1
|
Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
Collapse
Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| |
Collapse
|
2
|
Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
Collapse
Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
| |
Collapse
|
3
|
Farooqui S, Narayanan DL, Mascarenhas S, do Rosario MC, Nair KV, Periyasamy R, Shukla A. c.202_204del in NUP214 causes late onset form of febrile encephalopathy. Am J Med Genet A 2024; 194:e63529. [PMID: 38179855 DOI: 10.1002/ajmg.a.63529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024]
Abstract
Nucleoporins (NUPs) are a group of transporter proteins that maintain homeostasis of nucleocytoplasmic transport of proteins and ribonucleic acids under physiological conditions. Biallelic pathogenic variants in NUP214 are known to cause susceptibility to acute infection-induced encephalopathy-9 (IIAE9, MIM#618426), which is characterized by severe and early-onset febrile encephalopathy causing neuroregression, developmental delay, microcephaly, epilepsy, ataxia, brain atrophy, and early death. NUP214-related IIAE9 has been reported in eight individuals from four distinct families till date. We identified a novel in-frame deletion, c.202_204del p.(Leu68del), in NUP214 by exome sequencing in a 20-year-old male with episodic ataxia, seizures, and encephalopathy, precipitated by febrile illness. Neuroimaging revealed progressive cerebellar atrophy. In silico predictions show a change in the protein conformation that may alter the downstream protein interactions with the NUP214 N-terminal region, probably impacting the mRNA export. We report this novel deletion in NUP214 as a cause for a late onset and less severe form of IIAE9.
Collapse
Affiliation(s)
- Sheeba Farooqui
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- DBT/Wellcome Trust India Alliance Early Career Clinical and Public Health Research Fellow, Hyderabad, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Vijay Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Radhakrishnan Periyasamy
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
4
|
Laskin GR, Cabrera AR, Greene NP, Tomko RJ, Vied C, Gordon BS. The mechanosensitive gene arrestin domain containing 2 regulates myotube diameter with direct implications for disuse atrophy with aging. Am J Physiol Cell Physiol 2024; 326:C768-C783. [PMID: 38314723 PMCID: PMC11193484 DOI: 10.1152/ajpcell.00444.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
Arrestin domain containing 2 and 3 (Arrdc2/3) are genes whose mRNA contents are decreased in young skeletal muscle following mechanical overload. Arrdc3 is linked to the regulation of signaling pathways in nonmuscle cells that could influence skeletal muscle size. Despite a similar amino acid sequence, Arrdc2 function remains undefined. The purpose of this study was to further explore the relationship of Arrdc2/Arrdc3 expression with changes in mechanical load in young and aged muscle and define the effect of Arrdc2/3 expression on C2C12 myotube diameter. In young and aged mice, mechanical load was decreased using hindlimb suspension whereas mechanical load was increased by reloading previously unloaded muscle or inducing high-force contractions. Arrdc2 and Arrdc3 mRNAs were overexpressed in C2C12 myotubes using adenoviruses. Myotube diameter was determined 48-h posttransfection, and RNA sequencing was performed on those samples. Arrdc2 and Arrdc3 mRNA content was higher in the unloaded muscle within 1 day of disuse and remained higher up through 10 days. The induction of Arrdc2 mRNA was more pronounced in aged muscle than young muscle in response to unloading. Reloading previously unloaded muscle of young and aged mice restored Arrdc2 and Arrdc3 levels to ambulatory levels. Increasing mechanical load beyond normal ambulatory levels lowered Arrdc2 mRNA, but not Arrdc3 mRNA, in young and aged muscle. Arrdc2 overexpression only was sufficient to lower myotube diameter in C2C12 cells in part by altering the transcriptome favoring muscle atrophy. These data are consistent with Arrdc2 contributing to disuse atrophy, particularly in aged muscle.NEW & NOTEWORTHY We establish Arrdc2 as a novel mechanosensitive gene highly induced in response to mechanical unloading, particularly in aged muscle. Arrdc2 induction in C2C12 myotubes is sufficient to produce thinner myotubes and a transcriptional landscape consistent with muscle atrophy and disuse.
Collapse
Affiliation(s)
- Grant R Laskin
- Department of of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, United States
| | - Ana Regina Cabrera
- Department of Health, Human Performance and Recreation, Cachexia Research Laboratory, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - Nicholas P Greene
- Department of Health, Human Performance and Recreation, Cachexia Research Laboratory, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - Robert J Tomko
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, United States
| | - Cynthia Vied
- Translational Science Laboratory, Florida State University College of Medicine, Tallahassee, Florida, United States
| | - Bradley S Gordon
- Department of of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, United States
- Institute of Sports Sciences and Medicine, Florida State University, Tallahassee, Florida, United States
| |
Collapse
|
5
|
Arul Nambi Rajan A, Asada R, Montpetit B. Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and promote Dbp5-mediated tRNA export in vivo in Saccharomyces cerevisiae. eLife 2024; 12:RP89835. [PMID: 38189406 PMCID: PMC10945473 DOI: 10.7554/elife.89835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Cells must maintain a pool of processed and charged transfer RNAs (tRNA) to sustain translation capacity and efficiency. Numerous parallel pathways support the processing and directional movement of tRNA in and out of the nucleus to meet this cellular demand. Recently, several proteins known to control messenger RNA (mRNA) transport were implicated in tRNA export. The DEAD-box Protein 5, Dbp5, is one such example. In this study, genetic and molecular evidence demonstrates that Dbp5 functions parallel to the canonical tRNA export factor Los1. In vivo co-immunoprecipitation data further shows Dbp5 is recruited to tRNA independent of Los1, Msn5 (another tRNA export factor), or Mex67 (mRNA export adaptor), which contrasts with Dbp5 recruitment to mRNA that is abolished upon loss of Mex67 function. However, as with mRNA export, overexpression of Dbp5 dominant-negative mutants indicates a functional ATPase cycle and that binding of Dbp5 to Gle1 is required by Dbp5 to direct tRNA export. Biochemical characterization of the Dbp5 catalytic cycle demonstrates the direct interaction of Dbp5 with tRNA (or double-stranded RNA) does not activate Dbp5 ATPase activity, rather tRNA acts synergistically with Gle1 to fully activate Dbp5. These data suggest a model where Dbp5 directly binds tRNA to mediate export, which is spatially regulated via Dbp5 ATPase activation at nuclear pore complexes by Gle1.
Collapse
Affiliation(s)
- Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, DavisDavisUnited States
| | - Ryuta Asada
- Department of Viticulture and Enology, University of California, DavisDavisUnited States
| | - Ben Montpetit
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, DavisDavisUnited States
- Department of Viticulture and Enology, University of California, DavisDavisUnited States
| |
Collapse
|
6
|
Rajan AAN, Asada R, Montpetit B. Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and to promote Dbp5 mediated tRNA export in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547072. [PMID: 37425677 PMCID: PMC10327206 DOI: 10.1101/2023.06.29.547072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cells must maintain a pool of processed and charged transfer RNAs (tRNA) to sustain translation capacity and efficiency. Numerous parallel pathways support the processing and directional movement of tRNA in and out of the nucleus to meet this cellular demand. Recently, several proteins known to control messenger RNA (mRNA) transport were implicated in tRNA export. The DEAD-box Protein 5, Dbp5, is one such example. In this study, genetic and molecular evidence demonstrates that Dbp5 functions parallel to the canonical tRNA export factor Los1. In vivo co-immunoprecipitation data further shows Dbp5 is recruited to tRNA independent of Los1, Msn5 (another tRNA export factor), or Mex67 (mRNA export adaptor), which contrasts with Dbp5 recruitment to mRNA that is abolished upon loss of Mex67 function. However, as with mRNA export, overexpression of Dbp5 dominant-negative mutants indicates a functional ATPase cycle and that binding of Dbp5 to Gle1 is required by Dbp5 to direct tRNA export. Biochemical characterization of the Dbp5 catalytic cycle demonstrates the direct interaction of Dbp5 with tRNA (or double stranded RNA) does not activate Dbp5 ATPase activity, rather tRNA acts synergistically with Gle1 to fully activate Dbp5. These data suggest a model where Dbp5 directly binds tRNA to mediate export, which is spatially regulated via Dbp5 ATPase activation at nuclear pore complexes by Gle1.
Collapse
Affiliation(s)
- Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
| | - Ryuta Asada
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Ben Montpetit
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| |
Collapse
|
7
|
Querl L, Krebber H. The DEAD-box RNA helicase Dbp5 is a key protein that couples multiple steps in gene expression. Biol Chem 2023; 404:845-850. [PMID: 37436777 DOI: 10.1515/hsz-2023-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
Cell viability largely depends on the surveillance of mRNA export and translation. Upon pre-mRNA processing and nuclear quality control, mature mRNAs are exported into the cytoplasm via Mex67-Mtr2 attachment. At the cytoplasmic site of the nuclear pore complex, the export receptor is displaced by the action of the DEAD-box RNA helicase Dbp5. Subsequent quality control of the open reading frame requires translation. Our studies suggest an involvement of Dbp5 in cytoplasmic no-go-and non-stop decay. Most importantly, we have also identified a key function for Dbp5 in translation termination, which identifies this helicase as a master regulator of mRNA expression.
Collapse
Affiliation(s)
- Luisa Querl
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| |
Collapse
|
8
|
Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
Collapse
Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| |
Collapse
|
9
|
Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ, Wu Y. Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Front Oncol 2023; 12:1087989. [PMID: 36761420 PMCID: PMC9905851 DOI: 10.3389/fonc.2022.1087989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
Collapse
Affiliation(s)
- Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hardikkumar Patel
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan and Saskatchewan Cancer Agency, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| |
Collapse
|
10
|
Loughran G, Li X, O’Loughlin S, Atkins JF, Baranov P. Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts. Nucleic Acids Res 2022; 51:304-314. [PMID: 36533511 PMCID: PMC9841425 DOI: 10.1093/nar/gkac1180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/08/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
A stop codon entering the ribosome A-site is normally decoded by release factors that induce release of the polypeptide. Certain factors influence the efficiency of the termination which is in competition with elongation in either the same (readthrough) or an alternative (frameshifting) reading frame. To gain insight into the competition between these processes, we monitored translation in parallel from all three reading frames downstream of stop codons while changing the nucleotide context of termination sites or altering cellular conditions (polyamine levels). We found that P-site codon identity can have a major impact on the termination efficiency of the OPRL1 stop signal, whereas for the OAZ1 ORF1 stop signal, the P-site codon mainly influences the reading frame of non-terminating ribosomes. Changes to polyamine levels predominantly influence the termination efficiency of the OAZ1 ORF1 stop signal. In contrast, increasing polyamine levels stimulate readthrough of the OPRL1 stop signal by enhancing near-cognate decoding rather than by decreasing termination efficiency. Thus, by monitoring the four competing processes occurring at stop codons we were able to determine which is the most significantly affected upon perturbation. This approach may be useful for the interrogation of other recoding phenomena where alternative decoding processes compete with standard decoding.
Collapse
Affiliation(s)
- Gary Loughran
- Correspondence may also be addressed to Gary Loughran.
| | - Xiang Li
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sinead O’Loughlin
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland,Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | |
Collapse
|
11
|
Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
Collapse
Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
| |
Collapse
|
12
|
Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
Collapse
Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
| |
Collapse
|
13
|
Castelli LM, Benson BC, Huang WP, Lin YH, Hautbergue GM. RNA Helicases in Microsatellite Repeat Expansion Disorders and Neurodegeneration. Front Genet 2022; 13:886563. [PMID: 35646086 PMCID: PMC9133428 DOI: 10.3389/fgene.2022.886563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Short repeated sequences of 3-6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. Although considered rare diseases in relation to the relatively low number of cases, these primarily adult-onset conditions, often debilitating and fatal in absence of a cure, collectively pose a large burden on healthcare systems in an ageing world population. The pathological mechanisms driving disease onset are complex implicating several non-exclusive mechanisms of neuronal injury linked to RNA and protein toxic gain- and loss- of functions. Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. Finally, we will discuss the challenges and potential opportunities that are associated with the targeting of RNA helicases for the development of future therapeutic approaches.
Collapse
Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Bridget C Benson
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
14
|
Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
Collapse
Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| |
Collapse
|
15
|
Shuvalov A, Shuvalova E, Biziaev N, Sokolova E, Evmenov K, Pustogarov N, Arnautova A, Matrosova V, Egorova T, Alkalaeva E. Nsp1 of SARS-CoV-2 stimulates host translation termination. RNA Biol 2021; 18:804-817. [PMID: 34793288 PMCID: PMC8782162 DOI: 10.1080/15476286.2021.1999103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 10/19/2022] Open
Abstract
Nsp1 of SARS-CoV-2 regulates the translation of host and viral mRNAs in cells. Nsp1 inhibits host translation initiation by occluding the entry channel of the 40S ribosome subunit. The structural study of the Nsp1-ribosomal complexes reported post-termination 80S complex containing Nsp1, eRF1 and ABCE1. Considering the presence of Nsp1 in the post-termination 80S ribosomal complex, we hypothesized that Nsp1 may be involved in translation termination. Using a cell-free translation system and reconstituted in vitro translation system, we show that Nsp1 stimulates peptide release and formation of termination complexes. Detailed analysis of Nsp1 activity during translation termination stages reveals that Nsp1 facilitates stop codon recognition. We demonstrate that Nsp1 stimulation targets eRF1 and does not affect eRF3. Moreover, Nsp1 increases amount of the termination complexes at all three stop codons. The activity of Nsp1 in translation termination is provided by its N-terminal domain and the minimal required part of eRF1 is NM domain. We assume that the biological meaning of Nsp1 activity in translation termination is binding with the 80S ribosomes translating host mRNAs and remove them from the pool of the active ribosomes.
Collapse
Affiliation(s)
- Alexey Shuvalov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta Sokolova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Evmenov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Pustogarov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra Arnautova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vera Matrosova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Egorova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Alkalaeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
16
|
Egorova T, Biziaev N, Shuvalov A, Sokolova E, Mukba S, Evmenov K, Zotova M, Kushchenko A, Shuvalova E, Alkalaeva E. eIF3j facilitates loading of release factors into the ribosome. Nucleic Acids Res 2021; 49:11181-11196. [PMID: 34591963 PMCID: PMC8565342 DOI: 10.1093/nar/gkab854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/23/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
eIF3j is one of the eukaryotic translation factors originally reported as the labile subunit of the eukaryotic translation initiation factor eIF3. The yeast homolog of this protein, Hcr1, has been implicated in stringent AUG recognition as well as in controlling translation termination and stop codon readthrough. Using a reconstituted mammalian in vitro translation system, we showed that the human protein eIF3j is also important for translation termination. We showed that eIF3j stimulates peptidyl-tRNA hydrolysis induced by a complex of eukaryotic release factors, eRF1-eRF3. Moreover, in combination with the initiation factor eIF3, which also stimulates peptide release, eIF3j activity in translation termination increases. We found that eIF3j interacts with the pre-termination ribosomal complex, and eRF3 destabilises this interaction. In the solution, these proteins bind to each other and to other participants of translation termination, eRF1 and PABP, in the presence of GTP. Using a toe-printing assay, we determined the stage at which eIF3j functions – binding of release factors to the A-site of the ribosome before GTP hydrolysis. Based on these data, we assumed that human eIF3j is involved in the regulation of translation termination by loading release factors into the ribosome.
Collapse
Affiliation(s)
- Tatiana Egorova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| | - Sabina Mukba
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin Evmenov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Zotova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Artem Kushchenko
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia
| |
Collapse
|
17
|
Shuvalova E, Egorova T, Ivanov A, Shuvalov A, Biziaev N, Mukba S, Pustogarov N, Terenin I, Alkalaeva E. Discovery of a novel role of tumor suppressor PDCD4 in stimulation of translation termination. J Biol Chem 2021; 297:101269. [PMID: 34606825 PMCID: PMC8551656 DOI: 10.1016/j.jbc.2021.101269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Programmed cell death 4 protein (PDCD4) regulates many vital cell processes, although is classified as a tumor suppressor because it inhibits neoplastic transformation and tumor growth. For example, PCDC4 has been implicated in the regulation of transcription and mRNA translation. PDCD4 is known to inhibit translation initiation by binding to eukaryotic initiation factor 4A and elongation of oncogenic c- and A-myb mRNAs. Additionally, PDCD4 has been shown to interact with poly(A)-binding protein (PABP), which affects translation termination, although the significance of this interaction is not fully understood. Considering the interaction between PABP and PDCD4, we hypothesized that PDCD4 may also be involved in translation termination. Using in vitro translation systems, we revealed that PDCD4 directly activates translation termination. PDCD4 stimulates peptidyl-tRNA hydrolysis induced by a complex of eukaryotic release factors, eRF1-eRF3. Moreover, in combination with the PABP, which also stimulates peptide release, PDCD4 activity in translation termination increases. PDCD4 regulates translation termination by facilitating the binding of release factors to the ribosome, increasing the GTPase activity of eRF3, and dissociating eRF3 from the posttermination complex. Using a toe-printing assay, we determined the first stage at which PDCD4 functions-binding of release factors to the A-site of the ribosome. However, preventing binding of eRF3 with PABP, PDCD4 suppresses subsequent rounds of translation termination. Based on these data, we assumed that human PDCD4 controls protein synthesis during translation termination. The described mechanism of the activity of PDCD4 in translation termination provides a new insight into its functioning during suppression of protein biosynthesis.
Collapse
Affiliation(s)
- Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia
| | - Alexander Ivanov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia
| | - Sabina Mukba
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Pustogarov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia
| | - Ilya Terenin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia.
| |
Collapse
|
18
|
Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O, Oliveira C, Dumas C, Mariz FC, Papadopoulou B. Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res 2021; 49:9459-9478. [PMID: 34358325 PMCID: PMC8450092 DOI: 10.1093/nar/gkab667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
DDX3 is a multifaceted RNA helicase of the DEAD-box family that plays central roles in all aspects of RNA metabolism including translation initiation. Here, we provide evidence that the Leishmania DDX3 ortholog functions in post-initiation steps of translation. We show that genetic depletion of DDX3 slows down ribosome movement resulting in elongation-stalled ribosomes, impaired translation elongation and decreased de novo protein synthesis. We also demonstrate that the essential ribosome recycling factor Rli1/ABCE1 and termination factors eRF3 and GTPBP1 are less recruited to ribosomes upon DDX3 loss, suggesting that arrested ribosomes may be inefficiently dissociated and recycled. Furthermore, we show that prolonged ribosome stalling triggers co-translational ubiquitination of nascent polypeptide chains and a higher recruitment of E3 ubiquitin ligases and proteasome components to ribosomes of DDX3 knockout cells, which further supports that ribosomes are not elongating optimally. Impaired elongation of translating ribosomes also results in the accumulation of cytoplasmic protein aggregates, which implies that defects in translation overwhelm the normal quality controls. The partial recovery of translation by overexpressing Hsp70 supports this possibility. Collectively, these results suggest an important novel contribution of DDX3 to optimal elongation of translating ribosomes by preventing prolonged translation stalls and stimulating recycling of arrested ribosomes.
Collapse
Affiliation(s)
- Prasad Kottayil Padmanabhan
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Gabriel Reis Ferreira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Ouafa Zghidi-Abouzid
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Camila Oliveira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Filipe Colaço Mariz
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| |
Collapse
|
19
|
Park Y, Park J, Hwang HJ, Kim L, Jeong K, Song HK, Rufener SC, Mühlemann O, Kim YK. Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF-DDX19B interaction. Nucleic Acids Res 2021; 49:8261-8276. [PMID: 34232997 PMCID: PMC8373075 DOI: 10.1093/nar/gkab579] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 06/08/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Newly synthesized mRNA is translated during its export through the nuclear pore complex, when its 5′-cap structure is still bound by the nuclear cap-binding complex (CBC), a heterodimer of cap-binding protein (CBP) 80 and CBP20. Despite its critical role in mRNA surveillance, the mechanism by which CBC-dependent translation (CT) is regulated remains unknown. Here, we demonstrate that the CT initiation factor (CTIF) is tethered in a translationally incompetent manner to the perinuclear region by the DEAD-box helicase 19B (DDX19B). DDX19B hands over CTIF to CBP80, which is associated with the 5′-cap of a newly exported mRNA. The resulting CBP80–CTIF complex then initiates CT in the perinuclear region. We also show that impeding the interaction between CTIF and DDX19B leads to uncontrolled CT throughout the cytosol, consequently dysregulating nonsense-mediated mRNA decay. Altogether, our data provide molecular evidence supporting the importance of tight control of local translation in the perinuclear region.
Collapse
Affiliation(s)
- Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Leehyeon Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Kyu Song
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Simone C Rufener
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
20
|
Pinter S, Knodel F, Choudalakis M, Schnee P, Kroll C, Fuchs M, Broehm A, Weirich S, Roth M, Eisler SA, Zuber J, Jeltsch A, Rathert P. A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation. Nucleic Acids Res 2021; 49:4350-4370. [PMID: 33823549 PMCID: PMC8096265 DOI: 10.1093/nar/gkab180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
The lysine specific demethylase 1 (LSD1) plays a pivotal role in cellular differentiation by regulating the expression of key developmental genes in concert with different coregulatory proteins. This process is impaired in different cancer types and incompletely understood. To comprehensively identify functional coregulators of LSD1, we established a novel tractable fluorescent reporter system to monitor LSD1 activity in living cells. Combining this reporter system with a state-of-the-art multiplexed RNAi screen, we identify the DEAD-box helicase 19A (DDX19A) as a novel coregulator and demonstrate that suppression of Ddx19a results in an increase of R-loops and reduced LSD1-mediated gene silencing. We further show that DDX19A binds to tri-methylated lysine 27 of histone 3 (H3K27me3) and it regulates gene expression through the removal of transcription promoting R-loops. Our results uncover a novel transcriptional regulatory cascade where the downregulation of genes is dependent on the LSD1 mediated demethylation of histone H3 lysine 4 (H3K4). This allows the polycomb repressive complex 2 (PRC2) to methylate H3K27, which serves as a binding site for DDX19A. Finally, the binding of DDX19A leads to the efficient removal of R-loops at active promoters, which further de-represses LSD1 and PRC2, establishing a positive feedback loop leading to a robust repression of the target gene.
Collapse
Affiliation(s)
- Sabine Pinter
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Franziska Knodel
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Michel Choudalakis
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Philipp Schnee
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Carolin Kroll
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Marina Fuchs
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alexander Broehm
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Mareike Roth
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Stephan A Eisler
- Stuttgart Research Center Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| |
Collapse
|
21
|
Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
Collapse
Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
| |
Collapse
|
22
|
Susorov D, Egri S, Korostelev AA. Termi-Luc: a versatile assay to monitor full-protein release from ribosomes. RNA (NEW YORK, N.Y.) 2020; 26:2044-2050. [PMID: 32817446 PMCID: PMC7668252 DOI: 10.1261/rna.076588.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 05/05/2023]
Abstract
Termination of protein biosynthesis is an essential step of gene expression, during which a complete functional protein is released from the ribosome. Premature or inefficient termination results in truncated, nonfunctional, or toxic proteins that may cause disease. Indeed, more than 10% of human genetic diseases are caused by nonsense mutations leading to premature termination. Efficient and sensitive approaches are required to study eukaryotic termination mechanisms and to identify potential therapeutics that modulate termination. Canonical radioactivity-based termination assays are complex, report on a short peptide release, and are incompatible with high-throughput screening. Here we describe a robust and simple in vitro assay to study the kinetics of full-protein release. The assay monitors luminescence upon release of nanoluciferase from a mammalian pretermination complex. The assay can be used to record time-progress curves of protein release in a high-throughput format, making it optimal for studying release kinetics and for high-throughput screening for small molecules that modulate the efficiency of termination.
Collapse
Affiliation(s)
- Denis Susorov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Shawn Egri
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| |
Collapse
|
23
|
Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression. Cell Mol Life Sci 2020; 78:2019-2030. [PMID: 33205304 DOI: 10.1007/s00018-020-03680-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/21/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022]
Abstract
The DEAD-box protein (DBP) Dbp5, a member of the superfamily II (SFII) helicases, has multiple reported roles in gene expression. First identified as an essential regulator of mRNA export in Saccharomyces cerevisiae, the enzyme now has reported functions in non-coding RNA export, translation, transcription, and DNA metabolism. Localization of the protein to various cellular compartments (nucleoplasm, nuclear envelope, and cytoplasm) highlights the ability of Dbp5 to modulate different stages of the RNA lifecycle. While Dbp5 has been well studied for > 20 years, several critical questions remain regarding the mechanistic principles that govern Dbp5 localization, substrate selection, and functions in gene expression. This review aims to take a holistic view of the proposed functions of Dbp5 and evaluate models that accommodate current published data.
Collapse
|
24
|
Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| |
Collapse
|
25
|
Adams RL, Wente SR. Dbp5 associates with RNA-bound Mex67 and Nab2 and its localization at the nuclear pore complex is sufficient for mRNP export and cell viability. PLoS Genet 2020; 16:e1009033. [PMID: 33002012 PMCID: PMC7553267 DOI: 10.1371/journal.pgen.1009033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/13/2020] [Accepted: 08/06/2020] [Indexed: 01/04/2023] Open
Abstract
In Saccharomyces cerevisiae, the mRNA export receptor Mex67 is recruited to mature nuclear transcripts to mediate mRNA export through the nuclear pore complex (NPC) to the cytoplasm. Mex67 binds transcripts through adaptor proteins such as the poly(A) binding protein Nab2. When a transcript reaches the cytoplasmic face of the NPC, the DEAD-box protein Dbp5 acts to induce a local structural change to release Nab2 and Mex67 in an essential process termed mRNP remodeling. It is unknown how certain proteins (Nab2, Mex67) are released during Dbp5-mediated mRNP remodeling, whereas others remain associated. Here, we demonstrate that Dbp5 associates in close proximity with Mex67 and Nab2 in a cellular complex. Further, fusion of Dbp5 to Nup159 anchors Dbp5 at the cytoplasmic face of the NPC and is sufficient for cell viability. Thus, we speculate that the essential role of Dbp5 in remodeling exporting mRNPs requires its localization to the NPC and is separable from other subcellular functions of Dbp5. This work supports a model where the diverse nuclear, cytoplasmic and NPC functions of Dbp5 in the mRNA lifecycle are not interdependent and that Dbp5 is locally recruited through complex protein-protein interactions to select regions of transcripts for specific removal of transport proteins at the NPC.
Collapse
Affiliation(s)
- Rebecca L. Adams
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Susan R. Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| |
Collapse
|
26
|
CTELS: A Cell-Free System for the Analysis of Translation Termination Rate. Biomolecules 2020; 10:biom10060911. [PMID: 32560154 PMCID: PMC7356799 DOI: 10.3390/biom10060911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3′ UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a “leaky” stop codon context, which likely defines the basis of nonsense suppression.
Collapse
|
27
|
Beißel C, Grosse S, Krebber H. Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay. Int J Mol Sci 2020; 21:ijms21031085. [PMID: 32041247 PMCID: PMC7037193 DOI: 10.3390/ijms21031085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/21/2023] Open
Abstract
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination and NMD in the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
Collapse
|
28
|
Beißel C, Neumann B, Uhse S, Hampe I, Karki P, Krebber H. Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3. Nucleic Acids Res 2019; 47:4798-4813. [PMID: 30873535 PMCID: PMC6511868 DOI: 10.1093/nar/gkz177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/28/2019] [Accepted: 03/08/2019] [Indexed: 01/16/2023] Open
Abstract
Translation termination requires eRF1 and eRF3 for polypeptide- and tRNA-release on stop codons. Additionally, Dbp5/DDX19 and Rli1/ABCE1 are required; however, their function in this process is currently unknown. Using a combination of in vivo and in vitro experiments, we show that they regulate a stepwise assembly of the termination complex. Rli1 and eRF3-GDP associate with the ribosome first. Subsequently, Dbp5-ATP delivers eRF1 to the stop codon and in this way prevents a premature access of eRF3. Dbp5 dissociates upon placing eRF1 through ATP-hydrolysis. This in turn enables eRF1 to contact eRF3, as the binding of Dbp5 and eRF3 to eRF1 is mutually exclusive. Defects in the Dbp5-guided eRF1 delivery lead to premature contact and premature dissociation of eRF1 and eRF3 from the ribosome and to subsequent stop codon readthrough. Thus, the stepwise Dbp5-controlled termination complex assembly is essential for regular translation termination events. Our data furthermore suggest a possible role of Dbp5/DDX19 in alternative translation termination events, such as during stress response or in developmental processes, which classifies the helicase as a potential drug target for nonsense suppression therapy to treat cancer and neurodegenerative diseases.
Collapse
Affiliation(s)
- Christian Beißel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Bettina Neumann
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Simon Uhse
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Irene Hampe
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| |
Collapse
|
29
|
Lari A, Arul Nambi Rajan A, Sandhu R, Reiter T, Montpetit R, Young BP, Loewen CJ, Montpetit B. A nuclear role for the DEAD-box protein Dbp5 in tRNA export. eLife 2019; 8:48410. [PMID: 31453808 PMCID: PMC6711706 DOI: 10.7554/elife.48410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023] Open
Abstract
Dbp5 is an essential DEAD-box protein that mediates nuclear mRNP export. Dbp5 also shuttles between nuclear and cytoplasmic compartments with reported roles in transcription, ribosomal subunit export, and translation; however, the mechanism(s) by which nucleocytoplasmic transport occurs and how Dbp5 specifically contributes to each of these processes remains unclear. Towards understanding the functions and transport of Dbp5 in Saccharomyces cerevisiae, alanine scanning mutagenesis was used to generate point mutants at all possible residues within a GFP-Dbp5 reporter. Characterization of the 456 viable mutants led to the identification of an N-terminal Xpo1-dependent nuclear export signal in Dbp5, in addition to other separation-of-function alleles, which together provide evidence that Dbp5 nuclear shuttling is not essential for mRNP export. Rather, disruptions in Dbp5 nucleocytoplasmic transport result in tRNA export defects, including changes in tRNA shuttling dynamics during recovery from nutrient stress.
Collapse
Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States
| | - Rima Sandhu
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, United States
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Barry P Young
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Chris Jr Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, United States.,Food Science Graduate Group, University of California Davis, Davis, United States
| |
Collapse
|
30
|
Egorova T, Sokolova E, Shuvalova E, Matrosova V, Shuvalov A, Alkalaeva E. Fluorescent toeprinting to study the dynamics of ribosomal complexes. Methods 2019; 162-163:54-59. [PMID: 31201933 DOI: 10.1016/j.ymeth.2019.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Classical toeprinting is generally used to determine the position of ribosomes on mRNA; however, it has several disadvantages. We describe a fluorescent toeprinting assay that enables easier identification of ribosomal complexes bound to mRNA in vitro. The procedure involves the use of stable and safe fluorescently labeled oligonucleotides for reverse transcription reactions as primers, followed by the analysis of cDNA products using an automatic sequencer. This procedure allows the multiplexing and simultaneous analysis of a large number of samples. Over the past ten years, fluorescent toeprinting was applied to determine the activities of eukaryotic release factors and additional proteins involved in translation termination, to study the dynamics of translation initiation and elongation complexes, and to quantitatively evaluate the observed ribosomal complexes. Because of the simplicity and small amounts of material required, fluorescent toeprinting provides a highly scalable and versatile tool to study ribosomal complexes.
Collapse
Affiliation(s)
- Tatiana Egorova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vera Matrosova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia.
| |
Collapse
|
31
|
Volpon L, Osborne MJ, Borden KL. Biochemical and Structural Insights into the Eukaryotic Translation Initiation Factor eIF4E. Curr Protein Pept Sci 2019; 20:525-535. [DOI: 10.2174/1389203720666190110142438] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/04/2019] [Indexed: 12/18/2022]
Abstract
A major question in cell and cancer biology is concerned with understanding the flow of
information from gene to protein. Indeed, many studies indicate that the proteome can be decoupled
from the transcriptome. A major source of this decoupling is post-transcriptional regulation. The eukaryotic
translation initiation factor eIF4E serves as an excellent example of a protein that can modulate
the proteome at the post-transcriptional level. eIF4E is elevated in many cancers thus highlighting
the relevance of this mode of control to biology. In this review, we provide a brief overview of various
functions of eIF4E in RNA metabolism e.g. in nuclear-cytoplasmic RNA export, translation,
RNA stability and/or sequestration. We focus on the modalities of eIF4E regulation at the biochemical
and particularly structural level. In this instance, we describe not only the importance for the m7Gcap
eIF4E interaction but also of recently discovered non-traditional RNA-eIF4E interactions as well
as cap-independent activities of eIF4E. Further, we describe several distinct structural modalities used
by the cell and some viruses to regulate or co-opt eIF4E, substantially extending the types of proteins
that can regulate eIF4E from the traditional eIF4E-binding proteins (e.g. 4E-BP1 and eIF4G). Finally,
we provide an overview of the results of targeting eIF4E activity in the clinic.
Collapse
Affiliation(s)
- Laurent Volpon
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
| | - Michael J. Osborne
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
| | - Katherine L.B. Borden
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Universite de Montreal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, Quebec, Canada
| |
Collapse
|
32
|
Ivanov A, Shuvalova E, Egorova T, Shuvalov A, Sokolova E, Bizyaev N, Shatsky I, Terenin I, Alkalaeva E. Polyadenylate-binding protein-interacting proteins PAIP1 and PAIP2 affect translation termination. J Biol Chem 2019; 294:8630-8639. [PMID: 30992367 DOI: 10.1074/jbc.ra118.006856] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/29/2019] [Indexed: 12/29/2022] Open
Abstract
Polyadenylate-binding protein (PABP) stimulates translation termination via interaction of its C-terminal domain with eukaryotic polypeptide chain release factor, eRF3. Additionally, two other proteins, poly(A)-binding protein-interacting proteins 1 and 2 (PAIP1 and PAIP2), bind the same domain of PABP and regulate its translation-related activity. To study the biochemistry of eRF3 and PAIP1/2 competition for PABP binding, we quantified the effects of PAIPs on translation termination in the presence or absence of PABP. Our results demonstrated that both PAIP1 and PAIP2 prevented translation termination at the premature termination codon, by controlling PABP activity. Moreover, PAIP1 and PAIP2 inhibited the activity of free PABP on translation termination in vitro However, after binding the poly(A) tail, PABP became insensitive to suppression by PAIPs and efficiently activated translation termination in the presence of eRF3a. Additionally, we revealed that PAIP1 binds eRF3 in solution, which stabilizes the post-termination complex. These results indicated that PAIP1 and PAIP2 participate in translation termination and are important regulators of readthrough at the premature termination codon.
Collapse
Affiliation(s)
- Alexandr Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nikita Bizyaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan Shatsky
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya Terenin
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119146, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| |
Collapse
|
33
|
Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
Collapse
Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| |
Collapse
|
34
|
Barkovich KJ, Moore MK, Hu Q, Shokat KM. Chemical genetic inhibition of DEAD-box proteins using covalent complementarity. Nucleic Acids Res 2018; 46:8689-8699. [PMID: 30102385 PMCID: PMC6158709 DOI: 10.1093/nar/gky706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/07/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022] Open
Abstract
DEAD-box proteins are an essential class of enzymes involved in all stages of RNA metabolism. The study of DEAD-box proteins is challenging in a native setting since they are structurally similar, often essential and display dosage sensitivity. Pharmacological inhibition would be an ideal tool to probe the function of these enzymes. In this work, we describe a chemical genetic strategy for the specific inactivation of individual DEAD-box proteins with small molecule inhibitors using covalent complementarity. We identify a residue of low conservation within the P-loop of the nucleotide-binding site of DEAD-box proteins and show that it can be mutated to cysteine without a substantial loss of enzyme function to generate electrophile-sensitive mutants. We then present a series of small molecules that rapidly and specifically bind and inhibit electrophile-sensitive DEAD-box proteins with high selectivity over the wild-type enzyme. Thus, this approach can be used to systematically generate small molecule-sensitive alleles of DEAD-box proteins, allowing for pharmacological inhibition and functional characterization of members of this enzyme family.
Collapse
Affiliation(s)
- Krister J Barkovich
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Megan K Moore
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Qi Hu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
35
|
Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun 2018; 9:2319. [PMID: 29899397 PMCID: PMC5998080 DOI: 10.1038/s41467-018-04459-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 04/27/2018] [Indexed: 11/25/2022] Open
Abstract
The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1•Nup42•DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans. The export of mRNA to the cytosol depends on the nuclear pore complex (NPC) and the activation of the helicase DDX19, but their interplay in humans remains poorly understood. Here, the authors present a structural and functional analysis of DDX19 activation, revealing how the human NPC regulates mRNA export.
Collapse
Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Sarah W Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
| |
Collapse
|
36
|
Okamura M, Yamanaka Y, Shigemoto M, Kitadani Y, Kobayashi Y, Kambe T, Nagao M, Kobayashi I, Okumura K, Masuda S. Depletion of mRNA export regulator DBP5/DDX19, GLE1 or IPPK that is a key enzyme for the production of IP6, resulting in differentially altered cytoplasmic mRNA expression and specific cell defect. PLoS One 2018; 13:e0197165. [PMID: 29746542 PMCID: PMC5945018 DOI: 10.1371/journal.pone.0197165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/27/2018] [Indexed: 01/13/2023] Open
Abstract
DBP5, also known as DDX19, GLE1 and inositol hexakisphosphate (IP6) function in messenger RNA (mRNA) export at the cytoplasmic surface of the nuclear pore complex in eukaryotic cells. DBP5 is a DEAD-box RNA helicase, and its activity is stimulated by interactions with GLE1 and IP6. In addition, these three factors also have unique role(s). To investigate how these factors influenced the cytoplasmic mRNA expression and cell phenotype change, we performed RNA microarray analysis to detect the effect and function of DBP5, GLE1 and IP6 on the cytoplasmic mRNA expression. The expression of some cytoplasmic mRNA subsets (e.g. cell cycle, DNA replication) was commonly suppressed by the knock-down of DBP5, GLE1 and IPPK (IP6 synthetic enzyme). The GLE1 knock-down selectively reduced the cytoplasmic mRNA expression required for mitotic progression, results in an abnormal spindle phenotype and caused the delay of mitotic process. Meanwhile, G1/S cell cycle arrest was observed in DBP5 and IPPK knock-down cells. Several factors that function in immune response were also down-regulated in DBP5 or IPPK knock-down cells. Thereby, IFNβ-1 mRNA transcription evoked by poly(I:C) treatment was suppressed. These results imply that DBP5, GLE1 and IP6 have a conserved and individual function in the cytoplasmic mRNA expression. Variations in phenotype are due to the difference in each function of DBP5, GLE1 and IPPK in intracellular mRNA metabolism.
Collapse
Affiliation(s)
- Masumi Okamura
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Yasutaka Yamanaka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Maki Shigemoto
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Yuya Kitadani
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Yuhko Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Taiho Kambe
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Masaya Nagao
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Issei Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Katsuzumi Okumura
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
- * E-mail:
| |
Collapse
|
37
|
Cridge AG, Crowe-McAuliffe C, Mathew SF, Tate WP. Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel. Nucleic Acids Res 2018; 46:1927-1944. [PMID: 29325104 PMCID: PMC5829715 DOI: 10.1093/nar/gkx1315] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/07/2017] [Accepted: 01/05/2018] [Indexed: 01/01/2023] Open
Abstract
When a stop codon is at the 80S ribosomal A site, there are six nucleotides (+4 to +9) downstream that are inferred to be occupying the mRNA channel. We examined the influence of these downstream nucleotides on translation termination success or failure in mammalian cells at the three stop codons. The expected hierarchy in the intrinsic fidelity of the stop codons (UAA>UAG>>UGA) was observed, with highly influential effects on termination readthrough mediated by nucleotides at position +4 and position +8. A more complex influence was observed from the nucleotides at positions +5 and +6. The weakest termination contexts were most affected by increases or decreases in the concentration of the decoding release factor (eRF1), indicating that eRF1 binding to these signals was rate-limiting. When termination efficiency was significantly reduced by cognate suppressor tRNAs, the observed influence of downstream nucleotides was maintained. There was a positive correlation between experimentally measured signal strength and frequency of the signal in eukaryotic genomes, particularly in Saccharomyces cerevisiae and Drosophila melanogaster. We propose that termination efficiency is not only influenced by interrogation of the stop signal directly by the release factor, but also by downstream ribosomal interactions with the mRNA nucleotides in the entry channel.
Collapse
Affiliation(s)
- Andrew G Cridge
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | | | - Suneeth F Mathew
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Warren P Tate
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| |
Collapse
|