Translation initiation is a major target of gene regulation in eukaryotes. Internal ribosome entry sites (IRES) are RNA sequences that drive a non-canonical mechanism of translation initiation, bypassing the need for a 5'cap on the messenger RNA (mRNA). IRESs are central players in the infection cycles of many important viruses (e.g. hepatitis C, hepatitis A, poliovirus, HIV-1) and are significant regulators of gene expression. Many IRESs possess higher-order structures that interact with and manipulate the translation machinery, but our understanding of how they work is rudimentary. Thus, our knowledge of the viruses that employ IRESs remains incomplete, and our ability to exploit IRESs as drug targets is limited. Furthermore, because some IRESs are known to interact directly with the ribosome to alter its conformation and manipulate its function, IRESs offer a window into how ribosomes work, how structured RNAs can bind to ribosomes, and how ribosome function can be altered. The intergenic (IGR) IRESs of the Dicistroviridae provide a powerful model system to explore these phenomena. We propose to build upon our long-standing studies on the intergenic (IGR) IRESs of the Dicistroviridae, which drive a highly streamlined mode of ribosome recruitment and activation. Over the last few years, we have made discoveries that lead to a detailed structure-based model of IGR IRES function;we are now poised to test that model and explain the function of an IRES in unprecedented detail. We propose to do this with three specific aims. First, we will employ single molecule FRET (smFRET) to observe the motions of IRES RNAs, tRNAs, and ribosome components within an initiating complex. By watching how the structured IRES drives specific movements on the ribosome and comparing these motions to those of canonical elongation, we will gain insight at a level not yet achieved. Second, we will explore conformational changes within the IRES RNA structure itself, linking these dynamic changes to global changes in the initiating complex and in so doing, turn static pictures into dynamic pathways. Third, we will solve the structures of IRES-ribosome complexes by x-ray crystallography, which should reveal heretofore unseen intimate ribosome-IRES interactions that underlie conformational changes. These three independent but complementary aims promise to yield a cohesive, high-resolution, and dynamic mechanistic picture of how an IRES RNA manipulates a fundamental biological machine, lending wide-ranging insight into universal biological processes.

Public Health Relevance

to NIH Internal ribosome entry site (IRES) RNAs are used by many pathogenic viruses (e.g. hepatitis C virus, hepatitis A virus, poliovirus, HIV-1) as a critical part of their strategy to multiply inside a host cell and are also used to regulate gene expression in cells. However, we have a very limited understanding of how these IRES RNAs work;this prevents us from fully understanding these viruses, or targeting the IRES RNAs with drugs. We propose to employ state of the art methods in biochemistry, structural biology, and biophysics to gain new knowledge as to how these biologically important RNAs operate at the molecular level and also to gain critical insight into fundamental processes of biology.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Macromolecular Structure and Function C Study Section (MSFC)
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Bender, Michael T
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University of Colorado Denver
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Hartwick, Erik W; Costantino, David A; MacFadden, Andrea et al. (2018) Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun 9:5074
Akiyama, Benjamin M; Eiler, Daniel; Kieft, Jeffrey S (2016) Structured RNAs that evade or confound exonucleases: function follows form. Curr Opin Struct Biol 36:40-7
Hao, Yumeng; Kieft, Jeffrey S (2016) Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol 13:635-45
Batey, Robert T; Kieft, Jeffrey S (2016) Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol 1320:219-32
Hussain, Tanweer; Llácer, Jose L; Wimberly, Brian T et al. (2016) Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 167:133-144.e13
Ruehle, Marisa D; Zhang, Haibo; Sheridan, Ryan M et al. (2015) A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation. Elife 4:
Colussi, Timothy M; Costantino, David A; Zhu, Jianyu et al. (2015) Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature 519:110-3
Plank, Terra-Dawn M; Whitehurst, James T; Cencic, Regina et al. (2014) Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure. Translation (Austin) 2:e27694
Chapman, Erich G; Moon, Stephanie L; Wilusz, Jeffrey et al. (2014) RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA. Elife 3:e01892
Colussi, Timothy M; Costantino, David A; Hammond, John A et al. (2014) The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature 511:366-9

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