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Chapter 15 : Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites

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Abstract:

In December 1975, Hugh Pelham invented the micrococcal nuclease-treated (messenger-dependent) rabbit reticulocyte lysate. The sequencing of picornavirus RNAs in the early 1980s revealed that they had rather long 5' untranslated regions (5' UTRs) of between 610 and ~1400 nucleotides [nt], depending on the particular virus species. In due course, evidence for translation by direct internal ribosome entry was provided by the demonstration that the insertion of a picornavirus 5' UTR between the two cistrons of a laboratory-constructed dicistronic mRNA leads to dramatic enhancement of expression of the downstream cistron. Entero- and rhinovirus 2A and foot-and-mouth disease virus (FMDV) L proteases cleave eIF4G into an N-terminal one-third fragment, which has the eIF4E interaction site, and a C-terminal two-thirds fragment, which has the interaction site for eIF3, and both sites where eIF4A binds. Toe-printing and sucrose gradient analyses of initiation complexes formed with highly purified initiation factors have shown that the binding of the 40S subunit to the correct initiation site on the encephalomyocarditis virus (EMCV) internal ribosomal entry site (IRES) absolutely requires eIF2, 3, and 4A and either the complete native eIF4F complex (with associated eIF4A) or recombinant fragments of eIF4G, which include the central one-third domain. In conclusion, therefore, the most plausible hypothesis is that by binding at multiple points in the IRES element, polypyrimidine tract-binding protein (PTB), PCBP-2, and serve to help in the maintenance or the attainment of the appropriate three-dimensional RNA structure.

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15

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Figures

Image of FIGURE 1
FIGURE 1

Schematic diagram of eIF4G domain structure. The eIF4G polypeptide is depicted as an open rectangle, with binding/interaction sites of PABP, eIF3, eIF4A helicase (two interaction sites), and eIF4E cap-binding factor shown ( ). The putative RNP-1 and RNP-2 motifs of the hypothetical RRM in the central domain are shown as vertical black bars. The indicated central domain is (so far) the minimum eIF4G fragment able to support translation initiation dependent on the EMCV IRES. The diagram is based on the more abundant and better studied eIF4G species, eIF4GI. The other minor species (eIF4GII), although only 46% homologous to eIF4GI throughout the whole protein, shows much greater homology in certain specific regions, notably in the center and toward the C terminus, suggesting that the sites of interaction with PABP, eIF3, eIF4A, and eIF4E will be in similar positions as in eIF4GI ( ).

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15
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Image of FIGURE 2
FIGURE 2

Schematic diagram of the EMCV IRES. The sequence around the authentic initiation site (AUG-11, shown in bold) is given. The various subdomains (H through L) discussed in the text are indicated. The site at which eIF4G (or eIF4F) binds as determined by foot-printing ( ) is shown by stippling, and the self-consistent toe-print site ( ) is also indicated. Asterisks denote the regions protected when PTB binds to the IRES, as determined by foot-printing/protection experiments ( ). The A-rich bulge (sequence 5′-UAAAAAA-3′ in EMCV strain R) is denoted by a thickened checkered line; a fortuitous expansion of this bulge by a single additional A-residue renders the activity of the IRES highly dependent on PTB ( ).

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15
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Image of FIGURE 3
FIGURE 3

Schematic diagram of the domain structure of , PTB, and PCBPs. The diagrams are approximately to scale and show the five cold-shock domains (CSD) of in black, the four noncanonical RRMs of PTB as stippled rectangles, and the three KH-domains of PCBP-1/2 as vertically striped rectangles. The amino acid sequences of the core of each of the five CSDs of are given, with the amino acid residues believed to constitute the RNA-binding surface ( ) in bold. Note that all five CSDs of have the sequence FFH, which is unique to this member of the family, in contrast with the FVH motif found in all other CSD proteins ( ). At the bottom is the amino acid sequence of PCBP-2, with the differences found in PCPB-1 given below. These amino acid sequences are those published by Leffers et al. ( ), and the K-H domains identified by Leffers et al. are highlighted by boxed rectangles.

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15
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Tables

Generic image for table
TABLE 1

Canonical mammalian initiation factors and their roles

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15
Generic image for table
TABLE 2

Characteristics of different mechanisms of initiation of translation of eukaryotic cellular and viral RNAs

It is thought likely that the same pattern of requirements will be shown by all picornavirus IRESs except the HAV IRES.

Although initiation dependent on the EMCV IRES requires ATP hydrolysis ( ), significantly lower ATP concentrations are needed than for scanning-dependent initiation ( ).

Answers given in parentheses are considered to be the most probable outcome, but the issue has not yet been put to a direct test.

Citation: Jackson R. 2002. Proteins Involved in the Function of Picornavirus Internal Ribosomal Entry Sites, p 171-183. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch15

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