Dataset Information

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

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.

SUBMITTER: Yu Y

PROVIDER: S-EPMC3113573 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Yu Yingpu Y Abaeva Irina S IS Marintchev Assen A Pestova Tatyana V TV Hellen Christopher U T CU

Nucleic acids research 20110208 11

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 additi ...[more]

PMID: 21306989

Similar Datasets

Project description:Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY4741 (a laboratory strain) and RM11-1a (a wild strain), for their gene expression divergence first by microarray. By incorporating the obtained array data with ChIP-chip data, we generated a set of single-regulator-regulated genes that showed expression divergence between BY4741 and RM11-1a. We randomly selected 50 of these genes for further study. We found substantial variations in the DNA sequences of the promoter regions of these genes and in their regulators between the two strains, which are potential sources of expression divergence. We then developed a step-by-step approach to assess the relative contributions of cis- and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the two alleles of BY4741 and RM11-1a in co-cultures and in hybrid diploids. Among the 50 genes studied, 4 genes showed no significant expression difference when the two strains were grown in separate cultures or in the same culture (co-culture) and 6 genes showed significant expression difference in separate cultures but not in co-culture. The remaining 40 genes showed expression divergence between the two strains in co-culture. Among these 40 genes, pyrosequencing of diploids showed that 18 cases of expression divergence (45%=18/40) can be attributed to differences in trans-acting factors alone, 7 cases (17.5%) mainly to trans-variations, 8 cases (20%) to both cis- and trans-acting factors, 3 cases (7.5%) mainly to cis-variations, and 4 cases (10%) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed the cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important. Keywords: comparative gene expression between strains

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets