1
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Abaeva IS, Young C, Warsaba R, Khan N, Tran L, Jan E, Pestova T, Hellen CT. The structure and mechanism of action of a distinct class of dicistrovirus intergenic region IRESs. Nucleic Acids Res 2023; 51:9294-9313. [PMID: 37427788 PMCID: PMC10516663 DOI: 10.1093/nar/gkad569] [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: 04/07/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023] Open
Abstract
Internal ribosomal entry sites (IRESs) engage with the eukaryotic translation apparatus to promote end-independent initiation. We identified a conserved class of ∼150 nt long intergenic region (IGR) IRESs in dicistrovirus genomes derived from members of the phyla Arthropoda, Bryozoa, Cnidaria, Echinodermata, Entoprocta, Mollusca and Porifera. These IRESs, exemplified by Wenling picorna-like virus 2, resemble the canonical cricket paralysis virus (CrPV) IGR IRES in comprising two nested pseudoknots (PKII/PKIII) and a 3'-terminal pseudoknot (PKI) that mimics a tRNA anticodon stem-loop base-paired to mRNA. However, they are ∼50 nt shorter than CrPV-like IRESs, and PKIII is an H-type pseudoknot that lacks the SLIV and SLV stem-loops that are primarily responsible for the affinity of CrPV-like IRESs for the 40S ribosomal subunit and that restrict initial binding of PKI to its aminoacyl (A) site. Wenling-class IRESs bound strongly to 80S ribosomes but only weakly to 40S subunits. Whereas CrPV-like IRESs must be translocated from the A site to the peptidyl (P) site by elongation factor 2 for elongation to commence, Wenling-class IRESs bound directly to the P site of 80S ribosomes, and decoding begins without a prior translocation step. A chimeric CrPV clone containing a Wenling-class IRES was infectious, confirming that the IRES functioned in cells.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Christina Young
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Reid Warsaba
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nadiyah Khan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Lan Vy Tran
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
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2
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Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener 2023; 18:58. [PMID: 37626421 PMCID: PMC10464328 DOI: 10.1186/s13024-023-00642-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
RNA translation is tightly controlled in eukaryotic cells to regulate gene expression and maintain proteome homeostasis. RNA binding proteins, translation factors, and cell signaling pathways all modulate the translation process. Defective translation is involved in multiple neurological diseases including amyotrophic lateral sclerosis (ALS). ALS is a progressive neurodegenerative disorder and poses a major public health challenge worldwide. Over the past few years, tremendous advances have been made in the understanding of the genetics and pathogenesis of ALS. Dysfunction of RNA metabolisms, including RNA translation, has been closely associated with ALS. Here, we first introduce the general mechanisms of translational regulation under physiological and stress conditions and review well-known examples of translation defects in neurodegenerative diseases. We then focus on ALS-linked genes and discuss the recent progress on how translation is affected by various mutant genes and the repeat expansion-mediated non-canonical translation in ALS.
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Affiliation(s)
- Shaopeng Wang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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3
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Miścicka A, Lu K, Abaeva IS, Pestova TV, Hellen CUT. Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1051-1068. [PMID: 37041031 PMCID: PMC10275262 DOI: 10.1261/rna.079599.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
Initiation of translation on many viral mRNAs occurs by noncanonical mechanisms that involve 5' end-independent binding of ribosomes to an internal ribosome entry site (IRES). The ∼190-nt-long intergenic region (IGR) IRES of dicistroviruses such as cricket paralysis virus (CrPV) initiates translation without Met-tRNAi Met or initiation factors. Advances in metagenomics have revealed numerous dicistrovirus-like genomes with shorter, structurally distinct IGRs, such as nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1). Like canonical IGR IRESs, the ∼165-nt-long NediV-like IGRs comprise three domains, but they lack key canonical motifs, including L1.1a/L1.1b loops (which bind to the L1 stalk of the ribosomal 60S subunit) and the apex of stem-loop V (SLV) (which binds to the head of the 40S subunit). Domain 2 consists of a compact, highly conserved pseudoknot (PKIII) that contains a UACUA loop motif and a protruding CrPV-like stem--loop SLIV. In vitro reconstitution experiments showed that NediV-like IRESs initiate translation from a non-AUG codon and form elongation-competent 80S ribosomal complexes in the absence of initiation factors and Met-tRNAi Met Unlike canonical IGR IRESs, NediV-like IRESs bind directly to the peptidyl (P) site of ribosomes leaving the aminoacyl (A) site accessible for decoding. The related structures of NediV-like IRESs and their common mechanism of action indicate that they exemplify a distinct class of IGR IRES.
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Affiliation(s)
- Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Kristen Lu
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
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4
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Takallou S, Puchacz N, Allard D, Said KB, Nokhbeh MR, Samanfar B, Golshani A. IRES-mediated translation in bacteria. Biochem Biophys Res Commun 2023; 641:110-115. [PMID: 36527744 DOI: 10.1016/j.bbrc.2022.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Despite the similarity in fundamental goals of translation initiation between different domains of life, it is one of the most phylogenetically diverse steps of the central dogma of molecular biology. In a classical view, the translation signals for prokaryotes and eukaryotes are distinct from each other. This idea was challenged by the finding that the Internal Ribosome Entry Site (IRES) belonging to Plautia stali intestine virus (PSIV) could bypass the domain-specific boundaries and effectively initiate translation in E. coli. This finding led us to investigate whether the ability of PSIV IRES to initiate translation in E. coli is specific to this IRES and also to study features that allow this viral IRES to mediate prokaryotic translation initiation. We observed that certain IRESs may also possess the ability to initiate E. coli translation. Our results also indicated that the structural integrity of the PSIV IRES in translation in prokaryotes does not appear to be as critical as it is in eukaryotes. We also demonstrated that two regions of the PSIV IRES with complementarity to 16S ribosomal RNA are important for the ability of this IRES to initiate translation in E. coli.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Nathalie Puchacz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Saudi Arabia.
| | | | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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5
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Roberts L, Wieden HJ. The prokaryotic activity of the IGR IRESs is mediated by ribosomal protein S1. Nucleic Acids Res 2022; 50:9355-9367. [PMID: 36039756 PMCID: PMC9458429 DOI: 10.1093/nar/gkac697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
Internal ribosome entry sites (IRESs) are RNA elements capable of initiating translation on an internal portion of a messenger RNA. The intergenic region (IGR) IRES of the Dicistroviridae virus family folds into a triple pseudoknot tertiary structure, allowing it to recruit the ribosome and initiate translation in a structure dependent manner. This IRES has also been reported to drive translation in Escherichia coli and to date is the only described translation initiation signal that functions across domains of life. Here we show that unlike in the eukaryotic context the tertiary structure of the IGR IRES is not required for prokaryotic ribosome recruitment. In E. coli IGR IRES translation efficiency is dependent on ribosomal protein S1 in conjunction with an AG-rich Shine-Dalgarno-like element, supporting a model where the translational activity of the IGR IRESs is due to S1-mediated canonical prokaryotic translation.
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Affiliation(s)
- Luc Roberts
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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6
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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7
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Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Richards CM, Qiao W, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of eS25 loss drives resistance phenotypes. Nucleic Acids Res 2020; 48:7279-7297. [PMID: 32463448 PMCID: PMC7367175 DOI: 10.1093/nar/gkaa444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.
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Affiliation(s)
- Alex G Johnson
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Yaw Shin Ooi
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wenjie Qiao
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Shizuka B Yamada
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Couthouis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jan E Carette
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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8
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Miller CM, Selvam S, Fuchs G. Fatal attraction: The roles of ribosomal proteins in the viral life cycle. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1613. [PMID: 32657002 DOI: 10.1002/wrna.1613] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/30/2022]
Abstract
Upon viral infection of a host cell, each virus starts a program to generate many progeny viruses. Although viruses interact with the host cell in numerous ways, one critical step in the virus life cycle is the expression of viral proteins, which are synthesized by the host ribosomes in conjunction with host translation factors. Here we review different mechanisms viruses have evolved to effectively seize host cell ribosomes, the roles of specific ribosomal proteins and their posttranslational modifications on viral RNA translation, or the cellular response to infection. We further highlight ribosomal proteins with extra-ribosomal function during viral infection and put the knowledge of ribosomal proteins during viral infection into the larger context of ribosome-related diseases, known as ribosomopathies. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation.
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Affiliation(s)
- Clare M Miller
- Department of Biological Sciences, University at Albany, Albany, New York, USA
| | - Sangeetha Selvam
- Department of Biological Sciences, University at Albany, Albany, New York, USA
| | - Gabriele Fuchs
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
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9
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DiGiuseppe S, Rollins MG, Astar H, Khalatyan N, Savas JN, Walsh D. Proteomic and mechanistic dissection of the poxvirus-customized ribosome. J Cell Sci 2020; 134:jcs246603. [PMID: 32467327 PMCID: PMC7358139 DOI: 10.1242/jcs.246603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
Ribosomes are often viewed as protein synthesis machines that lack intrinsic regulatory capacity. However, studies have established that ribosomes can functionally diversify through changes in the composition of, or post-translational modifications to ribosomal subunit proteins (RPs). We recently found that poxviruses phosphorylate unique sites in the RP, receptor for activated C kinase 1 (RACK1) to enhance viral protein synthesis. Here, we developed approaches for large-scale proteomic analysis of ribosomes isolated from cells infected with different viruses. Beyond RACK1, we identified additional phosphorylation events within RPS2 and RPS28 that arise during poxvirus infection, but not other viruses tested. The modified sites lie within unstructured loop domains that position around the mRNA entry and exit channel, respectively, and site-substitution mutants revealed that each modified residue contributed differently to poxvirus replication. Our findings reveal the broader extent to which poxviruses customize host ribosomes and provide new insights into how ribosomes can functionally diversify.
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Affiliation(s)
- Stephen DiGiuseppe
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Madeline G Rollins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Helen Astar
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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10
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Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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11
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Barrera A, Olguín V, Vera-Otarola J, López-Lastra M. Cap-independent translation initiation of the unspliced RNA of retroviruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194583. [PMID: 32450258 DOI: 10.1016/j.bbagrm.2020.194583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Retroviruses are a unique family of RNA viruses that utilize a virally encoded reverse transcriptase (RT) to replicate their genomic RNA (gRNA) through a proviral DNA intermediate. The provirus is permanently integrated into the host cell chromosome and is expressed by the host cell transcription, RNA processing, and translation machinery. Retroviral messenger RNAs (mRNAs) entirely resemble a cellular mRNA as they have a 5'cap structure, 5'untranslated region (UTR), an open reading frame (ORF), 3'UTR, and a 3'poly(A) tail. The primary transcription product interacts with the cellular RNA processing machinery and is spliced, exported to the cytoplasm, and translated. However, a proportion of the pre-mRNA subverts typical RNA processing giving rise to the full-length RNA. In the cytoplasm, the full-length retroviral RNA fulfills a dual role acting as mRNA and as the gRNA. Simple retroviruses generate two pools of full-length RNA, one for each purpose. However, complex retroviruses have a single pool of full-length RNA, which is destined for translation or encapsidation. As for eukaryotic mRNAs, translational control of retroviral protein synthesis is mostly exerted at the step of initiation. Interestingly, some retroviral mRNAs, both simple and complex, use a dual mechanism to initiate protein synthesis, a cap-dependent initiation mechanism, or via internal initiation using an internal ribosome entry site (IRES). In this review, we describe and discuss data regarding the molecular mechanism driving the canonical cap-dependent and IRES-mediated translation initiation for retroviral mRNA, focusing the discussion mainly on the most studied retroviral mRNA, the HIV-1 mRNA.
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Affiliation(s)
- Aldo Barrera
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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12
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LaFontaine E, Miller CM, Permaul N, Martin ET, Fuchs G. Ribosomal protein RACK1 enhances translation of poliovirus and other viral IRESs. Virology 2020; 545:53-62. [PMID: 32308198 DOI: 10.1016/j.virol.2020.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 02/09/2023]
Abstract
Viruses have evolved strategies to ensure efficient translation using host cell ribosomes and translation factors. In addition to cleaving translation initiation factors required for host cell translation, poliovirus (PV) uses an internal ribosome entry site (IRES). Recent studies suggest that viruses exploit specific ribosomal proteins to enhance translation of their viral proteins. The ribosomal protein receptor for activated C kinase 1 (RACK1), a protein of the 40S ribosomal subunit, was previously shown to mediate translation from the 5' cricket paralysis virus and hepatitis C virus IRESs. Here we found that translation of a PV dual-luciferase reporter shows a moderate dependence on RACK1. However, in the context of a viral infection we observed significantly reduced poliovirus plaque size and titers and delayed host cell translational shut-off. Our findings further illustrate the involvement of the cellular translational machinery during PV infection and how viruses usurp the function of specific ribosomal proteins.
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Affiliation(s)
- Ethan LaFontaine
- Department of Biological Sciences, University at Albany, Albany, NY, 12222, USA
| | - Clare M Miller
- Department of Biological Sciences, University at Albany, Albany, NY, 12222, USA
| | - Natasha Permaul
- Department of Biological Sciences, University at Albany, Albany, NY, 12222, USA
| | - Elliot T Martin
- Department of Biological Sciences, University at Albany, Albany, NY, 12222, USA
| | - Gabriele Fuchs
- Department of Biological Sciences, University at Albany, Albany, NY, 12222, USA; The RNA Institute, University at Albany, NY, 12222, USA.
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13
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Hui KK, Chen YK, Endo R, Tanaka M. Translation from the Ribosome to the Clinic: Implication in Neurological Disorders and New Perspectives from Recent Advances. Biomolecules 2019; 9:E680. [PMID: 31683805 PMCID: PMC6920867 DOI: 10.3390/biom9110680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
De novo protein synthesis by the ribosome and its multitude of co-factors must occur in a tightly regulated manner to ensure that the correct proteins are produced accurately at the right time and, in some cases, also in the proper location. With novel techniques such as ribosome profiling and cryogenic electron microscopy, our understanding of this basic biological process is better than ever and continues to grow. Concurrently, increasing attention is focused on how translational regulation in the brain may be disrupted during the progression of various neurological disorders. In fact, translational dysregulation is now recognized as the de facto pathogenic cause for some disorders. Novel mechanisms including ribosome stalling, ribosome-associated quality control, and liquid-liquid phase separation are closely linked to translational regulation, and may thus be involved in the pathogenic process. The relationships between translational dysregulation and neurological disorders, as well as the ways through which we may be able to reverse those detrimental effects, will be examined in this review.
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Affiliation(s)
- Kelvin K Hui
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Yi-Kai Chen
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Ryo Endo
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
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14
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Yamada SB, Gendron TF, Niccoli T, Genuth NR, Grosely R, Shi Y, Glaria I, Kramer NJ, Nakayama L, Fang S, Dinger TJI, Thoeng A, Rocha G, Barna M, Puglisi JD, Partridge L, Ichida JK, Isaacs AM, Petrucelli L, Gitler AD. RPS25 is required for efficient RAN translation of C9orf72 and other neurodegenerative disease-associated nucleotide repeats. Nat Neurosci 2019; 22:1383-1388. [PMID: 31358992 PMCID: PMC6713615 DOI: 10.1038/s41593-019-0455-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
Nucleotide repeat expansions in the C9orf72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia. Unconventional translation (RAN translation) of C9orf72 repeats generates dipeptide repeat proteins that can cause neurodegeneration. We performed a genetic screen for regulators of RAN translation and identified small ribosomal protein subunit 25 (RPS25), presenting a potential therapeutic target for C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia and other neurodegenerative diseases caused by nucleotide repeat expansions.
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Affiliation(s)
- Shizuka B Yamada
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Teresa Niccoli
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Naomi R Genuth
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yingxiao Shi
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Idoia Glaria
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
| | - Nicholas J Kramer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Neurosciences Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Nakayama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirleen Fang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tai J I Dinger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Annora Thoeng
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Gabriel Rocha
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
| | | | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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15
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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16
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Li S. Regulation of Ribosomal Proteins on Viral Infection. Cells 2019; 8:E508. [PMID: 31137833 PMCID: PMC6562653 DOI: 10.3390/cells8050508] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins (RPs), in conjunction with rRNA, are major components of ribosomes involved in the cellular process of protein biosynthesis, known as "translation". The viruses, as the small infectious pathogens with limited genomes, must recruit a variety of host factors to survive and propagate, including RPs. At present, more and more information is available on the functional relationship between RPs and virus infection. This review focuses on advancements in my own understanding of critical roles of RPs in the life cycle of viruses. Various RPs interact with viral mRNA and proteins to participate in viral protein biosynthesis and regulate the replication and infection of virus in host cells. Most interactions are essential for viral translation and replication, which promote viral infection and accumulation, whereas the minority represents the defense signaling of host cells by activating immune pathway against virus. RPs provide a new platform for antiviral therapy development, however, at present, antiviral therapeutics with RPs involving in virus infection as targets is limited, and exploring antiviral strategy based on RPs will be the guides for further study.
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Affiliation(s)
- Shuo Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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17
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Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LYL, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA. Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate. Mol Cell 2018; 73:36-47.e10. [PMID: 30503772 DOI: 10.1016/j.molcel.2018.10.032] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/04/2018] [Accepted: 10/18/2018] [Indexed: 01/13/2023]
Abstract
Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked from or linked to cellular growth rate in RP-deficient yeast cells. Ribosome deficiency was associated with altered translation of gene subclasses, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.
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MESH Headings
- Cell Proliferation
- Gene Expression Regulation, Fungal
- Mutation
- Protein Processing, Post-Translational
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Time Factors
- Transcriptome
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Affiliation(s)
- Ze Cheng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Frederick Mugler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Abdurrahman Keskin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Leon Yen-Lee Chan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH, 8093 Zurich, Switzerland
| | - Philipp Mertins
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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18
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Li S, Li X, Zhou Y. Ribosomal protein L18 is an essential factor that promote rice stripe virus accumulation in small brown planthopper. Virus Res 2018; 247:15-20. [DOI: 10.1016/j.virusres.2018.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/13/2018] [Accepted: 01/22/2018] [Indexed: 01/10/2023]
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19
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Gazon H, Barbeau B, Mesnard JM, Peloponese JM. Hijacking of the AP-1 Signaling Pathway during Development of ATL. Front Microbiol 2018; 8:2686. [PMID: 29379481 PMCID: PMC5775265 DOI: 10.3389/fmicb.2017.02686] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of a fatal malignancy known as adult T-cell leukemia (ATL). One way to address the pathology of the disease lies on conducting research with a molecular approach. In addition to the analysis of ATL-relevant signaling pathways, understanding the regulation of important and relevant transcription factors allows researchers to reach this fundamental objective. HTLV-1 encodes for two oncoproteins, Tax and HTLV-1 basic leucine-zipper factor, which play significant roles in the cellular transformation and the activation of the host's immune responses. Activating protein-1 (AP-1) transcription factor has been linked to cancer and neoplastic transformation ever since the first representative members of the Jun and Fos gene family were cloned and shown to be cellular homologs of viral oncogenes. AP-1 is a dimeric transcription factor composed of proteins belonging to the Jun (c-Jun, JunB, and JunD), Fos (c-Fos, FosB, Fra1, and Fra2), and activating transcription factor protein families. Activation of AP-1 transcription factor family by different stimuli, such as inflammatory cytokines, stress inducers, or pathogens, results in innate and adaptive immunity. AP-1 is also involved in various cellular events including differentiation, proliferation, survival, and apoptosis. Deregulated expression of AP-1 transcription factors is implicated in various lymphomas such as classical Hodgkin lymphomas, anaplastic large cell lymphomas, diffuse large B-cell lymphomas, and adult T-cell leukemia. Here, we review the current thinking behind deregulation of the AP-1 pathway and its contribution to HTLV-induced cellular transformation.
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Affiliation(s)
- Hélène Gazon
- Belgium Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, Liège, Belgium
| | - Benoit Barbeau
- Département des Sciences Biologiques and Centre de Recherche BioMed, Université du Québec à Montréal, Montréal, QC, Canada
| | - Jean-Michel Mesnard
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Jean-Marie Peloponese
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
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20
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Au HHT, Elspass VM, Jan E. Functional Insights into the Adjacent Stem-Loop in Honey Bee Dicistroviruses That Promotes Internal Ribosome Entry Site-Mediated Translation and Viral Infection. J Virol 2018; 92:e01725-17. [PMID: 29093099 PMCID: PMC5752952 DOI: 10.1128/jvi.01725-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
All viruses must successfully harness the host translational apparatus and divert it towards viral protein synthesis. Dicistroviruses use an unusual internal ribosome entry site (IRES) mechanism whereby the IRES adopts a three-pseudoknot structure that accesses the ribosome tRNA binding sites to directly recruit the ribosome and initiate translation from a non-AUG start site. A subset of dicistroviruses, including the honey bee Israeli acute paralysis virus (IAPV), encode an extra stem-loop (SLVI) 5' -adjacent to the IGR IRES. Previously, the function of this additional stem-loop is unknown. Here, we provide mechanistic and functional insights into the role of SLVI in IGR IRES translation and in virus infection. Biochemical analyses of a series of mutant IRESs demonstrated that SLVI does not function in ribosome recruitment but is required for proper ribosome positioning on the IRES to direct translation. Using a chimeric infectious clone derived from the related Cricket paralysis virus, we showed that the integrity of SLVI is important for optimal viral translation and viral yield. Based on structural models of ribosome-IGR IRES complexes, the SLVI is predicted to be in the vicinity of the ribosome E site. We propose that SLVI of IAPV IGR IRES functionally mimics interactions of an E-site tRNA with the ribosome to direct positioning of the tRNA-like domain of the IRES in the A site.IMPORTANCEViral internal ribosome entry sites are RNA elements and structures that allow some positive-sense monopartite RNA viruses to hijack the host ribosome to start viral protein synthesis. We demonstrate that a unique stem-loop structure is essential for optimal viral protein synthesis and for virus infection. Biochemical evidence shows that this viral stem-loop RNA structure impacts a fundamental property of the ribosome to start protein synthesis.
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Affiliation(s)
- Hilda H T Au
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Valentina M Elspass
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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21
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Umegawachi T, Yoshida H, Koshida H, Yamada M, Ohkawa Y, Sato T, Suyama M, Krause HM, Yamaguchi M. Control of tissue size and development by a regulatory element in the yorkie 3'UTR. Am J Cancer Res 2017; 7:673-687. [PMID: 28401020 PMCID: PMC5385651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 06/07/2023] Open
Abstract
Regulation of the Hippo pathway via phosphorylation of Yorkie (Yki), the Drosophila homolog of human Yes-associated protein 1, is conserved from Drosophila to humans. Overexpression of a non-phosphorylatable form of Yki induces severe overgrowth in adult fly eyes. Here, we show that yki mRNA associates with microsomal fractions and forms foci that partially colocalize to processing bodies in the vicinity of endoplasmic reticulum. This localization is dependent on a stem-loop (SL) structure in the 3' untranslated region of yki. Surprisingly, expression of SL deleted yki in eye imaginal discs also results in severe overgrowth phenotypes. When the structure of the SL is disrupted, Yki protein levels increase without a significant effect on RNA levels. When the SL is completely removed, protein levels drastically increase, but in this case, due to increased RNA stability. In the latter case, we show that the increased RNA accumulation is due to removal of a putative miR-8 seed sequence in the SL. These data demonstrate the function of two novel regulatory mechanisms, both controlled by the yki SL element, that are essential for proper Hippo pathway mediated growth regulation.
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Affiliation(s)
- Takanari Umegawachi
- Department of Applied Biology, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- The Center for Advanced Insect Research Promotion, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hiromu Koshida
- Department of Applied Biology, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Momoko Yamada
- Department of Applied Biology, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yasuyuki Ohkawa
- Medical Institute of Bioregulation, Kyushu UniversityFukuoka 812-8582, Japan
| | - Tetsuya Sato
- Medical Institute of Bioregulation, Kyushu UniversityFukuoka 812-8582, Japan
| | - Mikita Suyama
- Medical Institute of Bioregulation, Kyushu UniversityFukuoka 812-8582, Japan
| | - Henry M Krause
- Banting and Best Department of Medical Research, University of TorontoToronto, Ontario M5G 1L6, Canada
- Department of Molecular Genetics, University of TorontoToronto, Ontario M5G 1L6, Canada
- Donnelly Centre, University of TorontoToronto, Ontario M5G 1L6, Canada
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- The Center for Advanced Insect Research Promotion, Kyoto Institute of TechnologyMatsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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22
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Molecular analysis of the factorless internal ribosome entry site in Cricket Paralysis virus infection. Sci Rep 2016; 6:37319. [PMID: 27853311 PMCID: PMC5112510 DOI: 10.1038/srep37319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/27/2016] [Indexed: 11/09/2022] Open
Abstract
The dicistrovirus Cricket Paralysis virus contains a unique dicistronic RNA genome arrangement, encoding two main open reading frames that are driven by distinct internal ribosome entry sites (IRES). The intergenic region (IGR) IRES adopts an unusual structure that directly recruits the ribosome and drives translation of viral structural proteins in a factor-independent manner. While structural, biochemical, and biophysical approaches have provided mechanistic details into IGR IRES translation, these studies have been limited to in vitro systems and little is known about the behavior of these IRESs during infection. Here, we examined the role of previously characterized IGR IRES mutations on viral yield and translation in CrPV-infected Drosophila S2 cells. Using a recently generated infectious CrPV clone, introduction of a subset of mutations that are known to disrupt IRES activity failed to produce virus, demonstrating the physiological relevance of specific structural elements within the IRES for virus infection. However, a subset of mutations still led to virus production, thus revealing the key IRES-ribosome interactions for IGR IRES translation in infected cells, which highlights the importance of examining IRES activity in its physiological context. This is the first study to examine IGR IRES translation in its native context during virus infection.
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23
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Fahl SP, Wang M, Zhang Y, Duc ACE, Wiest DL. Regulatory Roles of Rpl22 in Hematopoiesis: An Old Dog with New Tricks. Crit Rev Immunol 2016; 35:379-400. [PMID: 26853850 DOI: 10.1615/critrevimmunol.v35.i5.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribosomal proteins have long been known to serve critical roles in facilitating the biogenesis of the ribosome and its ability to synthesize proteins. However, evidence is emerging that suggests ribosomal proteins are also capable of performing tissue-restricted, regulatory functions that impact normal development and pathological conditions, including cancer. The challenge in studying such regulatory functions is that elimination of many ribosomal proteins also disrupts ribosome biogenesis and/or function. Thus, it is difficult to determine whether developmental abnormalities resulting from ablation of a ribosomal protein result from loss of core ribosome functions or from loss of the regulatory function of the ribosomal protein. Rpl22, a ribosomal protein component of the large 60S subunit, provides insight into this conundrum; Rpl22 is dispensable for both ribosome biogenesis and protein synthesis yet its ablation causes tissue-restricted disruptions in development. Here we review evidence supporting the regulatory functions of Rpl22 and other ribosomal proteins.
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Affiliation(s)
- Shawn P Fahl
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anne-Cecile E Duc
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
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24
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Dengue virus NS1 protein interacts with the ribosomal protein RPL18: This interaction is required for viral translation and replication in Huh-7 cells. Virology 2015; 484:113-126. [DOI: 10.1016/j.virol.2015.05.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/22/2015] [Accepted: 05/24/2015] [Indexed: 01/06/2023]
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25
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Joseph AP, Bhat P, Das S, Srinivasan N. Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA. RNA Biol 2015; 11:891-905. [PMID: 25268799 DOI: 10.4161/rna.29545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.
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Affiliation(s)
- Agnel Praveen Joseph
- Molecular Biophysics Unit. Indian Institute of Science, Bangalore, India; Present address: Science and Technology Facilities Council, RAL, Harwell, Didcot, UK
| | - Prasanna Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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26
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Affiliation(s)
- Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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27
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Zhou X, Liao WJ, Liao JM, Liao P, Lu H. Ribosomal proteins: functions beyond the ribosome. J Mol Cell Biol 2015; 7:92-104. [PMID: 25735597 DOI: 10.1093/jmcb/mjv014] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/05/2014] [Indexed: 01/05/2023] Open
Abstract
Although ribosomal proteins are known for playing an essential role in ribosome assembly and protein translation, their ribosome-independent functions have also been greatly appreciated. Over the past decade, more than a dozen of ribosomal proteins have been found to activate the tumor suppressor p53 pathway in response to ribosomal stress. In addition, these ribosomal proteins are involved in various physiological and pathological processes. This review is composed to overview the current understanding of how ribosomal stress provokes the accumulation of ribosome-free ribosomal proteins, as well as the ribosome-independent functions of ribosomal proteins in tumorigenesis, immune signaling, and development. We also propose the potential of applying these pieces of knowledge to the development of ribosomal stress-based cancer therapeutics.
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Affiliation(s)
- Xiang Zhou
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wen-Juan Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jun-Ming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Peng Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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28
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Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature 2015; 519:110-3. [PMID: 25652826 PMCID: PMC4352134 DOI: 10.1038/nature14219] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022]
Abstract
The central dogma of gene expression (DNA→RNA→protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive1,2. However, the core structures and conformational dynamics of ribosomes that are responsible for the steps of translation following initiation are ancient and conserved across the domains of life3,4. We asked whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here, we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by tRNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence as an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.
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Graifer D, Karpova G. Roles of ribosomal proteins in the functioning of translational machinery of eukaryotes. Biochimie 2015; 109:1-17. [DOI: 10.1016/j.biochi.2014.11.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
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Au HHT, Jan E. Novel viral translation strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:779-801. [PMID: 25045163 PMCID: PMC7169809 DOI: 10.1002/wrna.1246] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/03/2014] [Accepted: 05/08/2014] [Indexed: 01/06/2023]
Abstract
Viral genomes are compact and encode a limited number of proteins. Because they do not encode components of the translational machinery, viruses exhibit an absolute dependence on the host ribosome and factors for viral messenger RNA (mRNA) translation. In order to recruit the host ribosome, viruses have evolved unique strategies to either outcompete cellular transcripts that are efficiently translated by the canonical translation pathway or to reroute translation factors and ribosomes to the viral genome. Furthermore, viruses must evade host antiviral responses and escape immune surveillance. This review focuses on some recent major findings that have revealed unconventional strategies that viruses utilize, which include usurping the host translational machinery, modulating canonical translation initiation factors to specifically enhance or repress overall translation for the purpose of viral production, and increasing viral coding capacity. The discovery of these diverse viral strategies has provided insights into additional translational control mechanisms and into the viral host interactions that ensure viral protein synthesis and replication. WIREs RNA 2014, 5:779–801. doi: 10.1002/wrna.1246 This article is categorized under:
Translation > Translation Mechanisms Translation > Translation Regulation
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Affiliation(s)
- Hilda H T Au
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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31
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Fernández IS, Bai XC, Murshudov G, Scheres SHW, Ramakrishnan V. Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Cell 2014; 157:823-31. [PMID: 24792965 PMCID: PMC4017093 DOI: 10.1016/j.cell.2014.04.015] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/14/2014] [Accepted: 04/11/2014] [Indexed: 01/04/2023]
Abstract
The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation. The high-resolution structure of CrPV-IRES bound to the ribosome was solved by cryoEM Pseudoknot I of CrPV-IRES binds in the decoding center, thus blocking the A site CrPV-IRES mimics a pretranslocation rather than initiation complex of the ribosome Translocation of CrPV-IRES by eEF2 is required for the start of translation
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Affiliation(s)
- Israel S Fernández
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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32
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Mallo M, Alonso CR. The regulation of Hox gene expression during animal development. Development 2013; 140:3951-63. [PMID: 24046316 DOI: 10.1242/dev.068346] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hox genes encode a family of transcriptional regulators that elicit distinct developmental programmes along the head-to-tail axis of animals. The specific regional functions of individual Hox genes largely reflect their restricted expression patterns, the disruption of which can lead to developmental defects and disease. Here, we examine the spectrum of molecular mechanisms controlling Hox gene expression in model vertebrates and invertebrates and find that a diverse range of mechanisms, including nuclear dynamics, RNA processing, microRNA and translational regulation, all concur to control Hox gene outputs. We propose that this complex multi-tiered regulation might contribute to the robustness of Hox expression during development.
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Affiliation(s)
- Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
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The DNA virus white spot syndrome virus uses an internal ribosome entry site for translation of the highly expressed nonstructural protein ICP35. J Virol 2013; 87:13263-78. [PMID: 24089551 DOI: 10.1128/jvi.01732-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although shrimp white spot syndrome virus (WSSV) is a large double-stranded DNA virus (∼300 kbp), it expresses many polycistronic mRNAs that are likely to use internal ribosome entry site (IRES) elements for translation. A polycistronic mRNA encodes the gene of the highly expressed nonstructural protein ICP35, and here we use a dual-luciferase assay to demonstrate that this protein is translated cap independently by an IRES element located in the 5' untranslated region of icp35. A deletion analysis of this region showed that IRES activity was due to stem-loops VII and VIII. A promoterless assay, a reverse transcription-PCR together with quantitative real-time PCR analysis, and a stable stem-loop insertion upstream of the Renilla luciferase open reading frame were used, respectively, to rule out the possibility that cryptic promoter activity, abnormal splicing, or read-through was contributing to the IRES activity. In addition, a Northern blot analysis was used to confirm that only a single bicistronic mRNA was expressed. The importance of ICP35 to viral replication was demonstrated in a double-stranded RNA (dsRNA) interference knockdown experiment in which the mortality of the icp35 dsRNA group was significantly reduced. Tunicamycin was used to show that the α subunit of eukaryotic initiation factor 2 is required for icp35 IRES activity. We also found that the intercalating drug quinacrine significantly inhibited icp35 IRES activity in vitro and reduced the mortality rate and viral copy number in WSSV-challenged shrimp. Lastly, in Sf9 insect cells, we found that knockdown of the gene for the Spodoptera frugiperda 40S ribosomal protein RPS10 decreased icp35 IRES-regulated firefly luciferase activity but had no effect on cap-dependent translation.
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Boncristiani HF, Evans JD, Chen Y, Pettis J, Murphy C, Lopez DL, Simone-Finstrom M, Strand M, Tarpy DR, Rueppell O. In vitro infection of pupae with Israeli acute paralysis virus suggests disturbance of transcriptional homeostasis in honey bees (Apis mellifera). PLoS One 2013; 8:e73429. [PMID: 24039938 PMCID: PMC3764161 DOI: 10.1371/journal.pone.0073429] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 07/19/2013] [Indexed: 01/08/2023] Open
Abstract
The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. The infected pupae developed pronounced but variable patterns of disease. Symptoms varied from complete cessation of development with no visual evidence of disease to rapid darkening of a part or the entire body. Considerable differences in IAPV titer dynamics were observed, suggesting significant variation in resistance to IAPV among and possibly within honey bee colonies. Thus, selective breeding for virus resistance should be possible. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. These results provide first insights into the mechanisms of IAPV pathogenicity. They mirror a transcriptional survey of honey bees afflicted with Colony Collapse Disorder and thus support the hypothesis that viruses play a critical role in declining honey bee health.
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Affiliation(s)
- Humberto F. Boncristiani
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
- * E-mail:
| | - Jay D. Evans
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Yanping Chen
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Jeff Pettis
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Charles Murphy
- Soybean Genomics and Improvement, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Dawn L. Lopez
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Michael Simone-Finstrom
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Micheline Strand
- United States Army Research Office, Division of Life Sciences, Research Triangle Park, North Carolina, United States of America
| | - David R. Tarpy
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
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Xu XF, Xin Y, Zhang Y, Huang YM, Li WB, Li N, Lin Z, Zhou YJ, Zhang ZG. Expression of lymphocyte coding genes in peripheral blood and lymphocyte infiltration in cardiac tissues influenced by cyclosporin A in heterotopic heart transplantation model in rats. Transpl Immunol 2013; 29:82-7. [PMID: 23851154 DOI: 10.1016/j.trim.2013.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/24/2013] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
Abstract
UNLABELLED To systematically compare the expression of coding genes with pathological changes of transplanted cardiac tissue and peripheral blood lymphocytes in an allo-heterotopic rat cardiac transplant model. Using SD rats as donors and Wistar rats as recipients, animals were divided into two groups, control and cyclosporine A intervention plus heart transplant groups. After transplant at 1, 3, 7, 10 and 12d, we assessed the ability of lymphocytes to infiltrate into cardiac tissues and levels of leukocyte coding genes in peripheral blood. Histopathological changes were monitored in cardiac tissue to determine the level of transplant rejection. RESULTS (1) 24h after transplant peripheral blood lymphocytes' transcription and expression were temporarily reduced. (2) CD4(+) and CD8(+) lymphocytes infiltrate into cardiac tissue and Grade 1R pathological changes were observed 3d-7d after heart transplant. (3)Cyclosporine A was not able to completely block heart transplant rejection.(4) Although cyclosporine A was not able to effectively suppress CD4(+) T cell gene expression, it did suppress CD8(+) T cell gene transcription. (5) Cyclosporine A did not effectively reduce the rapid infiltration of CD4(+) or CD8(+) infiltration in 3d, but significantly reduced the degree of CD4(+) T cell infiltration in cardiac tissues between 3 and 7d. (6) Differential display (DD-PCR): Graft control group: there were differences in 2,3-bisphosphoglycerate, ribosomal protein S25, 12S ribosomal, gig18, MHC-III and ATPase H(+), which occurred 24h before CD4/CD8 surface protein expression. Cyclosporine A group: there were differences in thrombospondin-1, TCR, 2,3-bisphosphoglycerate, sodium channel beta-1, gig18 and TCR. In the cyclosporine A group 2,3-bisphosphoglycerate positive expression was observed 24h after the control group, which indicates that cyclosporine A slowed down the 2,3-bisphosphoglycerate transcription rate in peripheral lymphocytes and delayed its expression time. Cyclosporine A also suppressed gig18 transcription in peripheral lymphocytes. After 24h, sodium channel beta-1 was positively expressed in the cyclosporine A group. The relationship between molecular surface receptor expression and coding genes in cardiac tissue and peripheral blood after transplant indicates that early detection of acute rejection and anti-rejection drugs' curative effect can be assessed.
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Affiliation(s)
- Xiu-fang Xu
- Department of Molecular Biology, Capital Medical University Affiliated with Beijing Anzhen Hospital, Beijing Institute of Heart, Lung & Blood Vessel Diseases, Beijing 100029, PR China
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36
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Specialization from synthesis: How ribosome diversity can customize protein function. FEBS Lett 2013; 587:1189-97. [DOI: 10.1016/j.febslet.2013.02.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 11/20/2022]
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37
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Au HHT, Jan E. Insights into factorless translational initiation by the tRNA-like pseudoknot domain of a viral IRES. PLoS One 2012; 7:e51477. [PMID: 23236506 PMCID: PMC3517527 DOI: 10.1371/journal.pone.0051477] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/05/2012] [Indexed: 01/22/2023] Open
Abstract
The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors. The pseudoknot I (PKI) domain of the IRES mimics a tRNA-like codon:anticodon interaction in the ribosomal P site to direct translation initiation from a non-AUG initiation codon in the A site. In this study, we have performed a comprehensive mutational analysis of this region to delineate the molecular parameters that drive IRES translation. We demonstrate that IRES-mediated translation can initiate at an alternate adjacent and overlapping start site, provided that basepairing interactions within PKI remain intact. Consistent with this, IGR IRES translation tolerates increases in the variable loop region that connects the anticodon- and codon-like elements within the PKI domain, as IRES activity remains relatively robust up to a 4-nucleotide insertion in this region. Finally, elements from an authentic tRNA anticodon stem-loop can functionally supplant corresponding regions within PKI. These results verify the importance of the codon:anticodon interaction of the PKI domain and further define the specific elements within the tRNA-like domain that contribute to optimal initiator Met-tRNAi-independent IRES translation.
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Affiliation(s)
- Hilda H. T. Au
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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38
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A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs. Proc Natl Acad Sci U S A 2012; 110:324-9. [PMID: 23169626 DOI: 10.1073/pnas.1216454109] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Initiation is the primary target of translational control for all organisms. Regulation of eukaryotic translation is traditionally thought to occur through initiation factors and RNA structures. Here, we characterize a transcript-specific translation initiation mechanism that is mediated by the ribosome. By studying vesicular stomatitis virus (VSV), we identify the large ribosomal subunit protein rpL40 as requisite for VSV cap-dependent translation but not bulk cellular or internal ribosome entry site-driven translation. This requirement is conserved among members of the order Mononegavirales, including measles virus and rabies virus. Polysome analyses and in vitro reconstitution of initiation demonstrate that rpL40 is required for 80S formation on VSV mRNAs through a cis-regulatory element. Using deep sequencing, we further uncover a subset of cellular transcripts that are selectively sensitive to rpL40 depletion, suggesting VSV may have usurped an endogenous translation pathway. Together, these findings demonstrate that the ribosome acts as a translational regulator outside of its catalytic role during protein synthesis.
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39
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Thompson SR. Tricks an IRES uses to enslave ribosomes. Trends Microbiol 2012; 20:558-66. [PMID: 22944245 DOI: 10.1016/j.tim.2012.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/01/2012] [Accepted: 08/09/2012] [Indexed: 02/05/2023]
Abstract
In eukaryotes, mRNAs are primarily translated through a cap-dependent mechanism whereby initiation factors recruit the 40S ribosomal subunit to a cap structure at the 5' end of the mRNA. However, some viral and cellular messages initiate protein synthesis without a cap. They use a structured RNA element termed an internal ribosome entry site (IRES) to recruit the 40S ribosomal subunit. IRESs were discovered over 20 years ago, but only recently have studies using a model IRES from dicistroviruses expanded our understanding of how a 3D RNA structure can capture and manipulate the ribosome to initiate translation.
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Affiliation(s)
- Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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40
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Puglisi I, Faedda R, Sanzaro V, Lo Piero AR, Petrone G, Cacciola SO. Identification of differentially expressed genes in response to mercury I and II stress in Trichoderma harzianum. Gene 2012; 506:325-30. [PMID: 22789863 DOI: 10.1016/j.gene.2012.06.091] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/26/2012] [Accepted: 06/27/2012] [Indexed: 10/28/2022]
Abstract
Filamentous fungi are very promising organisms in both the control and the reduction of the amount of heavy metal released by human and industrial activities. In particular, Trichoderma harzianum demonstrated to be tolerant towards different heavy metals, such as mercury and cadmium, even though the mechanism underlying this tolerance is not fully understood. By using a particular strategy of the suppression subtractive hybridization technique, we were able to identify in the strain IMI 393899 of T. harzianum eight different genes up-regulated in the presence of mercury II with respect to cadmium. Among the genes identified, a possible role in the tolerance mechanism could be envisaged for hydrophobin, due to its ability to dissolve hydrophobic molecules into aqueous media. We also show that IMI 393899 grows at the same rate of control culture in the presence of mercury I and that all eight genes isolated were also up-regulated in this condition.
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Affiliation(s)
- Ivana Puglisi
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, University of Catania, Italy
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41
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Zhang X, Wang W, Wang H, Wang MH, Xu W, Zhang R. Identification of ribosomal protein S25 (RPS25)-MDM2-p53 regulatory feedback loop. Oncogene 2012; 32:2782-91. [PMID: 22777350 DOI: 10.1038/onc.2012.289] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
There is an increasing interest in determining the role of ribosomal proteins (RPs) in the regulation of MDM2-p53 pathway in coordinating cellular response to stress. Herein, we report a novel regulatory role of ribosomal protein S25 (RPS25) in MDM2-mediated p53 degradation and a feedback regulation of S25 by p53. We demonstrated that S25 interacted with MDM2 and inhibited its E3 ligase activity, resulting in the reduction of MDM2-mediated p53 ubiquitination and the stabilization and activation of p53. S25, MDM2 and p53 formed a ternary complex following ribosomal stress. The nucleolar localization and MDM2-binding domains of S25 were critical for its role in MDM2-mediated p53 regulation. Knockdown of S25 by siRNA attenuated the induction and activation of p53 following ribosomal stress. S25 stabilized and cooperated with MDMX to regulate MDM2 E3 ligase activity. Furthermore, S25 was identified to be a transcriptional target of p53; p53 directly bound to S25 promoter and suppressed S25 expression. Our results suggest that there is a S25-MDM2-p53 regulatory feedback loop, which may have an important role in cancer development and progression.
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Affiliation(s)
- X Zhang
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center, School of Pharmacy, Amarillo, TX 79106, USA
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42
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Kondrashov N, Pusic A, Stumpf CR, Shimizu K, Hsieh AC, Ishijima J, Shiroishi T, Barna M. Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell 2011; 145:383-397. [PMID: 21529712 DOI: 10.1016/j.cell.2011.03.028] [Citation(s) in RCA: 425] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 10/16/2010] [Accepted: 03/15/2011] [Indexed: 12/27/2022]
Abstract
Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than regulatory capacity in mRNA translation. Here we identify mutations of the Ribosomal Protein L38 (Rpl38) gene in mice exhibiting surprising tissue-specific patterning defects, including pronounced homeotic transformations of the axial skeleton. In Rpl38 mutant embryos, global protein synthesis is unchanged; however the translation of a select subset of Homeobox mRNAs is perturbed. Our data reveal that RPL38 facilitates 80S complex formation on these mRNAs as a regulatory component of the ribosome to confer transcript-specific translational control. We further show that Rpl38 expression is markedly enriched in regions of the embryo where loss-of-function phenotypes occur. Unexpectedly, a ribosomal protein (RP) expression screen reveals dynamic regulation of individual RPs within the vertebrate embryo. Collectively, these findings suggest that RP activity may be highly regulated to impart a new layer of specificity in the control of gene expression and mammalian development.
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Affiliation(s)
- Nadya Kondrashov
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, San Francisco, San Francisco, California
| | - Aya Pusic
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, San Francisco, San Francisco, California
| | - Craig R Stumpf
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, San Francisco, San Francisco, California
| | - Kunihiko Shimizu
- Department of Pediatric Dentistry, Nihon University School of Dentistry at Matsudo, Chiba 271-8587, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Mishima Shizuoka-ken 411-8540, Japan
| | - Andrew C Hsieh
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, San Francisco, San Francisco, California.,Division of Hematology/Oncology, University of California, San Francisco, San Francisco, California
| | - Junko Ishijima
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima Shizuoka-ken 411-8540, Japan
| | - Toshihiko Shiroishi
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima Shizuoka-ken 411-8540, Japan
| | - Maria Barna
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, San Francisco, San Francisco, California
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43
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Burks JM, Zwieb C, Müller F, Wower IK, Wower J. In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses. Arch Virol 2011; 156:1737-47. [PMID: 21681504 DOI: 10.1007/s00705-011-1043-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 05/26/2011] [Indexed: 02/05/2023]
Abstract
Foot-and-mouth disease virus (FMDV) uses an internal ribosome entry site (IRES), a highly structured segment of its genomic RNA, to hijack the translational apparatus of an infected host. Computational analysis of 162 type II picornavirus IRES RNA sequences yielded secondary structures that included only base pairs supported by comparative or experimental evidence. The deduced helical sections provided the foundation for a hypothetical three-dimensional model of FMDV IRES RNA. The model was further constrained by incorporation of data derived from chemical modification and enzymatic probing of IRES RNAs as well as high-resolution information about IRES RNA-bound proteins.
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Affiliation(s)
- Jody M Burks
- Department of Animal Sciences, Auburn University, 210 Upchurch Hall, Auburn, AL 36849-5415, USA
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44
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Hertz MI, Thompson SR. In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites. Nucleic Acids Res 2011; 39:7276-88. [PMID: 21646337 PMCID: PMC3167618 DOI: 10.1093/nar/gkr427] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Some viral and cellular messages use an alternative mechanism to initiate protein synthesis that involves internal recruitment of the ribosome to an internal ribosome entry site (IRES). The Dicistroviridae intergenic regions (IGR) have been studied as model IRESs to understand the mechanism of IRES-mediated translation. In this study, the in vivo activity of IGR IRESs were compared. Our analysis demonstrates that Class I and II IGR IRESs have comparable translation efficiency in yeast and that Class II is significantly more active in mammalian cells. Furthermore, while Class II IGR IRES activity was enhanced in yeast grown at a higher temperature, temperature did not affect IGR IRES activity in mammalian cells. This suggests that Class II IRESs may not function optimally with yeast ribosomes. Examination of chimeric IGR IRESs, established that the IRES strength and temperature sensitivity are mediated by the ribosome binding domain. In addition, the sequence of the first translated codon is also an important determinant of IRES activity. Our findings provide us with a comprehensive overview of IGR IRES activities and allow us to begin to understand the differences between Classes I and II IGR IRESs.
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Affiliation(s)
- Marla I Hertz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Muhs M, Yamamoto H, Ismer J, Takaku H, Nashimoto M, Uchiumi T, Nakashima N, Mielke T, Hildebrand PW, Nierhaus KH, Spahn CMT. Structural basis for the binding of IRES RNAs to the head of the ribosomal 40S subunit. Nucleic Acids Res 2011; 39:5264-75. [PMID: 21378123 PMCID: PMC3130280 DOI: 10.1093/nar/gkr114] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Some viruses exploit internal initiation for their propagation in the host cell. This type of initiation is facilitated by structured elements (internal ribosome entry site, IRES) upstream of the initiator AUG and requires only a reduced number of canonical initiation factors. An important example are IRES of the virus family Dicistroviridae that bind to the inter-subunit side of the small ribosomal 40S subunit and lead to the formation of elongation-competent 80S ribosomes without the help of any initiation factor. Here, we present a comprehensive functional and structural analysis of eukaryotic-specific ribosomal protein rpS25 in the context of this type of initiation and propose a structural model explaining the essential involvement of rpS25 for hijacking the ribosome.
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Affiliation(s)
- Margarita Muhs
- Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany
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46
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Mechanism of translation initiation by Dicistroviridae IGR IRESs. Virology 2011; 411:355-61. [PMID: 21284991 DOI: 10.1016/j.virol.2011.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 01/04/2011] [Indexed: 01/02/2023]
Abstract
The Dicistroviridae is a growing virus family characterized by a dicistronic genome, wherein each open reading frame (ORF) is translated from an independent internal ribosome entry site (IRES). The 5' IRES that translates the first open reading frame (ORF1) is similar to the picornaviral IRESs. However the second IRES, referred to as the intergenic region (IGR) IRES, - translates ORF2 by and uses an unusual mechanism of initiating protein synthesis. It folds into a compact RNA structure that can bind directly to 40S ribosomal subunits and form 80S complexes to initiate translation in the absence of any initiation factors. Despite its unusual mechanism, the IGR IRES has proven to be an elegant model for elucidating initiation mechanisms employed by IRESs, as well as making it a powerful research tool with diverse applications.
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47
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Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Söding J, Westhof E, Wilson DN, Beckmann R. Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A 2010; 107:19754-9. [PMID: 20974910 PMCID: PMC2993421 DOI: 10.1073/pnas.1010005107] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
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Affiliation(s)
- Jean-Paul Armache
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Alexander Jarasch
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Andreas M. Anger
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Elizabeth Villa
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Thomas Becker
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Shashi Bhushan
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Fabrice Jossinet
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Michael Habeck
- Department of Empirical Inference, Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 Tübingen, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Gülcin Dindar
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Sibylle Franckenberg
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Viter Marquez
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
- Institut für Medizinische Physik und Biophysik, Charité, Ziegelstrasse 5-8, 10117 Berlin, Germany; and
| | - Michael Thomm
- Universität Regensburg, Lehrstuhl für Mikrobiologie, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Otto Berninghausen
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Birgitta Beatrix
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Johannes Söding
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Daniel N. Wilson
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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48
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Jang CJ, Jan E. Modular domains of the Dicistroviridae intergenic internal ribosome entry site. RNA (NEW YORK, N.Y.) 2010; 16:1182-1195. [PMID: 20423979 PMCID: PMC2874170 DOI: 10.1261/rna.2044610] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/16/2010] [Indexed: 05/29/2023]
Abstract
The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae viral family can directly assemble 80S ribosomes and initiate translation at a non-AUG codon from the ribosomal A-site. These functions are directed by two independently folded domains of the IGR IRES. One domain, composed of overlapping pseudoknots II and III (PKII/III), mediates ribosome recruitment. The second domain, composed of PKI, mimics a tRNA anticodon-codon interaction to position the ribosome at the ribosomal A-site. Although adopting a common secondary structure, the dicistrovirus IGR IRESs can be grouped into two classes based on distinct features within each domain. In this study, we report on the modularity of the IGR IRESs and show that the ribosome-binding domain and the tRNA anticodon mimicry domain are functionally interchangeable between the Type I and the Type II IGR IRESs. Using structural probing, ribosome-binding assays, and ribosome positioning analysis by toeprinting assays, we show that the chimeric IRESs fold properly, assemble 80S ribosomes, and can mediate IRES translation in rabbit reticulocyte lysates. We also demonstrate that the chimeric IRESs can stimulate the ribosome-dependent GTPase activity of eEF2, which suggests that the ribosome is primed for a step downstream from IRES binding. Overall, the results demonstrate that the dicistrovirus IGR IRESs are composed of two modular domains that work in concert to manipulate the ribosome and direct translation initiation.
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Affiliation(s)
- Christopher J Jang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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49
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Landry DM, Hertz MI, Thompson SR. RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev 2009; 23:2753-64. [PMID: 19952110 PMCID: PMC2788332 DOI: 10.1101/gad.1832209] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 10/06/2009] [Indexed: 02/05/2023]
Abstract
Most eukaryotic mRNAs are translated using a cap-dependent mechanism of translation. However, approximately 10% of mammalian mRNAs initiate translation using a cap-independent mechanism that is not well understood. These mRNAs contain an internal ribosome entry site (IRES) located in the 5' untranslated region. The cricket paralysis virus (CrPV) intergenic region IRES (IGR IRES) functions in yeast, mammals, and plants, and does not require any translation initiation factors. We used yeast genetics to understand how ribosomes are recruited directly to the mRNA by an IRES. We found that Rps25p has an essential role in CrPV IGR IRES activity in yeast and mammalian cells but not in cap-dependent translation. Purified 40S ribosomal subunits lacking Rps25 are unable to bind to the IGR IRES in vitro. The hepatitis C virus (HCV) IRES also requires Rps25, demonstrating the function of Rps25 is conserved across IRES types. Yeast strains lacking Rps25 exhibit only slight defects in global translation, readthrough, ribosome biogenesis, and programmed ribosomal frameshifting. This work is the first demonstration of a ribosomal protein that is specifically required for IRES-mediated translation initiation. Our findings provide us with the beginnings of a model for the molecular interactions of an IRES with the ribosome.
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Affiliation(s)
- Dori M. Landry
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Marla I. Hertz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Sunnie R. Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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50
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Pfingsten JS, Castile AE, Kieft JS. Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol 2009; 395:205-17. [PMID: 19878683 DOI: 10.1016/j.jmb.2009.10.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/15/2009] [Accepted: 10/21/2009] [Indexed: 11/19/2022]
Abstract
Dicistroviridae intergenic region (IGR) internal ribosome entry site(s) (IRES) RNAs drive a cap-independent pathway of translation initiation, recruiting both small and large ribosomal subunits to viral RNA without the use of any canonical translation initiation factors. This ability is conferred by the folded three-dimensional structure of the IRES RNA, which has been solved by X-ray crystallography. Here, we report the chemical probing of Plautia stali intestine virus IGR IRES in the unbound form, in the 40S-subunit-bound form, and in the 80S-ribosome-bound form. The results, when combined with an analysis of crystal structures, suggest that parts of the IRES RNA change structure as the preinitiation complex forms. Using mutagenesis coupled with native gel electrophoresis, preinitiation complex assembly assays, and translation initiation assays, we show that these potentially structurally dynamic elements of the IRES are involved in different steps in the pathway of ribosome recruitment and translation initiation. Like tRNAs, it appears that the IGR IRES undergoes local structural changes that are coordinated with structural changes in the ribosome, and these are critical for the IRES mechanism of action.
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Affiliation(s)
- Jennifer S Pfingsten
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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