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Ryoo HD. The integrated stress response in metabolic adaptation. J Biol Chem 2024; 300:107151. [PMID: 38462161 PMCID: PMC10998230 DOI: 10.1016/j.jbc.2024.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024] Open
Abstract
The integrated stress response (ISR) refers to signaling pathways initiated by stress-activated eIF2α kinases. Distinct eIF2α kinases respond to different stress signals, including amino acid deprivation and mitochondrial stress. Such stress-induced eIF2α phosphorylation attenuates general mRNA translation and, at the same time, stimulates the preferential translation of specific downstream factors to orchestrate an adaptive gene expression program. In recent years, there have been significant new advances in our understanding of ISR during metabolic stress adaptation. Here, I discuss those advances, reviewing among others the ISR activation mechanisms in response to amino acid deprivation and mitochondrial stress. In addition, I review how ISR regulates the amino acid metabolic pathways and how changes in the ISR impact the physiology and pathology of various disease models.
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Affiliation(s)
- Hyung Don Ryoo
- Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA.
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Thompson KD, Suber W, Nicholas R, Arnosti DN. Long-range repression by ecdysone receptor on complex enhancers of the insulin receptor gene. Fly (Austin) 2023; 17:2242238. [PMID: 37621079 PMCID: PMC10461493 DOI: 10.1080/19336934.2023.2242238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
The insulin signalling pathway is evolutionarily conserved throughout metazoans, playing key roles in development, growth, and metabolism. Misregulation of this pathway is associated with a multitude of disease states including diabetes, cancer, and neurodegeneration. The human insulin receptor gene (INSR) is widely expressed throughout development and was previously described as a 'housekeeping' gene. Yet, there is abundant evidence that this gene is expressed in a cell-type specific manner, with dynamic regulation in response to environmental signals. The Drosophila insulin-like receptor gene (InR) is homologous to the human INSR gene and was previously shown to be regulated by multiple transcriptional elements located primarily within the introns of the gene. These elements were roughly defined in ~1.5 kbp segments, but we lack an understanding of the potential detailed mechanisms of their regulation. We characterized the substructure of these cis-regulatory elements in Drosophila S2 cells, focusing on regulation through the ecdysone receptor (EcR) and the dFOXO transcription factor. By identifying specific locations of activators and repressors within 300 bp subelements, we show that some previously identified enhancers consist of relatively compact clusters of activators, while others have a distributed architecture not amenable to further reduction. In addition, these assays uncovered a long-range repressive action of unliganded EcR. The complex transcriptional circuitry likely endows InR with a highly flexible and tissue-specific response to tune insulin signalling. Further studies will provide insights to demonstrate the impact of natural variation in this gene's regulation, applicable to human genetic studies.
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Affiliation(s)
- Katie D. Thompson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Will Suber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Rachel Nicholas
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - David N. Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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Harris MT, Marr MT. The intrinsically disordered region of eIF5B stimulates IRES usage and nucleates biological granule formation. Cell Rep 2023; 42:113283. [PMID: 37862172 PMCID: PMC10680144 DOI: 10.1016/j.celrep.2023.113283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 03/22/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Cells activate stress response pathways to survive adverse conditions. Such responses involve the inhibition of global cap-dependent translation. This inhibition is a block that essential transcripts must escape via alternative methods of translation initiation, e.g., an internal ribosome entry site (IRES). IRESs have distinct structures and generally require a limited repertoire of translation factors. Cellular IRESs have been identified in many critical cellular stress response transcripts. We previously identified cellular IRESs in the murine insulin receptor (Insr) and insulin-like growth factor 1 receptor (Igf1r) transcripts and demonstrated their resistance to eukaryotic initiation factor 4F (eIF4F) inhibition. Here, we find that eIF5B preferentially promotes Insr, Igf1r, and hepatitis C virus IRES activity through a non-canonical mechanism that requires its highly charged and disordered N terminus. We find that the N-terminal region of eIF5B can drive cytoplasmic granule formation. This eIF5B granule is triggered by cellular stress and is sufficient to specifically promote IRES activity.
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Affiliation(s)
- Meghan T Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA
| | - Michael T Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA.
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Clark NK, Harris MT, Dahl WB, Knotts Z, Marr MT. The Insulin Receptor and Insulin like Growth Factor Receptor 5' UTRs Support Translation Initiation Independently of EIF4G1. Mol Cell Biol 2023; 43:485-499. [PMID: 37724583 PMCID: PMC10569357 DOI: 10.1080/10985549.2023.2255120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
IRES mediated translation initiation requires a different repertoire of factors than canonical cap-dependent translation. Treatments that inhibit the canonical translation factor EIF4G1 have little or no effect on the ability of the Insr and Igf1r cellular IRESes to promote translation. Transcripts for two cellular receptors contain RNA elements that facilitate translation initiation without intact EIF4G1. Cellular IRES mechanisms may resemble viral type III IRESes allowing them to promote translate with a limited number of initiation factors allowing them to work under stress conditions when canonical translation is repressed.
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Affiliation(s)
- Nicholas K. Clark
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts, USA
| | - Meghan T. Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- Myeloid Therapeutics, Cambridge, Massachusetts, USA
| | - William B. Dahl
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Zachary Knotts
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Michael T. Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
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Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development. Biomedicines 2022; 10:biomedicines10081865. [PMID: 36009412 PMCID: PMC9405587 DOI: 10.3390/biomedicines10081865] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Many conditions can benefit from RNA-based therapies, namely, those targeting internal ribosome entry sites (IRESs) and their regulatory proteins, the IRES trans-acting factors (ITAFs). IRES-mediated translation is an alternative mechanism of translation initiation, known for maintaining protein synthesis when canonical translation is impaired. During a stress response, it contributes to cell reprogramming and adaptation to the new environment. The relationship between IRESs and ITAFs with tumorigenesis and resistance to therapy has been studied in recent years, proposing new therapeutic targets and treatments. In addition, IRES-dependent translation initiation dysregulation is also related to neurological and cardiovascular diseases, muscular atrophies, or other syndromes. The participation of these structures in the development of such pathologies has been studied, yet to a far lesser extent than in cancer. Strategies involving the disruption of IRES–ITAF interactions or the modification of ITAF expression levels may be used with great impact in the development of new therapeutics. In this review, we aim to comprehend the current data on groups of human pathologies associated with IRES and/or ITAF dysregulation and their application in the designing of new therapeutic approaches using them as targets or tools. Thus, we wish to summarise the evidence in the field hoping to open new promising lines of investigation toward personalised treatments.
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Tatar M. Aging Regulated Through a Stability Model of Insulin/Insulin Growth Factor Receptor Function. Front Endocrinol (Lausanne) 2021; 12:649880. [PMID: 33776941 PMCID: PMC7991905 DOI: 10.3389/fendo.2021.649880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
Mutations of the insulin-like receptor in Drosophila extend lifespan. New research suggests this receptor operates in two modes. The first extends lifespan while slowing reproduction and reducing growth. The second strongly extends lifespan without impairing growth or reproduction; it confers longevity assurance. The mutation that confers longevity assurance resides in the kinase insert domain, which contains a potential SH2 binding site for substrate proteins. We apply a recent model for the function of receptor tyrosine kinases to propose how insulin receptor structure can modulate aging. This concept hypothesizes that strong insulin-like ligands promote phosphorylation of high threshold substrate binding sites to robustly induce reproduction, which impairs survival as a consequence of trade-offs. Lower levels of receptor stimulation provide less kinase dimer stability, which reduces reproduction and extends lifespan by avoiding reproductive costs. Environmental conditions that favor diapause alter the expression of insulin ligands to further repress the stability of the interacting kinase domains, block phosphorylation of low threshold substrates and thus induce a unique molecular program that confers longevity assurance. Mutations of the insulin receptor that block low-phosphorylation site interactions, such as within the kinase insert domain, can extend lifespan while maintaining overall dimer stability. These flies are long-lived while maintaining reproduction and growth. The kinase insert domain of Drosophila provides a novel avenue from which to seek signaling of the insulin/insulin-like growth factor system of humans that modulate aging without impacting reproduction and growth, or incurring insulin resistance pathology.
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Jin H, Xu W, Rahman R, Na D, Fieldsend A, Song W, Liu S, Li C, Rosbash M. TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals. SCIENCE ADVANCES 2020; 6:eabb8771. [PMID: 32851185 PMCID: PMC7423359 DOI: 10.1126/sciadv.abb8771] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/30/2020] [Indexed: 05/04/2023]
Abstract
4E-BP (eIF4E-BP) represses translation initiation by binding to the 5' cap-binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity, and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used HyperTRIBE (targets of RNA binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. The protein associates with specific mRNAs, and ribosome profiling data show that mTOR inhibition changes the translational efficiency of 4E-BP TRIBE targets more substantially compared to nontargets. In both systems, these targets have specific motifs and are enriched in translation-related pathways, which correlate well with the known activity of 4E-BP and suggest that it modulates the binding specificity of eIF4E and contributes to mTOR translational specificity.
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Affiliation(s)
- Hua Jin
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Weijin Xu
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Daxiang Na
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Allegra Fieldsend
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Wei Song
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Shaobo Liu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Chong Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
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Jacobsen T, Yi G, Al Asafen H, Jermusyk AA, Beisel CL, Reeves GT. Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems. PLoS One 2020; 15:e0232046. [PMID: 32352996 PMCID: PMC7192461 DOI: 10.1371/journal.pone.0232046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/05/2020] [Indexed: 11/20/2022] Open
Abstract
Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5' vs. 3' untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.
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Affiliation(s)
- Thomas Jacobsen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
| | - Gloria Yi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
| | - Hadel Al Asafen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
| | - Ashley A Jermusyk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Gregory T Reeves
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States of America
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Signaling Network of Forkhead Family of Transcription Factors (FOXO) in Dietary Restriction. Cells 2019; 9:cells9010100. [PMID: 31906091 PMCID: PMC7016766 DOI: 10.3390/cells9010100] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/25/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023] Open
Abstract
Dietary restriction (DR), which is defined as a reduction of particular or total nutrient intake without causing malnutrition, has been proved to be a robust way to extend both lifespan and health-span in various species from yeast to mammal. However, the molecular mechanisms by which DR confers benefits on longevity were not yet fully elucidated. The forkhead box O transcription factors (FOXOs), identified as downstream regulators of the insulin/IGF-1 signaling pathway, control the expression of many genes regulating crucial biological processes such as metabolic homeostasis, redox balance, stress response and cell viability and proliferation. The activity of FOXOs is also mediated by AMP-activated protein kinase (AMPK), sirtuins and the mammalian target of rapamycin (mTOR). Therefore, the FOXO-related pathways form a complex network critical for coordinating a response to environmental fluctuations in order to maintain cellular homeostasis and to support physiological aging. In this review, we will focus on the role of FOXOs in different DR interventions. As different DR regimens or calorie (energy) restriction mimetics (CRMs) can elicit both distinct and overlapped DR-related signaling pathways, the benefits of DR may be maximized by combining diverse forms of interventions. In addition, a better understanding of the precise role of FOXOs in different mechanistic aspects of DR response would provide clear cellular and molecular insights on DR-induced increase of lifespan and health-span.
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Zhao CL, Singh K, Brodsky AS, Lu S, Graves TA, Fenton MA, Yang D, Sturtevant A, Resnick MB, Wang Y. Stromal ColXα1 expression correlates with tumor-infiltrating lymphocytes and predicts adjuvant therapy outcome in ER-positive/HER2-positive breast cancer. BMC Cancer 2019; 19:1036. [PMID: 31675929 PMCID: PMC6825361 DOI: 10.1186/s12885-019-6134-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background The breast cancer microenvironment contributes to tumor progression and response to chemotherapy. Previously, we reported that increased stromal Type X collagen α1 (ColXα1) and low TILs correlated with poor pathologic response to neoadjuvant therapy in estrogen receptor and HER2-positive (ER+/HER2+) breast cancer. Here, we investigate the relationship of ColXα1 and long-term outcome of ER+/HER2+ breast cancer patients in an adjuvant setting. Methods A total of 164 cases with at least 5-year follow-up were included. Immunohistochemistry for ColXα1 was performed on whole tumor sections. Associations between ColXα1expression, clinical pathological features, and outcomes were analyzed. Results ColXα1 expression was directly proportional to the amount of tumor associated stroma (p = 0.024) and inversely proportional to TILs. Increased ColXα1 was significantly associated with shorter disease free survival and overall survival by univariate analysis. In multivariate analysis, OS was lower in ColXα1 expressing (HR = 2.1; 95% CI = 1.2–3.9) tumors of older patients (> = 58 years) (HR = 5.3; 95% CI = 1.7–17) with higher stage (HR = 2.6; 95% CI = 1.3–5.2). Similarly, DFS was lower in ColXα1 expressing (HR = 1.8; 95% CI = 1.6–5.7) tumors of older patients (HR = 3.2; 95% CI = 1.3–7.8) with higher stage (HR = 2.7; 95% CI = 1.6–5.7) and low TILs. In low PR+ tumors, higher ColXα1 expression was associated with poorer prognosis. Conclusion ColXα1 expression is associated with poor disease free survival and overall survival in ER+/HER2+ breast cancer. This study provides further support for the prognostic utility of ColXα1 as a breast cancer associated stromal factor that predicts response to chemotherapy. Electronic supplementary material The online version of this article (10.1186/s12885-019-6134-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chaohui Lisa Zhao
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Kamaljeet Singh
- Department of Pathology and Laboratory Medicine, Women and Infant Hospital, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Theresa A Graves
- Department of Surgery, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Mary Anne Fenton
- Department of Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Ashlee Sturtevant
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Murray B Resnick
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA.
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Deletion of a Single LeishIF4E-3 Allele by the CRISPR-Cas9 System Alters Cell Morphology and Infectivity of Leishmania. mSphere 2019; 4:4/5/e00450-19. [PMID: 31484740 PMCID: PMC6731530 DOI: 10.1128/msphere.00450-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Leishmania species are the causative agents of a spectrum of diseases. Available drug treatment is toxic and expensive, with drug resistance a growing concern. Leishmania parasites migrate between transmitting sand flies and mammalian hosts, experiencing unfavorable extreme conditions. The parasites therefore developed unique mechanisms for promoting a stage-specific program for gene expression, with translation playing a central role. There are six paralogs of the cap-binding protein eIF4E, which vary in their function, expression profiles, and assemblages. Using the CRISPR-Cas9 system for Leishmania, we deleted one of the two LeishIF4E-3 alleles. Expression of LeishIF4E-3 in the deletion mutant was low, leading to reduction in global translation and growth of the mutant cells. Cell morphology also changed, affecting flagellum growth, cell shape, and infectivity. The importance of this study is in highlighting that LeishIF4E-3 is essential for completion of the parasite life cycle. Our study gives new insight into how parasite virulence is determined. The genomes of Leishmania and trypanosomes encode six paralogs of the eIF4E cap-binding protein, known in other eukaryotes to anchor the translation initiation complex. In line with the heteroxenous nature of these parasites, the different LeishIF4E paralogs vary in their biophysical features and their biological behavior. We therefore hypothesize that each has a specialized function, not limited to protein synthesis. Of the six paralogs, LeishIF4E-3 has a weak cap-binding activity. It participates in the assembly of granules that store inactive transcripts and ribosomal proteins during nutritional stress that is experienced in the sand fly. We investigated the role of LeishIF4E-3 in Leishmania mexicana promastigotes using the CRISPR-Cas9 system. We deleted one of the two LeishIF4E-3 alleles, generating a heterologous deletion mutant with reduced LeishIF4E-3 expression. The mutant showed a decline in de novo protein synthesis and growth kinetics, altered morphology, and impaired infectivity. The mutant cells were rounded and failed to transform into the nectomonad-like form, in response to purine starvation. Furthermore, the infectivity of macrophage cells by the LeishIF4E-3(+/−) mutant was severely reduced. These phenotypic features were not observed in the addback cells, in which expression of LeishIF4E-3 was restored. The observed phenotypic changes correlated with the profile of transcripts associated with LeishIF4E-3. These were enriched for cytoskeleton- and flagellum-encoding genes, along with genes for RNA binding proteins. Our data illustrate the importance of LeishIF4E-3 in translation and in the parasite virulence. IMPORTANCELeishmania species are the causative agents of a spectrum of diseases. Available drug treatment is toxic and expensive, with drug resistance a growing concern. Leishmania parasites migrate between transmitting sand flies and mammalian hosts, experiencing unfavorable extreme conditions. The parasites therefore developed unique mechanisms for promoting a stage-specific program for gene expression, with translation playing a central role. There are six paralogs of the cap-binding protein eIF4E, which vary in their function, expression profiles, and assemblages. Using the CRISPR-Cas9 system for Leishmania, we deleted one of the two LeishIF4E-3 alleles. Expression of LeishIF4E-3 in the deletion mutant was low, leading to reduction in global translation and growth of the mutant cells. Cell morphology also changed, affecting flagellum growth, cell shape, and infectivity. The importance of this study is in highlighting that LeishIF4E-3 is essential for completion of the parasite life cycle. Our study gives new insight into how parasite virulence is determined.
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Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
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Vella V, Milluzzo A, Scalisi NM, Vigneri P, Sciacca L. Insulin Receptor Isoforms in Cancer. Int J Mol Sci 2018; 19:ijms19113615. [PMID: 30453495 PMCID: PMC6274710 DOI: 10.3390/ijms19113615] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022] Open
Abstract
The insulin receptor (IR) mediates both metabolic and mitogenic effects especially when overexpressed or in clinical conditions with compensatory hyperinsulinemia, due to the metabolic pathway resistance, as obesity diabetes. In many cancers, IR is overexpressed preferentially as IR-A isoform, derived by alternative splicing of exon 11. The IR-A overexpression, and the increased IR-A:IR-B ratio, are mechanisms that promote the mitogenic response of cancer cells to insulin and IGF-2, which is produced locally by both epithelial and stromal cancer cells. In cancer IR-A, isoform predominance may occur for dysregulation at both mRNA transcription and post-transcription levels, including splicing factors, non-coding RNAs and protein degradation. The mechanisms that regulate IR isoform expression are complex and not fully understood. The IR isoform overexpression may play a role in cancer cell stemness, in tumor progression and in resistance to target therapies. From a clinical point of view, the IR-A overexpression in cancer may be a determinant factor for the resistance to IGF-1R target therapies for this issue. IR isoform expression in cancers may have the meaning of a predictive biomarker and co-targeting IGF-1R and IR-A may represent a new more efficacious treatment strategy.
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Affiliation(s)
- Veronica Vella
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Catania Medical School, Garibaldi-Nesima Hospital, via Palermo 636, 95122 Catania, Italy.
- School of Human and Social Science, University "Kore" of Enna, 94100 Enna, Italy.
| | - Agostino Milluzzo
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Catania Medical School, Garibaldi-Nesima Hospital, via Palermo 636, 95122 Catania, Italy.
| | - Nunzio Massimo Scalisi
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Catania Medical School, Garibaldi-Nesima Hospital, via Palermo 636, 95122 Catania, Italy.
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, University of Catania Medical School, Center of Experimental Oncology and Hematology, A.O.U. Policlinico Vittorio Emanuele, via Santa Sofia, 78, 95123 Catania, Italy.
| | - Laura Sciacca
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Catania Medical School, Garibaldi-Nesima Hospital, via Palermo 636, 95122 Catania, Italy.
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14
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The GCN2-ATF4 Signaling Pathway Induces 4E-BP to Bias Translation and Boost Antimicrobial Peptide Synthesis in Response to Bacterial Infection. Cell Rep 2018; 21:2039-2047. [PMID: 29166596 DOI: 10.1016/j.celrep.2017.10.096] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/25/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial infection often leads to suppression of mRNA translation, but hosts are nonetheless able to express immune response genes through as yet unknown mechanisms. Here, we use a Drosophila model to demonstrate that antimicrobial peptide (AMP) production during infection is paradoxically stimulated by the inhibitor of cap-dependent translation, 4E-BP (eIF4E-binding protein; encoded by the Thor gene). We found that 4E-BP is induced upon infection with pathogenic bacteria by the stress-response transcription factor ATF4 and its upstream kinase, GCN2. Loss of gcn2, atf4, or 4e-bp compromised immunity. While AMP transcription is unaffected in 4e-bp mutants, AMP protein levels are substantially reduced. The 5' UTRs of AMPs score positive in cap-independent translation assays, and this cap-independent activity is enhanced by 4E-BP. These results are corroborated in vivo using transgenic 5' UTR reporters. These observations indicate that ATF4-induced 4e-bp contributes to innate immunity by biasing mRNA translation toward cap-independent mechanisms, thus enhancing AMP synthesis.
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15
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Luhur A, Buddika K, Ariyapala IS, Chen S, Sokol NS. Opposing Post-transcriptional Control of InR by FMRP and LIN-28 Adjusts Stem Cell-Based Tissue Growth. Cell Rep 2018; 21:2671-2677. [PMID: 29212015 DOI: 10.1016/j.celrep.2017.11.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/01/2023] Open
Abstract
Although the intrinsic mechanisms that control whether stem cells divide symmetrically or asymmetrically underlie tissue growth and homeostasis, they remain poorly defined. We report that the RNA-binding protein fragile X mental retardation protein (FMRP) limits the symmetric division, and resulting expansion, of the stem cell population during adaptive intestinal growth in Drosophila. The elevated insulin sensitivity that FMRP-deficient progenitor cells display contributes to their accelerated expansion, which is suppressed by the depletion of insulin-signaling components. This FMRP activity is mediated solely via a second conserved RNA-binding protein, LIN-28, known to boost insulin signaling in stem cells. Via LIN-28, FMRP controls progenitor cell behavior by post-transcriptionally repressing the level of insulin receptor (InR). This study identifies the stem cell-based mechanism by which FMRP controls tissue adaptation, and it raises the possibility that defective adaptive growth underlies the accelerated growth, gastrointestinal, and other symptoms that affect fragile X syndrome patients.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Shengyao Chen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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16
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Willson NL, Forder REA, Tearle R, Williams JL, Hughes RJ, Nattrass GS, Hynd PI. Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential. BMC Genomics 2018; 19:309. [PMID: 29716547 PMCID: PMC5930858 DOI: 10.1186/s12864-018-4723-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/24/2018] [Indexed: 01/25/2023] Open
Abstract
Background Divergent selection for meat and egg production in poultry has resulted in strains of birds differing widely in traits related to these products. Modern strains of meat birds can reach live weights of 2 kg in 35 d, while layer strains are now capable of producing more than 300 eggs per annum but grow slowly. In this study, RNA-Seq was used to investigate hepatic gene expression between three groups of birds with large differences in growth potential; meat bird, layer strain as well as an F1 layer x meat bird. The objective was to identify differentially expressed (DE) genes between all three strains to elucidate biological factors underpinning variations in growth performance. Results RNA-Seq analysis was carried out on total RNA extracted from the liver of meat bird (n = 6), F1 layer x meat bird cross (n = 6) and layer strain (n = 6), males. Differential expression of genes were considered significant at P < 0.05, and a false discovery rate of < 0.05, with any fold change considered. In total, 6278 genes were found to be DE with 5832 DE between meat birds and layers (19%), 2935 DE between meat birds and the cross (9.6%) and 493 DE between the cross and layers (1.6%). Comparisons between the three groups identified 155 significant DE genes. Gene ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the 155 DE genes showed the FoxO signalling pathway was most enriched (P = 0.001), including genes related to cell cycle regulation and insulin signalling. Significant GO terms included ‘positive regulation of glucose import’ and ‘cellular response to oxidative stress’, which is also consistent with FoxOs regulation of glucose metabolism. There were high correlations between FoxO pathway genes and bodyweight, as well as genes related to glycolysis and bodyweight. Conclusions This study revealed large transcriptome differences between meat and layer birds. There was significant evidence implicating the FoxO signalling pathway (via cell cycle regulation and altered metabolism) as an active driver of growth variations in chicken. Functional analysis of the FoxO genes is required to understand how they regulate growth and egg production.
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Affiliation(s)
- Nicky-Lee Willson
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia. .,Poultry CRC, University of New England, PO Box U242, Armidale, NSW, 2351, Australia. .,Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia.
| | - Rebecca E A Forder
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Robert J Hughes
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia.,South Australian Research and Development Institute (SARDI), Pig and Poultry Production Institute, Roseworthy, SA, 5371, Australia
| | - Greg S Nattrass
- South Australian Research and Development Institute (SARDI), Livestock and Farming Systems, Roseworthy, SA, 5371, Australia
| | - Philip I Hynd
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia.,Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, 5371, Australia
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17
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Chen CY, Chen J, He L, Stiles BL. PTEN: Tumor Suppressor and Metabolic Regulator. Front Endocrinol (Lausanne) 2018; 9:338. [PMID: 30038596 PMCID: PMC6046409 DOI: 10.3389/fendo.2018.00338] [Citation(s) in RCA: 343] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/05/2018] [Indexed: 12/19/2022] Open
Abstract
Phosphatase and Tensin Homolog deleted on Chromosome 10 (PTEN) is a dual phosphatase with both protein and lipid phosphatase activities. PTEN was first discovered as a tumor suppressor with growth and survival regulatory functions. In recent years, the function of PTEN as a metabolic regulator has attracted significant attention. As the lipid phosphatase that dephosphorylates phosphatidylinositol-3, 4, 5-phosphate (PIP3), PTEN reduces the level of PIP3, a critical 2nd messenger mediating the signal of not only growth factors but also insulin. In this review, we introduced the discovery of PTEN, the PTEN-regulated canonical and nuclear signals, and PTEN regulation. We then focused on the role of PTEN and PTEN-regulated signals in metabolic regulation. This included the role of PTEN in glycolysis, gluconeogenesis, glycogen synthesis, lipid metabolism as well as mitochondrial metabolism. We also included how PTEN and PTEN regulated metabolic functions may act paradoxically toward insulin sensitivity and tumor metabolism and growth. Further understanding of how PTEN regulates metabolism and how such regulations lead to different biological outcomes is necessary for interventions targeting at the PTEN-regulated signals in either cancer or diabetes treatment.
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Affiliation(s)
- Chien-Yu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Jingyu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Lina He
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Bangyan L. Stiles
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Bangyan L. Stiles
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18
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Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny. PLoS One 2017; 12:e0188357. [PMID: 29200426 PMCID: PMC5714339 DOI: 10.1371/journal.pone.0188357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/06/2017] [Indexed: 01/01/2023] Open
Abstract
The insulin/TOR signal transduction pathway plays a critical role in determining such important traits as body and organ size, metabolic homeostasis and life span. Although this pathway is highly conserved across the animal kingdom, the affected traits can exhibit important differences even between closely related species. Evolutionary studies of regulatory regions require the reliable identification of transcription factor binding sites. Here we have focused on the Insulin Receptor (InR) expression from its P2 promoter in the Drosophila genus, which in D. melanogaster is up-regulated by hypophosphorylated Drosophila FOXO (dFOXO). We have finely characterized this transcription factor binding sites in vitro along the 1.3 kb region upstream of the InR P2 promoter in five Drosophila species. Moreover, we have tested the effect of mutations in the characterized dFOXO sites of D. melanogaster in transgenic flies. The number of experimentally established binding sites varies across the 1.3 kb region of any particular species, and their distribution also differs among species. In D. melanogaster, InR expression from P2 is differentially affected by dFOXO binding sites at the proximal and distal halves of the species 1.3 kb fragment. The observed uneven distribution of binding sites across this fragment might underlie their differential contribution to regulate InR transcription.
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19
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Thounaojam B, Keshan B. Modulation of gene expression by nutritional state and hormones in Bombyx larvae in relation to its growth period. Gene Expr Patterns 2017; 25-26:175-183. [DOI: 10.1016/j.gep.2017.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 08/05/2017] [Accepted: 08/22/2017] [Indexed: 10/19/2022]
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20
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Gonskikh Y, Polacek N. Alterations of the translation apparatus during aging and stress response. Mech Ageing Dev 2017; 168:30-36. [PMID: 28414025 DOI: 10.1016/j.mad.2017.04.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 01/03/2023]
Abstract
Aging is a biological process characterized by the irreversible and time-dependent deterioration of cell functions, tissues, and organs. Accumulating studies in a wide range of species from yeast to human revealed changes associated with the aging process to be conserved throughout evolution. The main characteristics of aging are (i) genomic instability, (ii) loss of telomere function, (iii) epigenetic changes,(iv) increased cellular senescence, (v) depletion of the stem cell pool, (vi) altered intercellular communication and (vii) loss of protein homeostasis. Among the multiple molecular mechanisms underlying aging, alterations of the translation machinery affecting the rate and selectivity of protein biosynthesis seem to play a central role. At the very heart of translation is the ribosome, a multifaceted and universally conserved RNA-protein particle responsible for accurate polypeptide synthesis and co-translational protein folding. Here we summarize and discuss recent developments on the contribution of altered translation and age-dependent modifications on the ribosome structure to aging and cellular senescence.
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Affiliation(s)
- Yulia Gonskikh
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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21
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Terenin IM, Smirnova VV, Andreev DE, Dmitriev SE, Shatsky IN. A researcher's guide to the galaxy of IRESs. Cell Mol Life Sci 2017; 74:1431-1455. [PMID: 27853833 PMCID: PMC11107752 DOI: 10.1007/s00018-016-2409-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022]
Abstract
The idea of internal initiation is frequently exploited to explain the peculiar translation properties or unusual features of some eukaryotic mRNAs. In this review, we summarize the methods and arguments most commonly used to address cases of translation governed by internal ribosome entry sites (IRESs). Frequent mistakes are revealed. We explain why "cap-independent" does not readily mean "IRES-dependent" and why the presence of a long and highly structured 5' untranslated region (5'UTR) or translation under stress conditions cannot be regarded as an argument for appealing to internal initiation. We carefully describe the known pitfalls and limitations of the bicistronic assay and artefacts of some commercially available in vitro translation systems. We explain why plasmid DNA transfection should not be used in IRES studies and which control experiments are unavoidable if someone decides to use it anyway. Finally, we propose a workflow for the validation of IRES activity, including fast and simple experiments based on a single genetic construct with a sequence of interest.
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Affiliation(s)
- Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Victoria V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitri E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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22
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Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S. Translation of CircRNAs. Mol Cell 2017; 66:9-21.e7. [PMID: 28344080 PMCID: PMC5387669 DOI: 10.1016/j.molcel.2017.02.021] [Citation(s) in RCA: 1256] [Impact Index Per Article: 179.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 01/04/2017] [Accepted: 02/21/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.
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Affiliation(s)
- Nagarjuna Reddy Pamudurti
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Christin Stottmeister
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Larissa Ruhe
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Emanuel Wyler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Daniel Perez-Hernandez
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Evelyn Ramberger
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shlomo Shenzis
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Samson
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gunnar Dittmar
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Marina Chekulaeva
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Starved epithelial cells uptake extracellular matrix for survival. Nat Commun 2017; 8:13989. [PMID: 28071763 PMCID: PMC5234072 DOI: 10.1038/ncomms13989] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/17/2016] [Indexed: 01/12/2023] Open
Abstract
Extracellular matrix adhesion is required for normal epithelial cell survival, nutrient uptake and metabolism. This requirement can be overcome by oncogene activation. Interestingly, inhibition of PI3K/mTOR leads to apoptosis of matrix-detached, but not matrix-attached cancer cells, suggesting that matrix-attached cells use alternate mechanisms to maintain nutrient supplies. Here we demonstrate that under conditions of dietary restriction or growth factor starvation, where PI3K/mTOR signalling is decreased, matrix-attached human mammary epithelial cells upregulate and internalize β4-integrin along with its matrix substrate, laminin. Endocytosed laminin localizes to lysosomes, results in increased intracellular levels of essential amino acids and enhanced mTORC1 signalling, preventing cell death. Moreover, we show that starved human fibroblasts secrete matrix proteins that maintain the growth of starved mammary epithelial cells contingent upon epithelial cell β4-integrin expression. Our study identifies a crosstalk between stromal fibroblasts and epithelial cells under starvation that could be exploited therapeutically to target tumours resistant to PI3K/mTOR inhibition. Inhibition of PI3K/mTOR, which mimics nutrient starvation, causes death of detached but not matrix-attached cancer cells. Here the authors show that nutrient restriction of epithelial cells causes uptake of the matrix protein laminin, which results in increased intracellular amino acids and enhanced mTORC1 signalling.
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24
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Kang MJ, Vasudevan D, Kang K, Kim K, Park JE, Zhang N, Zeng X, Neubert TA, Marr MT, Ryoo HD. 4E-BP is a target of the GCN2-ATF4 pathway during Drosophila development and aging. J Cell Biol 2017; 216:115-129. [PMID: 27979906 PMCID: PMC5223598 DOI: 10.1083/jcb.201511073] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 04/19/2016] [Accepted: 11/17/2016] [Indexed: 12/31/2022] Open
Abstract
Reduced amino acid availability attenuates mRNA translation in cells and helps to extend lifespan in model organisms. The amino acid deprivation-activated kinase GCN2 mediates this response in part by phosphorylating eIF2α. In addition, the cap-dependent translational inhibitor 4E-BP is transcriptionally induced to extend lifespan in Drosophila melanogaster, but through an unclear mechanism. Here, we show that GCN2 and its downstream transcription factor, ATF4, mediate 4E-BP induction, and GCN2 is required for lifespan extension in response to dietary restriction of amino acids. The 4E-BP intron contains ATF4-binding sites that not only respond to stress but also show inherent ATF4 activity during normal development. Analysis of the newly synthesized proteome through metabolic labeling combined with click chemistry shows that certain stress-responsive proteins are resistant to inhibition by 4E-BP, and gcn2 mutant flies have reduced levels of stress-responsive protein synthesis. These results indicate that GCN2 and ATF4 are important regulators of 4E-BP transcription during normal development and aging.
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Affiliation(s)
- Min-Ji Kang
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
- Department of Biomedical Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Deepika Vasudevan
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Kwonyoon Kang
- Department of Biomedical Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Kyunggon Kim
- Proteomics Core Laboratory, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Jung-Eun Park
- Department of Biomedical Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Nan Zhang
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Xiaomei Zeng
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Thomas A Neubert
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Michael T Marr
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453
| | - Hyung Don Ryoo
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
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25
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Alfa RW, Kim SK. Using Drosophila to discover mechanisms underlying type 2 diabetes. Dis Model Mech 2016; 9:365-76. [PMID: 27053133 PMCID: PMC4852505 DOI: 10.1242/dmm.023887] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mechanisms of glucose homeostasis are remarkably well conserved between the fruit flyDrosophila melanogasterand mammals. From the initial characterization of insulin signaling in the fly came the identification of downstream metabolic pathways for nutrient storage and utilization. Defects in these pathways lead to phenotypes that are analogous to diabetic states in mammals. These discoveries have stimulated interest in leveraging the fly to better understand the genetics of type 2 diabetes mellitus in humans. Type 2 diabetes results from insulin insufficiency in the context of ongoing insulin resistance. Although genetic susceptibility is thought to govern the propensity of individuals to develop type 2 diabetes mellitus under appropriate environmental conditions, many of the human genes associated with the disease in genome-wide association studies have not been functionally studied. Recent advances in the phenotyping of metabolic defects have positionedDrosophilaas an excellent model for the functional characterization of large numbers of genes associated with type 2 diabetes mellitus. Here, we examine results from studies modeling metabolic disease in the fruit fly and compare findings to proposed mechanisms for diabetic phenotypes in mammals. We provide a systematic framework for assessing the contribution of gene candidates to insulin-secretion or insulin-resistance pathways relevant to diabetes pathogenesis.
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Affiliation(s)
- Ronald W Alfa
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA Neuroscience Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, CA 94305, USA
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Luhur A, Sokol N. Starving for more: Nutrient sensing by LIN-28 in adult intestinal progenitor cells. Fly (Austin) 2016; 9:173-7. [PMID: 26934725 DOI: 10.1080/19336934.2016.1158366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In this Extra View, we extend our recent work on the protein LIN-28 and its role in adult stem cell divisions. LIN-28 is an mRNA- and microRNA-binding protein that is conserved from worms to humans. When expressed ectopically, it promotes the reprogramming of differentiated vertebrate cells into pluripotent stem cells as well as the regeneration of vertebrate tissues after injury. However, its endogenous function in stem cell populations is less clear. We recently reported that LIN-28 is specifically expressed in progenitor cells in the adult Drosophila intestine and enhances insulin signaling within this population. Loss of lin-28 alters the division patterns of these progenitor cells, limiting the growth of the intestinal epithelium that is ordinarily caused by feeding. Thus, LIN-28 is part of an uncharacterized circuit used to remodel a tissue in response to environmental cues like nutrition. Here, we extend this analysis by reporting that the levels of LIN-28 in progenitor cells are sensitive to nutrient availability. In addition, we speculate about the role of LIN-28 in the translational control of target mRNAs such as Insulin Receptor (InR) and how such translational control may be an important mechanism that underlies the stem cell dynamics needed for tissue homeostasis and growth.
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Affiliation(s)
- Arthur Luhur
- a Department of Biology ; Indiana University ; Bloomington , IN USA
| | - Nicholas Sokol
- a Department of Biology ; Indiana University ; Bloomington , IN USA
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Smylla TK, Preiss A, Maier D. In vivo analysis of internal ribosome entry at the Hairless locus by genome engineering in Drosophila. Sci Rep 2016; 6:34881. [PMID: 27713501 PMCID: PMC5054391 DOI: 10.1038/srep34881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/21/2016] [Indexed: 12/23/2022] Open
Abstract
Cell communication in metazoans requires the highly conserved Notch signaling pathway, which is subjected to strict regulation of both activation and silencing. In Drosophila melanogaster, silencing involves the assembly of a repressor complex by Hairless (H) on Notch target gene promoters. We previously found an in-frame internal ribosome entry site in the full length H transcript resulting in two H protein isoforms (Hp120 and Hp150). Hence, H may repress Notch signalling activity in situations where cap-dependent translation is inhibited. Here we demonstrate the in vivo importance of both H isoforms for proper fly development. To this end, we replaced the endogenous H locus by constructs specifically affecting translation of either Hp150 or Hp120 isoforms using genome engineering. Our findings indicate the functional relevance of both H proteins. Based on bristle phenotypes, the predominant isoform Hp150 appears to be of particular importance. In contrast, growth regulation and venation of the wing require the concomitant activity of both isoforms. Finally, the IRES dependent production of Hp120 during mitosis was verified in vivo. Together our data confirm IRES mediated translation of H protein in vivo, supporting strict regulation of Notch in different cellular settings.
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Affiliation(s)
- Thomas K Smylla
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599 Stuttgart, Germany
| | - Anette Preiss
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599 Stuttgart, Germany
| | - Dieter Maier
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599 Stuttgart, Germany
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28
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Musashe DT, Purice MD, Speese SD, Doherty J, Logan MA. Insulin-like Signaling Promotes Glial Phagocytic Clearance of Degenerating Axons through Regulation of Draper. Cell Rep 2016; 16:1838-50. [PMID: 27498858 DOI: 10.1016/j.celrep.2016.07.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 05/23/2016] [Accepted: 07/09/2016] [Indexed: 01/15/2023] Open
Abstract
Neuronal injury triggers robust responses from glial cells, including altered gene expression and enhanced phagocytic activity to ensure prompt removal of damaged neurons. The molecular underpinnings of glial responses to trauma remain unclear. Here, we find that the evolutionarily conserved insulin-like signaling (ILS) pathway promotes glial phagocytic clearance of degenerating axons in adult Drosophila. We find that the insulin-like receptor (InR) and downstream effector Akt1 are acutely activated in local ensheathing glia after axotomy and are required for proper clearance of axonal debris. InR/Akt1 activity, it is also essential for injury-induced activation of STAT92E and its transcriptional target draper, which encodes a conserved receptor essential for glial engulfment of degenerating axons. Increasing Draper levels in adult glia partially rescues delayed clearance of severed axons in glial InR-inhibited flies. We propose that ILS functions as a key post-injury communication relay to activate glial responses, including phagocytic activity.
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Affiliation(s)
- Derek T Musashe
- Department of Neurology, Jungers Center for Neurosciences Research, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA
| | - Maria D Purice
- Department of Neurology, Jungers Center for Neurosciences Research, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA
| | - Sean D Speese
- Department of Neurology, Jungers Center for Neurosciences Research, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA
| | - Johnna Doherty
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 55 North Lake Avenue, Worcester, MA 01605, USA
| | - Mary A Logan
- Department of Neurology, Jungers Center for Neurosciences Research, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA.
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29
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Wicki A, Mandalà M, Massi D, Taverna D, Tang H, Hemmings BA, Xue G. Acquired Resistance to Clinical Cancer Therapy: A Twist in Physiological Signaling. Physiol Rev 2016; 96:805-29. [DOI: 10.1152/physrev.00024.2015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Although modern therapeutic strategies have brought significant progress to cancer care in the last 30 years, drug resistance to targeted monotherapies has emerged as a major challenge. Aberrant regulation of multiple physiological signaling pathways indispensable for developmental and metabolic homeostasis, such as hyperactivation of pro-survival signaling axes, loss of suppressive regulations, and impaired functionalities of the immune system, have been extensively investigated aiming to understand the diversity of molecular mechanisms that underlie cancer development and progression. In this review, we intend to discuss the molecular mechanisms of how conventional physiological signal transduction confers to acquired drug resistance in cancer patients. We will particularly focus on protooncogenic receptor kinase inhibition-elicited tumor cell adaptation through two major core downstream signaling cascades, the PI3K/Akt and MAPK pathways. These pathways are crucial for cell growth and differentiation and are frequently hyperactivated during tumorigenesis. In addition, we also emphasize the emerging roles of the deregulated host immune system that may actively promote cancer progression and attenuate immunosurveillance in cancer therapies. Understanding these mechanisms may help to develop more effective therapeutic strategies that are able to keep the tumor in check and even possibly turn cancer into a chronic disease.
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Affiliation(s)
- Andreas Wicki
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Mario Mandalà
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Daniela Massi
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Daniela Taverna
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Huifang Tang
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Brian A. Hemmings
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Gongda Xue
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
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30
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Brodsky AS, Xiong J, Yang D, Schorl C, Fenton MA, Graves TA, Sikov WM, Resnick MB, Wang Y. Identification of stromal ColXα1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer. BMC Cancer 2016; 16:274. [PMID: 27090210 PMCID: PMC4835834 DOI: 10.1186/s12885-016-2302-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/07/2016] [Indexed: 12/15/2022] Open
Abstract
Background The influence of the tumor microenvironment and tumor-stromal interactions on the heterogeneity of response within breast cancer subtypes have just begun to be explored. This study focuses on patients with estrogen receptor-positive/human epidermal growth factor receptor 2-positive (ER+/HER2+) breast cancer receiving neoadjuvant chemotherapy and HER2-targeted therapy (NAC+H), and was designed to identify novel predictive biomarkers by combining gene expression analysis and immunohistochemistry with pathologic response. Methods We performed gene expression profiling on pre-NAC+H tumor samples from responding (no or minimal residual disease at surgery) and non-responding patients. Gene set enrichment analysis identified potentially relevant pathways, and immunohistochemical staining of pre-treatment biopsies was used to measure protein levels of those pathways, which were correlated with pathologic response in both univariate and multivariate analysis. Results Increased expression of genes encoding for stromal collagens, including Col10A1, and reduced expression of immune-associated genes, reflecting lower levels of total tumor-infiltrating lymphocytes (TILs), were strongly associated with poor pathologic response. Lower TILs in tumor biopsies correlated with reduced likelihood of achieving an optimal pathologic response, but increased expression of the Col10A1 gene product, colXα1, had greater predictive value than stromal abundance for poor response (OR = 18.9, p = 0.003), and the combination of increased colXα1 expression and low TILs was significantly associated with poor response in multivariate analysis. ROC analysis suggests strong specificity and sensitivity for this combination in predicting treatment response. Conclusions Increased expression of stromal colXα1 and low TILs correlate with poor pathologic response in ER+/HER2+ breast tumors. Further studies are needed to confirm their predictive value and impact on long-term outcomes, and to determine whether this collagen exerts a protective effect on the cancer cells or simply reflects other factors within the tumor microenvironment. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2302-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA. .,Department of Pathology, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, 02903, USA.
| | - Jinjun Xiong
- Department of Pathology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, USA
| | - Mary Anne Fenton
- Department of Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Theresa A Graves
- Department of Surgery, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - William M Sikov
- Program in Women's Oncology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, USA
| | - Murray B Resnick
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA. .,Department of Pathology, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, 02903, USA.
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31
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Chen CH, Luhur A, Sokol N. Lin-28 promotes symmetric stem cell division and drives adaptive growth in the adult Drosophila intestine. Development 2016; 142:3478-87. [PMID: 26487778 DOI: 10.1242/dev.127951] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Stem cells switch between asymmetric and symmetric division to expand in number as tissues grow during development and in response to environmental changes. The stem cell intrinsic proteins controlling this switch are largely unknown, but one candidate is the Lin-28 pluripotency factor. A conserved RNA-binding protein that is downregulated in most animals as they develop from embryos to adults, Lin-28 persists in populations of adult stem cells. Its function in these cells has not been previously characterized. Here, we report that Lin-28 is highly enriched in adult intestinal stem cells in the Drosophila intestine. lin-28 null mutants are homozygous viable but display defects in this population of cells, which fail to undergo a characteristic food-triggered expansion in number and have reduced rates of symmetric division as well as reduced insulin signaling. Immunoprecipitation of Lin-28-bound mRNAs identified Insulin-like Receptor (InR), forced expression of which completely rescues lin-28-associated defects in intestinal stem cell number and division pattern. Furthermore, this stem cell activity of lin-28 is independent of one well-known lin-28 target, the microRNA let-7, which has limited expression in the intestinal epithelium. These results identify Lin-28 as a stem cell intrinsic factor that boosts insulin signaling in intestinal progenitor cells and promotes their symmetric division in response to nutrients, defining a mechanism through which Lin-28 controls the adult stem cell division patterns that underlie tissue homeostasis and regeneration.
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Affiliation(s)
- Ching-Huan Chen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Arthur Luhur
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Nicholas Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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32
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Wu YB, Yang WJ, Xie YF, Xu KK, Tian Y, Yuan GR, Wang JJ. Molecular characterization and functional analysis of BdFoxO gene in the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae). Gene 2015; 578:219-24. [PMID: 26701614 DOI: 10.1016/j.gene.2015.12.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/11/2015] [Accepted: 12/11/2015] [Indexed: 11/15/2022]
Abstract
The forkhead box O transcription factor (FoxO) is an important downstream transcription factor in the well-conserved insulin signaling pathway, which regulates the body size and development of insects. In this study, the FoxO gene (BdFoxO) was identified from the oriental fruit fly, Bactrocera dorsalis (Hendel). The open reading frame of BdFoxO (2732 bp) encoded a 910 amino acid protein, and the sequence was well conserved with other insect species. The BdFoxO was highly expressed in larvae and pupae among different development stages, and the highest tissue-specific expression level was found in the fat bodies compared to the testis, ovary, head, thorax, midgut, and Malpighian tubules of adults. Interestingly, we found BdFoxO expression was also up-regulated by starvation, but down-regulated when re-fed. Moreover, the injection of BdFoxO double-stranded RNAs into third-instar larvae significantly reduced BdFoxO transcript levels, which in turn down-regulated the expression of other four genes in the insulin signaling pathway. The silencing of BdFoxO resulted in delayed pupation, and the insect body weight increased significantly compared with that of the control. These results suggested that BdFoxO plays an important role in body size and development in B. dorsalis.
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Affiliation(s)
- Yi-Bei Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Wen-Jia Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Yi-Fei Xie
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Kang-Kang Xu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Yi Tian
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
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33
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FOXO regulates RNA interference in Drosophila and protects from RNA virus infection. Proc Natl Acad Sci U S A 2015; 112:14587-92. [PMID: 26553999 DOI: 10.1073/pnas.1517124112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Small RNA pathways are important players in posttranscriptional regulation of gene expression. These pathways play important roles in all aspects of cellular physiology from development to fertility to innate immunity. However, almost nothing is known about the regulation of the central genes in these pathways. The forkhead box O (FOXO) family of transcription factors is a conserved family of DNA-binding proteins that responds to a diverse set of cellular signals. FOXOs are crucial regulators of cellular homeostasis that have a conserved role in modulating organismal aging and fitness. Here, we show that Drosophila FOXO (dFOXO) regulates the expression of core small RNA pathway genes. In addition, we find increased dFOXO activity results in an increase in RNA interference (RNAi) efficacy, establishing a direct link between cellular physiology and RNAi. Consistent with these findings, dFOXO activity is stimulated by viral infection and is required for effective innate immune response to RNA virus infection. Our study reveals an unanticipated connection among dFOXO, stress responses, and the efficacy of small RNA-mediated gene silencing and suggests that organisms can tune their gene silencing in response to environmental and metabolic conditions.
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34
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Reversible induction of translational isoforms of p53 in glucose deprivation. Cell Death Differ 2015; 22:1203-18. [PMID: 25721046 DOI: 10.1038/cdd.2014.220] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 02/01/2023] Open
Abstract
Tumor suppressor protein p53 is a master transcription regulator, indispensable for controlling several cellular pathways. Earlier work in our laboratory led to the identification of dual internal ribosome entry site (IRES) structure of p53 mRNA that regulates translation of full-length p53 and Δ40p53. IRES-mediated translation of both isoforms is enhanced under different stress conditions that induce DNA damage, ionizing radiation and endoplasmic reticulum stress, oncogene-induced senescence and cancer. In this study, we addressed nutrient-mediated translational regulation of p53 mRNA using glucose depletion. In cell lines, this nutrient-depletion stress relatively induced p53 IRES activities from bicistronic reporter constructs with concomitant increase in levels of p53 isoforms. Surprisingly, we found scaffold/matrix attachment region-binding protein 1 (SMAR1), a predominantly nuclear protein is abundant in the cytoplasm under glucose deprivation. Importantly under these conditions polypyrimidine-tract-binding protein, an established p53 ITAF did not show nuclear-cytoplasmic relocalization highlighting the novelty of SMAR1-mediated control in stress. In vivo studies in mice revealed starvation-induced increase in SMAR1, p53 and Δ40p53 levels that was reversible on dietary replenishment. SMAR1 associated with p53 IRES sequences ex vivo, with an increase in interaction on glucose starvation. RNAi-mediated-transient SMAR1 knockdown decreased p53 IRES activities in normal conditions and under glucose deprivation, this being reflected in changes in mRNAs in the p53 and Δ40p53 target genes involved in cell-cycle arrest, metabolism and apoptosis such as p21, TIGAR and Bax. This study provides a new physiological insight into the regulation of this critical tumor suppressor in nutrient starvation, also suggesting important functions of the p53 isoforms in these conditions as evident from the downstream transcriptional target activation.
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Abstract
The larval period of the Drosophila life cycle is characterized by immense growth. In nutrient rich conditions, larvae increase in mass approximately two hundred-fold in five days. However, upon nutrient deprivation, growth is arrested. The prevailing view is that dietary amino acids drive this larval growth by activating the conserved insulin/PI3 kinase and Target of rapamycin (TOR) pathways and promoting anabolic metabolism. One key anabolic process is protein synthesis. However, few studies have attempted to measure mRNA translation during larval development or examine the signaling requirements for nutrient-dependent regulation. Our work addresses this issue. Using polysome analyses, we observed that starvation rapidly (within thirty minutes) decreased larval mRNA translation, with a maximal decrease at 6–18 hours. By analyzing individual genes, we observed that nutrient-deprivation led to a general reduction in mRNA translation, regardless of any starvation-mediated changes (increase or decrease) in total transcript levels. Although sugars and amino acids are key regulators of translation in animal cells and are the major macronutrients in the larval diet, we found that they alone were not sufficient to maintain mRNA translation in larvae. The insulin/PI3 kinase and TOR pathways are widely proposed as the main link between nutrients and mRNA translation in animal cells. However, we found that genetic activation of PI3K and TOR signaling, or regulation of two effectors – 4EBP and S6K – could not prevent the starvation-mediated translation inhibition. Similarly, we showed that the nutrient stress-activated eIF2α kinases, GCN2 and PERK, were not required for starvation-induced inhibition of translation in larvae. These findings indicate that nutrient control of mRNA translation in larvae is more complex than simply amino acid activation of insulin and TOR signaling.
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Affiliation(s)
- Sabarish Nagarajan
- Department of Biochemistry and Molecular Biology, and Clark H. Smith Brain Tumour Centre, Southern Alberta Cancer Research Institute, University of Calgary, HRIC, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Savraj S Grewal
- Department of Biochemistry and Molecular Biology, and Clark H. Smith Brain Tumour Centre, Southern Alberta Cancer Research Institute, University of Calgary, HRIC, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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36
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Martínez-Salas E, Lozano G, Fernandez-Chamorro J, Francisco-Velilla R, Galan A, Diaz R. RNA-binding proteins impacting on internal initiation of translation. Int J Mol Sci 2013; 14:21705-26. [PMID: 24189219 PMCID: PMC3856030 DOI: 10.3390/ijms141121705] [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: 09/06/2013] [Revised: 10/17/2013] [Accepted: 10/22/2013] [Indexed: 12/20/2022] Open
Abstract
RNA-binding proteins (RBPs) are pivotal regulators of all the steps of gene expression. RBPs govern gene regulation at the post-transcriptional level by virtue of their capacity to assemble ribonucleoprotein complexes on certain RNA structural elements, both in normal cells and in response to various environmental stresses. A rapid cellular response to stress conditions is triggered at the step of translation initiation. Two basic mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism that operates in most mRNAs, and the internal ribosome entry site (IRES)-dependent mechanism activated under conditions that compromise the general translation pathway. IRES elements are cis-acting RNA sequences that recruit the translation machinery using a cap-independent mechanism often assisted by a subset of translation initiation factors and various RBPs. IRES-dependent initiation appears to use different strategies to recruit the translation machinery depending on the RNA organization of the region and the network of RBPs interacting with the element. In this review we discuss recent advances in understanding the implications of RBPs on IRES-dependent translation initiation.
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Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain.
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Chen J, Yang JT, Doctor DL, Rawlins BA, Shields BC, Vaughn JC. 5'-UTR mediated translational control of splicing assembly factor RNP-4F expression during development of the Drosophila central nervous system. Gene 2013; 528:154-62. [PMID: 23892091 DOI: 10.1016/j.gene.2013.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/17/2013] [Indexed: 11/24/2022]
Abstract
Drosophila RNP-4F is a highly conserved protein from yeast to human and functions as a spliceosome assembly factor during pre-mRNA splicing. Two major developmentally regulated rnp-4f mRNA isoforms have been described during fly development, designated "long" and "short," differing by a 177-nt tract in the 5'-UTR. This region potentially folds into a single long stable stem-loop by pairing of intron 0 and part of exon 2. Since the coding potential for the two isoforms is identical, the interesting question arises as to the functional significance of this evolutionarily-conserved 5'-UTR feature. Here we describe the effects of wild-type and mutated stem-loop on modulation of rnp-4f gene expression in embryos using a GFP reporter assay. In this work, a new GFP expression vector designated pUAS-Neostinger was constructed. The UAS-GAL4 system was utilized to trigger GFP expression using tissue-specific promoter driver fly lines. Fluorescence microscopy visualization, Western blotting and real-time qRT-PÇR were used to study and quantify GFP reporter protein and mRNA levels. A significant increase in GFP reporter protein expression due to presence of the wild-type stem-loop sequence/structure was unexpectedly observed with no concomitant increase in GFP reporter mRNA levels, showing that the 177-nt region enhancement acts posttranscriptionally. The effects of potential cis-acting elements within the stem-loop were evaluated using the reporter assay in two mutant constructs. Results of GFP reporter over-expression show that RNP-4F translational regulation is highly sensitive in the developing fly central nervous system. The potential molecular mechanism behind the observed translational enhancement is discussed.
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Affiliation(s)
- Jing Chen
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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38
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Olson CM, Donovan MR, Spellberg MJ, Marr MT. The insulin receptor cellular IRES confers resistance to eIF4A inhibition. eLife 2013; 2:e00542. [PMID: 23878722 PMCID: PMC3713452 DOI: 10.7554/elife.00542] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/11/2013] [Indexed: 11/17/2022] Open
Abstract
Under conditions of stress, such as limited growth factor signaling, translation is inhibited by the action of 4E-BP and PDCD4. These proteins, through inhibition of eIF4E and eIF4A, respectively, impair cap-dependent translation. Under stress conditions FOXO transcription factors activate 4E-BP expression amplifying the repression. Here we show that Drosophila FOXO binds the PDCD4 promoter and stimulates the transcription of PDCD4 in response to stress. We have shown previously that the 5′ UTR of the Drosophila insulin-like receptor (dINR) supports cap-independent translation that is resistant to 4E-BP. Using hippuristanol, an eIF4A inhibitor, we find that translation of dINR UTR containing transcripts are also resistant to eIF4A inhibition. In addition, the murine insulin receptor and insulin-like growth factor receptor 5′ UTRs support cap-independent translation and have a similar resistance to hippuristanol. This resistance to inhibition of eIF4E and eIF4A indicates a conserved strategy to allow translation of growth factor receptors under stress conditions. DOI:http://dx.doi.org/10.7554/eLife.00542.001 Protein synthesis in eukaryotes occurs in two stages: transcription of DNA into messenger RNA (mRNA) in the nucleus, and then translation of that mRNA into a protein by ribosomes in the cytoplasm. These processes are regulated by a complex network of signaling pathways that enables cells to tailor protein synthesis to match current conditions. This involves regulating the expression of the genes that code for these proteins. When cells experience stressful events, such as a shortage of oxygen or nutrients, they reduce the synthesis of most proteins. This response is regulated, in part, by a signaling pathway known as the insulin and insulin-like receptor pathway. In particular, stressful events inhibit a protein complex called eIF4F, which normally initiates the translation of mRNA molecules by binding to a structure on one end of the mRNA called the 5′ cap. Despite this general inhibition, the production of certain other proteins—including the insulin receptor itself—is actually increased in response to stress. Olson et al. have carried out a series of experiments to explore how inhibition of the eIF4F protein complex influences the translation of the mRNA for the insulin receptor. The eIF4F complex is made up of three proteins, including one that binds to the 5′ cap and a helicase that unwinds the RNA. Previous work in the fruit fly Drosophila showed that translation of this mRNA can continue even if formation of the eIF4F complex is inhibited by targeting the cap binding protein. Olsen et al. now show that translation of this mRNA is also independent of the helicase. Instead, translation is maintained under these conditions because the insulin receptor mRNA contains a sequence called an internal ribosome entry site, which allows ribosomes to bind to the mRNA without the influence of the 5′ cap. Olson et al. reveal the details of this regulatory pathway in Drosophila and show that similar mechanisms are at work in mammalian cells, suggesting this pathway represents a crucial regulatory process that has been conserved during evolution. A key question for future research is whether other genes within the insulin and insulin-receptor like signaling pathway use this same trick to evade translational inhibitors. DOI:http://dx.doi.org/10.7554/eLife.00542.002
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Affiliation(s)
- Calla M Olson
- Department of Biology and the Rosenstiel Basic Medical Sciences Research Center , Brandeis University , Waltham , United States
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39
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Yoshida Y, Fuchita M, Kimura-Koyanagi M, Kanno A, Matsuda T, Asahara SI, Hashimoto N, Isagawa T, Ogawa W, Aburatani H, Noda T, Seino S, Kasuga M, Kido Y. Contribution of insulin signaling to the regulation of pancreatic beta-cell mass during the catch-up growth period in a low birth weight mouse model. Diabetol Int 2013. [DOI: 10.1007/s13340-013-0127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Melnik BC, Zouboulis CC. Potential role of FoxO1 and mTORC1 in the pathogenesis of Western diet-induced acne. Exp Dermatol 2013; 22:311-5. [PMID: 23614736 PMCID: PMC3746128 DOI: 10.1111/exd.12142] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/13/2022]
Abstract
Acne in adolescents of developed countries is an epidemic skin disease and has currently been linked to the Western diet (WD). It is the intention of this viewpoint to discuss the possible impact of WD-mediated nutrient signalling in the pathogenesis of acne. High glycaemic load and dairy protein consumption both increase insulin/insulin-like growth factor-1 (IGF-1) signalling (IIS) that is superimposed on elevated IGF-1 signalling of puberty. The cell's nutritional status is primarily sensed by the forkhead box transcription factor O1 (FoxO1) and the serine/threonine kinase mammalian target of rapamycin complex 1 (mTORC1). Increased IIS extrudes FoxO1 into the cytoplasm, whereas nuclear FoxO1 suppresses hepatic IGF-1 synthesis and thus impairs somatic growth. FoxO1 attenuates androgen signalling, interacts with regulatory proteins important for sebaceous lipogenesis, regulates the activity of innate and adaptive immunity, antagonizes oxidative stress and most importantly functions as a rheostat of mTORC1, the master regulator of cell growth, proliferation and metabolic homoeostasis. Thus, FoxO1 links nutrient availability to mTORC1-driven processes: increased protein and lipid synthesis, cell proliferation, cell differentiation including hyperproliferation of acroinfundibular keratinocytes, sebaceous gland hyperplasia, increased sebaceous lipogenesis, insulin resistance and increased body mass index. Enhanced androgen, TNF-α and IGF-1 signalling due to genetic polymorphisms promoting the risk of acne all converge in mTORC1 activation, which is further enhanced by nutrient signalling of WD. Deeper insights into the molecular interplay of FoxO1/mTORC1-mediated nutrient signalling are thus of critical importance to understand the impact of WD on the promotion of epidemic acne and more serious mTORC1-driven diseases of civilization.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Osnabrück, Germany.
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41
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Ivanov DK, Papatheodorou I, Ziehm M, Thornton JM. Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster. MOLECULAR BIOSYSTEMS 2013; 9:1756-64. [PMID: 23624434 PMCID: PMC3693544 DOI: 10.1039/c3mb25485b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Several components have been previously identified, that modulate longevity in several species, including the target of rapamycin (TOR) and the Insulin/IGF-1 (IIS) signalling pathways. In order to infer paths and transcriptional feedback loops that are likely to modulate ageing, we manually built a comprehensive and computationally efficient signalling network model of the IIS and TOR pathways in worms. The core insulin transduction is signalling from the sole insulin receptor daf-2 to ultimately inhibit the translocation of the transcription factor daf-16 into the nucleus. Reduction in this core signalling is thought to increase longevity in several species. In addition to this core insulin signalling, we have also recorded in our worm model the transcription factors skn-1 and hif-1, those are also thought to modulate ageing in a daf-16 independent manner. Several paths that are likely to modulate ageing were inferred via a web-based service NetEffects, by utilising perturbed components (rheb-1, let-363, aak-2, daf-2;daf-16 and InR;foxo in worms and flies respectively) from freely available gene expression microarrays. These included "routes" from TOR pathway to transcription factors daf-16, skn-1, hif-1 and daf-16 independent paths via skn-1/hif-1. Paths that could be tested by experimental hypotheses, with respect to relative contribution to longevity, are also discussed. Direct comparison of the IIS and TOR pathways in both worm and fly suggest a remarkable similarity. While similarities in the paths that could modulate ageing in both organisms were noted, differences are also discussed. This approach can also be extended to other pathways and processes.
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Affiliation(s)
- Dobril K Ivanov
- EMBL-European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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42
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NAT1/DAP5/p97 and atypical translational control in the Drosophila Circadian Oscillator. Genetics 2012; 192:943-57. [PMID: 22904033 DOI: 10.1534/genetics.112.143248] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circadian rhythms are driven by gene expression feedback loops in metazoans. Based on the success of genetic screens for circadian mutants in Drosophila melanogaster, we undertook a targeted RNAi screen to study the impact of translation control genes on circadian locomotor activity rhythms in flies. Knockdown of vital translation factors in timeless protein-positive circadian neurons caused a range of effects including lethality. Knockdown of the atypical translation factor NAT1 had the strongest effect and lengthened circadian period. It also dramatically reduced PER protein levels in pigment dispersing factor (PDF) neurons. BELLE (BEL) protein was also reduced by the NAT1 knockdown, presumably reflecting a role of NAT1 in belle mRNA translation. belle and NAT1 are also targets of the key circadian transcription factor Clock (CLK). Further evidence for a role of NAT1 is that inhibition of the target of rapamycin (TOR) kinase increased oscillator activity in cultured wings, which is absent under conditions of NAT1 knockdown. Moreover, the per 5'- and 3'-UTRs may function together to facilitate cap-independent translation under conditions of TOR inhibition. We suggest that NAT1 and cap-independent translation are important for per mRNA translation, which is also important for the circadian oscillator. A circadian translation program may be especially important in fly pacemaker cells.
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Abstract
Research reported in this issue of Science Translational Medicine illustrates the benefits of short-term food withdrawal (fasting) in the treatment of cancer. Fasting exploited fundamental differences in the way tumor cells and normal cells respond to stress, simultaneously strengthening normal cell function and weakening tumor cell survival in the presence of toxic doses of chemotherapeutic drugs.
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Affiliation(s)
- Heidi Scrable
- Robert and Arlene Kogod Center on Aging, Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.
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Tebaldi T, Re A, Viero G, Pegoretti I, Passerini A, Blanzieri E, Quattrone A. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics 2012; 13:220. [PMID: 22672192 PMCID: PMC3441405 DOI: 10.1186/1471-2164-13-220] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/06/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome) and the polysome-associated mRNAs (the translatome) after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/translatome comparisons in mammalian cells following different stimuli or undergoing cell programs. RESULTS Triggering of the EGF pathway results in an early induction of transcriptome and translatome changes, but 90% of the significant variation is limited to the translatome and the degree of concordant changes is less than 5%. The survey of other 19 different transcriptome/translatome comparisons shows that extensive uncoupling is a general rule, in terms of both RNA movements and inferred cell activities, with a strong tendency of translation-related genes to be controlled purely at the translational level. By different statistical approaches, we finally provide evidence of the lack of dependence between changes at the transcriptome and translatome levels. CONCLUSIONS We propose a model of diffused independency between variation in transcript abundances and variation in their engagement on polysomes, which implies the existence of specific mechanisms to couple these two ways of regulating gene expression.
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Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
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Shang E, Cui Q, Wang X, Beseler C, Greenberg DA, Wolgemuth DJ. The bromodomain-containing gene BRD2 is regulated at transcription, splicing, and translation levels. J Cell Biochem 2012; 112:2784-93. [PMID: 21608014 DOI: 10.1002/jcb.23192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human BRD2 gene has been linked and associated with a form of common epilepsy and electroencephalographic abnormalities. Disruption of Brd2 in the mouse revealed that it is essential for embryonic neural development and that viable Brd2(+/-) heterozygotes show both decreased GABAergic neuron counts and increased susceptibility to seizures. To understand the molecular mechanisms by which mis-expression of BRD2 might contribute to epilepsy, we examined its regulation at multiple levels. We discovered that BRD2 expresses distinct tissue-specific transcripts that originate from different promoters and have strikingly different lengths of 5' untranslated regions (5'UTR). We also experimentally confirmed the presence of a highly conserved, alternatively spliced exon, inclusion of which would result in a premature termination of translation. Downstream of this alternative exon is a polymorphic microsatellite (GT-repeats). Manipulation of the number of the GT-repeats revealed that the length of the GT-repeats affects the ratio of the two alternative splicing products. In vitro translation and expression in cultured cells revealed that among the four different mRNAs (long and short 5'UTR combined with regular and alternative splicing), only the regularly spliced mRNA with the short 5'UTR yields full-length protein. In situ hybridization and immunohistochemical studies showed that although Brd2 mRNA is expressed in both the hippocampus and cerebellum, Brd2 protein only can be detected in the cerebellar Purkinje cells and not in hippocampal cells. These multiple levels of regulation would likely affect the production of functional BRD2 protein during neural development and hence, its role in the etiology of seizure susceptibility.
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Affiliation(s)
- Enyuan Shang
- Division of Statistical Genetics, Department of Biostatistics, Mailman School of Public Health, Columbia University Medical Center, New York, New York 10032, USA
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Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs. Comp Funct Genomics 2012; 2012:391546. [PMID: 22536116 PMCID: PMC3321441 DOI: 10.1155/2012/391546] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 01/20/2012] [Indexed: 12/13/2022] Open
Abstract
The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. The majority of eukaryotic cellular mRNAs initiates translation by the cap-dependent or scanning mode of translation initiation, a mechanism that depends on the recognition of the m(7)G(5')ppp(5')N, known as the cap. However, mRNAs encoding proteins required for cell survival under stress bypass conditions inhibitory to cap-dependent translation; these mRNAs often harbor internal ribosome entry site (IRES) elements in their 5'UTRs that mediate internal initiation of translation. This mechanism is also exploited by mRNAs expressed from the genome of viruses infecting eukaryotic cells. In this paper we discuss recent advances in understanding alternative ways to initiate translation across eukaryotic organisms.
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Muranen T, Selfors LM, Worster DT, Iwanicki MP, Song L, Morales FC, Gao S, Mills GB, Brugge JS. Inhibition of PI3K/mTOR leads to adaptive resistance in matrix-attached cancer cells. Cancer Cell 2012; 21:227-39. [PMID: 22340595 PMCID: PMC3297962 DOI: 10.1016/j.ccr.2011.12.024] [Citation(s) in RCA: 347] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 10/07/2011] [Accepted: 12/20/2011] [Indexed: 02/05/2023]
Abstract
The PI3K/mTOR-pathway is the most commonly dysregulated pathway in epithelial cancers and represents an important target for cancer therapeutics. Here, we show that dual inhibition of PI3K/mTOR in ovarian cancer-spheroids leads to death of inner matrix-deprived cells, whereas matrix-attached cells are resistant. This matrix-associated resistance is mediated by drug-induced upregulation of cellular survival programs that involve both FOXO-regulated transcription and cap-independent translation. Inhibition of any one of several upregulated proteins, including Bcl-2, EGFR, or IGF1R, abrogates resistance to PI3K/mTOR inhibition. These results demonstrate that acute adaptive responses to PI3K/mTOR inhibition in matrix-attached cells resemble well-conserved stress responses to nutrient and growth factor deprivation. Bypass of this resistance mechanism through rational design of drug combinations could significantly enhance PI3K-targeted drug efficacy.
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Affiliation(s)
- Taru Muranen
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Laura M. Selfors
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Devin T. Worster
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Marcin P. Iwanicki
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Loling Song
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Fabiana C. Morales
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Sizhen Gao
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Gordon B. Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Corresponding author , Department of Cell Biology, 240 Longwood Ave, Boston MA 02115, Phone: 617 432 3974, Fax: 617 432 3969
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Ferguson SB, Blundon MA, Klovstad MS, Schüpbach T. Modulation of gurken translation by insulin and TOR signaling in Drosophila. J Cell Sci 2012; 125:1407-19. [PMID: 22328499 DOI: 10.1242/jcs.090381] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Localized Gurken (Grk) translation specifies the anterior-posterior and dorsal-ventral axes of the developing Drosophila oocyte; spindle-class females lay ventralized eggs resulting from inefficient grk translation. This phenotype is thought to result from inhibition of the Vasa RNA helicase. In a screen for modifiers of the eggshell phenotype in spn-B flies, we identified a mutation in the lnk gene. We show that lnk mutations restore Grk expression but do not suppress the persistence of double-strand breaks nor other spn-B phenotypes. This suppression does not affect Egfr directly, but rather overcomes the translational block of grk messages seen in spindle mutants. Lnk was recently identified as a component of the insulin/insulin-like growth factor signaling (IIS) and TOR pathway. Interestingly, direct inhibition of TOR with rapamycin in spn-B or vas mutant mothers can also suppress the ventralized eggshell phenotype. When dietary protein is inadequate, reduced IIS-TOR activity inhibits cap-dependent translation by promoting the activity of the translation inhibitor eIF4E-binding protein (4EBP). We hypothesize that reduced TOR activity promotes grk translation independent of the canonical Vasa- and cap-dependent mechanism. This model might explain how flies can maintain the translation of developmentally important transcripts during periods of nutrient limitation when bulk cap-dependent translation is repressed.
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49
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Bolukbasi E, Vass S, Cobbe N, Nelson B, Simossis V, Dunbar DR, Heck MMS. Drosophila poly suggests a novel role for the Elongator complex in insulin receptor-target of rapamycin signalling. Open Biol 2012; 2:110031. [PMID: 22645656 PMCID: PMC3352090 DOI: 10.1098/rsob.110031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/21/2011] [Indexed: 01/06/2023] Open
Abstract
Multi-cellular organisms need to successfully link cell growth and metabolism to environmental cues during development. Insulin receptor-target of rapamycin (InR-TOR) signalling is a highly conserved pathway that mediates this link. Herein, we describe poly, an essential gene in Drosophila that mediates InR-TOR signalling. Loss of poly results in lethality at the third instar larval stage, but only after a stage of extreme larval longevity. Analysis in Drosophila demonstrates that Poly and InR interact and that poly mutants show an overall decrease in InR-TOR signalling, as evidenced by decreased phosphorylation of Akt, S6K and 4E-BP. Metabolism is altered in poly mutants, as revealed by microarray expression analysis and a decreased triglyceride : protein ratio in mutant animals. Intriguingly, the cellular distribution of Poly is dependent on insulin stimulation in both Drosophila and human cells, moving to the nucleus with insulin treatment, consistent with a role in InR-TOR signalling. Together, these data reveal that Poly is a novel, conserved (from flies to humans) mediator of InR signalling that promotes an increase in cell growth and metabolism. Furthermore, homology to small subunits of Elongator demonstrates a novel, unexpected role for this complex in insulin signalling.
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Affiliation(s)
| | | | | | | | | | | | - Margarete M. S. Heck
- University of Edinburgh, Queen's Medical
Research Institute, University/BHF Centre for
Cardiovascular Science, 47 Little France Crescent, Edinburgh EH16
4TJ, UK
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50
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Foss EJ, Radulovic D, Shaffer SA, Goodlett DR, Kruglyak L, Bedalov A. Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol 2011; 9:e1001144. [PMID: 21909241 PMCID: PMC3167781 DOI: 10.1371/journal.pbio.1001144] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 07/29/2011] [Indexed: 12/22/2022] Open
Abstract
Networks of co-regulated transcripts in genetically diverse populations have been studied extensively, but little is known about the degree to which these networks cause similar co-variation at the protein level. We quantified 354 proteins in a genetically diverse population of yeast segregants, which allowed for the first time construction of a coherent protein co-variation matrix. We identified tightly co-regulated groups of 36 and 93 proteins that were made up predominantly of genes involved in ribosome biogenesis and amino acid metabolism, respectively. Even though the ribosomal genes were tightly co-regulated at both the protein and transcript levels, genetic regulation of proteins was entirely distinct from that of transcripts, and almost no genes in this network showed a significant correlation between protein and transcript levels. This result calls into question the widely held belief that in yeast, as opposed to higher eukaryotes, ribosomal protein levels are regulated primarily by regulating transcript levels. Furthermore, although genetic regulation of the amino acid network was more similar for proteins and transcripts, regression analysis demonstrated that even here, proteins vary predominantly as a result of non-transcriptional variation. We also found that cis regulation, which is common in the transcriptome, is rare at the level of the proteome. We conclude that most inter-individual variation in levels of these particular high abundance proteins in this genetically diverse population is not caused by variation of their underlying transcripts.
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Affiliation(s)
- Eric J. Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center and Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Dragan Radulovic
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Scott A. Shaffer
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Leonid Kruglyak
- Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center and Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
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