Writing an introduction: Added Value Talk for Virology Students 5/13/2013 Anne Simon
Introduction Regulation of gene expression is an essential cellular process that occurs at multiple levels including translation of mRNAs into proteins. Most regulation at translation level is exerted at the translation initiation stage where the AUG start codon is identified and decoded by the methionyl tRNA specialized for initiation (1, 2). Canonical translation initiation in eukaryotes is a complex, multistep process in which 5’m7GpppN cap and 3’ poly(A) tail on a transcribed mRNA cooperate together to recruit translation initiation factors and 40S ribosomal subunits to form the preinitiation complex (PIC). Then the preinitiation complex (PIC) scans the message in a 5’ to 3’ direction and recognizes the AUG initiation codon where 60S ribosomal subunits join to form the 80S ribosome–mRNA complex to start the translation. Cellular gene expression is regulated at multiple steps including when mRNAs are translated into proteins. Post-transcriptional control of gene expression can occur during translation initiation, when the correct start codon is identified and decoded [1,2]. In eukaryotes, canonical translation initiation is a complex, multistep process in which the 5’m7GpppN cap and 3’ poly(A) tail cooperate to recruit translation initiation factors and ribosomal subunits. The 5’ cap is recognized by the cap-binding protein eIF4E, which along with scaffold protein eIF4G is a subunit of the eukaryotic translation initiation factor complex eIF4F . Simultaneous binding of eIF4G to eIF4E and poly(A)-binding protein forms a bridge that circularizes the mRNA, which is thought to recycle ribosomes leading to more efficient translation . The 43S ribosome preinitiation complex (PIC), consisting of the 40S ribosomal subunit and met-tRNA-containing ternary complex, is recruited to the 5’ end of mRNA via the interaction between eIF4G and additional initiation factors [3,5]. The PIC scans the message in a 5’ to 3’ direction until contacting an initiation codon in the proper context. The 60S ribosomal subunit then joins to form the 80S ribosome–mRNA complex, and translation elongation commences with the entry of the appropriate aminoacylated tRNA complex into the ribosome A-site.
Nonconventional mechanisms to translation are operative during cellular stress or utilized by atypical mRNAs that lack the cap structure at the 5’end or the poly(A) tail at the 3’end (1, 3). This mechanism depends on specific highly structured cis-acting RNA sequences called internal ribosome entry sites (IRESes) which are found in a broad range of RNA viruses and in some eukaryotic cellular mRNAs (4). IRESs are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5’m7GpppN cap structure. In addition to IRES, eukaryotic mRNAs can contain upstream open reading frames (uORFs), which allows a high frequency of reinitiation by post-termination 40S subunits or translation regulatory elements located in 3’UTR. Nonconventional mechanisms of translation operate during cellular stress and are also utilized by mRNAs lacking a 5’ cap and/or a 3’ poly(A) tail [1,6]. Cap-independent ribosome entry is frequently studied using animal RNA viruses that have replaced the 5’ cap with highly structured, cis-acting elements known as internal ribosome entry sites (IRESs) that encompass or are near the initiation codon . Attraction of the small ribosomal subunit to different viral IRES usually requires a subset of initiation factors but can also occur in the absence of factors .
Cap-independent translation elements (CITEs) in the 3’UTR is much more widespread in plant RNA viruses. Although the sequence and structure of plant virus 3’cap-independent translation enhancers (3’CITEs) diverse significantly, most of them involve in bridging 5’ UTR and 3’UTR by long-distance kissing-loop interactions, which is thought to deliver bound translation initiation factors to the 5’-terminal of viral RNA to mediate initiation of translation. In contrast with animal RNA viruses, plant RNA viruses whose genomes lack a 5’ cap and 3’ poly(A) tail have short 5’UTR that do not contain similar highly structured IRES elements. Translation of plant RNA viruses in the family Tombusviridae requires distinctive cap-independent translation elements (CITEs) located within the viral genomic RNA’s 3’ UTR and nearby coding region . 3’CITEs are currently divided into at least eight classes based mainly on their secondary structures, including Y-shaped, I-shaped, BTE-like, and TED-like . 3’CITEs are bound by various translation initiation factors and are generally associated with a long-distance, kissing-loop interaction that connects the 3’CITE with the 5’ UTR, resulting in genome circularization that delivers the bound factors to the viral 5’end [11-14]. How and when the 3’ CITE-bound factors contribute to ribosome recruitment, and how ribosomes are delivered at or near the 5’ terminus before scanning to the initiation codon [15-17], is not known.
Transfer RNAs (tRNA) are the adaptor molecules that serve as the physical link between the nucleotide sequence of nucleic acids and the amino acid sequence of proteins by carrying specific amino acids to the protein synthetic machinery as directed by a three-nucleotide codons in a messenger RNA (mRNA). In addition to their major role in protein biosynthesis, tRNAs participitates in a variety of cellular roles, such as amino acid biosynthesis (5), transcriptional regulation (6), viral packaging (7) and viral genome replication (8, 9). Many viruses has evolved to utilize elements that mimic of tRNA in terms of the structure or biochemical properties to perform various fundamental roles in viral life cycles. Transfer RNA-like structures (TLSs) are functional mimics of tRNAs that are found at the 3’ end of the genomes of a number of plant positive strand RNA plant viruses. TLSs have been found capable of valylation, tyrosylation or histidylation at the viral RNA’s 3’terminal CCA by a host cell aminoacyl tRNA-synthetase (AARS), which are represented by turnip yellow mosaic virus (TYMV) TLS, brome mosaic virus (BMV) TLS and tobacco mosaic virus (TMV) TLS respectively (10-12). The roles of TLSs vary widely among different viruses including regulation of translation, replication of the genome, fidelity of the 3’ end of the viral RNA and encapsidation of viral RNAs (13, 14). A tRNA anti-codon-like element (TLE) in the HIV-1 genome has been recently reported to mimics the anti-codon loop of tRNALys to increase the efficiency of tRNALys3 annealing to viral RNA which is crucial for viral replication. Other tRNA mimicry in RNA viruses includes the intergenic region (IGR) IRES region of cricket paralysis virus, which interacts with the ribosome’s decoding groove by mimicing the tRNA anticodon-mRNA codon interaction (15). In addition to a critical role translating mRNAs into proteins, tRNA-like structures also exist internally or at the 3' termini of genomes of a growing number of RNA viruses that have a variety of functions including being used as 3’CITEs. Some capped, positive-strand RNA plant viruses including tymo-, bromo, and tobamoviruses, contain 3’ terminal tRNA-like structures (TLS) that are aminoacylated by host aminoacyl tRNA-synthetases and function in replication, translation, packaging, and fidelity of the genome (7-14). The retrovirus HIV-1 contains an internal tRNA anticodon stem-like element that mimics the anti-codon loop of tRNALys and functions to increase the efficiency with which tRNALys3 anneals to the viral genome during replication . Other examples of tRNA mimicry in RNA viruses include a TLS replication enhancer in the RNA3 intergenic region of Brome mosaic virus and related cucomoviruses, which is a substrate for tRNA modification enzymes in vivo , and the IRES of Cricket paralysis virus, which interacts with the ribosome’s decoding groove by mimicking the tRNA anticodon-mRNA codon interaction .
An internally located tRNA-mimic that forms from three hairpins and two pseudoknots functions as a 3’CITE in the carmovirus Turnip crinkle virus (TCV) (family Tombusviridae) [23,24]. The TCV TSS binds to 80S ribosomes and 60S ribosomal subunits in the vicinity of the P-site  and is not associated with any long-distance kissing-loop interaction. Rather, circularization of the genome may result from 60S subunits bound to the 3’UTR TSS joining 40S subunits bound to a pyrimidine-rich sequence in the 5’UTR . A second tRNA mimic that functions as a 3’CITE was recently discovered in the 3’UTR of Pea enation mosaic virus (PEMV). PEMV is a bipartite virus with two single-stranded plus-sense RNAs that were originally independent viruses. PEMV RNA 2 (will be referred to throughout as PEMV) is classified as an umbravirus and is missing the 5’ cap and poly(A) tail, similar to viruses in the Tombusviridae. PEMV is a recombinant virus of 4.2 kb, encoding a carmovirus-like RNA-dependent RNA polymerase (RdRp) and two overlapping, movement-associated proteins (p26, p27) from a second, unknown virus  (Fig. 1). PEMV replicates independently in protoplasts, but requires products produced by the associated viral RNA for encapsidation and transmission from plant-to-plant . The central region of the PEMV 3’UTR (702 nt) contains a 3’CITE known as a Panicum mosaic virus(PMV)-like enhancer, or PTE  (Fig. 1). Rare examples of tRNA mimicry have also been reported in 3’ CITE of plant RNA viruses. An unique 3’CITE discovered in the 3’ UTR of carmovirus Turnip crinkle virus (TCV) folds into a T-shaped structure (TSS) and it is capable of binding to the P-site of 80S ribosomes and 60S ribosomal subunits, which is indispensable for the CITE activity (16-18). It has been suggested recently that circularization of the viral genome of TCV may be through the simultaneous binding of the 40S ribosomal subunit to a pyrimidine-rich sequence in the 5’UTR and the 60S subunit to the 3’UTR TSS (19). Our previous work has identified an 81-nt tRNA-shaped element (kl-TSS) near the center of the 3’UTR of Pea enation mosaic virus (PEMV) RNA2 that enhances translation by binding to ribosomes/40S/60S subunits, and engaging in a long distance RNA:RNA kissing-loop interaction with a 5’ coding region hairpin. A translation element just downstream from the kl-TSS (the PTE) binds to eIF4E and is needed for full activity of the kl-TSS (20, 21).
The PEMV PTE binds to eIF4E and binding efficiency correlates with translational enhancement [29,30]. Although PTE found in the 3’UTR of seven carmoviruses are known or postulated to engage in long-distance kissing-loop interactions with hairpins in the 5’UTR or nearby coding sequences , the PEMV PTE relies on an adjacent, upstream element for relocalization of itself and bound initiation factors to the 5’ end . The upstream element contains a two hairpin, three-way branched secondary structure with the 5’ side hairpin (3H1) participating in a kissing-loop interaction with a 12-bp hairpin (5H2) located at positions 60-88 near the 5’ end of the p33 ORF (Fig. 1). This 3’UTR branched element is predicted to fold into a TSS and is therefore designated as a “kissing-loop TSS” (kl-TSS) . Similar to the TCV TSS, the PEMV kl-TSS binds to 80S ribosomes and 60S ribosomal subunits; however, unlike the TCV TSS, the kl-TSS also binds to 40S subunits . Since both ribosome binding and long-distance RNA:RNA interaction activities of the kl-TSS are important for efficient translation, the kl-TSS has been designated as a 3’CITE.
In this report, we find that the kl-TSS and TCV TSS occupy different sites in the 80S ribosome and that the kl-TSS can simultaneously bind to ribosomes and interact with the 5’ hairpin, leading to a re-evaluation of the orientation of the kl-TSS with respect to canonical tRNAs. We also report that the kl-TSS inhibits translation more efficiently than the associated PTE when added to a reporter template in trans, and that both RNA:RNA interaction and ribosome binding activities contribute to translational inhibition. These results suggest: (i) the PTE may be contributing to kl-TSS ribosome binding and is not associated with an independent function; (ii) RNA viruses have evolved at least two different mechanisms for using TSS-type 3’CITEs; and (iii) the RNA:RNA interaction of the kl-TSS can directly place bound ribosomes/ribosomal subunits at the 5’ end for re-initiation of translation. In this work we provide evidence that binding of the kl-TSS to ribosomes and to the 5’89-nt of PEMV is mutually compatible, suggesting a model whereby the RNA:RNA interaction helps to recycle ribosomes/ribosomal subunits that bind to the kl-TSS located in cis to enhance re-initiation of translation at the 5’ end.