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Golebiowski F, Matic I, Tatham MH, Cole C, Yin Y, Nakamura A, Cox J, Barton GJ, Mann M, Hay RT. System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2009; 2:ra24. [PMID: 19471022 DOI: 10.1126/scisignal.2000282] [Citation(s) in RCA: 394] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Covalent conjugation of the small ubiquitin-like modifier (SUMO) proteins to target proteins regulates many important eukaryotic cellular mechanisms. Although the molecular consequences of the conjugation of SUMO proteins are relatively well understood, little is known about the cellular signals that regulate the modification of their substrates. Here, we show that SUMO-2 and SUMO-3 are required for cells to survive heat shock. Through quantitative labeling techniques, stringent purification of SUMOylated proteins, advanced mass spectrometric technology, and novel techniques of data analysis, we quantified heat shock-induced changes in the SUMOylation state of 766 putative substrates. In response to heat shock, SUMO was polymerized into polySUMO chains and redistributed among a wide range of proteins involved in cell cycle regulation; apoptosis; the trafficking, folding, and degradation of proteins; transcription; translation; and DNA replication, recombination, and repair. This comprehensive proteomic analysis of the substrates of a ubiquitin-like modifier (Ubl) identifies a pervasive role for SUMO proteins in the biologic response to hyperthermic stress.
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Affiliation(s)
- Filip Golebiowski
- 1Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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52
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Zabolotskaya MV, Grima DP, Lin MD, Chou TB, Newbury SF. The 5'-3' exoribonuclease Pacman is required for normal male fertility and is dynamically localized in cytoplasmic particles in Drosophila testis cells. Biochem J 2008; 416:327-35. [PMID: 18652574 DOI: 10.1042/bj20071720] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The exoribonuclease Xrn1 is widely recognised as a key component in the 5'-3' RNA degradation pathway. This enzyme is highly conserved between yeast and humans and is known to be involved in RNA interference and degradation of microRNAs as well as RNA turnover. In yeast and human tissue culture cells, Xrn1 has been shown to be a component of P-bodies (processing bodies), dynamic cytoplasmic granules where RNA degradation can take place. In this paper we show for the first time that Pacman, the Drosophila homologue of Xrn1, is localized in cytoplasmic particles in Drosophila testis cells. These particles are present in both the mitotically dividing spermatogonia derived from primordial stem cells and in the transcriptionally active spermatocytes. Pacman is co-localized with the decapping activator dDcp1 and the helicase Me31B (a Dhh1 homologue) in these particles, although this co-localization is not completely overlapping, suggesting that there are different compartments within these granules. Particles containing Pacman respond to stress and depletion of 5'-3' decay factors in the same way as yeast P-bodies, and therefore are likely to be sites of mRNA degradation or storage. Pacman is shown to be required for normal Drosophila spermatogenesis, suggesting that control of mRNA stability is crucial in the testis differentiation pathway.
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Affiliation(s)
- Maria V Zabolotskaya
- Brighton and Sussex Medical School, Medical Research Building, University of Sussex, Brighton BN1 9PS, UK
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53
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Nevarez L, Vasseur V, Le Dréan G, Tanguy A, Guisle-Marsollier I, Houlgatte R, Barbier G. Isolation and analysis of differentially expressed genes in Penicillium glabrum subjected to thermal stress. Microbiology (Reading) 2008; 154:3752-3765. [PMID: 19047743 DOI: 10.1099/mic.0.2008/021386-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- L. Nevarez
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - V. Vasseur
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - G. Le Dréan
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - A. Tanguy
- Evolution et Génétique des Populations Marines, UMR CNRS 7144, Université Pierre et Marie Curie, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff Cedex, France
| | - I. Guisle-Marsollier
- Plate-forme Transcriptomique Ouest-Génopôle, Institut du Thorax INSERM U533, 1 Rue Gaston Veil, BP 53508, 44035 Nantes, Cedex 1, France
| | - R. Houlgatte
- Plate-forme Transcriptomique Ouest-Génopôle, Institut du Thorax INSERM U533, 1 Rue Gaston Veil, BP 53508, 44035 Nantes, Cedex 1, France
| | - G. Barbier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
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54
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Lin MD, Jiao X, Grima D, Newbury SF, Kiledjian M, Chou TB. Drosophila processing bodies in oogenesis. Dev Biol 2008; 322:276-88. [PMID: 18708044 DOI: 10.1016/j.ydbio.2008.07.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 07/14/2008] [Accepted: 07/15/2008] [Indexed: 11/17/2022]
Abstract
Processing bodies (P-bodies) have emerged as important subcellular structures that are involved in mRNA metabolism. To date, a detailed description of P-bodies in Drosophila oogenesis is lacking. To this end, we first demonstrate that Drosophila decapping protein 2 (dDcp2) contains intrinsic decapping activity and its enzymatic activity was not detectably enhanced by Drosophila decapping protein 1 (dDcp1). dDcp1-containing bodies in the nurse cell cytoplasm can associate with the 5' to 3' exoribonuclease, Pacman in addition to dDcp2 and Me31B. The size and number of dDcp1 bodies are dynamic and dramatically increased in dDcp2 and pacman mutant backgrounds supporting the conclusion that dDcp1 bodies in nurse cell cytoplasm are Drosophila P-bodies. In stage 2-6 oocytes, dDcp1 bodies appear to be distinct from previously characterized P-bodies since they are insensitive to cycloheximide and RNase A treatments. Curiously, dDcp2 and Pacman do not colocalize with dDcp1 at the posterior end of the oocyte in stage 9-10 oocytes. This suggests that dDcp1 bodies are in a developmentally distinct state separate from the 5' end mRNA degradation enzymes at later stages in the oocyte. Interestingly, re-formation of maternally expressed dDcp1 with dDcp2 and Pacman was observed in early embryogenesis. With respect to developmental switching, the maternal dDcp1 is proposed to serve as a marker for the re-formation of P-bodies in early embryos. This also suggests that a regulated conversion occurs between maternal RNA granules and P-bodies from oogenesis to embryogenesis.
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Affiliation(s)
- Ming-Der Lin
- Institute of Molecular and Cellular Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
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55
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Kramer S, Queiroz R, Ellis L, Webb H, Hoheisel JD, Clayton C, Carrington M. Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. J Cell Sci 2008; 121:3002-14. [PMID: 18713834 PMCID: PMC2871294 DOI: 10.1242/jcs.031823] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In trypanosomes there is an almost total reliance on post-transcriptional mechanisms to alter gene expression; here, heat shock was used to investigate the response to an environmental signal. Heat shock rapidly and reversibly induced a decrease in polysome abundance, and the consequent changes in mRNA metabolism were studied. Both heat shock and polysome dissociation were necessary for (1) a reduction in mRNA levels that was more rapid than normal turnover, (2) an increased number of P-body-like granules that contained DHH1, SCD6 and XRNA, (3) the formation of stress granules that remained largely separate from the P-body-like granules and localise to the periphery of the cell and, (4) an increase in the size of a novel focus located at the posterior pole of the cell that contain XRNA, but neither DHH1 nor SCD6. The response differed from mammalian cells in that neither the decrease in polysomes nor stress-granule formation required phosphorylation of eIF2alpha at the position homologous to that of serine 51 in mammalian eIF2alpha and in the occurrence of a novel XRNA-focus.
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Affiliation(s)
- Susanne Kramer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA , UK
| | - Rafael Queiroz
- ZMBH, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Louise Ellis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA , UK
| | - Helena Webb
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA , UK
| | - Jörg D. Hoheisel
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | | | - Mark Carrington
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA , UK
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DeGracia DJ, Jamison JT, Szymanski JJ, Lewis MK. Translation arrest and ribonomics in post-ischemic brain: layers and layers of players. J Neurochem 2008; 106:2288-301. [PMID: 18627434 PMCID: PMC2574835 DOI: 10.1111/j.1471-4159.2008.05561.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A persistent translation arrest (TA) correlates precisely with the selective vulnerability of post-ischemic neurons. Mechanisms of post-ischemic TA that have been assessed include ribosome biochemistry, the link between TA and stress responses, and the inactivation of translational components via sequestration in subcellular structures. Each of these approaches provides a perspective on post-ischemic TA. Here, we develop the notion that mRNA regulation via RNA-binding proteins, or ribonomics, also contributes to post-ischemic TA. We describe the ribonomic network, or structures involved in mRNA regulation, including nuclear foci, polysomes, stress granules, embryonic lethal abnormal vision/Hu granules, processing bodies, exosomes, and RNA granules. Transcriptional, ribonomic, and ribosomal regulation together provide multiple layers mediating cell reprogramming. Stress gene induction via the heat-shock response, immediate early genes, and endoplasmic reticulum stress represents significant reprogramming of post-ischemic neurons. We present a model of post-ischemic TA in ischemia-resistant neurons that incorporates ribonomic considerations. In this model, selective translation of stress-induced mRNAs contributes to translation recovery. This model provides a basis to study dysfunctional stress responses in vulnerable neurons, with a key focus on the inability of vulnerable neurons to selectively translate stress-induced mRNAs. We suggest a ribonomic approach will shed new light on the roles of mRNA regulation in persistent TA in vulnerable post-ischemic neurons.
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Affiliation(s)
- Donald J DeGracia
- Department of Physiology, Wayne State University, Detroit, Michigan, USA.
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Skaggs HS, Xing H, Wilkerson DC, Murphy LA, Hong Y, Mayhew CN, Sarge KD. HSF1-TPR interaction facilitates export of stress-induced HSP70 mRNA. J Biol Chem 2007; 282:33902-7. [PMID: 17897941 PMCID: PMC2266631 DOI: 10.1074/jbc.m704054200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stress conditions inhibit mRNA export, but mRNAs encoding heat shock proteins continue to be efficiently exported from the nucleus during stress. How HSP mRNAs bypass this stress-associated export inhibition was not known. Here, we show that HSF1, the transcription factor that binds HSP promoters after stress to induce their transcription, interacts with the nuclear pore-associating TPR protein in a stress-responsive manner. TPR is brought into proximity of the HSP70 promoter after stress and preferentially associates with mRNAs transcribed from this promoter. Disruption of the HSF1-TPR interaction inhibits the export of mRNAs expressed from the HSP70 promoter, both endogenous HSP70 mRNA and a luciferase reporter mRNA. These results suggest that HSP mRNA export escapes stress inhibition via HSF1-mediated recruitment of the nuclear pore-associating protein TPR to HSP genes, thereby functionally connecting the first and last nuclear steps of the gene expression pathway, transcription and mRNA export.
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Affiliation(s)
- Hollie S Skaggs
- Department of Molecular and Cellular Biochemistry, Chandler Medical Center, University of Kentucky, 741 S. Limestone Street, Lexington, KY 40536-0084, USA
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58
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John Wiley & Sons, Ltd.. Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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59
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Jolly C, Lakhotia SC. Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res 2006; 34:5508-14. [PMID: 17020918 PMCID: PMC1636489 DOI: 10.1093/nar/gkl711] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Exposure of cells to stressful conditions elicits a highly conserved defense mechanism termed the heat shock response, resulting in the production of specialized proteins which protect the cells against the deleterious effects of stress. The heat shock response involves not only a widespread inhibition of the ongoing transcription and activation of heat shock genes, but also important changes in post-transcriptional processing. In particular, a blockade in splicing and other post-transcriptional processing has been described following stress in different organisms, together with an altered spatial distribution of the proteins involved in these activities. However, the specific mechanisms that regulate these activities under conditions of stress are little understood. Non-coding RNA molecules are increasingly known to be involved in the regulation of various activities in the cell, ranging from chromatin structure to splicing and RNA degradation. In this review, we consider two non-coding RNAs, the hsrω transcripts in Drosophila and the sat III transcripts in human cells, that seem to be involved in the dynamics of RNA-processing factors in normal and/or stressed cells, and thus provide new paradigms for understanding transcriptional and post-transcriptional regulations in normal and stressed cells.
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60
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Hilgers V, Teixeira D, Parker R. Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2006; 12:1835-45. [PMID: 16940550 PMCID: PMC1581975 DOI: 10.1261/rna.241006] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Post-transcriptional control mechanisms play an important role in regulating gene expression during cellular responses to stress. For example, many stresses inhibit translation, and at least some stresses inhibit mRNA turnover in yeast and mammalian cells. We show that hyperosmolarity, heat shock, and glucose deprivation stabilize multiple mRNAs in yeast, primarily through inhibition of deadenylation. Although these stresses inhibit translation and promote the movement of mRNAs into P-bodies, we also observed inhibition of deadenylation in cycloheximide-treated cells as well as in a mutant strain where translation initiation is impaired. This argues that inhibition of poly(A)-shortening is independent of the translational state of the mRNAs and can occur when mRNAs are localized in polysomes or are not engaged in translation. Analysis of pan2Delta or ccr4Delta strains indicates that stress inhibits the function of both the Ccr4p/Pop2p/Notp and the Pan2p/Pan3p deadenylases. We suggest that under stress, simultaneous repression of translation and deadenylation allows cells to selectively translate mRNAs specific to the stress response, while retaining the majority of the cytoplasmic pool of mRNAs for later reuse and recovery from stress. Moreover, because various cellular stresses also inhibit deadenylation in mammalian cells, this mechanism is likely to be a conserved aspect of the stress response.
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Affiliation(s)
- Valérie Hilgers
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721, USA
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61
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Small EC, Leggett SR, Winans AA, Staley JP. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol Cell 2006; 23:389-99. [PMID: 16885028 PMCID: PMC3777414 DOI: 10.1016/j.molcel.2006.05.043] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 05/30/2006] [Accepted: 05/31/2006] [Indexed: 11/26/2022]
Abstract
Binding of a pre-mRNA substrate triggers spliceosome activation, whereas the release of the mRNA product triggers spliceosome disassembly. The mechanisms that underlie the regulation of these rearrangements remain unclear. We find evidence that the GTPase Snu114p mediates the regulation of spliceosome activation and disassembly. Specifically, both unwinding of U4/U6, required for spliceosome activation, and disassembly of the postsplicing U2/U6.U5.intron complex are repressed by Snu114p bound to GDP and derepressed by Snu114p bound to GTP or nonhydrolyzable GTP analogs. Further, similar to U4/U6 unwinding, spliceosome disassembly requires the DExD/H box ATPase Brr2p. Together, our data define a common mechanism for regulating and executing spliceosome activation and disassembly. Although sequence similarity with EF-G suggests Snu114p functions as a molecular motor, our findings indicate that Snu114p functions as a classic regulatory G protein. We propose that Snu114p serves as a signal-dependent switch that transduces signals to Brr2p to control spliceosome dynamics.
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Affiliation(s)
- Eliza C. Small
- Department of Biochemistry and Molecular Biology, The University of Chicago Chicago, IL 60637
| | - Stephanie R. Leggett
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
| | - Adrienne A. Winans
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
| | - Jonathan P. Staley
- Department of Molecular Genetics and Cell Biology The University of Chicago Chicago, IL 60637
- Correspondence: 773-834-5886 (phone); 773-834-9064 (fax)
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