Conserved Element of the Dicistrovirus IGR IRES that Mimics an E-site tRNA/Ribosome Interaction Mediates Multiple Functions

Jang, Christopher J.; Lo, Miranda C.Y.; Jan, Eric

doi:10.1016/j.jmb.2009.01.042

Cited by 39 publications

(76 citation statements)

References 48 publications

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“…This has led to the hypothesis that distinct domains of the IRES interact with specific regions of the ribosome to direct IRES translation. Consistent with this, structural and biochemical studies have revealed that SLIV and SLV interact with rpS5 and rpS25 to mediate 40S binding, whereas the conserved L1.1 region is predicted to interact with the L1 stalk of the 60S subunit to direct 80S assembly (Pfingsten et al 2006(Pfingsten et al , 2010Schuler et al 2006;Nishiyama et al 2007;Costantino et al 2008;Jang et al 2009;Landry et al 2009). The L1.1 region is disordered in the unbound IRES, suggesting that this region is dynamic (Jan and Sarnow 2002;Pfingsten et al 2006Pfingsten et al , 2007Schuler et al 2006).…”

Section: Introductionmentioning

confidence: 70%

“…The L1.1 region is disordered in the unbound IRES, suggesting that this region is dynamic (Jan and Sarnow 2002;Pfingsten et al 2006Pfingsten et al , 2007Schuler et al 2006). Mutations within the L1.1 region disrupt IRES function and 80S assembly, indicating that specific nucleotides interact with the L1 stalk, thus contributing to 80S affinity (Pfingsten et al 2006(Pfingsten et al , 2010Jang et al 2009). …”

Section: Introductionmentioning

confidence: 99%

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Modular domains of the Dicistroviridae intergenic internal ribosome entry site

Jang¹,

Jan²

2010

RNA

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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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Section: Introductionmentioning

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Modular domains of the Dicistroviridae intergenic internal ribosome entry site

Jang¹,

Jan²

2010

RNA

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“…Although uncommon, there are examples of transcripts with specific requirement for large subunit proteins during translation initiation. For example, during initiation on the CrPV IRES, the RNA must associate with rpL1 for subunit joining of the 60S to the 40S and correct ribosome positioning (43,44). Furthermore, by studying mice with a short tail phenotype, rpL38 was found to be required for 80S formation on Homeobox mRNAs and thus correct tissue patterning during development (45).…”

Section: Discussionmentioning

confidence: 99%

A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs

Lee

Burdeinick-Kerr

Whelan

2012

Proc. Natl. Acad. Sci. U.S.A.

151

142

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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.ribosome code | rhabdovirus | alternative translation | uba52 | paramyxovirus T ranslation initiation in eukaryotes proceeds generally by a cap-dependent scanning mechanism. The rate-limiting step in this process is recognition of the 5′ m 7 GpppN mRNA cap structure by eukaryotic translation initiation factor 4E (eIF4E) (1). The cap-binding complex recruits the small 40S subunit in complex with initiation factors, which then scans along the mRNA until it reaches the initiation codon AUG. Start codon recognition causes the release of the initiation factors, and the large 60S subunit joins, forming an elongation competent 80S complex (2, 3).The study of viral gene expression has uncovered several exceptions to this general mechanism of translation initiation. Poliovirus mRNA contains an ∼750-nt highly structured 5′ UTR that directly recruits the ribosome to an internal RNA site independently of the cap-recognition complex (4). Such internal ribosome entry sites (IRESs) are present in many RNA viruses, and those used by members of the Dicistroviridae family, including Plautia stali intestine virus and cricket paralysis virus, remarkably do not require any initiation factors or the initiating methionine tRNA (5-7). Investigation of the mechanism by which capped but nonpolyadenylated viral mRNAs are translated has also demonstrated that structures or viral proteins can negate the need for poly(A) binding protein during mRNA translation (8, 9). Such studies on translation initiation in viruses have invariably led to subsequent identification of cellular RNAs that are translated by similar mechanisms (10, 11).Replication of negative-strand RNA viruses in the order Mononegavirales induces profound host shutoff, and inhibition of cellular translation effectively suppresses the host immune response and antiviral immunity (12). However, the mechanistic basis of selective viral translation by these viruses...

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“…Region 3 folds independently and does not make any contacts with the IRES domain in ribosome-bound or unbound states [28,33,41]. Region 3 is dispensable for ribosome binding [27], but is essential for initiation events that occur downstream of 80S ribosome assembly on the IRES [42,43].…”

Section: The Type 4 Igr Iresmentioning

confidence: 99%

Dynamics of IRES-mediated translation

Johnson

Grosely

Petrov

et al. 2017

Phil. Trans. R. Soc. B

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One contribution of 12 to a theme issue 'Perspectives on the ribosome'. Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of cap-binding and scanning. Owing to their simplicity and ribosomal affinity, the CrPV and HCV IRES have been important models for structural and functional studies of the eukaryotic ribosome during initiation, serving as excellent targets for recent technological breakthroughs in cryogenic electron microscopy (cryo-EM) and single-molecule analysis. High-resolution structural models of ribosome : IRES complexes, coupled with dynamics studies, have clarified decades of biochemical research and provided an outline of the conformational and compositional trajectory of the ribosome during initiation. Here we review recent progress in the study of HCV-and CrPV-type IRESs, highlighting important structural and dynamics insights and the synergy between cryo-EM and single-molecule studies.This article is part of the themed issue 'Perspectives on the ribosome'.

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Conserved Element of the Dicistrovirus IGR IRES that Mimics an E-site tRNA/Ribosome Interaction Mediates Multiple Functions

Cited by 39 publications

References 48 publications

Modular domains of the Dicistroviridae intergenic internal ribosome entry site

Modular domains of the Dicistroviridae intergenic internal ribosome entry site

A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs

Dynamics of IRES-mediated translation

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