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Hopkins KC, McLane LM, Maqbool T, Panda D, Gordesky-Gold B, Cherry S. A genome-wide RNAi screen reveals that mRNA decapping restricts bunyaviral replication by limiting the pools of Dcp2-accessible targets for cap-snatching. Genes Dev 2013; 27:1511-25. [PMID: 23824541 DOI: 10.1101/gad.215384.113] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bunyaviruses are an emerging group of medically important viruses, many of which are transmitted from insects to mammals. To identify host factors that impact infection, we performed a genome-wide RNAi screen in Drosophila and identified 131 genes that impacted infection of the mosquito-transmitted bunyavirus Rift Valley fever virus (RVFV). Dcp2, the catalytic component of the mRNA decapping machinery, and two decapping activators, DDX6 and LSM7, were antiviral against disparate bunyaviruses in both insect cells and adult flies. Bunyaviruses 5' cap their mRNAs by "cap-snatching" the 5' ends of poorly defined host mRNAs. We found that RVFV cap-snatches the 5' ends of Dcp2 targeted mRNAs, including cell cycle-related genes. Loss of Dcp2 allows increased viral transcription without impacting viral mRNA stability, while ectopic expression of Dcp2 impedes viral transcription. Furthermore, arresting cells in late S/early G2 led to increased Dcp2 mRNA targets and increased RVFV replication. Therefore, RVFV competes for the Dcp2-accessible mRNA pool, which is dynamically regulated and can present a bottleneck for viral replication.
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52
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Nishihara T, Zekri L, Braun JE, Izaurralde E. miRISC recruits decapping factors to miRNA targets to enhance their degradation. Nucleic Acids Res 2013; 41:8692-705. [PMID: 23863838 PMCID: PMC3794582 DOI: 10.1093/nar/gkt619] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNA (miRNA)-induced silencing complexes (miRISCs) repress translation and promote degradation of miRNA targets. Target degradation occurs through the 5′-to-3′ messenger RNA (mRNA) decay pathway, wherein, after shortening of the mRNA poly(A) tail, the removal of the 5′ cap structure by decapping triggers irreversible decay of the mRNA body. Here, we demonstrate that miRISC enhances the association of the decapping activators DCP1, Me31B and HPat with deadenylated miRNA targets that accumulate when decapping is blocked. DCP1 and Me31B recruitment by miRISC occurs before the completion of deadenylation. Remarkably, miRISC recruits DCP1, Me31B and HPat to engineered miRNA targets transcribed by RNA polymerase III, which lack a cap structure, a protein-coding region and a poly(A) tail. Furthermore, miRISC can trigger decapping and the subsequent degradation of mRNA targets independently of ongoing deadenylation. Thus, miRISC increases the local concentration of the decapping machinery on miRNA targets to facilitate decapping and irreversibly shut down their translation.
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Affiliation(s)
- Tadashi Nishihara
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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53
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Chiang PY, Shen YF, Su YL, Kao CH, Lin NY, Hsu PH, Tsai MD, Wang SC, Chang GD, Lee SC, Chang CJ. Phosphorylation of mRNA decapping protein Dcp1a by the ERK signaling pathway during early differentiation of 3T3-L1 preadipocytes. PLoS One 2013; 8:e61697. [PMID: 23637887 PMCID: PMC3630112 DOI: 10.1371/journal.pone.0061697] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 03/16/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Turnover of mRNA is a critical step in the regulation of gene expression, and an important step in mRNA decay is removal of the 5' cap. We previously demonstrated that the expression of some immediate early gene mRNAs is controlled by RNA stability during early differentiation of 3T3-L1 preadipocytes. METHODOLOGY/PRINCIPAL FINDINGS Here we show that the mouse decapping protein Dcp1a is phosphorylated via the ERK signaling pathway during early differentiation of preadipocytes. Mass spectrometry analysis and site-directed mutagenesis combined with a kinase assay identified ERK pathway-mediated dual phosphorylation at Ser 315 and Ser 319 of Dcp1a. To understand the functional effects of Dcp1a phosphorylation, we examined protein-protein interactions between Dcp1a and other decapping components with co-immunoprecipitation. Dcp1a interacted with Ddx6 and Edc3 through its proline-rich C-terminal extension, whereas the conserved EVH1 (enabled vasodilator-stimulated protein homology 1) domain in the N terminus of Dcp1a showed a stronger interaction with Dcp2. Once ERK signaling was activated, the interaction between Dcp1a and Ddx6, Edc3, or Edc4 was not affected by Dcp1a phosphorylation. Phosphorylated Dcp1a did, however, enhanced interaction with Dcp2. Protein complexes immunoprecipitated with the recombinant phosphomimetic Dcp1a(S315D/S319D) mutant contained more Dcp2 than did those immunoprecipitated with the nonphosphorylated Dcp1a(S315A/S319A) mutant. In addition, Dcp1a associated with AU-rich element (ARE)-containing mRNAs such as MAPK phosphatase-1 (MKP-1), whose mRNA stability was analyzed under the overexpression of Dcp1a constructs in the Dcp1a knockdown 3T3-L1 cells. CONCLUSIONS/SIGNIFICANCE Our findings suggest that ERK-phosphorylated Dcp1a enhances its interaction with the decapping enzyme Dcp2 during early differentiation of 3T3-L1 cells.
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Affiliation(s)
- Pei-Yu Chiang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Fang Shen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Lun Su
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Han Kao
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Nien-Yi Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ming-Daw Tsai
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Geen-Dong Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Sheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Jin Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J Mol Biol 2013; 425:3750-75. [PMID: 23467123 DOI: 10.1016/j.jmb.2013.02.029] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 01/15/2023]
Abstract
mRNA concentration depends on the balance between transcription and degradation rates. On both sides of the equilibrium, synthesis and degradation show, however, interesting differences that have conditioned the evolution of gene regulatory mechanisms. Here, we discuss recent genome-wide methods for determining mRNA half-lives in eukaryotes. We also review pre- and posttranscriptional regulons that coordinate the fate of functionally related mRNAs by using protein- or RNA-based trans factors. Some of these factors can regulate both transcription and decay rates, thereby maintaining proper mRNA homeostasis during eukaryotic cell life.
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55
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Ma J, Flemr M, Strnad H, Svoboda P, Schultz RM. Maternally recruited DCP1A and DCP2 contribute to messenger RNA degradation during oocyte maturation and genome activation in mouse. Biol Reprod 2013; 88:11. [PMID: 23136299 DOI: 10.1095/biolreprod.112.105312] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The oocyte-to-zygote transition entails transforming a highly differentiated oocyte into totipotent blastomeres and represents one of the earliest obstacles that must be successfully hurdled for continued development. Degradation of maternal mRNAs, which likely lies at the heart of this transition, is characterized by a transition from mRNA stability to instability during oocyte maturation. Although phosphorylation of the oocyte-specific RNA-binding protein MSY2 during maturation is implicated in making maternal mRNAs more susceptible to degradation, mechanisms underlying mRNA degradation during oocyte maturation remain poorly understood. We report that DCP1A and DCP2, proteins responsible for decapping mRNA, are encoded by maternal mRNAs recruited for translation during maturation via cytoplasmic polyadenylation elements located in their 3' untranslated regions. Both DCP1A and DCP2 are phosphorylated during maturation, with CDC2A being the kinase likely responsible for both, although MAPK may be involved in DCP1A phosphorylation. Inhibiting accumulation of DCP1A and DCP2 by RNA interference or morpholinos decreases not only degradation of mRNAs during meiotic maturation but also transcription of the zygotic genome. The results indicate that maternally recruited DCP1A and DCP2 are critical players in the transition from mRNA stability to instability during meiotic maturation and that proper maternal mRNA degradation must be successful to execute the oocyte-to-zygote transition.
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Affiliation(s)
- Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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56
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Aizer A, Kafri P, Kalo A, Shav-Tal Y. The P body protein Dcp1a is hyper-phosphorylated during mitosis. PLoS One 2013; 8:e49783. [PMID: 23300942 PMCID: PMC3534667 DOI: 10.1371/journal.pone.0049783] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/15/2012] [Indexed: 01/18/2023] Open
Abstract
Processing bodies (PBs) are non-membranous cytoplasmic structures found in all eukaryotes. Many of their components such as the Dcp1 and Dcp2 proteins are highly conserved. Using live-cell imaging we found that PB structures disassembled as cells prepared for cell division, and then began to reassemble during the late stages of cytokinesis. During the cell cycle and as cells passed through S phase, PB numbers increased. However, there was no memory of PB numbers between mother and daughter cells. Examination of hDcp1a and hDcp1b proteins by electrophoresis in mitotic cell extracts showed a pronounced slower migrating band, which was caused by hyper-phosphorylation of the protein. We found that hDcp1a is a phospho-protein during interphase that becomes hyper-phosphorylated in mitotic cells. Using truncations of hDcp1a we localized the region important for hyper-phosphorylation to the center of the protein. Mutational analysis demonstrated the importance of serine 315 in the hyper-phosphorylation process, while other serine residues tested had a minor affect. Live-cell imaging demonstrated that serine mutations in other regions of the protein affected the dynamics of hDcp1a association with the PB structure. Our work demonstrates the control of PB dynamics during the cell cycle via phosphorylation.
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Affiliation(s)
- Adva Aizer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Pinhas Kafri
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Alon Kalo
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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57
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The discovery and analysis of P Bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:23-43. [PMID: 23224963 DOI: 10.1007/978-1-4614-5107-5_3] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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58
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Abstract
Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNA-protein complexes (mRNPs) is essential to understanding these processes. In a global survey of Saccharomyces cerevisiae mRNA-binding proteins, we identified 120 proteins that cross-link to mRNA, including 66 new mRNA-binding proteins. These include kinases, RNA-modification enzymes, metabolic enzymes and tRNA- and rRNA-metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and processing bodies (P bodies). Cross-linking and immunoprecipitation (CLIP) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs, revealing positional binding preferences and co-assembly preferences. When taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress and begins to define assembly rules for P-body mRNPs.
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59
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Processing body and stress granule assembly occur by independent and differentially regulated pathways in Saccharomyces cerevisiae. Genetics 2012; 193:109-23. [PMID: 23105015 DOI: 10.1534/genetics.112.146993] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A variety of ribonucleoprotein (RNP) granules form in eukaryotic cells to regulate the translation, decay, and localization of the encapsulated messenger RNA (mRNAs). The work here examined the assembly and function of two highly conserved RNP structures, the processing body (P body) and the stress granule, in the yeast Saccharomyces cerevisiae. These granules are induced by similar stress conditions and contain translationally repressed mRNAs and a partially overlapping set of protein constituents. However, despite these similarities, the data indicate that these RNP complexes are independently assembled and that this assembly is controlled by different signaling pathways. In particular, the cAMP-dependent protein kinase (PKA) was found to control P body formation under all conditions examined. In contrast, the assembly of stress granules was not affected by changes in either PKA or TORC1 signalling activity. Both of these RNP granules were also detected in stationary-phase cells, but each appears at a distinct time. P bodies were formed prior to stationary-phase arrest, and the data suggest that these foci are important for the long-term survival of these quiescent cells. Stress granules, on the other hand, were not assembled until after the cells had entered into the stationary phase of growth and their appearance could therefore serve as a specific marker for the entry into this quiescent state. In all, the results here provide a framework for understanding the assembly of these RNP complexes and suggest that these structures have distinct but important activities in quiescent cells.
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60
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Abdelmohsen K, Tominaga-Yamanaka K, Srikantan S, Yoon JH, Kang MJ, Gorospe M. RNA-binding protein AUF1 represses Dicer expression. Nucleic Acids Res 2012; 40:11531-44. [PMID: 23066106 PMCID: PMC3526313 DOI: 10.1093/nar/gks930] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
MicroRNA (miRNA) biogenesis is tightly regulated by numerous proteins. Among them, Dicer is required for the processing of the precursor (pre-)miRNAs into the mature miRNA. Despite its critical function, the mechanisms that regulate Dicer expression are not well understood. Here we report that the RNA-binding protein (RBP) AUF1 (AU-binding factor 1) associates with the endogenous DICER1 mRNA and can interact with several segments of DICER1 mRNA within the coding region (CR) and the 3'-untranslated region (UTR). Through these interactions, AUF1 lowered DICER1 mRNA stability, since silencing AUF1 lengthened DICER1 mRNA half-life and increased Dicer expression, while overexpressing AUF1 lowered DICER1 mRNA and Dicer protein levels. Given that Dicer is necessary for the synthesis of mature miRNAs, the lowering of Dicer levels by AUF1 diminished the levels of miRNAs tested, but not the levels of the corresponding pre-miRNAs. In summary, AUF1 suppresses miRNA production by reducing Dicer production.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging-Intramural Research Program, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA.
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61
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Phosphorylation of the eukaryotic translation initiation factor 4E-transporter (4E-T) by c-Jun N-terminal kinase promotes stress-dependent P-body assembly. Mol Cell Biol 2012; 32:4572-84. [PMID: 22966201 DOI: 10.1128/mcb.00544-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Processing bodies (PBs, or P bodies) are cytoplasmic granules involved in mRNA storage and degradation that participate in the regulation of gene expression. PBs concentrate nontranslated mRNAs and several factors involved in mRNA decay and translational repression, including the eukaryotic translation initiation factor 4E-transporter (4E-T). 4E-T is required for PB assembly, but little is known about the molecular mechanisms that regulate its function. Here, we demonstrate that oxidative stress promotes multisite 4E-T phosphorylation. We show that the c-Jun N-terminal kinase (JNK) is targeted to PBs in response to oxidative stress and promotes the phosphorylation of 4E-T. Quantitative mass spectrometry analysis reveals that JNK phosphorylates 4E-T on six proline-directed sites that are required for the formation of the 4E-T complex upon stress. We have developed an image-based computational method to quantify the size, number, and density of PBs in cells, and we find that while 4E-T is required for steady-state PB assembly, its phosphorylation facilitates the formation of larger PBs upon oxidative stress. Using polysomal mRNA profiling, we assessed global and specific mRNA translation but did not find that 4E-T phosphorylation impacts translational control. Collectively, these data support a model whereby PB assembly is regulated by a two-step mechanism involving a 4E-T-dependent assembly stage in unstressed cells and a 4E-T phosphorylation-dependent aggregation stage in response to stress stimuli.
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62
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Abstract
All RNA species in yeast cells are subject to turnover. Work over the past 20 years has defined degradation mechanisms for messenger RNAs, transfer RNAs, ribosomal RNAs, and noncoding RNAs. In addition, numerous quality control mechanisms that target aberrant RNAs have been identified. Generally, each decay mechanism contains factors that funnel RNA substrates to abundant exo- and/or endonucleases. Key issues for future work include determining the mechanisms that control the specificity of RNA degradation and how RNA degradation processes interact with translation, RNA transport, and other cellular processes.
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Affiliation(s)
- Roy Parker
- Department of Molecular and Cellular Biology, University of Arizona and Howard Hughes Medical Institute, Tucson, AZ 85721, USA.
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63
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Abstract
Capped and polyadenylated long noncoding RNAs (lncRNAs) are shown to be degraded by a DCP2-mediated turnover mechanism by Geisler et al. (2012); this provides a new level of regulatory control for inducible genes by lncRNAs.
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Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
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64
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Juntawong P, Bailey-Serres J. Dynamic Light Regulation of Translation Status in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:66. [PMID: 22645595 DOI: 10.3389/fpls.2012.00066/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/20/2012] [Indexed: 05/26/2023]
Abstract
Light, a dynamic environmental parameter, is an essential regulator of plant growth and development. Light-regulated transcriptional networks are well documented, whereas light-regulated post-transcriptional regulation has received limited attention. In this study, dynamics in translation of cytosolic mRNAs were evaluated at the genome-level in Arabidopsis thaliana seedlings grown under a typical light/dark diurnal regime, shifted to darkness at midday, and then re-illuminated. One-hour of unanticipated darkness reduced levels of polysomes by 17% in a manner consistent with inhibition of initiation of translation. This down-regulation of translation was reversed within 10 min of re-illumination. Quantitative comparison of the total cellular population of transcripts (the transcriptome) to those associated with one or more 80S ribosome (the translatome) identified over 1600 mRNAs that were differentially translated in response to light availability. Unanticipated darkness limited both transcription and translation of mRNAs encoding components of the photosynthetic machinery. Many mRNAs encoding proteins associated with the energy demanding process of protein synthesis were stable but sequestered in the dark, in a rapidly reversible manner. A meta-analysis determined these same transcripts were similarly and coordinately regulated in response to changes in oxygen availability. The dark and hypoxia translationally repressed mRNAs lack highly supported candidate RNA-regulatory elements but are characterized by G + C-rich 5'-untranslated regions. We propose that modulation of translation of a subset of cellular mRNAs functions as an energy conservation mechanism.
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Affiliation(s)
- Piyada Juntawong
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, CA, USA
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65
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Hanson PJ, Zhang HM, Hemida MG, Ye X, Qiu Y, Yang D. IRES-Dependent Translational Control during Virus-Induced Endoplasmic Reticulum Stress and Apoptosis. Front Microbiol 2012; 3:92. [PMID: 22461781 PMCID: PMC3307021 DOI: 10.3389/fmicb.2012.00092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 02/23/2012] [Indexed: 12/11/2022] Open
Abstract
Many virus infections and stresses can induce endoplasmic reticulum (ER) stress response, a host self-defense mechanism against viral invasion and stress. During this event, viral and cellular gene expression is actively regulated and often encounters a switching of the translation initiation from cap-dependent to internal ribosome-entry sites (IRES)-dependent. This switching is largely dependent on the mRNA structure of the 5′ untranslated region (5′ UTR) and on the particular stress stimuli. Picornaviruses and some other viruses contain IRESs within their 5′ UTR of viral genome and employ an IRES-driven mechanism for translation initiation. Recently, a growing number of cellular genes involved in growth control, cell cycle progression and apoptosis were also found to contain one or more IRES within their long highly structured 5′ UTRs. These genes initiate translation usually by a cap-dependent mechanism under normal physiological conditions; however, in certain environments, such as infection, starvation, and heat shock they shift translation initiation to an IRES-dependent modality. Although the molecular mechanism is not entirely understood, a number of studies have revealed that several cellular biochemical processes are responsible for the switching of translation initiation to IRES-dependent. These include the cleavage of translation initiation factors by viral and/or host proteases, phosphorylation (inactivation) of host factors for translation initiation, overproduction of homologous proteins of cap-binding protein eukaryotic initiation factors (eIF)4E, suppression of cap-binding protein eIF4E expression by specific microRNA, activation of enzymes for mRNA decapping, as well as others. Here, we summarize the recent advances in our understanding of the molecular mechanisms for the switching of translation initiation, particularly for the proteins involved in cell survival and apoptosis in the ER stress pathways during viral infections.
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Affiliation(s)
- Paul J Hanson
- Department of Pathology and Laboratory Medicine, The Institute for Heart and Lung Health, St. Paul's Hospital, University of British Columbia Vancouver, BC, Canada
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66
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Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation. EMBO J 2012; 31:1975-84. [PMID: 22407295 DOI: 10.1038/emboj.2012.56] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 02/14/2012] [Indexed: 11/08/2022] Open
Abstract
Eukaryotic mRNA decapping proteins are essential for normal turnover of mRNA. Yet, the mechanism of bulk mRNA turnover during stress responses and its importance to stress tolerance are poorly understood. Here, we showed that dehydration stress activated MPK6 to phosphorylate serine 237 of Arabidopsis DCP1 and phospho-DCP1 preferentially associated with DCP5 to promote mRNA decapping in vivo. This process was essential for stress adaption as dcp5-1 and DCP1-S237A plants were hypersensitive to stress compared with wild-type (WT) plants. Microarray analysis revealed that dehydration-induced expression of many stress responsive genes was compromised in dcp5-1, whereas a subset of transcripts was over-represented in this mutant. Further analysis revealed that this subset of transcripts was likely the direct targets of stress-triggered mRNA decapping in WT. Our results suggest that mRNA decapping through MPK6-DCP1-DCP5 pathway serves as a rapid response to dehydration stress in Arabidopsis.
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67
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Regulation of vacuolar H+-ATPase activity by the Cdc42 effector Ste20 in Saccharomyces cerevisiae. EUKARYOTIC CELL 2012; 11:442-51. [PMID: 22327006 DOI: 10.1128/ec.05286-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the budding yeast Saccharomyces cerevisiae, the Cdc42 effector Ste20 plays a crucial role in the regulation of filamentous growth, a response to nutrient limitation. Using the split-ubiquitin technique, we found that Ste20 forms a complex with Vma13, an important regulatory subunit of vacuolar H(+)-ATPase (V-ATPase). This protein-protein interaction was confirmed by a pulldown assay and coimmunoprecipitation. We also demonstrate that Ste20 associates with vacuolar membranes and that Ste20 stimulates V-ATPase activity in isolated vacuolar membranes. This activation requires Ste20 kinase activity and does not depend on increased assembly of the V1 and V0 sectors of the V-ATPase, which is a major regulatory mechanism. Furthermore, loss of V-ATPase activity leads to a strong increase in invasive growth, possibly because these cells fail to store and mobilize nutrients efficiently in the vacuole in the absence of the vacuolar proton gradient. In contrast to the wild type, which grows in rather small, isolated colonies on solid medium during filamentation, hyperinvasive vma mutants form much bigger aggregates in which a large number of cells are tightly clustered together. Genetic data suggest that Ste20 and the protein kinase A catalytic subunit Tpk2 are both activated in the vma13Δ strain. We propose that during filamentous growth, Ste20 stimulates V-ATPase activity. This would sustain nutrient mobilization from vacuolar stores, which is beneficial for filamentous growth.
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68
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Kramer S. Developmental regulation of gene expression in the absence of transcriptional control: The case of kinetoplastids. Mol Biochem Parasitol 2012; 181:61-72. [PMID: 22019385 DOI: 10.1016/j.molbiopara.2011.10.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 11/25/2022]
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69
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Juntawong P, Bailey-Serres J. Dynamic Light Regulation of Translation Status in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:66. [PMID: 22645595 PMCID: PMC3355768 DOI: 10.3389/fpls.2012.00066] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/20/2012] [Indexed: 05/18/2023]
Abstract
Light, a dynamic environmental parameter, is an essential regulator of plant growth and development. Light-regulated transcriptional networks are well documented, whereas light-regulated post-transcriptional regulation has received limited attention. In this study, dynamics in translation of cytosolic mRNAs were evaluated at the genome-level in Arabidopsis thaliana seedlings grown under a typical light/dark diurnal regime, shifted to darkness at midday, and then re-illuminated. One-hour of unanticipated darkness reduced levels of polysomes by 17% in a manner consistent with inhibition of initiation of translation. This down-regulation of translation was reversed within 10 min of re-illumination. Quantitative comparison of the total cellular population of transcripts (the transcriptome) to those associated with one or more 80S ribosome (the translatome) identified over 1600 mRNAs that were differentially translated in response to light availability. Unanticipated darkness limited both transcription and translation of mRNAs encoding components of the photosynthetic machinery. Many mRNAs encoding proteins associated with the energy demanding process of protein synthesis were stable but sequestered in the dark, in a rapidly reversible manner. A meta-analysis determined these same transcripts were similarly and coordinately regulated in response to changes in oxygen availability. The dark and hypoxia translationally repressed mRNAs lack highly supported candidate RNA-regulatory elements but are characterized by G + C-rich 5'-untranslated regions. We propose that modulation of translation of a subset of cellular mRNAs functions as an energy conservation mechanism.
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Affiliation(s)
- Piyada Juntawong
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of CaliforniaRiverside, CA, USA
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of CaliforniaRiverside, CA, USA
- *Correspondence: Julia Bailey-Serres, Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA. e-mail:
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Jung JH, Kim J. Accumulation of P-bodies in Candida albicans under different stress and filamentous growth conditions. Fungal Genet Biol 2011; 48:1116-23. [DOI: 10.1016/j.fgb.2011.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 10/19/2011] [Accepted: 10/20/2011] [Indexed: 01/11/2023]
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71
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Rzeczkowski K, Beuerlein K, Müller H, Dittrich-Breiholz O, Schneider H, Kettner-Buhrow D, Holtmann H, Kracht M. c-Jun N-terminal kinase phosphorylates DCP1a to control formation of P bodies. ACTA ACUST UNITED AC 2011; 194:581-96. [PMID: 21859862 PMCID: PMC3160581 DOI: 10.1083/jcb.201006089] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytokines and stress-inducing stimuli signal through c-Jun N-terminal kinase (JNK) using a diverse and only partially defined set of downstream effectors. In this paper, the decapping complex subunit DCP1a was identified as a novel JNK target. JNK phosphorylated DCP1a at residue S315 in vivo and in vitro and coimmunoprecipitated and colocalized with DCP1a in processing bodies (P bodies). Sustained JNK activation by several different inducers led to DCP1a dispersion from P bodies, whereas IL-1 treatment transiently increased P body number. Inhibition of TAK1-JNK signaling also affected the number and size of P bodies and the localization of DCP1a, Xrn1, and Edc4. Transcriptome analysis further identified a central role for DCP1a in IL-1-induced messenger ribonucleic acid (mRNA) expression. Phosphomimetic mutation of S315 stabilized IL-8 but not IκBα mRNA, whereas overexpressed DCP1a blocked IL-8 transcription and suppressed p65 NF-κB nuclear activity. Collectively, these data reveal DCP1a as a multifunctional regulator of mRNA expression and suggest a novel mechanism controlling the subcellular localization of DCP1a in response to stress or inflammatory stimuli.
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Affiliation(s)
- Katharina Rzeczkowski
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University Giessen, 35392 Giessen, Germany
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Affiliation(s)
- Stacy L Erickson
- Division of Biology, University of California San Diego, La Jolla, CA 92093, USA
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73
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Xie W, Denman RB. Protein methylation and stress granules: posttranslational remodeler or innocent bystander? Mol Biol Int 2011; 2011:137459. [PMID: 22091395 PMCID: PMC3196864 DOI: 10.4061/2011/137459] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 01/10/2011] [Indexed: 01/06/2023] Open
Abstract
Stress granules contain a large number of post-translationally modified proteins, and studies have shown that these modifications serve as recruitment tags for specific proteins and even control the assembly and disassembly of the granules themselves. Work originating from our laboratory has focused on the role protein methylation plays in stress granule composition and function. We have demonstrated that both asymmetrically and symmetrically dimethylated proteins are core constituents of stress granules, and we have endeavored to understand when and how this occurs. Here we seek to integrate this data into a framework consisting of the currently known post-translational modifications affecting stress granules to produce a model of stress granule dynamics that, in turn, may serve as a benchmark for understanding and predicting how post-translational modifications regulate other granule types.
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Affiliation(s)
- Wen Xie
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 1065, USA
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Thomas MG, Loschi M, Desbats MA, Boccaccio GL. RNA granules: the good, the bad and the ugly. Cell Signal 2011; 23:324-34. [PMID: 20813183 PMCID: PMC3001194 DOI: 10.1016/j.cellsig.2010.08.011] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 08/20/2010] [Indexed: 12/13/2022]
Abstract
Processing bodies (PBs) and Stress Granules (SGs) are the founding members of a new class of RNA granules, known as mRNA silencing foci, as they harbour transcripts circumstantially excluded from the translationally active pool. PBs and SGs are able to release mRNAs thus allowing their translation. PBs are constitutive, but respond to stimuli that affect mRNA translation and decay, whereas SGs are specifically induced upon cellular stress, which triggers a global translational silencing by several pathways, including phosphorylation of the key translation initiation factor eIF2alpha, and tRNA cleavage among others. PBs and SGs with different compositions may coexist in a single cell. These macromolecular aggregates are highly conserved through evolution, from unicellular organisms to vertebrate neurons. Their dynamics is regulated by several signaling pathways, and depends on microfilaments and microtubules, and the cognate molecular motors myosin, dynein, and kinesin. SGs share features with aggresomes and related aggregates of unfolded proteins frequently present in neurodegenerative diseases, and may play a role in the pathology. Virus infections may induce or impair SG formation. Besides being important for mRNA regulation upon stress, SGs modulate the signaling balancing apoptosis and cell survival. Finally, the formation of Nuclear Stress Bodies (nSBs), which share components with SGs, and the assembly of additional cytosolic aggregates containing RNA -the UV granules and the Ire1 foci-, all of them induced by specific cell damage factors, contribute to cell survival.
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Key Words
- atxn2, ataxin-2
- bicd, bicaudal d
- cbp, creb binding protein
- cpeb, cytoplasmic polyadenylation element binding protein
- dhc, dynein heavy chain
- dic, dynein intermediate chain
- fak, focal adhesion kinase
- fus/tls/hnrnp p2, fused in sarcoma
- g3bp, ras-gap sh3 domain binding protein
- gcn2, general control nonderepressible-2
- grb7, growth factor receptor-bound protein 7
- hap, hnrnp a1 interacting protein
- hdac6, histone deacetylase 6
- hri, heme-regulated inhibitor
- hsf, heat shock transcription factor
- khc, kinesin heavy chain
- klc, kinesin light chain
- mln51, metastatic lymph node 51
- nmd, nonsense mediated decay
- nsbs, nuclear stress bodies
- ogfod1, 2–14 oxoglutarate and fe(ii)-dependent oxygenase domain containing 1
- pb, processing body
- perk, pancreatic endoplasmic reticulum eif2alpha kinase
- pkr/eif2ak2, double stranded rna-dependent protein kinase
- pp1, protein phosphatase 1
- prp, prion protein
- rbp, rna binding protein
- rnp, ribonucleoparticle
- sam68, src associated in mitosis 68 kda
- member of star, signal transducer and activator of rna
- sca, spinocerebellar ataxia
- sg, stress granule
- sma, spinal muscular atrophy
- fmrp, fragile x mental retardation protein
- smn, survival of motor neuron
- tdp43, tar dna-binding protein 43
- traf2, tnf receptor associated factor 2
- uvgs, uv rna granules
- processing body
- stress granule
- kinesin
- dynein
- bicaudal d
- aggresome
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Affiliation(s)
- María Gabriela Thomas
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - Mariela Loschi
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - María Andrea Desbats
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
| | - Graciela Lidia Boccaccio
- Instituto Leloir, Av. Patricias Argentinas 435, C1405 BWE Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
- University of Buenos Aires
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75
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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76
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The mitogen-activated protein kinase Slt2 regulates nuclear retention of non-heat shock mRNAs during heat shock-induced stress. Mol Cell Biol 2010; 30:5168-79. [PMID: 20823268 DOI: 10.1128/mcb.00735-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cellular adaptation to environmental stress conditions requires rapid and specific changes in gene expression. During heat shock, most polyadenylated mRNAs are retained in the nucleus, whereas the export of heat shock-induced mRNAs is allowed. Although essential mRNA export factors are known, the precise mechanism for regulating transport is not fully understood. Here we find that during heat shock in Saccharomyces cerevisiae, the mRNA-binding protein Nab2 is phosphorylated on threonine 178 and serine 180 by the mitogen-activated protein (MAP) kinase Slt2/Mpk1. Slt2 is required for nuclear poly(A(+)) mRNA accumulation upon heat shock, and thermotolerance is decreased in a nup42 nab2-T178A/S180A mutant. Coincident with phosphorylation, Nab2 and Yra1 colocalize in nuclear foci with Mlp1, a protein involved in mRNA retention. Nab2 nuclear focus formation and Nab2 phosphorylation are independent, suggesting that heat shock induces multiple cellular alterations that impinge upon transport efficiency. Under normal conditions, we find that the mRNA export receptor Mex67 and Nab2 directly interact. However, upon heat shock stress, Mex67 does not localize to the Mlp1 nuclear foci, and its association with Nab2 complexes is reduced. These results reveal a novel mechanism by which the MAP kinase Slt2 and Mlp1 control mRNA export factors during heat shock stress.
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Short B. Stress management for mRNAs. J Biophys Biochem Cytol 2010. [PMCID: PMC2878940 DOI: 10.1083/jcb.1895iti1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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