Limits...
Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors.

Yu Y, Abaeva IS, Marintchev A, Pestova TV, Hellen CU - Nucleic Acids Res. (2011)

Bottom Line: In addition to canonical translation factors, type 2 IRESs also require IRES trans-acting factors (ITAFs) that are hypothesized to stabilize the optimal IRES conformation that supports efficient ribosomal recruitment: the EMCV IRES is stimulated by pyrimidine tract binding protein (PTB), whereas the FMDV IRES requires PTB and ITAF(45).To test this hypothesis, we assessed the effect of ITAFs on the conformations of EMCV and FMDV IRESs by comparing their influence on hydroxyl radical cleavage of these IRESs from the central domain of eIF4G.The observed changes in cleavage patterns suggest that cognate ITAFs promote similar conformational changes that are consistent with adoption by the IRESs of comparable, more compact structures, in which domain J undergoes local conformational changes and is brought into closer proximity to the base of domain I.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA.

ABSTRACT
Type 2 internal ribosomal entry sites (IRESs) of encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV) and other picornaviruses comprise five major domains H-L. Initiation of translation on these IRESs begins with specific binding of the central domain of initiation factor, eIF4G to the J-K domains, which is stimulated by eIF4A. eIF4G/eIF4A then restructure the region of ribosomal attachment on the IRES and promote recruitment of ribosomal 43S pre-initiation complexes. In addition to canonical translation factors, type 2 IRESs also require IRES trans-acting factors (ITAFs) that are hypothesized to stabilize the optimal IRES conformation that supports efficient ribosomal recruitment: the EMCV IRES is stimulated by pyrimidine tract binding protein (PTB), whereas the FMDV IRES requires PTB and ITAF(45). To test this hypothesis, we assessed the effect of ITAFs on the conformations of EMCV and FMDV IRESs by comparing their influence on hydroxyl radical cleavage of these IRESs from the central domain of eIF4G. The observed changes in cleavage patterns suggest that cognate ITAFs promote similar conformational changes that are consistent with adoption by the IRESs of comparable, more compact structures, in which domain J undergoes local conformational changes and is brought into closer proximity to the base of domain I.

Show MeSH

Related in: MedlinePlus

Sites of hydroxyl radical cleavage in EMCV and FMDV IRESs from Fe(II)-tethered eIF4Gm in IRES/eIF4Gm/eIF4A complexes influenced by cognate ITAFs mapped onto the secondary structure of IRESs. Sites of hydroxyl radical cleavage from positions on eIF4Gm mapped onto the secondary structures of (A and B) the EMCV IRES and (C and D) the FMDV IRES (GenBank accession no. X00871). Models in panels B and D show only those sites at which cleavage was enhanced by nPTB or ITAF45. Nucleotide numbering of the EMCV IRES and nomenclature of IRES domains are as in (ref. 37). Cleavage sites are show in colors that match the colors of corresponding spheres in Figure 1A. Sites of strong cleavage are indicated by thick edging.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3113573&req=5

Figure 2: Sites of hydroxyl radical cleavage in EMCV and FMDV IRESs from Fe(II)-tethered eIF4Gm in IRES/eIF4Gm/eIF4A complexes influenced by cognate ITAFs mapped onto the secondary structure of IRESs. Sites of hydroxyl radical cleavage from positions on eIF4Gm mapped onto the secondary structures of (A and B) the EMCV IRES and (C and D) the FMDV IRES (GenBank accession no. X00871). Models in panels B and D show only those sites at which cleavage was enhanced by nPTB or ITAF45. Nucleotide numbering of the EMCV IRES and nomenclature of IRES domains are as in (ref. 37). Cleavage sites are show in colors that match the colors of corresponding spheres in Figure 1A. Sites of strong cleavage are indicated by thick edging.

Mentions: Type 2 IRESs, such as those of the picornaviruses encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV) and Theiler's murine encephalomyelitis virus (TMEV) are about 450-nt long, and consist of five major domains, designated H-L (Figure 2). Sequence variation between these IRESs can reach 50%, but a similar overall structure is maintained by compensatory base changes in helical elements. Biochemical reconstitution experiments have shown that 48S complex formation on type 2 IRESs requires eIF2, eIF3 and a 40S ribosomal subunit (which together form the core of the 43S complex), the RNA helicase eIF4A and the central domain of eIF4G, but is only modestly stimulated by eIF4B, eIF1 and eIF1A, and does not require the cap binding protein eIF4E or the N-terminal domain of eIF4G to which it binds (2–5). The key interaction of type 2 IRESs with the translational apparatus is the specific binding of the central HEAT-1 domain of eIF4G to the IRES's J-K domains, which is enhanced by eIF4A (3,5–8). The eIF4G/eIF4A complex induces Adenosine-5′-triphosphate (ATP)-dependent conformational changes at the 3′-border of the IRES (9) that likely prepare this region for binding of the 43S complex in a process that presumably involves the eIF4G/eIF3 interaction. However, the exact mechanism by which eIF4G/eIF4A promotes attachment of 43S complexes to the IRESs has not been determined.Figure 1.


Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors.

Yu Y, Abaeva IS, Marintchev A, Pestova TV, Hellen CU - Nucleic Acids Res. (2011)

Sites of hydroxyl radical cleavage in EMCV and FMDV IRESs from Fe(II)-tethered eIF4Gm in IRES/eIF4Gm/eIF4A complexes influenced by cognate ITAFs mapped onto the secondary structure of IRESs. Sites of hydroxyl radical cleavage from positions on eIF4Gm mapped onto the secondary structures of (A and B) the EMCV IRES and (C and D) the FMDV IRES (GenBank accession no. X00871). Models in panels B and D show only those sites at which cleavage was enhanced by nPTB or ITAF45. Nucleotide numbering of the EMCV IRES and nomenclature of IRES domains are as in (ref. 37). Cleavage sites are show in colors that match the colors of corresponding spheres in Figure 1A. Sites of strong cleavage are indicated by thick edging.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113573&req=5

Figure 2: Sites of hydroxyl radical cleavage in EMCV and FMDV IRESs from Fe(II)-tethered eIF4Gm in IRES/eIF4Gm/eIF4A complexes influenced by cognate ITAFs mapped onto the secondary structure of IRESs. Sites of hydroxyl radical cleavage from positions on eIF4Gm mapped onto the secondary structures of (A and B) the EMCV IRES and (C and D) the FMDV IRES (GenBank accession no. X00871). Models in panels B and D show only those sites at which cleavage was enhanced by nPTB or ITAF45. Nucleotide numbering of the EMCV IRES and nomenclature of IRES domains are as in (ref. 37). Cleavage sites are show in colors that match the colors of corresponding spheres in Figure 1A. Sites of strong cleavage are indicated by thick edging.
Mentions: Type 2 IRESs, such as those of the picornaviruses encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV) and Theiler's murine encephalomyelitis virus (TMEV) are about 450-nt long, and consist of five major domains, designated H-L (Figure 2). Sequence variation between these IRESs can reach 50%, but a similar overall structure is maintained by compensatory base changes in helical elements. Biochemical reconstitution experiments have shown that 48S complex formation on type 2 IRESs requires eIF2, eIF3 and a 40S ribosomal subunit (which together form the core of the 43S complex), the RNA helicase eIF4A and the central domain of eIF4G, but is only modestly stimulated by eIF4B, eIF1 and eIF1A, and does not require the cap binding protein eIF4E or the N-terminal domain of eIF4G to which it binds (2–5). The key interaction of type 2 IRESs with the translational apparatus is the specific binding of the central HEAT-1 domain of eIF4G to the IRES's J-K domains, which is enhanced by eIF4A (3,5–8). The eIF4G/eIF4A complex induces Adenosine-5′-triphosphate (ATP)-dependent conformational changes at the 3′-border of the IRES (9) that likely prepare this region for binding of the 43S complex in a process that presumably involves the eIF4G/eIF3 interaction. However, the exact mechanism by which eIF4G/eIF4A promotes attachment of 43S complexes to the IRESs has not been determined.Figure 1.

Bottom Line: In addition to canonical translation factors, type 2 IRESs also require IRES trans-acting factors (ITAFs) that are hypothesized to stabilize the optimal IRES conformation that supports efficient ribosomal recruitment: the EMCV IRES is stimulated by pyrimidine tract binding protein (PTB), whereas the FMDV IRES requires PTB and ITAF(45).To test this hypothesis, we assessed the effect of ITAFs on the conformations of EMCV and FMDV IRESs by comparing their influence on hydroxyl radical cleavage of these IRESs from the central domain of eIF4G.The observed changes in cleavage patterns suggest that cognate ITAFs promote similar conformational changes that are consistent with adoption by the IRESs of comparable, more compact structures, in which domain J undergoes local conformational changes and is brought into closer proximity to the base of domain I.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA.

ABSTRACT
Type 2 internal ribosomal entry sites (IRESs) of encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV) and other picornaviruses comprise five major domains H-L. Initiation of translation on these IRESs begins with specific binding of the central domain of initiation factor, eIF4G to the J-K domains, which is stimulated by eIF4A. eIF4G/eIF4A then restructure the region of ribosomal attachment on the IRES and promote recruitment of ribosomal 43S pre-initiation complexes. In addition to canonical translation factors, type 2 IRESs also require IRES trans-acting factors (ITAFs) that are hypothesized to stabilize the optimal IRES conformation that supports efficient ribosomal recruitment: the EMCV IRES is stimulated by pyrimidine tract binding protein (PTB), whereas the FMDV IRES requires PTB and ITAF(45). To test this hypothesis, we assessed the effect of ITAFs on the conformations of EMCV and FMDV IRESs by comparing their influence on hydroxyl radical cleavage of these IRESs from the central domain of eIF4G. The observed changes in cleavage patterns suggest that cognate ITAFs promote similar conformational changes that are consistent with adoption by the IRESs of comparable, more compact structures, in which domain J undergoes local conformational changes and is brought into closer proximity to the base of domain I.

Show MeSH
Related in: MedlinePlus