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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand J, Bensimon D, Croquette V. A mechanistic study of helicases with magnetic traps. Protein Sci 2017; 26:1314-1336. [PMID: 28474797 PMCID: PMC5477542 DOI: 10.1002/pro.3187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023]
Abstract
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
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Affiliation(s)
- Samar Hodeib
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Saurabh Raj
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Maria Manosas
- Departament de Física FonamentalFacultat de Física, Universitat de BarcelonaBarcelona08028Spain
- CIBER‐BBN de BioingenieriaBiomateriales y Nanomedicina, Instituto de Sanidad Carlos IIIMadridSpain
| | - Weiting Zhang
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Debjani Bagchi
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Present address: Physics DepartmentFaculty of Science, The M.S. University of BarodaVadodaraGujarat390002India
| | - Bertrand Ducos
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Francesca Fiorini
- Univ Lyon, Molecular Microbiology and Structural Biochemistry, MMSB‐IBCP UMR5086 CNRS/Lyon1Lyon Cedex 769367France
| | - Joanne Kanaan
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Jean‐François Allemand
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - David Bensimon
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia90095
| | - Vincent Croquette
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
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A helicase-independent activity of eIF4A in promoting mRNA recruitment to the human ribosome. Proc Natl Acad Sci U S A 2017; 114:6304-6309. [PMID: 28559306 DOI: 10.1073/pnas.1620426114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the scanning model of translation initiation, the decoding site and latch of the 40S subunit must open to allow the recruitment and migration of messenger RNA (mRNA); however, the precise molecular details for how initiation factors regulate mRNA accommodation into the decoding site have not yet been elucidated. Eukaryotic initiation factor (eIF) 3j is a subunit of eIF3 that binds to the mRNA entry channel and A-site of the 40S subunit. Previous studies have shown that a reduced affinity of eIF3j for the 43S preinitiation complex (PIC) occurs on eIF4F-dependent mRNA recruitment. Because eIF3j and mRNA bind anticooperatively to the 43S PIC, reduced eIF3j affinity likely reflects a state of full accommodation of mRNA into the decoding site. Here, we have used a fluorescence-based anisotropy assay to quantitatively determine how initiation components coordinate their activities to reduce the affinity of eIF3j during the recruitment of mRNA to the 43S PIC. Unexpectedly, we show that a full reduction in eIF3j affinity for the 43S PIC requires an ATP-dependent, but unwinding-independent, activity of eIF4A. This result suggests that in addition to its helicase activity, eIF4A uses the free energy of ATP binding and hydrolysis as a regulatory switch to control the conformation of the 43S PIC during mRNA recruitment. Therefore, our results define eIF4A as a universal initiation factor in cap-dependent translation initiation that functions beyond its role in RNA unwinding.
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Kumar P, Hellen CUT, Pestova TV. Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev 2017; 30:1573-88. [PMID: 27401559 PMCID: PMC4949329 DOI: 10.1101/gad.282418.116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/01/2016] [Indexed: 11/24/2022]
Abstract
Ribosomal attachment to mammalian capped mRNAs is achieved through the cap-eukaryotic initiation factor 4E (eIF4E)-eIF4G-eIF3-40S chain of interactions, but the mechanism by which mRNA enters the mRNA-binding channel of the 40S subunit remains unknown. To investigate this process, we recapitulated initiation on capped mRNAs in vitro using a reconstituted translation system. Formation of initiation complexes at 5'-terminal AUGs was stimulated by the eIF4E-cap interaction and followed "the first AUG" rule, indicating that it did not occur by backward scanning. Initiation complexes formed even at the very 5' end of mRNA, implying that Met-tRNAi (Met) inspects mRNA from the first nucleotide and that initiation does not have a "blind spot." In assembled initiation complexes, the cap was no longer associated with eIF4E. Omission of eIF4A or disruption of eIF4E-eIF4G-eIF3 interactions converted eIF4E into a specific inhibitor of initiation on capped mRNAs. Taken together, these results are consistent with the model in which eIF4E-eIF4G-eIF3-40S interactions place eIF4E at the leading edge of the 40S subunit, and mRNA is threaded into the mRNA-binding channel such that Met-tRNAi (Met) can inspect it from the first nucleotide. Before entering, eIF4E likely dissociates from the cap to overcome steric hindrance. We also found that the m(7)G cap specifically interacts with eIF3l.
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Affiliation(s)
- Parimal Kumar
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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Masvidal L, Hulea L, Furic L, Topisirovic I, Larsson O. mTOR-sensitive translation: Cleared fog reveals more trees. RNA Biol 2017; 14:1299-1305. [PMID: 28277937 PMCID: PMC5711451 DOI: 10.1080/15476286.2017.1290041] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Translation is fundamental for many biologic processes as it enables cells to rapidly respond to stimuli without requiring de novo mRNA synthesis. The mammalian/mechanistic target of rapamycin (mTOR) is a key regulator of translation. Although mTOR affects global protein synthesis, translation of a subset of mRNAs appears to be exceptionally sensitive to changes in mTOR activity. Recent efforts to catalog these mTOR-sensitive mRNAs resulted in conflicting results. Whereas ribosome-profiling almost exclusively identified 5'-terminal oligopyrimidine (TOP) mRNAs as mTOR-sensitive, polysome-profiling suggested that mTOR also regulates translation of non-TOP mRNAs. This inconsistency was explained by analytical and technical biases limiting the efficiency of ribosome-profiling in detecting mRNAs showing differential translation. Moreover, genome-wide characterization of 5'UTRs of non-TOP mTOR-sensitive mRNAs revealed 2 subsets of transcripts which differ in their requirement for translation initiation factors and biologic functions. We summarize these recent advances and their impact on the understanding of mTOR-sensitive translation.
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Affiliation(s)
- Laia Masvidal
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
| | - Laura Hulea
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Luc Furic
- d Cancer Program , Biomedicine Discovery Institute and Department of Anatomy & Developmental Biology, Monash University , Victoria , Australia.,e Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre , Melbourne , Victoria , Australia
| | - Ivan Topisirovic
- b Lady Davis Institute, SMBD Jewish General Hospital , Montreal , Canada.,c Gerald-Bronfman Department of Oncology, Departments of Experimental Medicine , and Biochemistry McGill University , Montreal , Canada
| | - Ola Larsson
- a Department of Oncology-Pathology , Science for Life Laboratory, Karolinska Institutet , Stockholm , Sweden
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55
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Andreou AZ, Harms U, Klostermeier D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol 2016; 14:113-123. [PMID: 27858515 DOI: 10.1080/15476286.2016.1259782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Eukaryotic translation initiation starts with binding of the eIF4F complex to the 5'-m7G cap of the mRNA. Recruitment of the 43S pre-initiation complex (PIC), formed by the 40S ribosomal subunit and other translation initiation factors, leads to formation of the 48S PIC that then scans the 5'-untranslated region (5'-UTR) toward the start codon. The eIF4F complex consists of eIF4E, the cap binding protein, eIF4A, a DEAD-box RNA helicase that is believed to unwind secondary structures in the 5'-UTR during scanning, and eIF4G, a scaffold protein that binds to both eIF4E and eIF4A. The ATPase and helicase activities of eIF4A are jointly stimulated by eIF4G and the translation initiation factor eIF4B. Yeast eIF4B mediates recruitment of the 43S PIC to the cap-bound eIF4F complex by interacting with the 40S subunit and possibly with eIF4A. However, a direct interaction between yeast eIF4A and eIF4B has not been demonstrated yet. Here we show that eIF4B binds to eIF4A in the presence of RNA and ADPNP, independent of the presence of eIF4G. A stretch of seven moderately conserved repeats, the r1-7 region, is responsible for complex formation, for modulation of the conformational energy landscape of eIF4A by eIF4B, and for stimulating the RNA-dependent ATPase- and ATP-dependent RNA unwinding activities of eIF4A. The isolated r1-7 region only slightly stimulates eIF4A conformational changes and activities, suggesting that communication of the repeats with other regions of eIF4B is required for full stimulation of eIF4A activity, for recruitment of the PIC to the mRNA and for translation initiation.
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Affiliation(s)
| | - Ulf Harms
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
| | - Dagmar Klostermeier
- a University of Muenster, Institute for Physical Chemistry , Muenster , Germany
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Toribio R, Díaz-López I, Ventoso I. New insights into the topology of the scanning ribosome during translation initiation: Lessons from viruses. RNA Biol 2016; 13:1223-1227. [PMID: 27824302 DOI: 10.1080/15476286.2016.1247146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Location of the translation initiation codon generally requires scanning of the 43S ribosomal preinitiation complex (43S PIC) from the 5' of the mRNA. Associated RNA helicases can facilitate movement of the 43S PIC by removing secondary structure present in the 5' UTR of mRNA, which is required for codon inspection. The canonical RNA-dependent helicase eIF4A is directly involved in this process, as part of the eIF4F complex (eIF4G + eIF4A + eIF4E) that associates first with mRNA and then recruits the 43S PIC to initiate scanning. The topology and operational mechanism of the scanning PIC are probably the least understood aspects of the initiation step. Recent findings from translation of alphavirus mRNA, together with new biochemical and structural data of the 43S PIC, suggest a role for the ES6S region of 40S as the gateway for mRNA entry during scanning. The presence of eIF4G-eIF4A complex in this region, interacting with the incoming mRNA, supports a model where eIF4A could work ahead of the scanning complex during translation initiation. Here we present additional data supporting this model.
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Affiliation(s)
- René Toribio
- a Centro de Biología Molecular Severo Ochoa (CSIC-UAM) and Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM) , Madrid , Spain
| | - Irene Díaz-López
- a Centro de Biología Molecular Severo Ochoa (CSIC-UAM) and Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM) , Madrid , Spain
| | - Iván Ventoso
- a Centro de Biología Molecular Severo Ochoa (CSIC-UAM) and Departamento de Biología Molecular , Universidad Autónoma de Madrid (UAM) , Madrid , Spain
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Das S, Das B. eIF4G—an integrator of mRNA metabolism? FEMS Yeast Res 2016; 16:fow087. [DOI: 10.1093/femsyr/fow087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 11/14/2022] Open
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Li L, Luo Q, Xie Z, Li G, Mao C, Liu Y, Wen X, Yin N, Cao J, Wang J, Li L, Yu J, Wang F, Yi P. Characterization of the Expression of the RNA Binding Protein eIF4G1 and Its Clinicopathological Correlation with Serous Ovarian Cancer. PLoS One 2016; 11:e0163447. [PMID: 27668427 PMCID: PMC5036801 DOI: 10.1371/journal.pone.0163447] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 09/08/2016] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ovarian cancer is the most lethal type of malignant tumor in gynecological cancers and is associated with a high percentage of late diagnosis and chemotherapy resistance. Thus, it is urgent to identify a tumor marker or a molecular target that allows early detection and effective treatment. RNA-binding proteins (RBPs) are crucial in various cellular processes at the post-transcriptional level. The eukaryotic translation initiation factor 4 gamma, 1(eIF4G1), an RNA-binding protein, facilitates the recruitment of mRNA to the ribosome, which is a rate-limiting step during the initiation phase of protein synthesis. However, little is known regarding the characteristics of eIF4G1 expression and its clinical significance in ovarian cancer. Therefore, we propose to investigate the expression and clinicopathological significance of eIF4G1 in ovarian cancer patients. METHODS We performed Real-time PCR in 40 fresh serous ovarian cancer tissues and 27 normal ovarian surface epithelial cell specimens to assess eIF4G1mRNA expression. Immunohistochemistry (IHC) was used to examine the expression of eIF4G1 at the protein level in 134 patients with serous ovarian cancer and 18 normal ovarian tissues. Statistical analysis was conducted to determine the correlation of the eIF4G1 protein levels with the clinicopathological characteristics and prognosis in ovarian cancer. RESULTS The expression of eIF4G1 was upregulated in serous ovarian cancer tissues at both the mRNA (P = 0.0375) and the protein (P = 0.0007) levels. The eIF4G1 expression was significantly correlated with the clinical tumor stage (P = 0.0004) and omentum metastasis (P = 0.024). Moreover, patients with low eIF4G1 protein expression had a longer overall survival time (P = 0.026). CONCLUSIONS These data revealed that eIF4G1 is markedly expressed in serous ovarian cancer and that upregulation of the eIF4G1 protein expression is significantly associated with an advanced tumor stage. Besides, the patients with lower expression of eIF4G1 tend to have a longer overall survival time. Thus, eIF4G1 may contribute to the occurrence and metastasis of ovarian cancer and can serve as a potential therapeutic target for the treatment of ovarian cancer.
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Affiliation(s)
- Lanfang Li
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Qingya Luo
- Department of Pathology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Zhe Xie
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Guiqin Li
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Chengyi Mao
- Department of Pathology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Xin Wen
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, PR China
| | - Na Yin
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Jianzhong Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Li Li
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Jianhua Yu
- The Ohio State University of Comprehensive Cancer Center, Columbus, Oh 43210, United States of America
| | - Fang Wang
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, PR China
| | - Ping Yi
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China
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eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. Proc Natl Acad Sci U S A 2016; 113:10464-72. [PMID: 27601676 DOI: 10.1073/pnas.1612398113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DEAD-box RNA helicases eukaryotic translation initiation factor 4A (eIF4A) and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. Eukaryotic translation initiation factor 4B (eIF4B) is a cofactor for eIF4A but also might function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. However, either eliminating eIF4B or inactivating eIF4A preferentially impacts mRNAs with longer, more structured 5' untranslated regions (UTRs). These findings reveal an eIF4A-independent role for eIF4B in addition to its function as eIF4A cofactor in promoting PIC attachment or scanning on structured mRNAs. eIF4B, eIF4A, and Ded1 mutations also preferentially impair translation of longer mRNAs in a fashion mitigated by the ability to form closed-loop messenger ribonucleoprotein particles (mRNPs) via eIF4F-poly(A)-binding protein 1 (Pab1) association, suggesting cooperation between closed-loop assembly and eIF4B/helicase functions. Remarkably, depleting eukaryotic translation initiation factor 4G (eIF4G), the scaffold subunit of eukaryotic translation initiation factor 4F (eIF4F), preferentially impacts short mRNAs with strong closed-loop potential and unstructured 5' UTRs, exactly the opposite features associated with hyperdependence on the eIF4B/helicases. We propose that short, highly efficient mRNAs preferentially depend on the stimulatory effects of eIF4G-dependent closed-loop assembly.
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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Allemand JF, Bensimon D, Croquette V. Single molecule studies of helicases with magnetic tweezers. Methods 2016; 105:3-15. [DOI: 10.1016/j.ymeth.2016.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/31/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022] Open
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Chu J, Cargnello M, Topisirovic I, Pelletier J. Translation Initiation Factors: Reprogramming Protein Synthesis in Cancer. Trends Cell Biol 2016; 26:918-933. [PMID: 27426745 DOI: 10.1016/j.tcb.2016.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Control of mRNA translation plays a crucial role in the regulation of gene expression and is critical for cellular homeostasis. Dysregulation of translation initiation factors has been documented in several pathologies including cancer. Aberrant function of translation initiation factors leads to translation reprogramming that promotes proliferation, survival, angiogenesis, and metastasis. In such context, understanding how altered levels (and presumably activity) of initiation factors can contribute to tumor initiation and/or maintenance is of major interest for the development of novel therapeutic strategies. In this review we provide an overview of translation initiation mechanisms and focus on recent findings describing the role of individual initiation factors and their aberrant activity in cancer.
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Affiliation(s)
- Jennifer Chu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Marie Cargnello
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada
| | - Ivan Topisirovic
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada.
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada; The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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GPRC5A suppresses protein synthesis at the endoplasmic reticulum to prevent radiation-induced lung tumorigenesis. Nat Commun 2016; 7:11795. [PMID: 27273304 PMCID: PMC4899846 DOI: 10.1038/ncomms11795] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
GPRC5A functions as a lung tumour suppressor to prevent spontaneous and environmentally induced lung carcinogenesis; however, the underlying mechanism remains unclear. Here we reveal that GPRC5A at the endoplasmic reticulum (ER) membrane suppresses synthesis of the secreted or membrane-bound proteins including a number of oncogenes, the most important one being Egfr. The ER-located GPRC5A disturbs the assembly of the eIF4F-mediated translation initiation complex on the mRNA cap through directly binding to the eIF4F complex with its two middle extracellular loops. Particularly, suppression of EGFR by GPRC5A contributes significantly to preventing ionizing radiation (IR)-induced lung tumorigenesis. Thus, GPRC5A deletion enhances IR-promoted EGFR expression through an increased translation rate, thereby significantly increasing lung tumour incidence in Gprc5a−/− mice. Our findings indicate that under-expressed GPRC5A during lung tumorigenesis enhances any transcriptional stimulation through an active translational status, which can be used to control oncogene expression and potentially the resulting related disease. GPRC5A is a retinoic acid inducible gene that is preferentially expressed in lung tissue. Here the authors report that GPRC5A suppresses the translation of EGFR by interfering with the eIF4F complex assembly, thereby limiting lung tumorigenesis, particularly radiation-induced lung tumorigenesis.
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Nandakumar D, Patel SS. Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork. Methods 2016; 108:65-78. [PMID: 27173619 DOI: 10.1016/j.ymeth.2016.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/26/2023] Open
Abstract
Replicative helicases work closely with the replicative DNA polymerases to ensure that the genomic DNA is copied in a timely and error free manner. In the replisomes of prokaryotes, mitochondria, and eukaryotes, the helicase and DNA polymerase enzymes are functionally and physically coupled at the leading strand replication fork and rely on each other for optimal DNA strand separation and synthesis activities. In this review, we describe pre-steady state kinetic methods to quantify the base pair unwinding-synthesis rate constant, a fundamental parameter to understand how the helicase and polymerase help each other during leading strand replication. We describe a robust method to measure the chemical step size of the helicase-polymerase complex that determines how the two motors are energetically coupled while tracking along the DNA. The 2-aminopurine fluorescence-based method provide structural information on the leading strand helicase-polymerase complex, such as the distance between the two enzymes, their relative positions at the replication fork, and their roles in fork junction melting. The combined information garnered from these methods informs on the mutual dependencies between the helicase and DNA polymerase enzymes, their stepping mechanism, and their individual functions at the replication fork during leading strand replication.
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Affiliation(s)
- Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway 08854, NJ, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway 08854, NJ, USA.
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Gandin V, Masvidal L, Hulea L, Gravel SP, Cargnello M, McLaughlan S, Cai Y, Balanathan P, Morita M, Rajakumar A, Furic L, Pollak M, Porco JA, St-Pierre J, Pelletier J, Larsson O, Topisirovic I. nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs. Genome Res 2016; 26:636-48. [PMID: 26984228 PMCID: PMC4864462 DOI: 10.1101/gr.197566.115] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 03/14/2016] [Indexed: 12/12/2022]
Abstract
The diversity of MTOR-regulated mRNA translation remains unresolved. Whereas ribosome-profiling suggested that MTOR almost exclusively stimulates translation of the TOP (terminal oligopyrimidine motif) and TOP-like mRNAs, polysome-profiling indicated that MTOR also modulates translation of mRNAs without the 5' TOP motif (non-TOP mRNAs). We demonstrate that in ribosome-profiling studies, detection of MTOR-dependent changes in non-TOP mRNA translation was obscured by low sensitivity and methodology biases. Transcription start site profiling using nano-cap analysis of gene expression (nanoCAGE) revealed that not only do many MTOR-sensitive mRNAs lack the 5' TOP motif but that 5' UTR features distinguish two functionally and translationally distinct subsets of MTOR-sensitive mRNAs: (1) mRNAs with short 5' UTRs enriched for mitochondrial functions, which require EIF4E but are less EIF4A1-sensitive; and (2) long 5' UTR mRNAs encoding proliferation- and survival-promoting proteins, which are both EIF4E- and EIF4A1-sensitive. Selective inhibition of translation of mRNAs harboring long 5' UTRs via EIF4A1 suppression leads to sustained expression of proteins involved in respiration but concomitant loss of those protecting mitochondrial structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5' UTR mRNAs by MTOR inhibitors results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5' UTR features define different modes of MTOR-sensitive translation of functionally distinct subsets of mRNAs, which may explain the diverse impact of MTOR and EIF4A inhibitors on neoplastic cells.
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Affiliation(s)
- Valentina Gandin
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6; Department of Experimental Medicine, McGill University, Montreal, Canada H3G 1Y6; Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6
| | - Laia Masvidal
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| | - Laura Hulea
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6
| | - Simon-Pierre Gravel
- Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6; Goodman Cancer Research Centre, McGill University, Montreal, Canada H3A 1A3
| | - Marie Cargnello
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6
| | - Shannon McLaughlan
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6
| | - Yutian Cai
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6
| | - Preetika Balanathan
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Victoria 3800, Australia
| | - Masahiro Morita
- Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6; Goodman Cancer Research Centre, McGill University, Montreal, Canada H3A 1A3
| | - Arjuna Rajakumar
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2
| | - Luc Furic
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Victoria 3800, Australia
| | - Michael Pollak
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6; Department of Experimental Medicine, McGill University, Montreal, Canada H3G 1Y6
| | - John A Porco
- Center for Chemical Methodology and Library Development, Boston University, Boston, Massachusetts 02215, USA
| | - Julie St-Pierre
- Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6; Goodman Cancer Research Centre, McGill University, Montreal, Canada H3A 1A3
| | - Jerry Pelletier
- Department of Oncology, McGill University, Montreal, Canada H3G 1Y6; Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6; Goodman Cancer Research Centre, McGill University, Montreal, Canada H3A 1A3
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD Jewish General Hospital, Montreal, Canada H3T 1E2; Department of Oncology, McGill University, Montreal, Canada H3G 1Y6; Department of Experimental Medicine, McGill University, Montreal, Canada H3G 1Y6; Department of Biochemistry, McGill University, Montreal, Canada H3G 1Y6
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66
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Toribio R, Díaz-López I, Boskovic J, Ventoso I. An RNA trapping mechanism in Alphavirus mRNA promotes ribosome stalling and translation initiation. Nucleic Acids Res 2016; 44:4368-80. [PMID: 26984530 PMCID: PMC4872096 DOI: 10.1093/nar/gkw172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 02/29/2016] [Indexed: 02/05/2023] Open
Abstract
During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pathway in mammals. However, some viral mRNAs can initiate translation in the presence of phosphorylated eIF2 via stable RNA stem-loop structures (DLP; Downstream LooP) located in their coding sequence (CDS), which promote 43S preinitiation complex stalling on the initiation codon. We show here that during the scanning process, DLPs of Alphavirus mRNA become trapped in ES6S region (680–914 nt) of 18S rRNA that are projected from the solvent side of 40S subunit. This trapping can lock the progress of the 40S subunit on the mRNA in a way that places the upstream initiator AUGi on the P site of 40S subunit, obviating the participation of eIF2. Notably, the DLP structure is released from 18S rRNA upon 60S ribosomal subunit joining, suggesting conformational changes in ES6Ss during the initiation process. These novel findings illustrate how viral mRNA is threaded into the 40S subunit during the scanning process, exploiting the topology of the 40S subunit solvent side to enhance its translation in vertebrate hosts.
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Affiliation(s)
- René Toribio
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology and Biocomputing Programme, Electron Microscopy Unit, Spanish Nacional Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
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Cencic R, Pelletier J. Hippuristanol - A potent steroid inhibitor of eukaryotic initiation factor 4A. ACTA ACUST UNITED AC 2016; 4:e1137381. [PMID: 27335721 DOI: 10.1080/21690731.2015.1137381] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/08/2015] [Accepted: 12/24/2015] [Indexed: 01/02/2023]
Abstract
Protein synthesis and its regulatory signaling pathways play essential roles in the initiation and maintenance of the cancer phenotype. Insight obtained over the last 3 decades on the mechanisms regulating translation in normal and transformed cells have revealed that perturbed control in cancer cells may offer an Achilles' heel for the development of novel anti-neoplastic agents. Several small molecule inhibitors have been identified and characterized that target translation initiation - more specifically, the rate-limiting step where ribosomes are recruited to mRNA templates. Among these, hippuristanol, a polyhydroxysteroid from the gorgonian Isis hippuris has been found to inhibit translation initiation by blocking the activity of eukaryotic initiation factor (eIF) 4A, an essential RNA helicase involved in this process. Herein, we highlight the biological properties of this compound, its potential development as an anti-cancer agent, and its use to validate eIF4A as an anti-neoplastic target.
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Affiliation(s)
- Regina Cencic
- Department of Biochemistry, McGill University , Montreal, Québec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Québec, Canada; The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Québec, Canada; Department of Oncology, McGill University, Montreal, Québec, Canada
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68
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Abstract
The original purification of the heterotrimeric eIF4F was published over 30 years ago (Grifo, J. A., Tahara, S. M., Morgan, M. A., Shatkin, A. J., and Merrick, W. C. (1983) J. Biol. Chem. 258, 5804-5810). Since that time, numerous studies have been performed with the three proteins specifically required for the translation initiation of natural mRNAs, eIF4A, eIF4B, and eIF4F. These have involved enzymatic and structural studies of the proteins and a number of site-directed mutagenesis studies. The regulation of translation exhibited through the mammalian target of rapamycin (mTOR) pathway is predominately seen as the phosphorylation of 4E-BP, an inhibitor of protein synthesis that functions by binding to the cap binding subunit of eIF4F (eIF4E). A hypothesis that requires the disassembly of eIF4F during translation initiation to yield free subunits (eIF4A, eIF4E, and eIF4G) is presented.
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Affiliation(s)
- William C Merrick
- From the Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4935
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