA that is present under normal growth conditions and explains the observed differences in gene expression profiles. This interaction is increased in a redox-dependent manner in response to nascent protein misfolding, via Tsa1-mediated oxidation of Bcy1. Oxidation of Bcy1 causes a reduction in cAMP binding by Bcy1, which dampens PKA pathway activity, leading to a targeted reprogramming of gene expression. Redox regulation of the regulatory subunit of PKA provides a mechanism to mitigate the toxic consequences of protein misfolding stress that is distinct to stress caused by exogenous sources of reactive oxygen species.
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Affiliation(s)
| | - Karol Nowicki-Osuch
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Zorana Carter
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Chris J Kershaw
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Declan R Creamer
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Alan J Weids
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
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12
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Molecular Characterization of Paralichthys olivaceus MAF1 and Its Potential Role as an Anti-Viral Hemorrhagic Septicaemia Virus Factor in Hirame Natural Embryo Cells. Int J Mol Sci 2021; 22:ijms22031353. [PMID: 33572970 PMCID: PMC7866426 DOI: 10.3390/ijms22031353] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
MAF1 is a global suppressor of RNA polymerase III-dependent transcription, and is conserved from yeast to human. Growing evidence supports the involvement of MAF1 in the immune response of mammals, but its biological functions in fish are unknown. We isolated and characterized Maf1 from the olive flounder Paralichthys olivaceus (PoMaf1). The coding region of PoMaf1 comprised 738 bp encoding a 245-amino-acid protein. The deduced PoMAF1 amino acid sequence shared features with those of MAF1 orthologues from vertebrates. PoMaf1 mRNA was detected in all tissues examined, and the levels were highest in eye and muscle tissue. The PoMaf1 mRNA level increased during early development. In addition, the PoMaf1 transcript level decreased during viral hemorrhagic septicemia virus (VHSV) infection of flounder hirame natural embryo (HINAE) cells. To investigate the role of PoMaf1 in VHSV infection, single-cell-derived PoMaf1 knockout HINAE cells were generated using the clustered regularly interspaced short palindromic repeats/CRISPR-associated-9 (CRISPR/Cas9) system, and cell clones with complete disruption of PoMaf1 were selected. PoMaf1 disruption increased the VHSV glycoprotein (G) mRNA levels during VHSV infection of HINAE cells, implicating PoMAF1 in the immune response to VSHV infection. To our knowledge, this is the first study to characterize fish Maf1, which may play a role in the response to viral infection.
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13
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Oliveira Andrade M, Sforça ML, Batista FAH, Figueira ACM, Benedetti CE. The MAF1 Phosphoregulatory Region Controls MAF1 Interaction with the RNA Polymerase III C34 Subunit and Transcriptional Repression in Plants. THE PLANT CELL 2020; 32:3019-3035. [PMID: 32641350 PMCID: PMC7474290 DOI: 10.1105/tpc.20.00297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/18/2020] [Accepted: 07/06/2020] [Indexed: 05/13/2023]
Abstract
MAF1 is a phosphoprotein that plays a critical role in cell growth control as the central regulator of RNA polymerase (Pol) III activity. Citrus MAF1 (CsMAF1) was identified as a direct target of PthA4, a bacterial effector protein required to induce tumors in citrus. CsMAF1 binds to Pol III to restrict transcription; however, exactly how CsMAF1 interacts with the polymerase and how phosphorylation modulates this interaction is unknown. Moreover, how CsMAF1 binds PthA4 is also obscure. Here we show that CsMAF1 binds predominantly to the WH1 domain of the citrus Pol III subunit C34 (CsC34) and that its phosphoregulatory region, comprising loop-3 and α-helix-2, contributes to this interaction. We also show that phosphorylation of this region decreases CsMAF1 affinity to CsC34, leading to Pol III derepression, and that Ser 45, found only in plant MAF1 proteins, is critical for CsC34 interaction and is phosphorylated by a new citrus AGC1 kinase. Additionally, we show that the C-terminal region of the citrus TFIIIB component BRF1 competes with CsMAF1 for CsC34 interaction, whereas the C-terminal region of CsMAF1 is essential for PthA4 binding. Based on CsMAF1 structural data, we propose a mechanism for how CsMAF1 represses Pol III transcription and how phosphorylation controls this process.
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Affiliation(s)
- Maxuel Oliveira Andrade
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-100 Campinas, São Paulo, Brazil
| | - Mauricio Luis Sforça
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-100 Campinas, São Paulo, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-100 Campinas, São Paulo, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-100 Campinas, São Paulo, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, 13083-100 Campinas, São Paulo, Brazil
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14
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Otsubo Y, Kamada Y, Yamashita A. Novel Links between TORC1 and Traditional Non-Coding RNA, tRNA. Genes (Basel) 2020; 11:E956. [PMID: 32825021 PMCID: PMC7563549 DOI: 10.3390/genes11090956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Target of rapamycin (TOR) is a serine/threonine kinase that modulates cell growth and metabolism in response to environmental changes. Transfer RNA (tRNA) is an abundant and ubiquitous small non-coding RNA that is essential in the translation of mRNAs. Beyond its canonical role, it has been revealed that tRNAs have more diverse functions. TOR complex 1 (TORC1), which is one of the two TOR complexes, regulates tRNA synthesis by controlling RNA polymerase III. In addition to tRNA synthesis regulation, recent studies have revealed hidden connections between TORC1 and tRNA, which are both essential players in eukaryotic cellular activities. Here, we review the accumulating findings on the regulatory links between TORC1 and tRNA-particularly those links in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.
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Affiliation(s)
- Yoko Otsubo
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoshiaki Kamada
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Yamashita
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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15
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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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16
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Trotta E. RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. J Biol Chem 2019; 294:12349-12358. [PMID: 31235518 PMCID: PMC6699833 DOI: 10.1074/jbc.ra119.008529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/19/2019] [Indexed: 07/24/2023] Open
Abstract
In yeast (Saccharomyces cerevisiae), the synthesis of tRNAs by RNA polymerase III (RNAP III) down-regulates the transcription of the nearby RNAP II-transcribed genes by a mechanism that is poorly understood. To clarify the basis of this tRNA gene-mediated (TGM) silencing, here, conducting a bioinformatics analysis of available ChIP-chip and ChIP-sequencing genomic data from yeast, we investigated whether the RNAP III transcriptional machinery can recruit protein factors required for RNAP II transcription. An analysis of 46 genome-wide protein-density profiles revealed that 12 factors normally implicated in RNAP II-mediated gene transcription are more enriched at tRNA than at mRNA loci. These 12 factors typically have RNA-binding properties, participate in the termination stage of the RNAP II transcription, and preferentially localize to the tRNA loci by a mechanism that apparently is based on the RNAP III transcription level. The factors included two kinases of RNAP II (Bur1 and Ctk1), a histone demethylase (Jhd2), and a mutated form of a nucleosome-remodeling factor (Spt6) that have never been reported to be recruited to tRNA loci. Moreover, we show that the expression levels of RNAP II-transcribed genes downstream of tRNA loci correlate with the distance from the tRNA gene by a mechanism that depends on their orientation. These results are consistent with the notion that pre-tRNAs recruit RNAP II-associated factors, thereby reducing the availability of these factors for RNAP II transcription and contributing, at least in part, to the TGM-silencing mechanism.
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Affiliation(s)
- Edoardo Trotta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche (CNR), Roma 00133, Italy.
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17
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Ciesla M, Skowronek E, Boguta M. Function of TFIIIC, RNA polymerase III initiation factor, in activation and repression of tRNA gene transcription. Nucleic Acids Res 2019; 46:9444-9455. [PMID: 30053100 PMCID: PMC6182151 DOI: 10.1093/nar/gky656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 01/09/2023] Open
Abstract
Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC directly competes with Pol III for chromatin occupancy as demonstrated by inversely correlated tDNA binding. The association of TFIIIC with tDNA was stronger under unfavorable respiratory conditions and in the presence of Maf1. Induction of tDNA transcription by glucose-activated protein kinase A (PKA) was correlated with the down-regulation of TFIIIC occupancy on tDNA. The conditions that activate the PKA signaling pathway promoted the binding of TFIIIB subunits, Brf1 and Bdp1, with tDNA, but decreased their interaction with TFIIIC. Association of Brf1 and Bdp1 with TFIIIC was much stronger under repressive conditions, potentially restricting TFIIIB recruitment to tDNA and preventing Pol III recruitment. Altogether, we propose a model in which, depending on growth conditions, TFIIIC promotes activation or repression of tDNA transcription.
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Affiliation(s)
- Malgorzata Ciesla
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Ewa Skowronek
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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18
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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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19
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Herrera MC, Chymkowitch P, Robertson JM, Eriksson J, Bøe SO, Alseth I, Enserink JM. Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity. Nucleic Acids Res 2019; 46:11698-11711. [PMID: 30247619 PMCID: PMC6294503 DOI: 10.1093/nar/gky846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023] Open
Abstract
tRNA genes are transcribed by RNA polymerase III (RNAPIII). During recent years it has become clear that RNAPIII activity is strictly regulated by the cell in response to environmental cues and the homeostatic status of the cell. However, the molecular mechanisms that control RNAPIII activity to regulate the amplitude of tDNA transcription in normally cycling cells are not well understood. Here, we show that tRNA levels fluctuate during the cell cycle and reveal an underlying molecular mechanism. The cyclin Clb5 recruits the cyclin dependent kinase Cdk1 to tRNA genes to boost tDNA transcription during late S phase. At tDNA genes, Cdk1 promotes the recruitment of TFIIIC, stimulates the interaction between TFIIIB and TFIIIC, and increases the dynamics of RNA polymerase III in vivo. Furthermore, we identified Bdp1 as a putative Cdk1 substrate in this process. Preventing Bdp1 phosphorylation prevented cell cycle-dependent recruitment of TFIIIC and abolished the cell cycle-dependent increase in tDNA transcription. Our findings demonstrate that under optimal growth conditions Cdk1 gates tRNA synthesis in S phase by regulating the RNAPIII machinery, revealing a direct link between the cell cycle and RNAPIII activity.
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Affiliation(s)
- Maria C Herrera
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
| | - Joseph M Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Eriksson
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Stig Ove Bøe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
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20
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Davis RB, Likhite N, Jackson CA, Liu T, Yu MC. Robust repression of tRNA gene transcription during stress requires protein arginine methylation. Life Sci Alliance 2019; 2:2/3/e201800261. [PMID: 31160378 PMCID: PMC6549136 DOI: 10.26508/lsa.201800261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Protein arginine methylation is an important means by which protein function can be regulated. In the budding yeast, this modification is catalyzed by the major protein arginine methyltransferase Hmt1. Here, we provide evidence that the Hmt1-mediated methylation of Rpc31, a subunit of RNA polymerase III, plays context-dependent roles in tRNA gene transcription: under conditions optimal for growth, it positively regulates tRNA gene transcription, and in the setting of stress, it promotes robust transcriptional repression. In the context of stress, methylation of Rpc31 allows for its optimal interaction with RNA polymerase III global repressor Maf1. Interestingly, mammalian Hmt1 homologue is able to methylate one of Rpc31's human homologue, RPC32β, but not its paralogue, RPC32α. Our data led us to propose an efficient model whereby protein arginine methylation facilitates metabolic economy and coordinates protein-synthetic capacity.
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Affiliation(s)
- Richoo B Davis
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Neah Likhite
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Christopher A Jackson
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Michael C Yu
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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21
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Comprehensive Analysis of Aspergillus nidulans PKA Phosphorylome Identifies a Novel Mode of CreA Regulation. mBio 2019; 10:mBio.02825-18. [PMID: 31040248 PMCID: PMC6495382 DOI: 10.1128/mbio.02825-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cyclic AMP (cAMP)-dependent protein kinase A (PKA) signaling pathway is well conserved across eukaryotes, and previous work has shown that it plays an important role in regulating development, growth, and virulence in a number of fungi. PKA is activated in response to extracellular nutrients and acts to regulate metabolism and growth. While a number of components in the PKA pathway have been defined in filamentous fungi, current understanding does not provide a global perspective on PKA function. Thus, this work is significant in that it comprehensively identifies proteins and functional pathways regulated by PKA in a model filamentous fungus. This information enhances our understanding of PKA action and may provide information on how to manipulate it for specific purposes. In filamentous fungi, an important kinase responsible for adaptation to changes in available nutrients is cyclic AMP (cAMP)-dependent protein kinase (protein kinase A [PKA]). This kinase has been well characterized at a molecular level, but its systemic action and direct/indirect targets are generally not well understood in filamentous fungi. In this work, we used a pkaA deletion strain (ΔpkaA) to identify Aspergillus nidulans proteins for which phosphorylation is dependent (either directly or indirectly) on PKA. A combination of phosphoproteomic and transcriptomic analyses revealed both direct and indirect targets of PKA and provided a global perspective on its function. One of these targets was the transcription factor CreA, the main repressor responsible for carbon catabolite repression (CCR). In the ΔpkaA strain, we identified a previously unreported phosphosite in CreA, S319, which (based on motif analysis) appears to be a direct target of Stk22 kinase (AN5728). Upon replacement of CreA S319 with an alanine (i.e., phosphonull mutant), the dynamics of CreA import to the nucleus are affected. Collectively, this work provides a global overview of PKA function while also providing novel insight regarding significance of a specific PKA-mediated phosphorylation event.
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22
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Szatkowska R, Garcia-Albornoz M, Roszkowska K, Holman SW, Furmanek E, Hubbard SJ, Beynon RJ, Adamczyk M. Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1. Biochem J 2019; 476:1053-1082. [PMID: 30885983 PMCID: PMC6448137 DOI: 10.1042/bcj20180701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023]
Abstract
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, Maf1 elicit broad changes in the abundance profiles of enzymes engaged in fundamental metabolism in S. cerevisiae In a mutant compromised in RNAP III activity, there is a repartitioning towards amino acids synthesis de novo at the expense of glycolytic throughput. Conversely, cells lacking Maf1 protein have greater potential for glycolytic flux.
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Affiliation(s)
- Roza Szatkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Manuel Garcia-Albornoz
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Katarzyna Roszkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Emil Furmanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Simon J Hubbard
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Malgorzata Adamczyk
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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23
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Ahn CS, Lee DH, Pai HS. Characterization of Maf1 in Arabidopsis: function under stress conditions and regulation by the TOR signaling pathway. PLANTA 2019; 249:527-542. [PMID: 30293201 DOI: 10.1007/s00425-018-3024-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Maf1 repressor activity is critical for plant survival during environmental stresses, and is regulated by its phosphorylation/dephosphorylation through the activity of TOR and PP4/PP2A phosphatases. Maf1 is a global repressor of RNA polymerase III (Pol III), and is conserved in eukaryotes. Pol III synthesizes small RNAs, 5S rRNA, and tRNAs that are essential for protein translation and cell growth. Maf1 is a phosphoprotein and dephosphorylation of Maf1 promotes its repressor activity in yeast and mammals. Plant Maf1 was identified in citrus plants as a canker elicitor-binding protein, and citrus Maf1 represses cell growth associated with canker development. However, functions of plant Maf1 under diverse stress conditions and its regulation by the target of rapamycin (TOR) signaling components are poorly understood. In this study, the Arabidopsis maf1 mutants were more susceptible to diverse stresses and treatment with the TOR inhibitor Torin-1 than wild-type plants. The maf1 mutants expressed higher levels of Maf1 target RNAs, including 5S rRNA and pre-tRNAs in leaf cells, supporting Pol III repressor activity of Arabidopsis Maf1. Cellular stresses and Torin-1 treatment induced dephosphorylation of Maf1, suggesting Maf1 activation under diverse stress conditions. TOR silencing also stimulated Maf1 dephosphorylation, while silencing of catalytic subunit genes of PP4 and PP2A repressed it. Thus, TOR kinase and PP4/PP2A phosphatases appeared to oppositely modulate the Maf1 phosphorylation status. TOR silencing decreased the abundance of the target RNAs, while silencing of the PP4 and PP2A subunit genes increased it, supporting the positive correlation between Maf1 dephosphorylation and its repressor activity. Taken together, these results suggest that repressor activity of Maf1, regulated by the TOR signaling pathway, is critical for plant cell survival during environmental stresses.
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Affiliation(s)
- Chang Sook Ahn
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Future Technology Research Center, Corporate R&D, LG Chem/LG Science Park, Seoul, 07796, Korea
| | - Du-Hwa Lee
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea.
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24
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Wang Z, Wu C, Aslanian A, Yates JR, Hunter T. Defective RNA polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 pathway. eLife 2018; 7:35447. [PMID: 30192228 PMCID: PMC6128692 DOI: 10.7554/elife.35447] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/21/2018] [Indexed: 12/26/2022] Open
Abstract
Transcription by RNA polymerase III (Pol III) is an essential cellular process, and mutations in Pol III can cause neurodegenerative disease in humans. However, in contrast to Pol II transcription, which has been extensively studied, the knowledge of how Pol III is regulated is very limited. We report here that in budding yeast, Saccharomyces cerevisiae, Pol III is negatively regulated by the Small Ubiquitin-like MOdifier (SUMO), an essential post-translational modification pathway. Besides sumoylation, Pol III is also targeted by ubiquitylation and the Cdc48/p97 segregase; these three processes likely act in a sequential manner and eventually lead to proteasomal degradation of Pol III subunits, thereby repressing Pol III transcription. This study not only uncovered a regulatory mechanism for Pol III, but also suggests that the SUMO and ubiquitin modification pathways and the Cdc48/p97 segregase can be potential therapeutic targets for Pol III-related human diseases.
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Affiliation(s)
- Zheng Wang
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Catherine Wu
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Aaron Aslanian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,The Scripps Research Institute, La Jolla, United States
| | - John R Yates
- The Scripps Research Institute, La Jolla, United States
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
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25
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Asghar F, Yan H, Jiang L. The putative transcription factor CaMaf1 controls the sensitivity to lithium and rapamycin and represses RNA polymerase III transcription in Candida albicans. FEMS Yeast Res 2018; 18:5047891. [PMID: 29982370 DOI: 10.1093/femsyr/foy068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/23/2018] [Indexed: 12/19/2022] Open
Abstract
Maf1 is a repressor of RNA polymerase (Pol) III transcription for tRNA. Nutrient deprivation and environmental stress repress Pol III transcription through Maf1 in Saccharomyces cerevisiae. The sole Candida albicans homolog CaMaf1 is a protein of 380 amino acids with conserved domains and motifs of the eukaryotic Maf1 family. Here, we show that C. albicans cells lacking CaMAF1 show elevated levels of tRNA. Deletion of CaMAF1 increases the sensitivity of C. albicans cells to lithium cation and SDS as well as tolerance to rapamycin and azole. In addition, deletion of CaMAF1 reduces the level of filamentation and alters the surface morphology of colonies. CaMaf1 is localized in the nucleus of log-phase growing cells. However, a dynamic change of subcellular localization of CaMaf1 exists during serum-induced morphological transition, with CaMaf1 being localized in the nuclei of cells with germ tubes and short filaments but outside of the nuclei of cells with long filaments. In addition, CaMaf1 is required for rapamycin-induced repression of CaERG20, encoding the farnesyl pyrophosphate synthetase involved in ergosterol biosynthesis. Therefore, CaMaf1 plays a role as a general repressor of Pol III transcription in C. albicans.
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Affiliation(s)
- Faiza Asghar
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 XiCunXi Road, Zibo 255000, China
| | - Hongbo Yan
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 XiCunXi Road, Zibo 255000, China
| | - Linghuo Jiang
- Laboratory for Yeast Molecular and Cell Biology, the Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 XiCunXi Road, Zibo 255000, China
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MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
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Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
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27
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Graczyk D, Cieśla M, Boguta M. Regulation of tRNA synthesis by the general transcription factors of RNA polymerase III - TFIIIB and TFIIIC, and by the MAF1 protein. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:320-329. [DOI: 10.1016/j.bbagrm.2018.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/20/2018] [Accepted: 01/21/2018] [Indexed: 01/03/2023]
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Sriskanthadevan-Pirahas S, Deshpande R, Lee B, Grewal SS. Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila. PLoS Genet 2018; 14:e1007202. [PMID: 29401457 PMCID: PMC5814106 DOI: 10.1371/journal.pgen.1007202] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 02/15/2018] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
The small G-protein Ras is a conserved regulator of cell and tissue growth. These effects of Ras are mediated largely through activation of a canonical RAF-MEK-ERK kinase cascade. An important challenge is to identify how this Ras/ERK pathway alters cellular metabolism to drive growth. Here we report on stimulation of RNA polymerase III (Pol III)-mediated tRNA synthesis as a growth effector of Ras/ERK signalling in Drosophila. We find that activation of Ras/ERK signalling promotes tRNA synthesis both in vivo and in cultured Drosophila S2 cells. We also show that Pol III function is required for Ras/ERK signalling to drive proliferation in both epithelial and stem cells in Drosophila tissues. We find that the transcription factor Myc is required but not sufficient for Ras-mediated stimulation of tRNA synthesis. Instead we show that Ras signalling promotes Pol III function and tRNA synthesis by phosphorylating, and inhibiting the nuclear localization and function of the Pol III repressor Maf1. We propose that inhibition of Maf1 and stimulation of tRNA synthesis is one way by which Ras signalling enhances protein synthesis to promote cell and tissue growth.
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Affiliation(s)
- Shrivani Sriskanthadevan-Pirahas
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, and Department of Biochemistry and Molecular Biology Calgary, University of Calgary, Calgary, Alberta, Canada
| | - Rujuta Deshpande
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, and Department of Biochemistry and Molecular Biology Calgary, University of Calgary, Calgary, Alberta, Canada
| | - Byoungchun Lee
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, and Department of Biochemistry and Molecular Biology Calgary, University of Calgary, Calgary, Alberta, Canada
| | - Savraj S. Grewal
- Clark H Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Alberta Children’s Hospital Research Institute, and Department of Biochemistry and Molecular Biology Calgary, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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29
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Zhang S, Li X, Wang HY, Steven Zheng XF. Beyond regulation of pol III: Role of MAF1 in growth, metabolism, aging and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:338-343. [PMID: 29407795 DOI: 10.1016/j.bbagrm.2018.01.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 11/24/2022]
Abstract
MAF1 was discovered as a master repressor of Pol III-dependent transcription in response to diverse extracellular signals, including growth factor, nutrient and stress. It is regulated through posttranslational mechanisms such as phosphorylation. A prominent upstream regulator of MAF1 is the mechanistic target of rapamycin (mTOR) pathway. mTOR kinase directly phosphorylates MAF1, controlling its localization and transcriptional activity. In mammals, MAF1 has also been shown to regulate Pol I- and Pol II-dependent transcription. Interestingly, MAF1 modulates Pol II activity both as a repressor and activator, depending on specific target genes, to impact on cellular growth and metabolism. While MAF1 represses genes such as TATA-binding protein (TBP) and fatty acid synthase (FASN), it activates the expression of PTEN, a major tumor suppressor and an inhibitor of the mTOR signaling. Increasing evidence indicates that MAF1 plays an important role in different aspects of normal physiology, lifespan and oncogenesis. Here we will review the current knowledge on MAF1 in growth, metabolism, aging and cancer. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Shanshan Zhang
- State Key Laboratory of Oncology in South China, and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaoxing Li
- State Key Laboratory of Oncology in South China, and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Hui-Yun Wang
- State Key Laboratory of Oncology in South China, and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Rutgers Cancer Institute of New Jersey and Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - X F Steven Zheng
- State Key Laboratory of Oncology in South China, and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Rutgers Cancer Institute of New Jersey and Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.
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30
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Willis IM, Moir RD. Signaling to and from the RNA Polymerase III Transcription and Processing Machinery. Annu Rev Biochem 2018; 87:75-100. [PMID: 29328783 DOI: 10.1146/annurev-biochem-062917-012624] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities. In this review, we consider how nutrients and stress control Pol III transcription via its factors and its negative regulator, Maf1. We highlight recent work showing that the composition of the tRNA population and the function of individual tRNAs is dynamically controlled and that unrestrained Pol III transcription can reprogram central metabolic pathways.
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Affiliation(s)
- Ian M Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , .,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Robyn D Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; ,
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31
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Willis IM. Maf1 phenotypes and cell physiology. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:330-337. [PMID: 29248739 DOI: 10.1016/j.bbagrm.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/27/2017] [Indexed: 01/16/2023]
Abstract
As a master regulator of transcription by RNA polymerase (Pol) III, Maf1 represses the synthesis of highly abundant non-coding RNAs as anabolic signals dissipate, as the quality or quantity of nutrients decreases, and under a wide range of cellular and environmental stress conditions. Thus, Maf1 responds to changes in cell physiology to conserve metabolic energy and to help maintain appropriate levels of tRNAs and other essential non-coding RNAs. Studies in different model organisms and cell-based systems show that perturbations of Maf1 can also impact cell physiology and metabolism. These effects are mediated by changes in Pol III transcription and/or by effects of Maf1 on the expression of select Pol II-transcribed genes. Maf1 phenotypes can vary between different systems and are sometimes conflicting as in comparisons between Maf1 KO mice and cultured mammalian cells. These studies are reviewed in an effort to better appreciate the relationship between Maf1 function and cell physiology. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Ian M Willis
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
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32
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Chymkowitch P, Enserink JM. Regulation of tRNA synthesis by posttranslational modifications of RNA polymerase III subunits. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:310-319. [PMID: 29127063 DOI: 10.1016/j.bbagrm.2017.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/18/2022]
Abstract
RNA polymerase III (RNAPIII) transcribes tRNA genes, 5S RNA as well as a number of other non-coding RNAs. Because transcription by RNAPIII is an energy-demanding process, its activity is tightly linked to the stress levels and nutrient status of the cell. Multiple signaling pathways control RNAPIII activity in response to environmental cues, but exactly how these pathways regulate RNAPIII is still poorly understood. One major target of these pathways is the transcriptional repressor Maf1, which inhibits RNAPIII activity under conditions that are detrimental to cell growth. However, recent studies have found that the cell can also directly regulate the RNAPIII machinery through phosphorylation and sumoylation of RNAPIII subunits. In this review we summarize post-translational modifications of RNAPIII subunits that mainly have been identified in large-scale proteomics studies, and we highlight several examples to discuss their relevance for regulation of RNAPIII.
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Affiliation(s)
- Pierre Chymkowitch
- Department of Microbiology, Oslo University Hospital, NO-0027 Oslo, Norway.
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway.
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33
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Anda S, Zach R, Grallert B. Activation of Gcn2 in response to different stresses. PLoS One 2017; 12:e0182143. [PMID: 28771613 PMCID: PMC5542535 DOI: 10.1371/journal.pone.0182143] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
All organisms have evolved pathways to respond to different forms of cellular stress. The Gcn2 kinase is best known as a regulator of translation initiation in response to starvation for amino acids. Work in budding yeast has showed that the molecular mechanism of GCN2 activation involves the binding of uncharged tRNAs, which results in a conformational change and GCN2 activation. This pathway requires GCN1, which ensures delivery of the uncharged tRNA onto GCN2. However, Gcn2 is activated by a number of other stresses which do not obviously involve accumulation of uncharged tRNAs, raising the question how Gcn2 is activated under these conditions. Here we investigate the requirement for ongoing translation and tRNA binding for Gcn2 activation after different stresses in fission yeast. We find that mutating the tRNA-binding site on Gcn2 or deleting Gcn1 abolishes Gcn2 activation under all the investigated conditions. These results suggest that tRNA binding to Gcn2 is required for Gcn2 activation not only in response to starvation but also after UV irradiation and oxidative stress.
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Affiliation(s)
- Silje Anda
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Róbert Zach
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- * E-mail:
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34
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Soprano AS, Giuseppe POD, Shimo HM, Lima TB, Batista FAH, Righetto GL, Pereira JGDC, Granato DC, Nascimento AFZ, Gozzo FC, de Oliveira PSL, Figueira ACM, Smetana JHC, Paes Leme AF, Murakami MT, Benedetti CE. Crystal Structure and Regulation of the Citrus Pol III Repressor MAF1 by Auxin and Phosphorylation. Structure 2017; 25:1360-1370.e4. [PMID: 28781084 DOI: 10.1016/j.str.2017.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/16/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022]
Abstract
MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrus.
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Affiliation(s)
- Adriana Santos Soprano
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Hugo Massayoshi Shimo
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Tatiani Brenelli Lima
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil; Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Germanna Lima Righetto
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - José Geraldo de Carvalho Pereira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Daniela Campos Granato
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Andrey Fabricio Ziem Nascimento
- XALOC Beamline, Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain; Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Carrer Baldiri Reixac 15, 3 A17, 08028 Barcelona, Spain
| | - Fabio Cesar Gozzo
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Paulo Sérgio Lopes de Oliveira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Juliana Helena Costa Smetana
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Nacional Biosciences Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas, São Paulo, Brazil.
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35
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Transcription by RNA polymerase III: insights into mechanism and regulation. Biochem Soc Trans 2017; 44:1367-1375. [PMID: 27911719 PMCID: PMC5095917 DOI: 10.1042/bst20160062] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/07/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022]
Abstract
The highly abundant, small stable RNAs that are synthesized by RNA polymerase III (RNAPIII) have key functional roles, particularly in the protein synthesis apparatus. Their expression is metabolically demanding, and is therefore coupled to changing demands for protein synthesis during cell growth and division. Here, we review the regulatory mechanisms that control the levels of RNAPIII transcripts and discuss their potential physiological relevance. Recent analyses have revealed differential regulation of tRNA expression at all steps on its biogenesis, with significant deregulation of mature tRNAs in cancer cells.
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36
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TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity. Proc Natl Acad Sci U S A 2017; 114:1039-1044. [PMID: 28096404 DOI: 10.1073/pnas.1615093114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Maintaining cellular homeostasis under changing nutrient conditions is essential for the growth and development of all organisms. The mechanisms that maintain homeostasis upon loss of nutrient supply are not well understood. By mapping the SUMO proteome in Saccharomyces cerevisiae, we discovered a specific set of differentially sumoylated proteins mainly involved in transcription. RNA polymerase III (RNAPIII) components, including Rpc53, Rpc82, and Ret1, are particularly prominent nutrient-dependent SUMO targets. Nitrogen starvation, as well as direct inhibition of the master nutrient response regulator target of rapamycin complex 1 (TORC1), results in rapid desumoylation of these proteins, which is reflected by loss of SUMO at tRNA genes. TORC1-dependent sumoylation of Rpc82 in particular is required for robust tRNA transcription. Mechanistically, sumoylation of Rpc82 is important for assembly of the RNAPIII holoenzyme and recruitment of Rpc82 to tRNA genes. In conclusion, our data show that TORC1-dependent sumoylation of Rpc82 bolsters the transcriptional capacity of RNAPIII under optimal growth conditions.
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37
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Pradhan A, Hammerquist AM, Khanna A, Curran SP. The C-Box Region of MAF1 Regulates Transcriptional Activity and Protein Stability. J Mol Biol 2016; 429:192-207. [PMID: 27986570 DOI: 10.1016/j.jmb.2016.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 11/15/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022]
Abstract
MAF1 is a conserved negative regulator of RNA polymerase (pol) III and intracellular lipid homeostasis across species. Here, we show that the MAF1 C-box region negatively regulates its activity. Mutations in Caenorhabditis elegans mafr-1 that truncate the C-box retain the ability to inhibit the transcription of RNA pol III targets, reduce lipid biogenesis, and lower reproductive output. In human cells, C-box deletion of MAF1 leads to increased MAF1 nuclear localization and enhanced repression of ACC1 and FASN, but with impaired repression of RNA pol III targets. Surprisingly, C-box mutations render MAF1 insensitive to rapamycin, further defining a regulatory role for this region. Two MAF1 species, MAF1L and MAF1S, are regulated by the C-box YSY motif, which, when mutated, alters species stoichiometry and proteasome-dependent turnover of nuclear MAF1. Our results reveal a role for the C-box region as a critical determinant of MAF1 stability, activity, and response to cellular stress.
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Affiliation(s)
- Ajay Pradhan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy M Hammerquist
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Akshat Khanna
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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38
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Romero-Meza G, Vélez-Ramírez DE, Florencio-Martínez LE, Román-Carraro FC, Manning-Cela R, Hernández-Rivas R, Martínez-Calvillo S. Maf1 is a negative regulator of transcription in Trypanosoma brucei. Mol Microbiol 2016; 103:452-468. [PMID: 27802583 DOI: 10.1111/mmi.13568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
RNA polymerase III (Pol III) produces small RNA molecules that play essential roles in mRNA processing and translation. Maf1, originally described as a negative regulator of Pol III transcription, has been studied from yeast to human. Here we characterized Maf1 in the parasitic protozoa Trypanosoma brucei (TbMaf1), representing the first report to analyse Maf1 in an early-diverged eukaryote. While Maf1 is generally encoded by a single-copy gene, the T. brucei genome contains two almost identical TbMaf1 genes. The TbMaf1 protein has the three conserved sequences and is predicted to fold into a globular structure. Unlike in yeast, TbMaf1 localizes to the nucleus in procyclic forms of T. brucei under normal growth conditions. Cell lines that either downregulate or overexpress TbMaf1 were generated, and growth curve analysis with them suggested that TbMaf1 participates in the regulation of cell growth of T. brucei. Nuclear run-on and chromatin immunoprecipitation analyses demonstrated that TbMaf1 represses Pol III transcription of tRNA and U2 snRNA genes by associating with their promoters. Interestingly, 5S rRNA levels do not change after TbMaf1 ablation or overexpression. Notably, our data also revealed that TbMaf1 regulates Pol I transcription of procyclin gene and Pol II transcription of SL RNA genes.
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Affiliation(s)
- Gabriela Romero-Meza
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México.,Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Daniel E Vélez-Ramírez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Fiordaliso C Román-Carraro
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
| | - Rebeca Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, México, DF, 07360, México
| | - Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP, 54090, México
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Attenuation of transcriptional and signaling responses limits viability of ρ(0)Saccharomyces cerevisiae during periods of glucose deprivation. Biochim Biophys Acta Gen Subj 2016; 1860:2563-2575. [PMID: 27478089 DOI: 10.1016/j.bbagen.2016.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/09/2016] [Accepted: 07/27/2016] [Indexed: 01/31/2023]
Abstract
BACKGROUND The maintenance of viability during periods when a glycolytic carbon source is limited (or absent) is a major obstacle for cells whose mitochondrial DNA (mtDNA) has been damaged or lost. METHODS We utilized genome wide transcriptional profiling and in gel mobility analyses to examine the transcriptional response and characterize defects in the phosphorylation dependent signaling events that occur during acute glucose starvation in ρ(0) cells that lack mtDNA. Genetic and pharmacological interventions were employed to clarify the contribution of nutrient responsive kinases to regulation of the transcription factors that displayed abnormal phosphoregulation in ρ(0) cells. RESULTS The transcriptional response to glucose deprivation is dampened but not blocked in ρ(0) cells. Genes regulated by the transcription factors Mig1, Msn2, Gat1, and Ume6 were noticeably affected and phosphorylation of these factors in response to nutrient depletion is abnormal in ρ(0) cells. Regulation of the nutrient responsive kinases PKA and Snf1 remains normal in ρ(0) cells. The phosphorylation defect results from ATP depletion and loss of the activity of kinases including GSK3β, Rim15, and Yak1. Interventions which rescue phosphoregulation of transcription factors bolster maintenance of viability in ρ(0) cells during subsequent glucose deprivation. CONCLUSIONS A subset of nutrient responsive kinases is especially sensitive to ATP levels and their misregulation may underlie regulatory defects presented by ρ(0) cells. GENERAL SIGNIFICANCE Abnormal regulation of mitochondrial function is implicated in numerous human disorders. This work illustrates that some signaling pathways are more sensitive than others to metabolic defects caused by mitochondrial dysfunction.
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Li Y, Tsang CK, Wang S, Li X, Yang Y, Fu L, Huang W, Li M, Wang H, Zheng XS. MAF1 suppresses AKT-mTOR signaling and liver cancer through activation of PTEN transcription. Hepatology 2016; 63:1928-42. [PMID: 26910647 PMCID: PMC5021206 DOI: 10.1002/hep.28507] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED The phosphatidylinositol 3-kinase/phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase/protein kinase B/mammalian target of rapamycin (PI3K-PTEN-AKT-mTOR) pathway is a central controller of cell growth and a key driver for human cancer. MAF1 is an mTOR downstream effector and transcriptional repressor of ribosomal and transfer RNA genes. MAF1 expression is markedly reduced in hepatocellular carcinomas, which is correlated with disease progression and poor prognosis. Consistently, MAF1 displays tumor-suppressor activity toward in vitro and in vivo cancer models. Surprisingly, blocking the synthesis of ribosomal and transfer RNAs is insufficient to account for MAF1's tumor-suppressor function. Instead, MAF1 down-regulation paradoxically leads to activation of AKT-mTOR signaling, which is mediated by decreased PTEN expression. MAF1 binds to the PTEN promoter, enhancing PTEN promoter acetylation and activity. CONCLUSION In contrast to its canonical function as a transcriptional repressor, MAF1 can also act as a transcriptional activator for PTEN, which is important for MAF1's tumor-suppressor function. These results have implications in disease staging, prognostic prediction, and AKT-mTOR-targeted therapy in liver cancer. (Hepatology 2016;63:1928-1942).
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Affiliation(s)
- Yue Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Chi Kwan Tsang
- Rutgers Cancer Institute of New Jersey and Department of Pharmacology, Robert Wood Johnson Medical School, Rutgersthe State University of New JerseyNew BrunswickNJ
| | - Suihai Wang
- State Key Laboratory of Organ Failure Research, Institute of Antibody Engineering, School of BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Xiao‐Xing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yang Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Liwu Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Wenlin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Ming Li
- State Key Laboratory of Organ Failure Research, Institute of Antibody Engineering, School of BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Hui‐Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina,Rutgers Cancer Institute of New Jersey and Department of Pharmacology, Robert Wood Johnson Medical School, Rutgersthe State University of New JerseyNew BrunswickNJ
| | - X.F. Steven Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina,Rutgers Cancer Institute of New Jersey and Department of Pharmacology, Robert Wood Johnson Medical School, Rutgersthe State University of New JerseyNew BrunswickNJ
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Orioli A, Praz V, Lhôte P, Hernandez N. Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest. Genome Res 2016; 26:624-35. [PMID: 26941251 PMCID: PMC4864463 DOI: 10.1101/gr.201400.115] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/24/2016] [Indexed: 12/04/2022]
Abstract
RNA polymerase III (Pol III) is tightly controlled in response to environmental cues, yet a genomic-scale picture of Pol III regulation and the role played by its repressor MAF1 is lacking. Here, we describe genome-wide studies in human fibroblasts that reveal a dynamic and gene-specific adaptation of Pol III recruitment to extracellular signals in an mTORC1-dependent manner. Repression of Pol III recruitment and transcription are tightly linked to MAF1, which selectively localizes at Pol III loci, even under serum-replete conditions, and increasingly targets transcribing Pol III in response to serum starvation. Combining Pol III binding profiles with EU-labeling and high-throughput sequencing of newly synthesized small RNAs, we show that Pol III occupancy closely reflects ongoing transcription. Our results exclude the long-term, unproductive arrest of Pol III on the DNA as a major regulatory mechanism and identify previously uncharacterized, differential coordination in Pol III binding and transcription under different growth conditions.
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Affiliation(s)
- Andrea Orioli
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Philippe Lhôte
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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42
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Kaya Okur HS, Das A, Taylor RN, Bagchi IC, Bagchi MK. Roles of Estrogen Receptor-α and the Coactivator MED1 During Human Endometrial Decidualization. Mol Endocrinol 2016; 30:302-13. [PMID: 26849466 DOI: 10.1210/me.2015-1274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The steroid hormones 17β-estradiol and progesterone are critical regulators of endometrial stromal cell differentiation, known as decidualization, which is a prerequisite for successful establishment of pregnancy. The present study using primary human endometrial stromal cells (HESCs) addressed the role of estrogen receptor-α (ESR1) in decidualization. Knockdown of ESR1 transcripts by RNA interference led to a marked reduction in decidualization of HESCs. Gene expression profiling at an early stage of decidualization indicated that ESR1 negatively regulates several cell cycle regulatory factors, thereby suppressing the proliferation of HESCs as these cells enter the differentiation program. ESR1 also controls the expression of WNT4, FOXO1, and progesterone receptor (PGR), well-known mediators of decidualization. Whereas ESR1 knockdown strongly inhibited the expression of FOXO1 and WNT4 transcripts within 24 hours of the initiation of decidualization, PGR expression remained unaffected at this early time point. Our study also revealed a major role of cAMP signaling in influencing the function of ESR1 during decidualization. Using a proteomic approach, we discovered that the cAMP-dependent protein kinase A (PKA) phosphorylates Mediator 1 (MED1), a subunit of the mediator coactivator complex, during HESC differentiation. Using immunoprecipitation, we demonstrated that PKA-phosphorylated MED1 interacts with ESR1. The PKA-dependent phosphorylation of MED1 was also correlated with its enhanced recruitment to estrogen-responsive elements in the WNT4 gene. Knockdown of MED1 transcripts impaired the expression of ESR1-induced WNT4 and FOXO1 transcripts and blocked decidualization. Based on these findings, we conclude that modulation of ESR1-MED1 interactions by cAMP signaling plays a critical role in human decidualization.
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Affiliation(s)
- Hatice S Kaya Okur
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Amrita Das
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Robert N Taylor
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Indrani C Bagchi
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Milan K Bagchi
- Departments of Molecular and Integrative Physiology (H.S.K.O., M.K.B.) and Comparative Biosciences (A.D., I.C.B.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; and Department of Obstetrics and Gynecology (R.N.T.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
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Akdoğan E, Tardu M, Garipler G, Baytek G, Kavakli İH, Dunn CD. Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA. PLoS One 2016; 11:e0146511. [PMID: 26751567 PMCID: PMC4709096 DOI: 10.1371/journal.pone.0146511] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/19/2015] [Indexed: 12/12/2022] Open
Abstract
Damage to the mitochondrial genome (mtDNA) can lead to diseases for which there are no clearly effective treatments. Since mitochondrial function and biogenesis are controlled by the nutrient environment of the cell, it is possible that perturbation of conserved, nutrient-sensing pathways may successfully treat mitochondrial disease. We found that restricting glucose or otherwise reducing the activity of the protein kinase A (PKA) pathway can lead to improved proliferation of Saccharomyces cerevisiae cells lacking mtDNA and that the transcriptional response to mtDNA loss is reduced in cells with diminished PKA activity. We have excluded many pathways and proteins from being individually responsible for the benefits provided to cells lacking mtDNA by PKA inhibition, and we found that robust import of mitochondrial polytopic membrane proteins may be required in order for cells without mtDNA to receive the full benefits of PKA reduction. Finally, we have discovered that the transcription of genes involved in arginine biosynthesis and aromatic amino acid catabolism is altered after mtDNA damage. Our results highlight the potential importance of nutrient detection and availability on the outcome of mitochondrial dysfunction.
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Affiliation(s)
- Emel Akdoğan
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul, 34450, Turkey
| | - Mehmet Tardu
- Department of Chemical and Biological Engineering, Koç University, Sarıyer, İstanbul, 34450, Turkey
| | - Görkem Garipler
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul, 34450, Turkey
| | - Gülkız Baytek
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul, 34450, Turkey
| | - İ. Halil Kavakli
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul, 34450, Turkey
- Department of Chemical and Biological Engineering, Koç University, Sarıyer, İstanbul, 34450, Turkey
| | - Cory D. Dunn
- Department of Molecular Biology and Genetics, Koç University, Sarıyer, İstanbul, 34450, Turkey
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Mierzejewska J, Chreptowicz K. Lack of Maf1 enhances pyruvate kinase activity and fermentative metabolism while influencing lipid homeostasis in Saccharomyces cerevisiae. FEBS Lett 2015; 590:93-100. [PMID: 26787463 DOI: 10.1002/1873-3468.12033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/18/2015] [Accepted: 11/24/2015] [Indexed: 12/17/2022]
Abstract
The Maf1 protein is a general negative repressor of RNA polymerase III, which is conserved in eukaryotes from yeast to humans. Herein, we show the yeast maf1Δ mutant increases pyruvate kinase activity, the key enzyme in glycolysis and an important player in switching between fermentative and oxidative metabolism. We observed enhanced ethanol production and elevated lipid content in the maf1Δ strain grown on glucose. However, after shifting to a non-fermentable carbon source, the opposite effect was observed, and the mutant cells accumulated smaller lipid droplets. Thus, it has been concluded that the Maf1 protein is essential for regulation of glucose metabolism and lipid homeostasis.
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Affiliation(s)
- Jolanta Mierzejewska
- Department of Drug Technology and Biotechnology, Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Karolina Chreptowicz
- Department of Drug Technology and Biotechnology, Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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Endres L, Dedon PC, Begley TJ. Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. RNA Biol 2015; 12:603-14. [PMID: 25892531 DOI: 10.1080/15476286.2015.1031947] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
tRNA (tRNA) is a key molecule used for protein synthesis, with multiple points of stress-induced regulation that can include transcription, transcript processing, localization and ribonucleoside base modification. Enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and has the potential to influence specific anticodon-codon interactions and regulate translation. Notably, altered tRNA modification has been linked to mitochondrial diseases and cancer progression. In this review, specific to Eukaryotic systems, we discuss how recent systems-level analyses using a bioanalytical platform have revealed that there is extensive reprogramming of tRNA modifications in response to cellular stress and during cell cycle progression. Combined with genome-wide codon bias analytics and gene expression studies, a model emerges in which stress-induced reprogramming of tRNA drives the translational regulation of critical response proteins whose transcripts display a distinct codon bias. Termed Modification Tunable Transcripts (MoTTs), (1) we define them as (1) transcripts that use specific degenerate codons and codon biases to encode critical stress response proteins, and (2) transcripts whose translation is influenced by changes in wobble base tRNA modification. In this review we note that the MoTTs translational model is also applicable to the process of stop-codon recoding for selenocysteine incorporation, as stop-codon recoding involves a selective codon bias and modified tRNA to decode selenocysteine during the translation of a key subset of oxidative stress response proteins. Further, we discuss how in addition to RNA modification analytics, the comprehensive characterization of translational regulation of specific transcripts requires a variety of tools, including high coverage codon-reporters, ribosome profiling and linked genomic and proteomic approaches. Together these tools will yield important new insights into the role of translational elongation in cell stress response.
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Affiliation(s)
- Lauren Endres
- a College of Nanoscale Science and Engineering; State University of New York ; Albany , NY USA
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A Gβ protein and the TupA Co-Regulator Bind to Protein Kinase A Tpk2 to Act as Antagonistic Molecular Switches of Fungal Morphological Changes. PLoS One 2015; 10:e0136866. [PMID: 26334875 PMCID: PMC4559445 DOI: 10.1371/journal.pone.0136866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/09/2015] [Indexed: 11/19/2022] Open
Abstract
The human pathogenic fungus Paracoccidioides brasiliensis (Pb) undergoes a morphological transition from a saprobic mycelium to pathogenic yeast that is controlled by the cAMP-signaling pathway. There is a change in the expression of the Gβ-protein PbGpb1, which interacts with adenylate cyclase, during this morphological transition. We exploited the fact that the cAMP-signaling pathway of Saccharomyces cerevisiae does not include a Gβ-protein to probe the functional role of PbGpb1. We present data that indicates that PbGpb1 and the transcriptional regulator PbTupA both bind to the PKA protein PbTpk2. PbTPK2 was able to complement a TPK2Δ strain of S. cerevisiae, XPY5a/α, which was defective in pseudohyphal growth. Whilst PbGPB1 had no effect on the parent S. cerevisiae strain, MLY61a/α, it repressed the filamentous growth of XPY5a/α transformed with PbTPK2, behaviour that correlated with a reduced expression of the floculin FLO11. In vitro, PbGpb1 reduced the kinase activity of PbTpk2, suggesting that inhibition of PbTpk2 by PbGpb1 reduces the level of expression of Flo11, antagonizing the filamentous growth of the cells. In contrast, expressing the co-regulator PbTUPA in XPY5a/α cells transformed with PbTPK2, but not untransformed cells, induced hyperfilamentous growth, which could be antagonized by co-transforming the cells with PbGPB1. PbTUPA was unable to induce the hyperfilamentous growth of a FLO8Δ strain, suggesting that PbTupA functions in conjunction with the transcription factor Flo8 to control Flo11 expression. Our data indicates that P. brasiliensis PbGpb1 and PbTupA, both of which have WD/β-propeller structures, bind to PbTpk2 to act as antagonistic molecular switches of cell morphology, with PbTupA and PbGpb1 inducing and repressing filamentous growth, respectively. Our findings define a potential mechanism for controlling the morphological switch that underpins the virulence of dimorphic fungi.
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Cai Y, Wei YH. Distinct regulation of Maf1 for lifespan extension by Protein kinase A and Sch9. Aging (Albany NY) 2015; 7:133-43. [PMID: 25720796 PMCID: PMC4359695 DOI: 10.18632/aging.100727] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Protein kinase A (PKA) and Sch9 regulates cell growth as well as lifespan in Saccharomyces cerevisiae. Maf1 is a RNA polymerase III (PolIII) inhibitor that tailors 5S rRNA and tRNA production in response to various environmental cues. Both PKA and Sch9 have been shown to phosphorylate Maf1 in vitro at similar amino acids, suggesting a redundancy in Maf1 regulation. However, here we find that activating PKA by bcy1 deletion cannot replace Sch9 for Maf1 phosphorylation and cytoplasmic retention; instead, such modulation lowers Maf1 protein levels. Consistently, loss of MAF1 or constitutive PKA activity reverses the stress resistance and the extended lifespan of sch9Δ cells. Overexpression of MAF1 partially rescues the extended lifespan of sch9Δ in bcy1Δsch9Δ mutant, suggesting that PKA suppresses sch9Δ longevity at least partly through Maf1 abundance. Constitutive PKA activity also reverses the reduced tRNA synthesis and slow growth of sch9Δ, which, however, is not attributed to Maf1 protein abundance. Therefore, regulation of lifespan and growth can be decoupled. Together, we reveal that lifespan regulation by PKA and Sch9 are mediated by Maf1 through distinct mechanisms.
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Affiliation(s)
- Ying Cai
- No. 3 People's Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai 201900, China
| | - Yue-Hua Wei
- No. 3 People's Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai 201900, China
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Shin SH, Lee EJ, Chun J, Hyun S, Kang SS. ULK2 Ser 1027 Phosphorylation by PKA Regulates Its Nuclear Localization Occurring through Karyopherin Beta 2 Recognition of a PY-NLS Motif. PLoS One 2015; 10:e0127784. [PMID: 26052940 PMCID: PMC4460075 DOI: 10.1371/journal.pone.0127784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/18/2015] [Indexed: 11/23/2022] Open
Abstract
Uncoordinated 51-like kinase 2 (ULK2), a member of the serine/threonine kinase family, plays an essential role in the regulation of autophagy in mammalian cells. Given the role of autophagy in normal cellular homeostasis and in multiple diseases, improved mechanistic insight into this process may result in the development of novel therapeutic approaches. Here, we present evidence that ULK2 associates with karyopherin beta 2 (Kapβ2) for its transportation into the nucleus. We identify a potential PY-NLS motif (774gpgfgssppGaeaapslRyvPY795) in the S/P space domain of ULK2, which is similar to the consensus PY-NLS motif (R/K/H)X2–5PY. Using a pull-down approach, we observe that ULK2 interacts physically with Kapβ2 both in vitro and in vivo. Confocal microscopy confirmed the co-localization of ULK2 and Kapβ2. Localization of ULK2 to the nuclear region was disrupted by mutations in the putative Kapβ2-binding motif (P794A). Furthermore, in transient transfection assays, the presence of the Kapβ2 binding site mutant (the cytoplasmic localization form) was associated with a substantial increase in autophagy activity (but a decrease in the in vitro serine-phosphorylation) compared with the wild type ULK2. Mutational analysis showed that the phosphorylation on the Ser1027 residue of ULK2 by Protein Kinase A (PKA) is the regulatory point for its functional dissociation from Atg13 and FIP 200, nuclear localization, and autophagy. Taken together, our observations indicate that Kapβ2 interacts with ULK2 through ULK2’s putative PY-NLS motif, and facilitates transport from the cytoplasm to the nucleus, depending on its Ser1027 residue phosphorylation by PKA, thereby reducing autophagic activity.
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Affiliation(s)
- Sung Hwa Shin
- Department of Biology Education, Chungbuk National University, 1, Chungdae-ro, Seowon-gu, Cheongju, Chungbuk, Republic of Korea
| | - Eun Jeoung Lee
- Department of Internal Medicine, Chungbuk National University, 1, Chungdae-ro, Seowon-gu, Cheongju, Chungbuk, Republic of Korea
| | - Jaesun Chun
- Department of Biology Education, Korea National University of Education, Taeseongtabyeon-ro, Heungdeok-gu, Cheongju, Chungbuk, Republic of Korea
| | - Sunghee Hyun
- Department of Biomedical Laboratory Science, Eulji University, Daejeon, Republic of Korea
| | - Sang Sun Kang
- Department of Biology Education, Chungbuk National University, 1, Chungdae-ro, Seowon-gu, Cheongju, Chungbuk, Republic of Korea
- * E-mail:
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Liu C, Li S, Dai X, Ma J, Wan J, Jiang H, Wang P, Liu Z, Zhang H. PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex. Nucleic Acids Res 2015; 43:6270-84. [PMID: 26038315 PMCID: PMC4513857 DOI: 10.1093/nar/gkv574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polycomb repression complex 2 (PRC2) component EZH2 tri-methylates H3K27 and exerts epigenetic repression on target gene expression. EZH2-mediated epigenetic control of RNA polymerase II (Pol II) transcribed coding gene transcription has been well established. However, little is known about EZH2-mediated epigenetic regulation of RNA polymerase III (Pol III) transcription. Here we present a paradigm that EZH2 is involved in the repression of Pol III transcription via interaction with transcriptional factor complex IIIC (TFIIIC). EZH2 and H3K27me3 co-occupy the promoter of tRNATyr, 5S rRNA and 7SL RNA genes. Depletion of EZH2 or inhibition of EZH2 methyltransferase activity led to upregulation of Pol III target gene transcription. EZH2-mediated repression of Pol III transcribed gene expression requires presence of SUZ12. SUZ12 was able to interact with TFIIIC complex and knockdown of SUZ12 decreased occupancy of EZH2 and H3K27me3 at the promoter of Pol III target genes. Our findings pointed out a previously unidentified role of PRC2 complex in suppressing transcription of Pol III transcribed non-translated RNA genes, putting Pol III on a new layer of epigenetic regulation.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Shuai Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Xiaoyan Dai
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Ji Ma
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Junhu Wan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hao Jiang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Peng Wang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Zhaoli Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
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Lee J, Moir RD, Willis IM. Differential Phosphorylation of RNA Polymerase III and the Initiation Factor TFIIIB in Saccharomyces cerevisiae. PLoS One 2015; 10:e0127225. [PMID: 25970584 PMCID: PMC4430316 DOI: 10.1371/journal.pone.0127225] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The production of ribosomes and tRNAs for protein synthesis has a high energetic cost and is under tight transcriptional control to ensure that the level of RNA synthesis is balanced with nutrient availability and the prevailing environmental conditions. In the RNA polymerase (pol) III system in yeast, nutrients and stress affect transcription through a bifurcated signaling pathway in which protein kinase A (PKA) and TORC1 activity directly or indirectly, through downstream kinases, alter the phosphorylation state and function of the Maf1 repressor and Rpc53, a TFIIF-like subunit of the polymerase. However, numerous lines of evidence suggest greater complexity in the regulatory network including the phosphoregulation of other pol III components. To address this issue, we systematically examined all 17 subunits of pol III along with the three subunits of the initiation factor TFIIIB for evidence of differential phosphorylation in response to inhibition of TORC1. A relatively high stoichiometry of phosphorylation was observed for several of these proteins and the Rpc82 subunit of the polymerase and the Bdp1 subunit of TFIIIB were found to be differentially phosphorylated. Bdp1 is phosphorylated on four major sites during exponential growth and the protein is variably dephosphorylated under conditions that inhibit tRNA gene transcription. PKA, the TORC1-regulated kinase Sch9 and protein kinase CK2 are all implicated in the phosphorylation of Bdp1. Alanine substitutions at the four phosphosites cause hyper-repression of transcription indicating that phosphorylation of Bdp1 opposes Maf1-mediated repression. The new findings suggest an integrated regulatory model for signaling events controlling pol III transcription.
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Affiliation(s)
- Jaehoon Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (RDM); (IMW)
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (RDM); (IMW)
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