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Mandelboum S, Herrero M, Atzmon A, Ehrlich M, Elroy-Stein O. Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes. Nucleic Acids Res 2023; 51:3375-3390. [PMID: 36881761 PMCID: PMC10123121 DOI: 10.1093/nar/gkad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/01/2023] [Accepted: 02/12/2023] [Indexed: 03/09/2023] Open
Abstract
Regulation of mRNA translation in astrocytes gains a growing interest. However, until now, successful ribosome profiling of primary astrocytes has not been reported. Here, we optimized the standard 'polysome profiling' method and generated an effective protocol for polyribosome extraction, which enabled genome-wide assessment of mRNA translation dynamics along the process of astrocyte activation. Transcriptome (RNAseq) and translatome (Riboseq) data generated at 0, 24 and 48 h after cytokines treatment, revealed dynamic genome-wide changes in the expression level of ∼12 000 genes. The data clarify whether a change in protein synthesis rate results from a change in mRNA level or translation efficiency per se. It exhibit different expression strategies, based on changes in mRNA abundance and/or translation efficiency, which are specifically assigned to gene subsets depending on their function. Moreover, the study raises an important take-home message related to the possible presence of 'difficult to extract' polyribosome sub-groups, in all cell types, thus illuminating the impact of ribosomes extraction methodology on experiments addressing translation regulation.
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Affiliation(s)
- Shir Mandelboum
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Melisa Herrero
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrea Atzmon
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Orna Elroy-Stein
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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2
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Biembengut ÍV, Silva ILZ, Souza TDACBD, Shigunov P. Cytoplasmic FMR1 interacting protein (CYFIP) family members and their function in neural development and disorders. Mol Biol Rep 2021; 48:6131-6143. [PMID: 34327661 DOI: 10.1007/s11033-021-06585-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022]
Abstract
In humans, the cytoplasmic FMR1 interacting protein (CYFIP) family is composed of CYFIP1 and CYFIP2. Despite their high similarity and shared interaction with many partners, CYFIP1 and CYFIP2 act at different points in cellular processes. CYFIP1 and CYFIP2 have different expression levels in human tissues, and knockout animals die at different time points of development. CYFIP1, similar to CYFIP2, acts in the WAVE regulatory complex (WRC) and plays a role in actin dynamics through the activation of the Arp2/3 complex and in a posttranscriptional regulatory complex with the fragile X mental retardation protein (FMRP). Previous reports have shown that CYFIP1 and CYFIP2 may play roles in posttranscriptional regulation in different ways. While CYFIP1 is involved in translation initiation via the 5'UTR, CYFIP2 may regulate mRNA expression via the 3'UTR. In addition, this CYFIP protein family is involved in neural development and maturation as well as in different neural disorders, such as intellectual disabilities, autistic spectrum disorders, and Alzheimer's disease. In this review, we map diverse studies regarding the functions, regulation, and implications of CYFIP proteins in a series of molecular pathways. We also highlight mutations and their structural effects both in functional studies and in neural diseases.
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Affiliation(s)
- Ísis Venturi Biembengut
- Carlos Chagas Institute-FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775, CIC, Curitiba, Paraná, 81830-010, Brazil
| | | | | | - Patrícia Shigunov
- Carlos Chagas Institute-FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775, CIC, Curitiba, Paraná, 81830-010, Brazil.
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3
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Roy N, Sundar S, Pillai M, Patell-Socha F, Ganesh S, Aloysius A, Rumman M, Gala H, Hughes SM, Zammit PS, Dhawan J. mRNP granule proteins Fmrp and Dcp1a differentially regulate mRNP complexes to contribute to control of muscle stem cell quiescence and activation. Skelet Muscle 2021; 11:18. [PMID: 34238354 PMCID: PMC8265057 DOI: 10.1186/s13395-021-00270-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/28/2021] [Indexed: 01/28/2023] Open
Abstract
Background During skeletal muscle regeneration, satellite stem cells use distinct pathways to repair damaged myofibers or to self-renew by returning to quiescence. Cellular/mitotic quiescence employs mechanisms that promote a poised or primed state, including altered RNA turnover and translational repression. Here, we investigate the role of mRNP granule proteins Fragile X Mental Retardation Protein (Fmrp) and Decapping protein 1a (Dcp1a) in muscle stem cell quiescence and differentiation. Methods Using isolated single muscle fibers from adult mice, we established differential enrichment of mRNP granule proteins including Fmrp and Dcp1a in muscle stem cells vs. myofibers. We investigated muscle tissue homeostasis in adult Fmr1-/- mice, analyzing myofiber cross-sectional area in vivo and satellite cell proliferation ex vivo. We explored the molecular mechanisms of Dcp1a and Fmrp function in quiescence, proliferation and differentiation in a C2C12 culture model. Here, we used polysome profiling, imaging and RNA/protein expression analysis to establish the abundance and assembly status of mRNP granule proteins in different cellular states, and the phenotype of knockdown cells. Results Quiescent muscle satellite cells are enriched for puncta containing the translational repressor Fmrp, but not the mRNA decay factor Dcp1a. MuSC isolated from Fmr1-/- mice exhibit defective proliferation, and mature myofibers show reduced cross-sectional area, suggesting a role for Fmrp in muscle homeostasis. Expression and organization of Fmrp and Dcp1a varies during primary MuSC activation on myofibers, with Fmrp puncta prominent in quiescence, but Dcp1a puncta appearing during activation/proliferation. This reciprocal expression of Fmrp and Dcp1a puncta is recapitulated in a C2C12 culture model of quiescence and activation: consistent with its role as a translational repressor, Fmrp is enriched in non-translating mRNP complexes abundant in quiescent myoblasts; Dcp1a puncta are lost in quiescence, suggesting stabilized and repressed transcripts. The function of each protein differs during proliferation; whereas Fmrp knockdown led to decreased proliferation and lower cyclin expression, Dcp1a knockdown led to increased cell proliferation and higher cyclin expression. However, knockdown of either Fmrp or Dcp1a led to compromised differentiation. We also observed cross-regulation of decay versus storage mRNP granules; knockdown of Fmrp enhances accumulation of Dcp1a puncta, whereas knockdown of Dcp1a leads to increased Fmrp in puncta. Conclusions Taken together, our results provide evidence that the balance of mRNA turnover versus utilization is specific for distinct cellular states. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-021-00270-9.
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Affiliation(s)
- Nainita Roy
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Swetha Sundar
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malini Pillai
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Farah Patell-Socha
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sravya Ganesh
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ajoy Aloysius
- National Center for Biological Sciences, Bangalore, India
| | - Mohammed Rumman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Hardik Gala
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Simon M Hughes
- King's College London, Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, London, UK
| | - Peter S Zammit
- King's College London, Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, London, UK
| | - Jyotsna Dhawan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India. .,Centre for Cellular and Molecular Biology, Hyderabad, India.
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4
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Sobhany M, Stanley RE. Polysome Profiling without Gradient Makers or Fractionation Systems. J Vis Exp 2021. [PMID: 34152326 DOI: 10.3791/62680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Polysome fractionation by sucrose density gradient centrifugation is a powerful tool that can be used to create ribosome profiles, identify specific mRNAs being translated by ribosomes, and analyze polysome associated factors. While automated gradient makers and gradient fractionation systems are commonly used with this technique, these systems are generally expensive and can be cost-prohibitive for laboratories that have limited resources or cannot justify the expense due to their infrequent or occasional need to perform this method for their research. Here, a protocol is presented to reproducibly generate polysome profiles using standard equipment available in most molecular biology laboratories without specialized fractionation instruments. Moreover, a comparison of polysome profiles generated with and without a gradient fractionation system is provided. Strategies to optimize and produce reproducible polysome profiles are discussed. Saccharomyces cerevisiae is utilized as a model organism in this protocol. However, this protocol can be easily modified and adapted to generate ribosome profiles for many different organisms and cell types.
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Affiliation(s)
- Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
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5
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Reis RS, Deforges J, Schmidt RR, Schippers JHM, Poirier Y. An antisense noncoding RNA enhances translation via localized structural rearrangements of its cognate mRNA. THE PLANT CELL 2021; 33:1381-1397. [PMID: 33793857 DOI: 10.1093/plcell/koab010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/22/2020] [Indexed: 05/20/2023]
Abstract
A large portion of eukaryotic genes are associated with noncoding, natural antisense transcripts (NATs). Despite sharing extensive sequence complementarity with their sense mRNAs, mRNA-NAT pairs elusively often evade dsRNA-cleavage and siRNA-triggered silencing. More surprisingly, some NATs enhance translation of their sense mRNAs by yet unknown mechanism(s). Here, we show that translation enhancement of the rice (Oryza sativa) PHOSPHATE1.2 (PHO1.2) mRNA is enabled by specific structural rearrangements guided by its noncoding antisense RNA (cis-NATpho1.2). Their interaction in vitro revealed no evidence of widespread intermolecular dsRNA formation, but rather specific local changes in nucleotide base pairing, leading to higher flexibility of PHO1.2 mRNA at a key high guanine-cytosine�(GC) regulatory region inhibiting translation, ∼350-nt downstream of the start codon. Sense-antisense RNA interaction increased formation of the 80S complex in PHO1.2, possibly by inducing structural rearrangement within this inhibitory region, thus making this mRNA more accessible to 60S. This work presents a framework for nucleotide resolution studies of functional mRNA-antisense pairs.
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Affiliation(s)
- Rodrigo S Reis
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Romy R Schmidt
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany
| | - Jos H M Schippers
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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6
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Chen Y, Wu R, Chen W, Liu Y, Liao X, Zeng B, Guo G, Lou F, Xiang Y, Wang Y, Wang X. Curcumin prevents obesity by targeting TRAF4-induced ubiquitylation in m 6 A-dependent manner. EMBO Rep 2021; 22:e52146. [PMID: 33880847 PMCID: PMC8097347 DOI: 10.15252/embr.202052146] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
Obesity has become a major health problem that has rapidly prevailed over the past several decades worldwide. Curcumin, a natural polyphenolic compound present in turmeric, has been shown to have a protective effect on against obesity and metabolic diseases. However, its underlying mechanism remains largely unknown. Here, we show that the administration of curcumin significantly prevents HFD-induced obesity and decreases the fat mass of the subcutaneous inguinal WAT (iWAT) and visceral epididymal WAT (eWAT) in mice. Mechanistically, curcumin inhibits adipogenesis by reducing the expression of AlkB homolog 5 (ALKHB5), an m6 A demethylase, which leads to higher m6 A-modified TNF receptor-associated factor 4 (TRAF4) mRNA. TRAF4 mRNA with higher m6 A level is recognized and bound by YTHDF1, leading to enhanced translation of TRAF4. TRAF4, acting as an E3 RING ubiquitin ligase, promotes degradation of adipocyte differentiation regulator PPARγ by a ubiquitin-proteasome pathway thereby inhibiting adipogenesis. Thus, m6 A-dependent TRAF4 expression upregulation by ALKBH5 and YTHDF1 contributes to curcumin-induced obesity prevention. Our findings provide mechanistic insights into how m6 A is involved in the anti-obesity effect of curcumin.
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Affiliation(s)
- Yushi Chen
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Ruifan Wu
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Wei Chen
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Youhua Liu
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Xing Liao
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Botao Zeng
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Guanqun Guo
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Fangfang Lou
- Jinhua Academy of Agricultural SciencesJinhuaChina
| | - Yun Xiang
- Jinhua Academy of Agricultural SciencesJinhuaChina
| | - Yizhen Wang
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
| | - Xinxia Wang
- College of Animal SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University)Ministry of EducationHangzhouChina
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China)Ministry of Agriculture and Rural AffairsHangzhouChina
- Key Laboratory of Animal Feed and Nutrition of Zhejiang ProvinceHangzhouChina
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7
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Lin CH, Liao CC, Chen MY, Chou TY. Feedback Regulation of O-GlcNAc Transferase through Translation Control to Maintain Intracellular O-GlcNAc Homeostasis. Int J Mol Sci 2021; 22:ijms22073463. [PMID: 33801653 PMCID: PMC8037101 DOI: 10.3390/ijms22073463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Protein O-GlcNAcylation is a dynamic post-translational modification involving the attachment of N-acetylglucosamine (GlcNAc) to the hydroxyl groups of Ser/Thr residues on numerous nucleocytoplasmic proteins. Two enzymes are responsible for O-GlcNAc cycling on substrate proteins: O-GlcNAc transferase (OGT) catalyzes the addition while O-GlcNAcase (OGA) helps the removal of GlcNAc. O-GlcNAcylation modifies protein functions; therefore, dysregulation of O-GlcNAcylation affects cell physiology and contributes to pathogenesis. To maintain homeostasis of cellular O-GlcNAcylation, there exists feedback regulation of OGT and OGA expression responding to fluctuations of O-GlcNAc levels; yet, little is known about the molecular mechanisms involved. In this study, we investigated the O-GlcNAc-feedback regulation of OGT and OGA expression in lung cancer cells. Results suggest that, upon alterations in O-GlcNAcylation, the regulation of OGA expression occurs at the mRNA level and likely involves epigenetic mechanisms, while modulation of OGT expression is through translation control. Further analyses revealed that the eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) contributes to the downregulation of OGT induced by hyper-O-GlcNAcylation; the S5A/S6A O-GlcNAcylation-site mutant of 4E-BP1 cannot support this regulation, suggesting an important role of O-GlcNAcylation. The results provide additional insight into the molecular mechanisms through which cells may fine-tune intracellular O-GlcNAc levels to maintain homeostasis.
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Affiliation(s)
- Chia-Hung Lin
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Chen-Chung Liao
- Metabolomics-Proteomics Research Center, National Yang-Ming University, Taipei 11221, Taiwan;
- Metabolomics-Proteomics Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Mei-Yu Chen
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Cancer Progression Research Center, National Yang-Ming University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Correspondence: (M.-Y.C.); (T.-Y.C.); Tel.: +886-2-2826-7269 (M.-Y.C.); +886-2-2875-7022 (T.-Y.C.)
| | - Teh-Ying Chou
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Cancer Progression Research Center, National Yang-Ming University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Correspondence: (M.-Y.C.); (T.-Y.C.); Tel.: +886-2-2826-7269 (M.-Y.C.); +886-2-2875-7022 (T.-Y.C.)
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8
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Bressler KR, Ross JA, Ilnytskyy S, Vanden Dungen K, Taylor K, Patel K, Zovoilis A, Kovalchuk I, Thakor N. Depletion of eukaryotic initiation factor 5B (eIF5B) reprograms the cellular transcriptome and leads to activation of endoplasmic reticulum (ER) stress and c-Jun N-terminal kinase (JNK). Cell Stress Chaperones 2021; 26:253-264. [PMID: 33123915 PMCID: PMC7736443 DOI: 10.1007/s12192-020-01174-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 12/17/2022] Open
Abstract
During the integrated stress response (ISR), global translation initiation is attenuated; however, noncanonical mechanisms allow for the continued translation of specific transcripts. Eukaryotic initiation factor 5B (eIF5B) has been shown to play a critical role in canonical translation as well as in noncanonical mechanisms involving internal ribosome entry site (IRES) and upstream open reading frame (uORF) elements. The uORF-mediated translation regulation of activating transcription factor 4 (ATF4) mRNA plays a pivotal role in the cellular ISR. Our recent study confirmed that eIF5B depletion removes uORF2-mediated repression of ATF4 translation, which results in the upregulation of growth arrest and DNA damage-inducible protein 34 (GADD34) transcription. Accordingly, we hypothesized that eIF5B depletion may reprogram the transcriptome profile of the cell. Here, we employed genome-wide transcriptional analysis on eIF5B-depleted cells. Further, we validate the up- and downregulation of several transcripts from our RNA-seq data using RT-qPCR. We identified upregulated pathways including cellular response to endoplasmic reticulum (ER) stress, and mucin-type O-glycan biosynthesis, as well as downregulated pathways of transcriptional misregulation in cancer and T cell receptor signaling. We also confirm that depletion of eIF5B leads to activation of the c-Jun N-terminal kinase (JNK) arm of the mitogen-activated protein kinase (MAPK) pathway. This data suggests that depletion of eIF5B reprograms the cellular transcriptome and influences critical cellular processes such as ER stress and ISR.
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Affiliation(s)
- Kamiko R Bressler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
- Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
| | - Joseph A Ross
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
- Chinook Contract Research Inc., 97 East Lake Ramp NE, Airdrie, Alberta, T4A 2 K4, Canada
| | - Slava Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
| | - Keiran Vanden Dungen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
| | - Katrina Taylor
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
| | - Kush Patel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
- Canadian Centre for Behavioral Neuroscience (CCBN), Department of Neuroscience, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3 M4, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3 M4, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada.
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada.
- Canadian Centre for Behavioral Neuroscience (CCBN), Department of Neuroscience, University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3M4, Canada.
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, 4401 University Drive W, Lethbridge, Alberta, T1K 3 M4, Canada.
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada.
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9
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Toki N, Takahashi H, Sharma H, Valentine MNZ, Rahman FUM, Zucchelli S, Gustincich S, Carninci P. SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. Nucleic Acids Res 2020; 48:11626-11644. [PMID: 33130894 PMCID: PMC7672464 DOI: 10.1093/nar/gkaa814] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/26/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
SINEUPs are long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA. They have been studied in a wide range of applications, as both biological and therapeutic tools, although the underpinning molecular mechanism is unclear. Here, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs, performing co-transfection of expression vectors for these transcripts into human embryonic kidney cells (HEK293T/17), to investigate the network of translational regulation. The results showed that co-localization of target mRNAs and SINEUP RNAs in the cytoplasm was a key phenomenon. We identified PTBP1 and HNRNPK as essential RNA binding proteins. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhanced target mRNA translation. These findings will promote a better understanding of the mechanisms employed by regulatory RNAs implicated in efficient protein translation.
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Affiliation(s)
- Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Ferdous-Ur M Rahman
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
| | - Silvia Zucchelli
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases (CAAD) and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, Novara, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045 Japan
- Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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10
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Liu L, Lu JY, Li F, Xing X, Li T, Yang X, Shen X. IDH1 fine-tunes cap-dependent translation initiation. J Mol Cell Biol 2020; 11:816-828. [PMID: 31408165 PMCID: PMC6884706 DOI: 10.1093/jmcb/mjz082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.
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Affiliation(s)
- Lichao Liu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fajin Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xudong Xing
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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11
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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12
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Reis RS, Deforges J, Sokoloff T, Poirier Y. Modulation of Shoot Phosphate Level and Growth by PHOSPHATE1 Upstream Open Reading Frame. PLANT PHYSIOLOGY 2020; 183:1145-1156. [PMID: 32327548 PMCID: PMC7333697 DOI: 10.1104/pp.19.01549] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/02/2020] [Indexed: 05/19/2023]
Abstract
Inorganic orthophosphate (Pi) is an essential nutrient for plant growth, and its availability strongly impacts crop yield. PHOSPHATE1 (PHO1) transfers Pi from root to shoot via Pi export into root xylem vessels. In this work, we demonstrate that an upstream open reading frame (uORF) present in the 5' untranslated region of the Arabidopsis (Arabidopsis thaliana) PHO1 inhibits its translation and influences Pi homeostasis. The presence of the uORF strongly inhibited the translation of a PHO1 5'UTR-luciferase construct in protoplasts. A point mutation removing the PHO1 uORF (ΔuORF) in transgenic Arabidopsis resulted in increased association of its mRNA with polysomes and led to higher PHO1 protein levels, independent of Pi availability. Interestingly, deletion of the uORF led to higher shoot Pi content and was associated with improved shoot growth under low external Pi supply and no deleterious effects under Pi-sufficient conditions. We further show that natural accessions lacking the PHO1 uORF exhibit higher PHO1 protein levels and shoot Pi content. Increased shoot Pi content was linked to the absence of the PHO1 uORF in a population of F2 segregants. We identified the PHO1 uORF in genomes of crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aesativum), and we verified the inhibitory effect of the rice PHO1 uORF on translation in protoplasts. Our work suggests that regulation of PHO1 expression via its uORF might be a genetic resource useful-both in natural populations and in the context of genome editing-toward improving plant growth under Pi-deficient conditions.
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Affiliation(s)
- Rodrigo S Reis
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tatiana Sokoloff
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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13
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Pereira IT, Spangenberg L, Cabrera G, Dallagiovanna B. Polysome-associated lncRNAs during cardiomyogenesis of hESCs. Mol Cell Biochem 2020; 468:35-45. [PMID: 32125578 DOI: 10.1007/s11010-020-03709-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been found to be involved in many biological processes, including the regulation of cell differentiation, but a complete characterization of lncRNA is still lacking. Additionally, there is evidence that lncRNAs interact with ribosomes, raising questions about their functions in cells. Here, we used a developmentally staged protocol to induce cardiogenic commitment of hESCs and then investigated the differential association of lncRNAs with polysomes. Our results identified lncRNAs in both the ribosome-free and polysome-bound fractions during cardiogenesis and showed a very well-defined temporal lncRNA association with polysomes. Clustering of lncRNAs was performed according to the gene expression patterns during the five timepoints analyzed. In addition, differential lncRNA recruitment to polysomes was observed when comparing the differentially expressed lncRNAs in the ribosome-free and polysome-bound fractions or when calculating the polysome-bound vs ribosome-free ratio. The association of lncRNAs with polysomes could represent an additional cytoplasmic role of lncRNAs, e.g., in translational regulation of mRNA expression.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Guillermo Cabrera
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-Cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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14
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Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:cells9010162. [PMID: 31936572 PMCID: PMC7017053 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.
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15
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Lu H, Ye Z, Zhai Y, Wang L, Liu Y, Wang J, Zhang W, Luo W, Lu Z, Chen J. QKI regulates adipose tissue metabolism by acting as a brake on thermogenesis and promoting obesity. EMBO Rep 2020; 21:e47929. [PMID: 31868295 PMCID: PMC6944952 DOI: 10.15252/embr.201947929] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 12/31/2022] Open
Abstract
Adipose tissue controls numerous physiological processes, and its dysfunction has a causative role in the development of systemic metabolic disorders. The role of posttranscriptional regulation in adipose metabolism has yet to be fully understood. Here, we show that the RNA-binding protein quaking (QKI) plays an important role in controlling metabolic homeostasis of the adipose tissue. QKI-deficient mice are resistant to high-fat-diet (HFD)-induced obesity. Additionally, QKI depletion increased brown fat energy dissipation and browning of subcutaneous white fat. Adipose tissue-specific depletion of QKI in mice enhances cold-induced thermogenesis, thereby preventing hypothermia in response to cold stimulus. Further mechanistic analysis reveals that QKI is transcriptionally induced by the cAMP-cAMP response element-binding protein (CREB) axis and restricts adipose tissue energy consumption by decreasing stability, nuclear export, and translation of mRNAs encoding UCP1 and PGC1α. These findings extend our knowledge of the significance of posttranscriptional regulation in adipose metabolic homeostasis and provide a potential therapeutic target to defend against obesity and its related metabolic diseases.
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Affiliation(s)
- Huanyu Lu
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
| | - Zichen Ye
- State Key Laboratory of Cancer BiologyDepartment of PharmacogenomicsSchool of PharmacyFourth Military Medical UniversityXi'anChina
| | - Yue Zhai
- Department of Cell BiologyFourth Military Medical UniversityXi'anChina
| | - Li Wang
- State Key Laboratory of Cancer BiologyDepartment of PharmacogenomicsSchool of PharmacyFourth Military Medical UniversityXi'anChina
| | - Ying Liu
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
| | - Jiye Wang
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
| | - Wenbin Zhang
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
| | - Wenjing Luo
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
| | - Zifan Lu
- State Key Laboratory of Cancer BiologyDepartment of PharmacogenomicsSchool of PharmacyFourth Military Medical UniversityXi'anChina
| | - Jingyuan Chen
- Department of Occupational and Environmental Healththe Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational EnvironmentSchool of Public HealthFourth Military Medical UniversityXi'anChina
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16
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Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Hart-Smith G, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y. Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. PLANT PHYSIOLOGY 2019; 180:305-322. [PMID: 30760640 PMCID: PMC6501089 DOI: 10.1104/pp.19.00043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/03/2019] [Indexed: 05/06/2023]
Abstract
Cis-Natural Antisense Transcripts (cis-NATs), which overlap protein coding genes and are transcribed from the opposite DNA strand, constitute an important group of noncoding RNAs. Whereas several examples of cis-NATs regulating the expression of their cognate sense gene are known, most cis-NATs function by altering the steady-state level or structure of mRNA via changes in transcription, mRNA stability, or splicing, and very few cases involve the regulation of sense mRNA translation. This study was designed to systematically search for cis-NATs influencing cognate sense mRNA translation in Arabidopsis (Arabidopsis thaliana). Establishment of a pipeline relying on sequencing of total polyA+ and polysomal RNA from Arabidopsis grown under various conditions (i.e. nutrient deprivation and phytohormone treatments) allowed the identification of 14 cis-NATs whose expression correlated either positively or negatively with cognate sense mRNA translation. With use of a combination of cis-NAT stable over-expression in transgenic plants and transient expression in protoplasts, the impact of cis-NAT expression on mRNA translation was confirmed for 4 out of 5 tested cis-NAT:sense mRNA pairs. These results expand the number of cis-NATs known to regulate cognate sense mRNA translation and provide a foundation for future studies of their mode of action. Moreover, this study highlights the role of this class of noncoding RNAs in translation regulation.
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Affiliation(s)
- Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Rodrigo S Reis
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Philippe Jacquet
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Shaoline Sheppard
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Veerendra P Gadekar
- Institute of Theoretical Chemistry, University of Vienna, Wahringer Str 17, A-1090 Vienna, Austria
| | - Gene Hart-Smith
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Andrea Tanzer
- Institute of Theoretical Chemistry, University of Vienna, Wahringer Str 17, A-1090 Vienna, Austria
| | - Ivo L Hofacker
- Institute of Theoretical Chemistry, University of Vienna, Wahringer Str 17, A-1090 Vienna, Austria
| | - Christian Iseli
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ioannis Xenarios
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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17
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Manganese-induced cellular disturbance in the baker's yeast, Saccharomyces cerevisiae with putative implications in neuronal dysfunction. Sci Rep 2019; 9:6563. [PMID: 31024033 PMCID: PMC6484083 DOI: 10.1038/s41598-019-42907-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
Manganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.
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18
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Pereira IT, Spangenberg L, Robert AW, Amorín R, Stimamiglio MA, Naya H, Dallagiovanna B. Cardiomyogenic differentiation is fine-tuned by differential mRNA association with polysomes. BMC Genomics 2019; 20:219. [PMID: 30876407 PMCID: PMC6420765 DOI: 10.1186/s12864-019-5550-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination between transcription and post-transcriptional regulation during the differentiation processes. Here, we took advantage of the polysome profiling technique to isolate and high-throughput sequence ribosome-free and polysome-bound RNAs during cardiomyogenesis. RESULTS We showed that polysome-bound RNAs exhibit the cardiomyogenic commitment gene expression and that mesoderm-to-cardiac progenitor stages are strongly regulated. Additionally, we compared ribosome-free and polysome-bound RNAs and found that the post-transcriptional regulation vastly contributes to cardiac phenotype determination, including RNA recruitment to and dissociation from ribosomes. Moreover, we found that protein synthesis is decreased in cardiomyocytes compared to human embryonic stem-cells (hESCs), possibly due to the down-regulation of translation-related genes. CONCLUSIONS Our data provided a powerful tool to investigate genes potentially controlled by post-transcriptional mechanisms during the cardiac differentiation of hESC. This work could prospect fundamental tools to develop new therapy and research approaches.
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Affiliation(s)
- Isabela Tiemy Pereira
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Lucia Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Anny Waloski Robert
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Rocío Amorín
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Marco Augusto Stimamiglio
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil
| | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Bruno Dallagiovanna
- Basic Stem-cell Biology Laboratory, Instituto Carlos Chagas - FIOCRUZ-PR, Rua Professor Algacyr Munhoz Mader, 3775, Curitiba, PR, 81.350-010, Brazil.
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19
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Ross JA, Dungen KV, Bressler KR, Fredriksen M, Khandige Sharma D, Balasingam N, Thakor N. Eukaryotic initiation factor 5B (eIF5B) provides a critical cell survival switch to glioblastoma cells via regulation of apoptosis. Cell Death Dis 2019; 10:57. [PMID: 30670698 PMCID: PMC6342974 DOI: 10.1038/s41419-018-1283-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/29/2018] [Accepted: 12/07/2018] [Indexed: 12/26/2022]
Abstract
Physiological stress conditions attenuate global mRNA translation via modifications of key eukaryotic initiation factors. However, non-canonical translation initiation mechanisms allow cap-independent translation of certain mRNAs. We have previously demonstrated that eIF5B promotes cap-independent translation of the mRNA encoding the antiapoptotic factor, XIAP, during cellular stress. Here, we show that depletion of eIF5B sensitizes glioblastoma multiforme cells to TRAIL-induced apoptosis by a pathway involving caspases-8, −9, and −7, with no significant effect on cell cycle progression. eIF5B promotes evasion of apoptosis by promoting the translation of several IRES-containing mRNAs, encoding the antiapoptotic proteins XIAP, Bcl-xL, cIAP1, and c-FLIPS. We also show that eIF5B promotes translation of nuclear factor erythroid 2-related factor 2 and suggest that reactive oxygen species contribute to increased apoptosis under conditions of eIF5B depletion. Finally, eIF5B depletion leads to decreased activation of the canonical NF-κB pathway. Taken together, our data suggest that eIF5B represents a regulatory node, allowing cancer cells to evade apoptosis by promoting the translation of pro-survival proteins from IRES-containing mRNAs.
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Affiliation(s)
- Joseph A Ross
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Keiran Vanden Dungen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Kamiko R Bressler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Mikayla Fredriksen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Divya Khandige Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Nirujah Balasingam
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada. .,Canadian Centre for Behavioral Neuroscience (CCBN), Department of Neuroscience, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada. .,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
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20
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Ross JA, Bressler KR, Thakor N. Eukaryotic Initiation Factor 5B (eIF5B) Cooperates with eIF1A and eIF5 to Facilitate uORF2-Mediated Repression of ATF4 Translation. Int J Mol Sci 2018; 19:E4032. [PMID: 30551605 PMCID: PMC6321046 DOI: 10.3390/ijms19124032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022] Open
Abstract
A variety of cellular stresses lead to global translation attenuation due to phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2), which decreases the availability of the eIF2-GTP-Met-tRNAi ternary complex. However, a subset of mRNAs continues to be translated by non-canonical mechanisms under these conditions. In fact, although translation initiation of activating transcription factor 4 (ATF4) is normally repressed by an upstream open reading frame (uORF), a decreased availability of ternary complex leads to increased translation of the main ATF4-coding ORF. We show here that siRNA-mediated depletion of eIF5B-which can substitute for eIF2 in delivering Met-tRNAi-leads to increased levels of ATF4 protein in mammalian cells. This de-repression is not due to phosphorylation of eIF2α under conditions of eIF5B depletion. Although eIF5B depletion leads to a modest increase in the steady-state levels of ATF4 mRNA, we show by polysome profiling that the depletion of eIF5B enhances ATF4 expression primarily at the level of translation. Moreover, eIF5B silencing increases the expression of an ATF4-luciferase translational reporter by a mechanism requiring the repressive uORF2. Further experiments suggest that eIF5B cooperates with eIF1A and eIF5, but not eIF2A, to facilitate the uORF2-mediated repression of ATF4 translation.
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Affiliation(s)
- Joseph A Ross
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.
| | - Kamiko R Bressler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.
- Canadian Centre for Behavioral Neuroscience (CCBN), Department of Neuroscience, University of Lethbridge, 4401 University Drive W, Lethbridge, AB T1K 3M4, Canada.
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada.
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21
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Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs. Sci Data 2018; 5:180287. [PMID: 30512016 PMCID: PMC6278691 DOI: 10.1038/sdata.2018.287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
The regulation of gene expression acts at numerous complementary levels to control and refine protein abundance. The analysis of mRNAs associated with polysomes, called polysome profiling, has been used to investigate the post-transcriptional mechanisms that are involved in different biological processes. Pluripotent stem cells are able to differentiate into a variety of cell lineages, and the cell commitment progression is carefully orchestrated. Genome-wide expression profiling has provided the possibility to investigate transcriptional changes during cardiomyogenesis; however, a more accurate study regarding post-transcriptional regulation is required. In the present work, we isolated and high-throughput sequenced ribosome-free and polysome-bound RNAs from NKX2-5eGFP/w HES3 undifferentiated pluripotent stem cells at the subsequent differentiation stages of cardiomyogenesis: embryoid body aggregation, mesoderm, cardiac progenitor and cardiomyocyte. The expression of developmental markers was followed by flow cytometry, and quality analyses were performed as technical controls to ensure high quality data. Our dataset provides valuable information about hESC cardiac differentiation and can be used to investigate genes potentially controlled by post-transcriptional mechanisms.
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Heavy metal sensitivities of gene deletion strains for ITT1 and RPS1A connect their activities to the expression of URE2, a key gene involved in metal detoxification in yeast. PLoS One 2018; 13:e0198704. [PMID: 30231023 PMCID: PMC6145592 DOI: 10.1371/journal.pone.0198704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 11/19/2022] Open
Abstract
Heavy metal and metalloid contaminations are among the most concerning types of pollutant in the environment. Consequently, it is important to investigate the molecular mechanisms of cellular responses and detoxification pathways for these compounds in living organisms. To date, a number of genes have been linked to the detoxification process. The expression of these genes can be controlled at both transcriptional and translational levels. In baker’s yeast, Saccharomyces cerevisiae, resistance to a wide range of toxic metals is regulated by glutathione S-transferases. Yeast URE2 encodes for a protein that has glutathione peroxidase activity and is homologous to mammalian glutathione S-transferases. The URE2 expression is critical to cell survival under heavy metal stress. Here, we report on the finding of two genes, ITT1, an inhibitor of translation termination, and RPS1A, a small ribosomal protein, that when deleted yeast cells exhibit similar metal sensitivity phenotypes to gene deletion strain for URE2. Neither of these genes were previously linked to metal toxicity. Our gene expression analysis illustrates that these two genes affect URE2 mRNA expression at the level of translation.
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Ross JA, Thakor N. Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs. J Vis Exp 2018. [PMID: 29806829 DOI: 10.3791/57519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Translation initiation is the rate-limiting step of protein synthesis and represents a key point at which cells regulate their protein output. Regulation of protein synthesis is the key to cellular stress-response, and dysregulation is central to many disease states, such as cancer. For instance, although cellular stress leads to the inhibition of global translation by attenuating cap-dependent initiation, certain stress-response proteins are selectively translated in a cap-independent manner. Discreet RNA regulatory elements, such as cellular internal ribosome entry sites (IRESes), allow for the translation of these specific mRNAs. Identification of such mRNAs, and the characterization of their regulatory mechanisms, have been a key area in molecular biology. Toeprinting is a method for the study of RNA structure and function as it pertains to translation initiation. The goal of toeprinting is to assess the ability of in vitro transcribed RNA to form stable complexes with ribosomes under a variety of conditions, in order to determine which sequences, structural elements, or accessory factors are involved in ribosome binding-a pre-cursor for efficient translation initiation. Alongside other techniques, such as western analysis and polysome profiling, toeprinting allows for a robust characterization of mechanisms for the regulation of translation initiation.
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Affiliation(s)
- Joseph A Ross
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge;
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge; Department of Neuroscience and the Canadian Centre for Behavioral Neuroscience (CCBN), University of Lethbridge; Arnie Charbonneau Cancer Institute, University of Calgary;
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A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Rep 2018; 22:3427-3439. [DOI: 10.1016/j.celrep.2018.02.104] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022] Open
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Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signaling and malignant features in vitro and in vivo. Oncotarget 2017; 8:114856-114876. [PMID: 29383126 PMCID: PMC5777738 DOI: 10.18632/oncotarget.23145] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the most prevalent malignancy in women and there is an urgent need for new therapeutic drugs targeting aggressive and metastatic subtypes, such as hormone-refractory triple-negative breast cancer (TNBC). Control of protein synthesis is vital to cell growth and tumour progression and permits increased resistance to therapy and cellular stress. Hypoxic cancer cells attain invasive and metastatic properties and chemotherapy resistance, but the regulation and role of protein synthesis in this setting is poorly understood. We performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. Integrin beta 3 (ITGB3) was translationally activated in hypoxia and its knockdown increased apoptosis and reduced survival and migration, particularly under hypoxic conditions. Moreover, ITGB3 was required for sustained TGF-β pathway activation and for the induction of Snail and associated epithelial-mesenchymal transition markers. ITGB3 downregulation significantly reduced lung metastasis and improved overall survival in mice. Collectively, these data suggest that ITGB3 is translationally activated in hypoxia and regulates malignant features, including epithelial-mesenchymal transition and cell migration, through the TGF-β pathway, revealing a novel angle for the treatment of therapy-resistant hypoxic tumours.
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Shaikho S, Dobson CC, Naing T, Samanfar B, Moteshareie H, Hajikarimloo M, Golshani A, Holcik M. Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma. ACTA ACUST UNITED AC 2016; 4:e1244395. [PMID: 28090422 DOI: 10.1080/21690731.2016.1244395] [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] [Received: 06/28/2016] [Revised: 09/13/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023]
Abstract
Mammalian 90 kDa heat shock protein (Hsp90) is a ubiquitous molecular chaperone whose expression is selectively upregulated during stress, although the precise control mechanism of this increase is yet to be fully elucidated. We used polysome profiling to show that Hsp90α mRNA is selectively translated, while global translation is inhibited during heat stress. Furthermore, we have identified 2 ribosomal proteins, eL36 and eL42 that modulate Hsp90α expression under both normal and heat shock conditions. Importantly, we noted that expression of eL36 and eL42 is elevated in a panel of human rhabdomyosarcomas where it drives high expression of Hsp90 and modulates sensitivity of these cells to an Hsp90 inhibitor 17-AAG.
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Affiliation(s)
- Sarah Shaikho
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Christine C Dobson
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Thet Naing
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Maryam Hajikarimloo
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Martin Holcik
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
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27
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Chassé H, Mulner-Lorillon O, Boulben S, Glippa V, Morales J, Cormier P. Cyclin B Translation Depends on mTOR Activity after Fertilization in Sea Urchin Embryos. PLoS One 2016; 11:e0150318. [PMID: 26962866 PMCID: PMC4786324 DOI: 10.1371/journal.pone.0150318] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/11/2016] [Indexed: 12/11/2022] Open
Abstract
The cyclin B/CDK1 complex is a key regulator of mitotic entry. Using PP242, a specific ATP-competitive inhibitor of mTOR kinase, we provide evidence that the mTOR signalling pathway controls cyclin B mRNA translation following fertilization in Sphaerechinus granularis and Paracentrotus lividus. We show that PP242 inhibits the degradation of the cap-dependent translation repressor 4E-BP (eukaryotic initiation factor 4E-Binding Protein). PP242 inhibits global protein synthesis, delays cyclin B accumulation, cyclin B/CDK1 complex activation and consequently entry into the mitotic phase of the cell cycle triggered by fertilization. PP242 inhibits cyclin B mRNA recruitment into active polysomes triggered by fertilization. An amount of cyclin B mRNA present in active polysomes appears to be insensitive to PP242 treatment. Taken together, our results suggest that, following sea urchin egg fertilization, cyclin B mRNA translation is controlled by two independent mechanisms: a PP242-sensitive and an additional PP242-insentitive mechanism.
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Affiliation(s)
- Héloïse Chassé
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Odile Mulner-Lorillon
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- * E-mail: (PC); (JM); (OML)
| | - Sandrine Boulben
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Virginie Glippa
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Julia Morales
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- * E-mail: (PC); (JM); (OML)
| | - Patrick Cormier
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Translation Cell Cycle and Development, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- * E-mail: (PC); (JM); (OML)
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Machinaga A, Ishihara S, Shirai A, Takase-Yoden S. Splicing of Friend Murine Leukemia Virus env-mRNA Enhances Its Ability to Form Polysomes. Front Microbiol 2016; 7:160. [PMID: 26909075 PMCID: PMC4754430 DOI: 10.3389/fmicb.2016.00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
Friend murine leukemia virus (MLV) belongs to the gamma retroviruses of the Retroviridae family. The positive-sense RNA of its genome contains a 5' long terminal repeat (LTR), 5' leader sequence, gag, pol, env, and 3' LTR. Transcription from proviral DNA begins from the R region of the 5' LTR and ends at the polyadenylation signal located at the R region of the other end of the 3' LTR. There is a 5' splice site in the 5' leader sequence and a 3' splice site at the 3' end of the pol region. Both full-length unspliced mRNAs and a singly spliced mRNA (env-mRNA) are produced in MLV-infected cells. The MLV Env protein plays important roles both in viral adsorption to host cells and in neuropathogenic disease in MLV-infected mice and rats. Understanding the regulatory mechanisms controlling Env expression is important for determining the functions of the Env protein. We have previously shown that splicing increases env-mRNA stability and translation efficiency. Generally, mRNA polysome formation correlates with translation efficiency. Therefore, here we investigated the effects of env-mRNA splicing on polysome formation to identify mechanisms for Env up-regulation due to splicing. We performed polysome profile analyses using Env-expression plasmids producing spliced or unspliced env-mRNA and showed that the former formed polysomes more efficiently than the latter. Thus, splicing of env-mRNA facilitated polysome formation, suggesting that this contributes to up-regulation of Env expression. We replaced the env region of the expression plasmids with a luciferase (luc) gene, and found that in this case both unspliced and spliced luc-mRNA formed polysomes to a similar extent. Thus, we conclude that whether mRNA polysome formation is affected by splicing depends on the structure of gene in question.
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Affiliation(s)
- Akihito Machinaga
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Syuhei Ishihara
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Akiko Shirai
- Department of Bioinformatics, Graduate School of Engineering, Soka University Tokyo, Japan
| | - Sayaka Takase-Yoden
- Department of Bioinformatics, Graduate School of Engineering, Soka UniversityTokyo, Japan; Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka UniversityTokyo, Japan
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29
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Qi W, Zhu J, Wu Q, Wang Q, Li X, Yao D, Jin Y, Wang G, Wang G, Song R. Maize reas1 Mutant Stimulates Ribosome Use Efficiency and Triggers Distinct Transcriptional and Translational Responses. PLANT PHYSIOLOGY 2016; 170:971-88. [PMID: 26645456 PMCID: PMC4734584 DOI: 10.1104/pp.15.01722] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/07/2015] [Indexed: 05/19/2023]
Abstract
Ribosome biogenesis is a fundamental cellular process in all cells. Impaired ribosome biogenesis causes developmental defects; however, its molecular and cellular bases are not fully understood. We cloned a gene responsible for a maize (Zea mays) small seed mutant, dek* (for defective kernel), and found that it encodes Ribosome export associated1 (ZmReas1). Reas1 is an AAA-ATPase that controls 60S ribosome export from the nucleus to the cytoplasm after ribosome maturation. dek* is a weak mutant allele with decreased Reas1 function. In dek* cells, mature 60S ribosome subunits are reduced in the nucleus and cytoplasm, but the proportion of actively translating polyribosomes in cytosol is significantly increased. Reduced phosphorylation of eukaryotic initiation factor 2α and the increased elongation factor 1α level indicate an enhancement of general translational efficiency in dek* cells. The mutation also triggers dramatic changes in differentially transcribed genes and differentially translated RNAs. Discrepancy was observed between differentially transcribed genes and differentially translated RNAs, indicating distinct cellular responses at transcription and translation levels to the stress of defective ribosome processing. DNA replication and nucleosome assembly-related gene expression are selectively suppressed at the translational level, resulting in inhibited cell growth and proliferation in dek* cells. This study provides insight into cellular responses due to impaired ribosome biogenesis.
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Affiliation(s)
- Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Jie Zhu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Qiao Wu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Qun Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Xia Li
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Dongsheng Yao
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Ying Jin
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Gang Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Guifeng Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China (W.Q., J.Z., Q.Wu., Q.Wa., X.L., D.Y., Y.J., Ga.W., Gu.W., R.S.); and Coordinated Crop Biology Research Center, Beijing 100193, China (W.Q., Ga.W., Gu.W., R.S.) and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China (R.S)
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