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de Oya IG, Jiménez-Gutiérrez E, Gaillard H, Molina M, Martín H, Wellinger RE. Manganese Stress Tolerance Depends on Yap1 and Stress-Activated MAP Kinases. Int J Mol Sci 2022; 23:ijms232415706. [PMID: 36555348 PMCID: PMC9779322 DOI: 10.3390/ijms232415706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Understanding which intracellular signaling pathways are activated by manganese stress is crucial to decipher how metal overload compromise cellular integrity. Here, we unveil a role for oxidative and cell wall stress signaling in the response to manganese stress in yeast. We find that the oxidative stress transcription factor Yap1 protects cells against manganese toxicity. Conversely, extracellular manganese addition causes a rapid decay in Yap1 protein levels. In addition, manganese stress activates the MAPKs Hog1 and Slt2 (Mpk1) and leads to an up-regulation of the Slt2 downstream transcription factor target Rlm1. Importantly, Yap1 and Slt2 are both required to protect cells from oxidative stress in mutants impaired in manganese detoxification. Under such circumstances, Slt2 activation is enhanced upon Yap1 depletion suggesting an interplay between different stress signaling nodes to optimize cellular stress responses and manganese tolerance.
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Affiliation(s)
- Inés G. de Oya
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - Elena Jiménez-Gutiérrez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Humberto Martín
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain
| | - Ralf Erik Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
- Correspondence:
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2
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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3
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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4
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Whole-genome sequencing of Cryptococcus podzolicus Y3 and data-independent acquisition-based proteomic analysis during OTA degradation. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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5
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Sanz AB, García R, Pavón-Vergés M, Rodríguez-Peña JM, Arroyo J. Control of Gene Expression via the Yeast CWI Pathway. Int J Mol Sci 2022; 23:ijms23031791. [PMID: 35163713 PMCID: PMC8836261 DOI: 10.3390/ijms23031791] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/18/2022] Open
Abstract
Living cells exposed to stressful environmental situations can elicit cellular responses that guarantee maximal cell survival. Most of these responses are mediated by mitogen-activated protein kinase (MAPK) cascades, which are highly conserved from yeast to humans. Cell wall damage conditions in the yeast Saccharomyces cerevisiae elicit rescue mechanisms mainly associated with reprogramming specific transcriptional responses via the cell wall integrity (CWI) pathway. Regulation of gene expression by this pathway is coordinated by the MAPK Slt2/Mpk1, mainly via Rlm1 and, to a lesser extent, through SBF (Swi4/Swi6) transcription factors. In this review, we summarize the molecular mechanisms controlling gene expression upon cell wall stress and the role of chromatin structure in these processes. Some of these mechanisms are also discussed in the context of other stresses governed by different yeast MAPK pathways. Slt2 regulates both transcriptional initiation and elongation by interacting with chromatin at the promoter and coding regions of CWI-responsive genes but using different mechanisms for Rlm1- and SBF-dependent genes. Since MAPK pathways are very well conserved in eukaryotic cells and are essential for controlling cellular physiology, improving our knowledge regarding how they regulate gene expression could impact the future identification of novel targets for therapeutic intervention.
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Wang C, Barr K, Neutel D, Roy K, Liu Y, Chanfreau GF. Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the BDF2 mRNA. RNA (NEW YORK, N.Y.) 2021; 27:1545-1556. [PMID: 34497070 PMCID: PMC8594472 DOI: 10.1261/rna.078880.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The expression of bromodomain-containing proteins that regulate chromatin structure and accessibility must be tightly controlled to ensure the appropriate regulation of gene expression. In the yeast S. cerevisiae, Bromodomain Factor 2 (BDF2) expression is extensively regulated post-transcriptionally during stress by RNase III-mediated decay (RMD), which is triggered by cleavage of the BDF2 mRNA in the nucleus by the RNase III homolog Rnt1p. Previous studies have shown that RMD-mediated down-regulation of BDF2 is hyperactivated in osmotic stress conditions, yet the mechanisms driving the enhanced nuclear cleavage of BDF2 RNA under these conditions remain unknown. Here, we show that RMD hyperactivation can be detected in multiple stress conditions that inhibit mRNA export, and that Rnt1p remains primarily localized in the nucleus during salt stress. We show that globally inhibiting mRNA nuclear export by anchoring away mRNA biogenesis or export factors out of the nucleus can recapitulate RMD hyperactivation in the absence of stress. RMD hyperactivation requires Rnt1p nuclear localization but does not depend on the BDF2 gene endogenous promoter, and its efficiency is affected by the structure of the stem-loop cleaved by Rnt1p. Because multiple stress conditions have been shown to mediate global inhibition of mRNA export, our results suggest that the hyperactivation of RMD is primarily the result of the increased nuclear retention of the BDF2 mRNA during stress.
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Affiliation(s)
- Charles Wang
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Keaton Barr
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Dean Neutel
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
| | - Yanru Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, USA
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7
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Singh P, Chaudhuri A, Banerjea M, Marathe N, Das B. Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae. Nucleic Acids Res 2021; 49:11512-11536. [PMID: 34664673 PMCID: PMC8599857 DOI: 10.1093/nar/gkab930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Nuclear degradation of aberrant mRNAs in Saccharomyces cerevisiae is accomplished by the nuclear exosome and its cofactors TRAMP/CTEXT. Evidence from this investigation establishes a universal role of the Nrd1p-Nab3p-Sen1p (NNS) complex in the nuclear decay of all categories of aberrant mRNAs. In agreement with this, both nrd1-1 and nrd1-2 mutations impaired the decay of all classes of aberrant messages. This phenotype is similar to that displayed by GAL::RRP41 and rrp6-Δ mutant yeast strains. Remarkably, however, nrd1ΔCID mutation (lacking the C-terminal domain required for interaction of Nrd1p with RNAPII) only diminished the decay of aberrant messages with defects occurring during the early stage of mRNP biogenesis, without affecting other messages with defects generated later in the process. Co-transcriptional recruitment of Nrd1p on the aberrant mRNAs was vital for their concomitant decay. Strikingly, this recruitment on to mRNAs defective in the early phases of biogenesis is solely dependent upon RNAPII. In contrast, Nrd1p recruitment onto export-defective transcripts with defects occurring in the later stage of biogenesis is independent of RNAPII and dependent on the CF1A component, Pcf11p, which explains the observed characteristic phenotype of nrd1ΔCID mutation. Consistently, pcf11-2 mutation displayed a selective impairment in the degradation of only the export-defective messages.
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Affiliation(s)
- Pragyan Singh
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata - 700032, West Bengal, India
| | - Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata - 700032, West Bengal, India
| | - Mayukh Banerjea
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata - 700032, West Bengal, India
| | - Neeraja Marathe
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata - 700032, West Bengal, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata - 700032, West Bengal, India
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8
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Regulation of Pkc1 Hyper-Phosphorylation by Genotoxic Stress. J Fungi (Basel) 2021; 7:jof7100874. [PMID: 34682295 PMCID: PMC8541566 DOI: 10.3390/jof7100874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 01/02/2023] Open
Abstract
The cell wall integrity (CWI) signaling pathway is best known for its roles in cell wall biogenesis. However, it is also thought to participate in the response to genotoxic stress. The stress-activated protein kinase Mpk1 (Slt2, is activated by DNA damaging agents through an intracellular mechanism that does not involve the activation of upstream components of the CWI pathway. Additional observations suggest that protein kinase C (Pkc1), the top kinase in the CWI signaling cascade, also has a role in the response to genotoxic stress that is independent of its recognized function in the activation of Mpk1. Pkc1 undergoes hyper-phosphorylation specifically in response to genotoxic stress; we have found that this requires the DNA damage checkpoint kinases Mec1 (Mitosis Entry Checkpoint) and Tel1 (TELomere maintenance), but not their effector kinases. We demonstrate that the casein kinase 1 (CK1) ortholog, Hrr25 (HO and Radiation Repair), previously implicated in the DNA damage transcriptional response, associates with Pkc1 under conditions of genotoxic stress. We also found that the induced association of Hrr25 with Pkc1 requires Mec1 and Tel1, and that Hrr25 catalytic activity is required for Pkc1-hyperphosphorylation, thereby delineating a pathway from the checkpoint kinases to Pkc1. We used SILAC mass spectrometry to identify three residues within Pkc1 the phosphorylation of which was stimulated by genotoxic stress. We mutated these residues as well as a collection of 13 phosphorylation sites within the regulatory domain of Pkc1 that fit the consensus for CK1 sites. Mutation of the 13 Pkc1 phosphorylation sites blocked hyper-phosphorylation and diminished RNR3 (RiboNucleotide Reductase) basal expression and induction by genotoxic stress, suggesting that Pkc1 plays a role in the DNA damage transcriptional response.
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9
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Francette AM, Tripplehorn SA, Arndt KM. The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin. J Mol Biol 2021; 433:166979. [PMID: 33811920 PMCID: PMC8184591 DOI: 10.1016/j.jmb.2021.166979] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The regulation of transcription by RNA polymerase II is closely intertwined with the regulation of chromatin structure. A host of proteins required for the disassembly, reassembly, and modification of nucleosomes interacts with Pol II to aid its movement and counteract its disruptive effects on chromatin. The highly conserved Polymerase Associated Factor 1 Complex, Paf1C, travels with Pol II and exerts control over transcription elongation and chromatin structure, while broadly impacting the transcriptome in both single cell and multicellular eukaryotes. Recent studies have yielded exciting new insights into the mechanisms by which Paf1C regulates transcription elongation, epigenetic modifications, and post-transcriptional steps in eukaryotic gene expression. Importantly, these functional studies are now supported by an extensive foundation of high-resolution structural information, providing intimate views of Paf1C and its integration into the larger Pol II elongation complex. As a global regulatory factor operating at the interface between chromatin and transcription, the impact of Paf1C is broad and its influence reverberates into other domains of nuclear regulation, including genome stability, telomere maintenance, and DNA replication.
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Affiliation(s)
- Alex M Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sarah A Tripplehorn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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10
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Wang C, Liu Y, DeMario SM, Mandric I, Gonzalez-Figueroa C, Chanfreau GF. Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress. Cell Rep 2021; 31:107754. [PMID: 32521279 PMCID: PMC7587046 DOI: 10.1016/j.celrep.2020.107754] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The nuclear RNA exosome is essential for RNA processing and degradation. Here, we show that the exosome nuclear-specific subunit Rrp6p promotes cell survival during heat stress through the cell wall integrity (CWI) pathway, independently of its catalytic activity or association with the core exosome. Rrp6p exhibits negative genetic interactions with the Slt2/Mpk1p or Paf1p elongation factors required for expression of CWI genes during stress. Overexpression of Rrp6p or of its catalytically inactive or exosome-independent mutants can partially rescue the growth defect of the mpk1Δ mutant and stimulates expression of the Mpk1 p target gene FKS2. The rrp6Δ and mpk1Δ mutants show similarities in deficient expression of CWI genes during heat shock, and overexpression of the CWI gene HSP150 can rescue the stress-induced lethality of the mpk1Δrp6Δ mutant. These results demonstrate that Rrp6p moonlights independently from the exosome to ensure proper expression of CWI genes and to promote cell survival during stress. Wang et al. show that Rrp6 functions with the Slt2/Mpk1 and Paf1 elongation factors for the proper expression of CWI genes during heat stress. The role of Rrp6p in promoting heat-stress-induced gene expression does not require Rrp6 catalytic activity or interaction with the nuclear RNA exosome.
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Affiliation(s)
- Charles Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanru Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel M DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Igor Mandric
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos Gonzalez-Figueroa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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11
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Villa T, Barucco M, Martin-Niclos MJ, Jacquier A, Libri D. Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Rep 2021; 32:107942. [PMID: 32698007 DOI: 10.1016/j.celrep.2020.107942] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/08/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. Here, we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, circular RNA containing a natural NNS target in exosome-proficient cells. Our results have important implications for the mechanism of termination, the general impact of ncRNAs abundance, and the importance of nuclear ncRNA degradation.
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Affiliation(s)
- Tommaso Villa
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
| | - Mara Barucco
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | | | - Alain Jacquier
- Institut Pasteur, Centre National de la Recherche Scientifique, UMR3525 Paris, France
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
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12
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The MAP kinase AflSlt2 modulates aflatoxin biosynthesis and peanut infection in the fungus Aspergillus flavus. Int J Food Microbiol 2020; 322:108576. [PMID: 32240921 DOI: 10.1016/j.ijfoodmicro.2020.108576] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/21/2020] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Aflatoxin contamination in food and feed products has been brought into sharp focus over the last few decades in the world. However, there is no effective strategy for solving the problem thus far. Therefore, basic research on the aflatoxin-producer Aspergillus flavus is an urgent need. The vital role of mitogen-activated protein kinases (MAPKs) in signal transduction has been documented in various pathogenic fungi, but their functions in A. flavus have rarely been investigated. Herein, we characterized the detailed function of one of these MAPKs, AflSlt2. Targeted deletion of AflSlt2 gene indicates that this kinase is required for vegetative growth, conidia generation, and sclerotium formation. The analysis of AflSlt2 deletion mutant revealed hypersensitivity to cell wall-damaging chemicals and resistance against hydrogen peroxide. Interestingly, the ability of the ΔAflSlt2 mutant to generate aflatoxins in medium was significantly increased compared to wild type. However, a pathogenicity assay indicated that the ΔAflSlt2 mutant was deficient in peanut infection. Site-directed mutation study uncovered that the function of AflSlt2 was dependent on the phosphorylated residues (Thr-186 and Tyr-188) within the activation loop and the phosphotransfer residue (Lys-52) within the subdomain II. Interestingly, an autophosphorylation mutant of AflSlt2 (AflSlt2R66S) displayed wild type-like phenotypes. Bringing these observations together, we propose that Slt2-MAPK pathway is involved in development, stress response, aflatoxin biosynthesis, and pathogenicity in A. flavus. This study may be useful to unveil the regulation mechanism of aflatoxin biosynthesis and provide strategy to control A. flavus contamination.
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13
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Pearson AJ, Fullwood P, Toro Tapia G, Prise I, Smith MP, Xu Q, Jordan A, Giurisato E, Whitmarsh AJ, Francavilla C, Tournier C. Discovery of a Gatekeeper Residue in the C-Terminal Tail of the Extracellular Signal-Regulated Protein Kinase 5 (ERK5). Int J Mol Sci 2020; 21:E929. [PMID: 32023819 PMCID: PMC7037328 DOI: 10.3390/ijms21030929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
The extracellular signal-regulated protein kinase 5 (ERK5) is a non-redundant mitogen-activated protein kinase (MAPK) that exhibits a unique C-terminal extension which comprises distinct structural and functional properties. Here, we sought to elucidate the significance of phosphoacceptor sites in the C-terminal transactivation domain of ERK5. We have found that Thr732 acted as a functional gatekeeper residue controlling C-terminal-mediated nuclear translocation and transcriptional enhancement. Consistently, using a non-bias quantitative mass spectrometry approach, we demonstrated that phosphorylation at Thr732 conferred selectivity for binding interactions of ERK5 with proteins related to chromatin and RNA biology, whereas a number of metabolic regulators were associated with full-length wild type ERK5. Additionally, our proteomic analysis revealed that phosphorylation of the Ser730-Glu-Thr732-Pro motif could occur independently of dual phosphorylation at Thr218-Glu-Tyr220 in the activation loop. Collectively, our results firmly establish the significance of C-terminal phosphorylation in regulating ERK5 function. The post-translational modification of ERK5 on its C-terminal tail might be of particular relevance in cancer cells where ERK5 has be found to be hyperphosphoryated.
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Affiliation(s)
- Adam J. Pearson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (A.J.P.); (Q.X.); (E.G.)
| | - Paul Fullwood
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (P.F.); (G.T.T.); (M.P.S.); (A.J.W.); (C.F.)
| | - Gabriela Toro Tapia
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (P.F.); (G.T.T.); (M.P.S.); (A.J.W.); (C.F.)
| | - Ian Prise
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK;
| | - Michael P. Smith
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (P.F.); (G.T.T.); (M.P.S.); (A.J.W.); (C.F.)
| | - Qiuping Xu
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (A.J.P.); (Q.X.); (E.G.)
| | - Allan Jordan
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M13 9PT, UK;
| | - Emanuele Giurisato
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (A.J.P.); (Q.X.); (E.G.)
- Department of Biotechnology Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Alan J. Whitmarsh
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (P.F.); (G.T.T.); (M.P.S.); (A.J.W.); (C.F.)
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (P.F.); (G.T.T.); (M.P.S.); (A.J.W.); (C.F.)
| | - Cathy Tournier
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; (A.J.P.); (Q.X.); (E.G.)
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14
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Wagener J, Striegler K, Wagener N. α- and β-1,3-Glucan Synthesis and Remodeling. Curr Top Microbiol Immunol 2020; 425:53-82. [PMID: 32193600 DOI: 10.1007/82_2020_200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glucans are characteristic and major constituents of fungal cell walls. Depending on the species, different glucan polysaccharides can be found. These differ in the linkage of the D-glucose monomers which can be either in α- or β-conformation and form 1,3, 1,4 or 1,6 O-glycosidic bonds. The linkages and polymer lengths define the physical properties of the glucan macromolecules, which may form a scaffold for other cell wall structures and influence the rigidity and elasticity of the wall. β-1,3-glucan is essential for the viability of many fungal pathogens. Therefore, the β-1,3-glucan synthase complex represents an excellent and primary target structure for antifungal drugs. Fungal cell wall β-glucan is also an important pathogen-associated molecular pattern (PAMP). To hide from innate immunity, many fungal pathogens depend on the synthesis of cell wall α-glucan, which functions as a stealth molecule to mask the β-glucans itself or links other masking structures to the cell wall. Here, we review the current knowledge about the biosynthetic machineries that synthesize β-1,3-glucan, β-1,6-glucan, and α-1,3-glucan. We summarize the discovery of the synthases, major regulatory traits, and the impact of glucan synthesis deficiencies on the fungal organisms. Despite all efforts, many aspects of glucan synthesis remain yet unresolved, keeping research directed toward cell wall biogenesis an exciting and continuously challenging topic.
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Affiliation(s)
- Johannes Wagener
- Institut Für Hygiene Und Mikrobiologie, University of Würzburg, Würzburg, Germany. .,National Reference Center for Invasive Fungal Infections (NRZMyk), Jena, Germany.
| | - Kristina Striegler
- Institut Für Hygiene Und Mikrobiologie, University of Würzburg, Würzburg, Germany
| | - Nikola Wagener
- Department of Cell Biology, Medical Faculty, University of Munich, Martinsried, Germany
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15
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Sariki SK, Kumawat R, Singh V, Tomar RS. Flocculation ofSaccharomyces cerevisiaeis dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway. Mol Microbiol 2019; 112:1350-1369. [DOI: 10.1111/mmi.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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16
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Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics 2019; 212:153-174. [PMID: 30902808 DOI: 10.1534/genetics.119.302058] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 11/18/2022] Open
Abstract
RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of DBP2 results in RNA polymerase II accumulation at the 3' ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2∆ cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 3' ends and a requirement for Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.
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17
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Sauvaget M, Hutton F, Coull R, Vavassori S, Wang K, Reznik A, Chyker T, Newfield CG, Euston E, Benary G, Schweizer LM, Schweizer M. The NHR1-1 of Prs1 and the pentameric motif 284KKCPK288 of Prs3 permit multi-functionality of the PRPP synthetase in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:5288342. [PMID: 30649305 DOI: 10.1093/femsyr/foz006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/10/2019] [Indexed: 12/23/2022] Open
Abstract
The five-membered PRS gene family of Saccharomyces cerevisiae is an example of gene duplication allowing the acquisition of novel functions. Each of the five Prs polypeptides is theoretically capable of synthesising PRPP but at least one of the following heterodimers is required for survival: Prs1/Prs3, Prs2/Prs5 and Prs4/Prs5. Prs3 contains a pentameric motif 284KKCPK288 found only in nuclear proteins. Deletion of 284KKCPK288 destabilises the Prs1/Prs3 complex resulting in a cascade of events, including reduction in PRPP synthetase activity and altered cell wall integrity (CWI) as measured by caffeine sensitivity and Rlm1 expression. Prs3 also interacts with the kinetochore-associated protein, Nuf2. Following the possibility of 284KKCPK288-mediated transport of the Prs1/Prs3 complex to the nucleus, it may interact with Nuf2 and phosphorylated Slt2 permitting activation of Rlm1. This scenario explains the breakdown of CWI encountered in mutants lacking PRS3 or deleted for 284KKCPK288. However, removal of NHR1-1 from Prs1 does not disrupt the Prs1/Prs3 interaction as shown by increased PRPP synthetase activity. This is evidence for the separation of the two metabolic functions of the PRPP-synthesising machinery: provision of PRPP and maintenance of CWI and is an example of evolutionary development when multiple copies of a gene were present in the ancestral organism.
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Affiliation(s)
- Maëlle Sauvaget
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Fraser Hutton
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Robert Coull
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Stefano Vavassori
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Ke Wang
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Aleksandra Reznik
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Tatsiana Chyker
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Chelsea G Newfield
- Institute of Life & Earth Sciences, School of Energy, Geoscience, Infrastructure & Society, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Eloise Euston
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Gerrit Benary
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Lilian M Schweizer
- School of Life Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Edinburgh EH14 4AS, UK
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18
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Sanz AB, García R, Rodríguez-Peña JM, Nombela C, Arroyo J. Slt2 MAPK association with chromatin is required for transcriptional activation of Rlm1 dependent genes upon cell wall stress. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1029-1039. [DOI: 10.1016/j.bbagrm.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/25/2018] [Accepted: 09/12/2018] [Indexed: 11/26/2022]
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19
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Liu L, Levin DE. Intracellular mechanism by which genotoxic stress activates yeast SAPK Mpk1. Mol Biol Cell 2018; 29:2898-2909. [PMID: 30230955 PMCID: PMC6249863 DOI: 10.1091/mbc.e18-07-0441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Stress-activated MAP kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPKs are not known. The Saccharomyces cerevisiae SAPK Mpk1 (Slt2) is a well-characterized component of the cell-wall integrity (CWI) signaling pathway, which responds to physical and chemical challenges to the cell wall. However, Mpk1 is also activated in response to genotoxic stress through an unknown pathway. We show that, in contrast to cell-wall stress, the pathway for Mpk1 activation by genotoxic stress does not involve the stimulation of the MAP kinase kinases (MEKs) that function immediately upstream of Mpk1. Instead, DNA damage activates Mpk1 through induction of proteasomal degradation of Msg5, the dual-specificity protein phosphatase principally responsible for maintaining Mpk1 in a low-activity state in the absence of stress. Blocking Msg5 degradation in response to genotoxic stress prevented Mpk1 activation. This work raises the possibility that other Mpk1-activating stressors act intracellularly at different points along the canonical Mpk1 activation pathway.
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Affiliation(s)
- Li Liu
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118
| | - David E Levin
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118.,Department of Microbiology, Boston University School of Medicine, Boston, MA 02118
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20
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Willis SD, Stieg DC, Ong KL, Shah R, Strich AK, Grose JH, Cooper KF. Snf1 cooperates with the CWI MAPK pathway to mediate the degradation of Med13 following oxidative stress. MICROBIAL CELL 2018; 5:357-370. [PMID: 30175106 PMCID: PMC6116281 DOI: 10.15698/mic2018.08.641] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells, when faced with unfavorable environmental conditions, mount either pro-survival or pro-death programs. The conserved cyclin C-Cdk8 kinase plays a key role in this decision. Both are members of the Cdk8 kinase module that, along with Med12 and Med13, associate with the core Mediator complex of RNA polymerase II. In Saccharomyces cerevisiae, oxidative stress triggers Med13 destruction, which releases cyclin C into the cytoplasm to promote mitochondrial fission and programmed cell death. The SCFGrr1 ubiquitin ligase mediates Med13 degradation dependent on the cell wall integrity pathway, MAPK Slt2. Here we show that the AMP kinase Snf1 activates a second SCFGrr1 responsive degron in Med13. Deletion of Snf1 resulted in nuclear retention of cyclin C and failure to induce mitochondrial fragmentation. This degron was able to confer oxidative-stress-induced destruction when fused to a heterologous protein in a Snf1 dependent manner. Although snf1∆ mutants failed to destroy Med13, deleting the degron did not prevent destruction. These results indicate that the control of Med13 degradation following H2O2 stress is complex, being controlled simultaneously by CWI and MAPK pathways.
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Affiliation(s)
- Stephen D Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA
| | - David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA
| | - Kai Li Ong
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Ravina Shah
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA.,Current address: Department of Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028. USA
| | - Alexandra K Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA.,Current address: Shawnee High School, Medford, New Jersey 08055, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA
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21
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RNA Polymerase II Transcription Attenuation at the Yeast DNA Repair Gene, DEF1, Involves Sen1-Dependent and Polyadenylation Site-Dependent Termination. G3-GENES GENOMES GENETICS 2018; 8:2043-2058. [PMID: 29686108 PMCID: PMC5982831 DOI: 10.1534/g3.118.200072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Termination of RNA Polymerase II (Pol II) activity serves a vital cellular role by separating ubiquitous transcription units and influencing RNA fate and function. In the yeast Saccharomyces cerevisiae, Pol II termination is carried out by cleavage and polyadenylation factor (CPF-CF) and Nrd1-Nab3-Sen1 (NNS) complexes, which operate primarily at mRNA and non-coding RNA genes, respectively. Premature Pol II termination (attenuation) contributes to gene regulation, but there is limited knowledge of its prevalence and biological significance. In particular, it is unclear how much crosstalk occurs between CPF-CF and NNS complexes and how Pol II attenuation is modulated during stress adaptation. In this study, we have identified an attenuator in the DEF1 DNA repair gene, which includes a portion of the 5′-untranslated region (UTR) and upstream open reading frame (ORF). Using a plasmid-based reporter gene system, we conducted a genetic screen of 14 termination mutants and their ability to confer Pol II read-through defects. The DEF1 attenuator behaved as a hybrid terminator, relying heavily on CPF-CF and Sen1 but without Nrd1 and Nab3 involvement. Our genetic selection identified 22 cis-acting point mutations that clustered into four regions, including a polyadenylation site efficiency element that genetically interacts with its cognate binding-protein Hrp1. Outside of the reporter gene context, a DEF1 attenuator mutant increased mRNA and protein expression, exacerbating the toxicity of a constitutively active Def1 protein. Overall, our data support a biologically significant role for transcription attenuation in regulating DEF1 expression, which can be modulated during the DNA damage response.
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22
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Karmakar S, Dey P, Vaz AP, Bhaumik SR, Ponnusamy MP, Batra SK. PD2/PAF1 at the Crossroads of the Cancer Network. Cancer Res 2018; 78:313-319. [PMID: 29311159 DOI: 10.1158/0008-5472.can-17-2175] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/29/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Pancreatic differentiation 2 (PD2)/RNA polymerase II-associated factor 1 (PAF1) is the core subunit of the human PAF1 complex (PAF1C) that regulates the promoter-proximal pausing of RNA polymerase II as well as transcription elongation and mRNA processing and coordinates events in mRNA stability and quality control. As an integral part of its transcription-regulatory function, PD2/PAF1 plays a role in posttranslational histone covalent modifications as well as regulates expression of critical genes of the cell-cycle machinery. PD2/PAF1 alone, and as a part of PAF1C, provides distinct roles in the maintenance of self-renewal of embryonic stem cells and cancer stem cells, and in lineage differentiation. Thus, PD2/PAF1 malfunction or its altered abundance is likely to affect normal cellular functions, leading to disease states. Indeed, PD2/PAF1 is found to be upregulated in poorly differentiated pancreatic cancer cells and has the capacity for neoplastic transformation when ectopically expressed in mouse fibroblast cells. Likewise, PD2/PAF1 is upregulated in pancreatic and ovarian cancer stem cells. Here, we concisely describe multifaceted roles of PD2/PAF1 associated with oncogenic transformation and implicate PD2/PAF1 as an attractive target for therapeutic development to combat malignancy. Cancer Res; 78(2); 313-9. ©2018 AACR.
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Affiliation(s)
- Saswati Karmakar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Parama Dey
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Arokia P Vaz
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska.,Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. .,Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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23
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Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell 2017; 68:913-925.e3. [PMID: 29220656 DOI: 10.1016/j.molcel.2017.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/21/2017] [Accepted: 11/15/2017] [Indexed: 12/28/2022]
Abstract
The RNA polymerase II largest subunit C-terminal domain consists of repeated YSPTSPS heptapeptides. The role of tyrosine-1 (Tyr1) remains incompletely understood, as, for example, mutating all Tyr1 residues to Phe (Y1F) is lethal in vertebrates but a related mutant has only a mild phenotype in S. pombe. Here we show that Y1F substitution in budding yeast resulted in a strong slow-growth phenotype. The Y1F strain was also hypersensitive to several different cellular stresses that involve MAP kinase signaling. These phenotypes were all linked to transcriptional changes, and we also identified genetic and biochemical interactions between Tyr1 and both transcription initiation and termination factors. Further studies uncovered defects related to MAP kinase I (Slt2) pathways, and we provide evidence that Slt2 phosphorylates Tyr1 in vitro and in vivo. Our study has thus identified Slt2 as a Tyr1 kinase, and in doing so provided links between stress response activation and Tyr1 phosphorylation.
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Affiliation(s)
- Nathan Yurko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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24
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The CWI Pathway: Regulation of the Transcriptional Adaptive Response to Cell Wall Stress in Yeast. J Fungi (Basel) 2017; 4:jof4010001. [PMID: 29371494 PMCID: PMC5872304 DOI: 10.3390/jof4010001] [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: 11/08/2017] [Revised: 12/11/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Fungi are surrounded by an essential structure, the cell wall, which not only confers cell shape but also protects cells from environmental stress. As a consequence, yeast cells growing under cell wall damage conditions elicit rescue mechanisms to provide maintenance of cellular integrity and fungal survival. Through transcriptional reprogramming, yeast modulate the expression of genes important for cell wall biogenesis and remodeling, metabolism and energy generation, morphogenesis, signal transduction and stress. The yeast cell wall integrity (CWI) pathway, which is very well conserved in other fungi, is the key pathway for the regulation of this adaptive response. In this review, we summarize the current knowledge of the yeast transcriptional program elicited to counterbalance cell wall stress situations, the role of the CWI pathway in the regulation of this program and the importance of the transcriptional input received by other pathways. Modulation of this adaptive response through the CWI pathway by positive and negative transcriptional feedbacks is also discussed. Since all these regulatory mechanisms are well conserved in pathogenic fungi, improving our knowledge about them will have an impact in the developing of new antifungal therapies.
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25
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Yurko NM, Manley JL. The RNA polymerase II CTD "orphan" residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7. Transcription 2017; 9:30-40. [PMID: 28771071 DOI: 10.1080/21541264.2017.1338176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of a unique repeated heptad sequence of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. An important function of the CTD is to couple transcription with RNA processing reactions that occur during the initiation, elongation, and termination phases of transcription. During this transcription cycle, the CTD is subject to extensive modification, primarily phosphorylation, on its non-proline residues. Reversible phosphorylation of Ser2 and Ser5 is well known to play important and general functions during transcription in all eukaryotes. More recent studies have enhanced our understanding of Tyr1, Thr4, and Ser7, and what have been previously characterized as unknown or specialized functions for these residues has changed to a more fine-detailed map of transcriptional regulation that highlights similarities as well as significant differences between organisms. Here, we review recent findings on the function and modification of these three residues, which further illustrate the importance of the CTD in precisely modulating gene expression.
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Affiliation(s)
- Nathan M Yurko
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - James L Manley
- a Department of Biological Sciences , Columbia University , New York , NY , USA
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26
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Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS Genet 2017; 13:e1006863. [PMID: 28665995 PMCID: PMC5513554 DOI: 10.1371/journal.pgen.1006863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/17/2017] [Accepted: 06/10/2017] [Indexed: 01/04/2023] Open
Abstract
Transcriptome studies on eukaryotic cells have revealed an unexpected abundance and diversity of noncoding RNAs synthesized by RNA polymerase II (Pol II), some of which influence the expression of protein-coding genes. Yet, much less is known about biogenesis of Pol II non-coding RNA than mRNAs. In the budding yeast Saccharomyces cerevisiae, initiation of non-coding transcripts by Pol II appears to be similar to that of mRNAs, but a distinct pathway is utilized for termination of most non-coding RNAs: the Sen1-dependent or “NNS” pathway. Here, we examine the effect on the S. cerevisiae transcriptome of conditional mutations in the genes encoding six different essential proteins that influence Sen1-dependent termination: Sen1, Nrd1, Nab3, Ssu72, Rpb11, and Hrp1. We observe surprisingly diverse effects on transcript abundance for the different proteins that cannot be explained simply by differing severity of the mutations. Rather, we infer from our results that termination of Pol II transcription of non-coding RNA genes is subject to complex combinatorial control that likely involves proteins beyond those studied here. Furthermore, we identify new targets and functions of Sen1-dependent termination, including a role in repression of meiotic genes in vegetative cells. In combination with other recent whole-genome studies on termination of non-coding RNAs, our results provide promising directions for further investigation. The information stored in the DNA of a cell’s chromosomes is transmitted to the rest of the cell by transcribing the DNA into RNA copies or “transcripts”. The fidelity of this process, and thus the health of the cell, depends critically on the proper function of proteins that direct transcription. Since hundreds of genes, each specifying a unique RNA transcript, are arranged in tandem along each chromosome, the beginning and end of each gene must be marked in the DNA sequence. Although encoded in DNA, the signal for terminating an RNA transcript is usually recognized in the transcript itself. We examined the genome-wide functional targets of six proteins implicated in transcription termination by identifying transcripts whose structure or abundance is altered by a mutation that compromises the activity of each protein. For a small minority of transcripts, a mutation in any of the six proteins disrupts termination. Much more commonly, a transcript is affected by a mutation in only one or a few of the six proteins, revealing the varying extent to which the proteins cooperate with one another. We discovered affected transcripts that were not known to be controlled by any of the six proteins, including a cohort of genes required for meiosis.
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Affiliation(s)
- Xin Chen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Melissa N. Carver
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Ulrika Müller
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (DAB); (DTA)
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail: (DAB); (DTA)
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27
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Fischl H, Howe FS, Furger A, Mellor J. Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate. Mol Cell 2017; 65:685-698.e8. [PMID: 28190769 PMCID: PMC5316414 DOI: 10.1016/j.molcel.2017.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
RNA polymerase II (Pol2) movement through chromatin and the co-transcriptional processing and fate of nascent transcripts is coordinated by transcription elongation factors (TEFs) such as polymerase-associated factor 1 (Paf1), but it is not known whether TEFs have gene-specific functions. Using strand-specific nucleotide resolution techniques, we show that levels of Paf1 on Pol2 vary between genes, are controlled dynamically by environmental factors via promoters, and reflect levels of processing and export factors on the encoded transcript. High levels of Paf1 on Pol2 promote transcript nuclear export, whereas low levels reflect nuclear retention. Strains lacking Paf1 show marked elongation defects, although low levels of Paf1 on Pol2 are sufficient for transcription elongation. Our findings support distinct Paf1 functions: a core general function in transcription elongation, satisfied by the lowest Paf1 levels, and a regulatory function in determining differential transcript fate by varying the level of Paf1 on Pol2.
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Affiliation(s)
- Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Françoise S Howe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andre Furger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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28
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Bresson S, Tuck A, Staneva D, Tollervey D. Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast. Mol Cell 2017; 65:787-800.e5. [PMID: 28190770 PMCID: PMC5344683 DOI: 10.1016/j.molcel.2017.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/10/2016] [Accepted: 01/05/2017] [Indexed: 12/31/2022]
Abstract
In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprogramming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV crosslinking immediately following glucose withdrawal (0, 4, and 8 min). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many growth-related mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. We conclude that transcription termination is followed by TRAMP-mediated RNA decay. Upregulated transcripts evaded increased surveillance factor binding following glucose withdrawal. Some upregulated genes showed use of alternative transcription starts to bypass strong NNS binding sites. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability. Changes in nuclear surveillance factor binding very rapidly follow nutritional shift Downregulated genes frequently show strongly increased surveillance factor binding Upregulated genes are protected against elevated surveillance factor binding The behavior of functionally related genes indicates posttranscriptional coregulation
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MESH Headings
- Adaptation, Physiological
- Binding Sites
- Cell Nucleus/metabolism
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Gene Expression Regulation, Fungal
- Glucose/deficiency
- Glucose/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA Processing, Post-Transcriptional
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Nuclear/genetics
- RNA, Nuclear/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Time Factors
- Transcription, Genetic
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Affiliation(s)
- Stefan Bresson
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Desislava Staneva
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland.
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29
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SHIN YK, KIM KY. Ampicillin activates Mpk1 phosphorylation in Saccharomyces cerevisiaeand ERK1/2 phosphorylation in HepG2 cells. Turk J Biol 2017. [DOI: 10.3906/biy-1611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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30
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Ugbogu EA, Wang K, Schweizer LM, Schweizer M. Metabolic gene products have evolved to interact with the cell wall integrity pathway inSaccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow092. [DOI: 10.1093/femsyr/fow092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
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31
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Sanz AB, García R, Rodríguez-Peña JM, Nombela C, Arroyo J. Cooperation between SAGA and SWI/SNF complexes is required for efficient transcriptional responses regulated by the yeast MAPK Slt2. Nucleic Acids Res 2016; 44:7159-72. [PMID: 27112564 PMCID: PMC5009723 DOI: 10.1093/nar/gkw324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 12/21/2022] Open
Abstract
The transcriptional response of Saccharomyces cerevisiae to cell wall stress is mainly mediated by the cell wall integrity (CWI) pathway through the MAPK Slt2 and the transcription factor Rlm1. Once activated, Rlm1 interacts with the chromatin remodeling SWI/SNF complex which locally alters nucleosome positioning at the target promoters. Here we show that the SAGA complex plays along with the SWI/SNF complex an important role for eliciting both early induction and sustained gene expression upon stress. Gcn5 co-regulates together with Swi3 the majority of the CWI transcriptional program, except for a group of genes which are only dependent on the SWI/SNF complex. SAGA subunits are recruited to the promoter of CWI-responsive genes in a Slt2, Rlm1 and SWI/SNF-dependent manner. However, Gcn5 mediates acetylation and nucleosome eviction only at the promoters of the SAGA-dependent genes. This process is not essential for pre-initiation transcriptional complex assembly but rather increase the extent of the remodeling mediated by SWI/SNF. As a consequence, H3 eviction and Rlm1 recruitment is completely blocked in a swi3Δ gcn5Δ double mutant. Therefore, SAGA complex, through its histone acetylase activity, cooperates with the SWI/SNF complex for the mandatory nucleosome displacement required for full gene expression through the CWI pathway.
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Affiliation(s)
- Ana Belén Sanz
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - Raúl García
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - José Manuel Rodríguez-Peña
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - César Nombela
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - Javier Arroyo
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
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32
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Goshen-Lago T, Goldberg-Carp A, Melamed D, Darlyuk-Saadon I, Bai C, Ahn NG, Admon A, Engelberg D. Variants of the yeast MAPK Mpk1 are fully functional independently of activation loop phosphorylation. Mol Biol Cell 2016; 27:2771-83. [PMID: 27413009 PMCID: PMC5007096 DOI: 10.1091/mbc.e16-03-0167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
MAPKs are catalytically and biologically active only when dually phosphorylated on a TEY motif. Mutations in the yeast MAPK Mpk1 are described that render it fully functional when mutated in its TEY motif and even when it carries a kinase-dead mutation. MAP kinases of the ERK family are conserved from yeast to humans. Their catalytic activity is dependent on dual phosphorylation of their activation loop’s TEY motif, catalyzed by MAPK kinases (MEKs). Here we studied variants of Mpk1, a yeast orthologue of Erk, which is essential for cell wall integrity. Cells lacking MPK1, or the genes encoding the relevant MEKs, MKK1 and MKK2, do not proliferate under cell wall stress, imposed, for example, by caffeine. Mutants of Mpk1, Mpk1(Y268C) and Mpk1(Y268A), function independently of Mkk1 and Mkk2. We show that these variants are phosphorylated at their activation loop in mkk1∆mkk2∆ and mkk1∆mkk2∆pbs2∆ste7∆ cells, suggesting that they autophosphorylate. However, strikingly, when Y268C/A mutations were combined with the kinase-dead mutation, K54R, or mutations at the TEY motif, T190A+Y192F, the resulting proteins still allowed mkk1∆mkk2∆ cells to proliferate under caffeine stress. Mutating the equivalent residue, Tyr-280/Tyr-261, in Erk1/Erk2 significantly impaired Erk1/2’s catalytic activity. This study describes the first case in which a MAPK, Erk/Mpk1, imposes a phenotype via a mechanism that is independent of TEY phosphorylation and an unusual case in which an equivalent mutation in a highly conserved domain of yeast and mammalian Erks causes an opposite effect.
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Affiliation(s)
- Tal Goshen-Lago
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Anat Goldberg-Carp
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dganit Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ilona Darlyuk-Saadon
- CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
| | - Chen Bai
- CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - David Engelberg
- Department of Biological Chemistry, Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 91904, Israel CREATE-NUS-HUJ, Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore, Singapore 138602 Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
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33
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García R, Sanz AB, Rodríguez-Peña JM, Nombela C, Arroyo J. Rlm1 mediates positive autoregulatory transcriptional feedback that is essential for Slt2-dependent gene expression. J Cell Sci 2016; 129:1649-60. [PMID: 26933180 DOI: 10.1242/jcs.180190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/22/2016] [Indexed: 11/20/2022] Open
Abstract
Activation of the yeast cell wall integrity (CWI) pathway induces an adaptive transcriptional programme that is largely dependent on the transcription factor Rlm1 and the mitogen-activated protein kinase (MAPK) Slt2. Upon cell wall stress, the transcription factor Rlm1 is recruited to the promoters of RLM1 and SLT2, and exerts positive-feedback mechanisms on the expression of both genes. Activation of the MAPK Slt2 by cell wall stress is not impaired in strains with individual blockade of any of the two feedback pathways. Abrogation of the autoregulatory feedback mechanism on RLM1 severely affects the transcriptional response elicited by activation of the CWI pathway. In contrast, a positive trans-acting feedback mechanism exerted by Rlm1 on SLT2 also regulates CWI output responses but to a lesser extent. Therefore, a complete CWI transcriptional response requires not only phosphorylation of Rlm1 by Slt2 but also concurrent SLT2- and RLM1-mediated positive-feedback mechanisms; sustained patterns of gene expression are mainly achieved by positive autoregulatory circuits based on the transcriptional activation of Rlm1.
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Affiliation(s)
- Raúl García
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid 28040, Spain
| | - Ana Belén Sanz
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid 28040, Spain
| | - José Manuel Rodríguez-Peña
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid 28040, Spain
| | - César Nombela
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid 28040, Spain
| | - Javier Arroyo
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid 28040, Spain
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34
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The regulation and functions of the nuclear RNA exosome complex. Nat Rev Mol Cell Biol 2016; 17:227-39. [PMID: 26726035 DOI: 10.1038/nrm.2015.15] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA exosome complex is the most versatile RNA-degradation machine in eukaryotes. The exosome has a central role in several aspects of RNA biogenesis, including RNA maturation and surveillance. Moreover, it is emerging as an important player in regulating the expression levels of specific mRNAs in response to environmental cues and during cell differentiation and development. Although the mechanisms by which RNA is targeted to (or escapes from) the exosome are still not fully understood, general principles have begun to emerge, which we discuss in this Review. In addition, we introduce and discuss novel, previously unappreciated functions of the nuclear exosome, including in transcription regulation and in the maintenance of genome stability.
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35
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Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO Rep 2015; 16:1673-87. [PMID: 26518661 PMCID: PMC4687421 DOI: 10.15252/embr.201541214] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/05/2015] [Indexed: 11/21/2022] Open
Abstract
The maintenance of open and repressed chromatin states is crucial for the regulation of gene expression. To study the genes involved in maintaining chromatin states, we generated a random mutant library in Schizosaccharomyces pombe and monitored the silencing of reporter genes inserted into the euchromatic region adjacent to the heterochromatic mating type locus. We show that Leo1–Paf1 [a subcomplex of the RNA polymerase II‐associated factor 1 complex (Paf1C)] is required to prevent the spreading of heterochromatin into euchromatin by mapping the heterochromatin mark H3K9me2 using high‐resolution genomewide ChIP (ChIP–exo). Loss of Leo1–Paf1 increases heterochromatin stability at several facultative heterochromatin loci in an RNAi‐independent manner. Instead, deletion of Leo1 decreases nucleosome turnover, leading to heterochromatin stabilization. Our data reveal that Leo1–Paf1 promotes chromatin state fluctuations by enhancing histone turnover.
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Affiliation(s)
- Laia Sadeghi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Punit Prasad
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Amikam Cohen
- Department of Microbiology and Molecular Genetics, IMRIC The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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36
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Flocculation inSaccharomyces cerevisiaeis regulated by RNA/DNA helicase Sen1p. FEBS Lett 2015; 589:3165-74. [DOI: 10.1016/j.febslet.2015.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/13/2022]
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37
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Abstract
The immunoglobulin diversification processes of somatic hypermutation and class switch recombination critically rely on transcription-coupled targeting of activation-induced cytidine deaminase (AID) to Ig loci in activated B lymphocytes. AID catalyzes deamination of cytidine deoxynucleotides on exposed single-stranded DNA. In addition to driving immunoglobulin diversity, promiscuous targeting of AID mutagenic activity poses a deleterious threat to genomic stability. Recent genome-wide studies have uncovered pervasive AID activity throughout the B cell genome. It is increasingly apparent that AID activity is frequently targeted to genomic loci undergoing early transcription termination where RNA exosome promotes the resolution of stalled transcription complexes via cotranscriptional RNA degradation mechanisms. Here, we review aspects and consequences of eukaryotic transcription that lead to early termination, RNA exosome recruitment, and ultimately targeting of AID mutagenic activity.
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Affiliation(s)
- Evangelos Pefanis
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
| | - Uttiya Basu
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
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38
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Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Differential genetic interactions of yeast stress response MAPK pathways. Mol Syst Biol 2015; 11:800. [PMID: 25888283 PMCID: PMC4422557 DOI: 10.15252/msb.20145606] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. However, most studies have been performed under optimal growth conditions even though many functional interactions are known to occur under specific cellular conditions. In this study, we have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. We found an extensive number of conditional genetic interactions that recapitulate known stress-specific functional associations. Furthermore, we have also uncovered previously unrecognized roles involving the phosphatase regulator Bud14, the histone methylation complex COMPASS and membrane trafficking complexes in modulating the cell wall integrity pathway. Finally, the osmotic stress differential genetic interactions showed enrichment for genes coding for proteins with conditional changes in phosphorylation but not for genes with conditional changes in gene expression. This suggests that conditional genetic interactions are a powerful tool to dissect the functional importance of the different response mechanisms of the cell.
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Affiliation(s)
- Humberto Martin
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA
| | - Pablo Fernandez-Piñar
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Ping Wei
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Maria Molina
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Dorothea Fiedler
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Kevan M Shokat
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK iBiMED and Department of Health Sciences, University of Aveiro, Aveiro, Portugal
| | - Wendell Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA Howard Hughes Medical Institute, University of California, San Francisco, CA, USA Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA J. David Gladstone Institutes, San Francisco, CA, USA
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39
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Miller MS, Rialdi A, Ho JSY, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JAT, Feagins AR, Basler CF, Fernandez-Sesma A, Becherel OJ, Lavin MF, van Bakel H, Marazzi I. Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis. Nat Immunol 2015; 16:485-94. [PMID: 25822250 PMCID: PMC4406851 DOI: 10.1038/ni.3132] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/27/2015] [Indexed: 12/14/2022]
Abstract
The human helicase senataxin (SETX) has been linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2). Here we identified a role for SETX in controlling the antiviral response. Cells that had undergone depletion of SETX and SETX-deficient cells derived from patients with AOA2 had higher expression of antiviral mediators in response to infection than did wild-type cells. Mechanistically, we propose a model whereby SETX attenuates the activity of RNA polymerase II (RNAPII) at genes stimulated after a virus is sensed and thus controls the magnitude of the host response to pathogens and the biogenesis of various RNA viruses (e.g., influenza A virus and West Nile virus). Our data indicate a potentially causal link among inborn errors in SETX, susceptibility to infection and the development of neurologic disorders.
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Affiliation(s)
- Matthew S Miller
- 1] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Biochemistry and Biomedical Sciences, Institute for Infectious Diseases Research, McMaster Immunology Research Centre, McMaster University, Hamilton, Canada
| | - Alexander Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Sook Yuin Ho
- Laboratory of Methyltransferases in Development and Disease, Institute of Molecular and Cell Biology, Singapore
| | - Micah Tilove
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luis Martinez-Gil
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Natasha P Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zuleyma Peralta
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Justine Noel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Camilla Melegari
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana M Maestre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Panagiotis Mitsopoulos
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Joaquín Madrenas
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Sven Heinz
- The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Chris Benner
- The Salk Institute for Biological Studies, La Jolla, California, USA
| | | | - Alicia R Feagins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Olivier J Becherel
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Martin F Lavin
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Harm van Bakel
- 1] Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ivan Marazzi
- 1] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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40
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Abstract
The RNA polymerase II transcription cycle is often divided into three major stages: initiation, elongation, and termination. Research over the last decade has blurred these divisions and emphasized the tightly regulated transitions that occur as RNA polymerase II synthesizes a transcript from start to finish. Transcription termination, the process that marks the end of transcription elongation, is regulated by proteins that interact with the polymerase, nascent transcript, and/or chromatin template. The failure to terminate transcription can cause accumulation of aberrant transcripts and interfere with transcription at downstream genes. Here, we review the mechanism, regulation, and physiological impact of a termination pathway that targets small noncoding transcripts produced by RNA polymerase II. We emphasize the Nrd1-Nab3-Sen1 pathway in yeast, in which the process has been extensively studied. The importance of understanding small RNA termination pathways is underscored by the need to control noncoding transcription in eukaryotic genomes.
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Affiliation(s)
- Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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41
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Porrua O, Libri D. Transcription termination and the control of the transcriptome: why, where and how to stop. Nat Rev Mol Cell Biol 2015; 16:190-202. [DOI: 10.1038/nrm3943] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sakata T, Fujii K, Ohno M, Kitabatake M. Crt10 directs the cullin-E3 ligase Rtt101 to nonfunctional 25S rRNA decay. Biochem Biophys Res Commun 2014; 457:90-4. [PMID: 25534857 DOI: 10.1016/j.bbrc.2014.12.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/13/2014] [Indexed: 01/04/2023]
Abstract
Nonfunctional mutant ribosomal RNAs in 40S or 60S subunits are selectively degraded in eukaryotic cells (nonfunctional rRNA decay, NRD). We previously reported that NRD of 25S rRNA required cullin-E3 ligase Rtt101 and its associating factor Mms1, both of which are involved in DNA repair. Although Mms22, an accessory component of the E3 complex, was suggested to direct the E3 complex to DNA repair, the factor that directs the complex to 25S NRD currently remains unknown. We herein demonstrated that another accessory component, Crt10 was required for 25S NRD, but not for DNA repair, suggesting that this accessory component specifies the function of the E3 complex differently. We also identified two distinct Crt10-containing E3 complexes, one of which contained the Paf1 complex, a Pol-II binding complex that modulates the transcription of stress-related genes. Our results showed the convergence of multiple pathways for stresses that harm nucleic acids and provided a molecular framework for the substrate diversity of the E3 complex.
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Affiliation(s)
- Tomoko Sakata
- Institute for Virus Research, Kyoto University, Shogoin-Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kotaro Fujii
- Institute for Virus Research, Kyoto University, Shogoin-Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Virus Research, Kyoto University, Shogoin-Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Makoto Kitabatake
- Institute for Virus Research, Kyoto University, Shogoin-Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan.
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Chen Y, Zhang L, Estarás C, Choi SH, Moreno L, Karn J, Moresco JJ, Yates JR, Jones KA. A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. Genes Dev 2014; 28:2261-75. [PMID: 25319827 PMCID: PMC4201287 DOI: 10.1101/gad.250449.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HIV-1 Tat stimulates transcription elongation by recruiting the P-TEFb (positive transcription elongation factor-b) (CycT1:CDK9) C-terminal domain (CTD) kinase to the HIV-1 promoter. Here we show that Tat transactivation also requires the Ssu72 CTD Ser5P (S5P)-specific phosphatase, which mediates transcription termination and intragenic looping at eukaryotic genes. Importantly, HIV-1 Tat interacts directly with Ssu72 and strongly stimulates its CTD phosphatase activity. We found that Ssu72 is essential for Tat:P-TEFb-mediated phosphorylation of the S5P-CTD in vitro. Interestingly, Ssu72 also stimulates nascent HIV-1 transcription in a phosphatase-dependent manner in vivo. Chromatin immunoprecipitation (ChIP) experiments reveal that Ssu72, like P-TEFb and AFF4, is recruited by Tat to the integrated HIV-1 proviral promoter in TNF-α signaling 2D10 T cells and leaves the elongation complex prior to the termination site. ChIP-seq (ChIP combined with deep sequencing) and GRO-seq (genome-wide nuclear run-on [GRO] combined with deep sequencing) analysis further reveals that Ssu72 predominantly colocalizes with S5P-RNAPII (RNA polymerase II) at promoters in human embryonic stem cells, with a minor peak in the terminator region. A few genes, like NANOG, also have high Ssu72 at the terminator. Ssu72 is not required for transcription at most cellular genes but has a modest effect on cotranscriptional termination. We conclude that Tat alters the cellular function of Ssu72 to stimulate viral gene expression and facilitate the early S5P-S2P transition at the integrated HIV-1 promoter.
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Affiliation(s)
- Yupeng Chen
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lirong Zhang
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Conchi Estarás
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Seung H Choi
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Luis Moreno
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - James J Moresco
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John R Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
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Engelsdorf T, Hamann T. An update on receptor-like kinase involvement in the maintenance of plant cell wall integrity. ANNALS OF BOTANY 2014; 114:1339-47. [PMID: 24723447 PMCID: PMC4195549 DOI: 10.1093/aob/mcu043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant cell walls form the interface between the cells and their environment. They perform different functions, such as protecting cells from biotic and abiotic stress and providing structural support during development. Maintenance of the functional integrity of cell walls during these different processes is a prerequisite that enables the walls to perform their particular functions. The available evidence suggests that an integrity maintenance mechanism exists in plants that is capable of both detecting wall integrity impairment caused by cell wall damage and initiating compensatory responses to maintain functional integrity. The responses involve 1-aminocyclopropane-1-carboxylic acid (ACC), jasmonic acid, reactive oxygen species and calcium-based signal transduction cascades as well as the production of lignin and other cell wall components. Experimental evidence implicates clearly different signalling molecules, but knowledge regarding contributions of receptor-like kinases to this process is less clear. Different receptor-like kinase families have been considered as possible sensors for perception of cell wall damage; however, strong experimental evidence that provides insights into functioning exists for very few kinases. SCOPE AND CONCLUSIONS This review examines the involvement of cell wall integrity maintenance in different biological processes, defines what constitutes plant cell wall damage that impairs functional integrity, clarifies which stimulus perception and signal transduction mechanisms are required for integrity maintenance and assesses the available evidence regarding the functions of receptor-like kinases during cell wall integrity maintenance. The review concludes by discussing how the plant cell wall integrity maintenance mechanism could form an essential component of biotic stress responses and of plant development, functions that have not been fully recognized to date.
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Affiliation(s)
- Timo Engelsdorf
- Department of Biology, Høgskoleringen 5, Realfagbygget, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Thorsten Hamann
- Department of Biology, Høgskoleringen 5, Realfagbygget, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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45
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Engelberg D, Perlman R, Levitzki A. Transmembrane signaling in Saccharomyces cerevisiae as a model for signaling in metazoans: state of the art after 25 years. Cell Signal 2014; 26:2865-78. [PMID: 25218923 DOI: 10.1016/j.cellsig.2014.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/02/2014] [Indexed: 02/07/2023]
Abstract
In the very first article that appeared in Cellular Signalling, published in its inaugural issue in October 1989, we reviewed signal transduction pathways in Saccharomyces cerevisiae. Although this yeast was already a powerful model organism for the study of cellular processes, it was not yet a valuable instrument for the investigation of signaling cascades. In 1989, therefore, we discussed only two pathways, the Ras/cAMP and the mating (Fus3) signaling cascades. The pivotal findings concerning those pathways undoubtedly contributed to the realization that yeast is a relevant model for understanding signal transduction in higher eukaryotes. Consequently, the last 25 years have witnessed the discovery of many signal transduction pathways in S. cerevisiae, including the high osmotic glycerol (Hog1), Stl2/Mpk1 and Smk1 mitogen-activated protein (MAP) kinase pathways, the TOR, AMPK/Snf1, SPS, PLC1 and Pkr/Gcn2 cascades, and systems that sense and respond to various types of stress. For many cascades, orthologous pathways were identified in mammals following their discovery in yeast. Here we review advances in the understanding of signaling in S. cerevisiae over the last 25 years. When all pathways are analyzed together, some prominent themes emerge. First, wiring of signaling cascades may not be identical in all S. cerevisiae strains, but is probably specific to each genetic background. This situation complicates attempts to decipher and generalize these webs of reactions. Secondly, the Ras/cAMP and the TOR cascades are pivotal pathways that affect all processes of the life of the yeast cell, whereas the yeast MAP kinase pathways are not essential. Yeast cells deficient in all MAP kinases proliferate normally. Another theme is the existence of central molecular hubs, either as single proteins (e.g., Msn2/4, Flo11) or as multisubunit complexes (e.g., TORC1/2), which are controlled by numerous pathways and in turn determine the fate of the cell. It is also apparent that lipid signaling is less developed in yeast than in higher eukaryotes. Finally, feedback regulatory mechanisms seem to be at least as important and powerful as the pathways themselves. In the final chapter of this essay we dare to imagine the essence of our next review on signaling in yeast, to be published on the 50th anniversary of Cellular Signalling in 2039.
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Affiliation(s)
- David Engelberg
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; CREATE-NUS-HUJ, Cellular & Molecular Mechanisms of Inflammation Programme, National University of Singapore, 1 CREATE Way, Innovation Wing, #03-09, Singapore 138602, Singapore.
| | - Riki Perlman
- Hematology Division, Hadassah Hebrew University Medical Center, POB 12000, 91120 Jerusalem, Israel
| | - Alexander Levitzki
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Strich R, Cooper KF. The dual role of cyclin C connects stress regulated gene expression to mitochondrial dynamics. MICROBIAL CELL 2014; 1:318-324. [PMID: 28357211 PMCID: PMC5349174 DOI: 10.15698/mic2014.10.169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Following exposure to cytotoxic agents, cellular damage is first recognized by a
variety of sensor mechanisms. Thenceforth, the damage signal is transduced to
the nucleus to install the correct gene expression program including the
induction of genes whose products either detoxify destructive compounds or
repair the damage they cause. Next, the stress signal is disseminated throughout
the cell to effect the appropriate changes at organelles including the
mitochondria. The mitochondria represent an important signaling platform for the
stress response. An initial stress response of the mitochondria is extensive
fragmentation. If the damage is prodigious, the mitochondria fragment (fission)
and lose their outer membrane integrity leading to the release of pro-apoptotic
factors necessary for programmed cell death (PCD) execution. As this complex
biological process contains many moving parts, it must be exquisitely
coordinated as the ultimate decision is life or death. The conserved C-type
cyclin plays an important role in executing this molecular Rubicon by coupling
changes in gene expression to mitochondrial fission and PCD. Cyclin C, along
with its cyclin dependent kinase partner Cdk8, associates with the RNA
polymerase holoenzyme to regulate transcription. In particular, cyclin C-Cdk8
repress many stress responsive genes. To relieve this repression, cyclin C is
destroyed in cells exposed to pro-oxidants and other stressors. However, prior
to its destruction, cyclin C, but not Cdk8, is released from its nuclear anchor
(Med13), translocates from the nucleus to the cytoplasm where it interacts with
the fission machinery and is both necessary and sufficient to induce extensive
mitochondria fragmentation. Furthermore, cytoplasmic cyclin C promotes PCD
indicating that it mediates both mitochondrial fission and cell death pathways.
This review will summarize the role cyclin C plays in regulating
stress-responsive transcription. In addition, we will detail this new function
mediating mitochondrial fission and PCD. Although both these roles of cyclin C
are conserved, this review will concentrate on cyclin C's dual role in the
budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Randy Strich
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford NJ, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford NJ, USA
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Grzechnik P, Tan-Wong SM, Proudfoot NJ. Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 2014; 39:319-27. [PMID: 24928762 PMCID: PMC4085477 DOI: 10.1016/j.tibs.2014.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 01/28/2023]
Abstract
Transcriptional directionality is controlled by premature transcription termination. Transcriptional directionality is enforced by gene looping. mRNA-specific termination signals and factors are required for gene looping.
Bidirectional promoters are a common feature of many eukaryotic organisms from yeast to humans. RNA Polymerase II that is recruited to this type of promoter can start transcribing in either direction using alternative DNA strands as the template. Such promiscuous transcription can lead to the synthesis of unwanted transcripts that may have negative effects on gene expression. Recent studies have identified transcription termination and gene looping as critical players in the enforcement of promoter directionality. Interestingly, both mechanisms share key components. Here, we focus on recent findings relating to the transcriptional output of bidirectional promoters.
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Affiliation(s)
- Pawel Grzechnik
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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The PAF1 complex is involved in embryonic epidermal morphogenesis in Caenorhabditis elegans. Dev Biol 2014; 391:43-53. [PMID: 24721716 DOI: 10.1016/j.ydbio.2014.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 03/29/2014] [Accepted: 04/02/2014] [Indexed: 11/21/2022]
Abstract
The PAF1 complex (PAF1C) is an evolutionarily conserved protein complex involved in transcriptional regulation and chromatin remodeling. How the PAF1C is involved in animal development is still not well understood. Here, we report that, in the nematode Caenorhabditis elegans, the PAF1C is involved in epidermal morphogenesis in late embryogenesis. From an RNAi screen we identified the C. elegans ortholog of a component of the PAF1C, CTR-9, as a gene whose depletion caused various defects during embryonic epidermal morphogenesis, including epidermal cell positioning, ventral enclosure and epidermal elongation. RNAi of orthologs of other four components of the PAF1C (PAFO-1, LEO-1, CDC-73 and RTFO-1) caused similar epidermal defects. In these embryos, whereas the number and cell fate determination of epidermal cells were apparently unaffected, their position and shape were severely disorganized. PAFO-1::mCherry, mCherry::LEO-1 and GFP::RTFO-1 driven by the authentic promoters were detected in the nuclei of a wide range of cells. Nuclear localization of GFP::RTFO-1 was independent of other PAF1C components, while PAFO-1::mCherry and mCherry::LEO-1 dependent on other components except RTFO-1. Epidermis-specific expression of mCherry::LEO-1 rescued embryonic lethality of the leo-1 deletion mutant. Thus, although the PAF1C is universally expressed in C. elegans embryos, its epidermal function is crucial for the viability of this animal.
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49
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Jin C, Strich R, Cooper KF. Slt2p phosphorylation induces cyclin C nuclear-to-cytoplasmic translocation in response to oxidative stress. Mol Biol Cell 2014; 25:1396-407. [PMID: 24554767 PMCID: PMC3983003 DOI: 10.1091/mbc.e13-09-0550] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The conserved transcription factor cyclin C is both translocated to the cytoplasm and destroyed after oxidative stress. The signaling pathway that transmits the stress signal to cyclin C is complex and uses both the MAPK Slt2p and its pseudokinase homologue, Kdx1, via different mechanisms. The yeast C-type cyclin represses the transcription of genes required for the stress response and meiosis. To relieve this repression, cyclin C undergoes nuclear-to-cytoplasmic translocation in response to many stressors, including hydrogen peroxide, where it is destroyed by ubiquitin-mediated proteolysis. Before its destruction, cyclin C promotes stress-induced mitochondrial fission and programmed cell death, indicating that relocalization is an important cell fate regulator. Here we show that cyclin C cytoplasmic translocation requires the cell wall integrity (CWI) mitogen-activated protein kinase Slt2p, its pseudokinase paralogue, Kdx1p, and an associating transcription factor, Ask10p. Furthermore, Slt2p and Kdx1p regulate cyclin C stability through different but required mechanisms. Slt2p associates with, and directly phosphorylates, cyclin C at Ser-266. Eliminating or mimicking phosphorylation at this site restricts or enhances cyclin C cytoplasmic translocation and degradation, respectively. Conversely, Kdx1p does not bind cyclin C but instead coimmunoprecipitates with Ask10p, a transcription factor previously identified as a regulator of cyclin C destruction. These results reveal a complex regulatory circuitry involving both downstream effectors of the CWI mitogen-activated protein kinase signal transduction pathway to target the relocalization and consequent destruction of a single transcriptional repressor.
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Affiliation(s)
- Chunyan Jin
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084
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50
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Madak-Erdogan Z, Ventrella R, Petry L, Katzenellenbogen BS. Novel roles for ERK5 and cofilin as critical mediators linking ERα-driven transcription, actin reorganization, and invasiveness in breast cancer. Mol Cancer Res 2014; 12:714-27. [PMID: 24505128 DOI: 10.1158/1541-7786.mcr-13-0588] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
UNLABELLED Cancer cell motility and invasiveness are fundamental characteristics of the malignant phenotype and are regulated through diverse signaling networks involving kinases and transcription factors. This study establishes an estrogen receptor (ERα)/MAPK (ERK5)/cofilin (CFL1) network that specifies the degree of breast cancer cell aggressiveness through coupling of actin reorganization and hormone receptor-mediated transcription. Using dominant negative and constitutively active forms, as well as small-molecule inhibitors of extracellular signal-regulated kinase (ERK)5 and MAP-ERK kinase (MEK)5, it was revealed that hormone activation of ERα determined the subcellular localization of ERK5, which functions as a coregulator of ERα-dependent gene transcription. Notably, ERK5 acted in concert with the actin remodeling protein, CFL1, and upon hormone exposure, both localized to active nuclear transcriptional hubs as verified by immunofluorescence and proximity ligation assays. Both ERK5 and CFL1 facilitated PAF1 recruitment to the RNA Pol II complex and both were required for regulation of gene transcription. In contrast, in cells lacking ERα, ERK5 and CFL1 localized to cytoplasmic membrane regions of high actin remodeling, promoting cell motility and invasion, thereby revealing a mechanism likely contributing to the generally poorer prognosis of patients with ERα-negative breast cancer. Thus, this study uncovers the dynamic interplay of nuclear receptor-mediated transcription and actin reorganization in phenotypes of breast cancer aggressiveness. IMPLICATIONS Identification of the ER/ERK5/CFL1 axis suggests new prognostic biomarkers and novel therapeutic avenues to moderate cancer aggressiveness.
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Affiliation(s)
- Zeynep Madak-Erdogan
- Authors' Affiliation: Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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