title: Role of polypyrimidine tract binding protein in mediating internal initiation of translation of interferon regulatory factor 2 RNA.
abstract: BACKGROUND
  Earlier we have reported translational control of interferon regulatory factor 2 (IRF2) by internal initiation (Dhar et al, Nucleic Acids Res, 2007). The results implied possible role of IRF2 in controlling the intricate balance of cellular gene expression under stress conditions in general. Here we have investigated the secondary structure of the Internal Ribosome Entry Site of IRF2 RNA and demonstrated the role of PTB protein in ribosome assembly to facilitate internal initiation.
  
  
  RESULTS
  We have probed the putative secondary structure of the IRF2 5'UTR RNA using various enzymatic and chemical modification agents to constrain the secondary structure predicted from RNA folding algorithm Mfold. The IRES activity was found to be influenced by the interaction of trans-acting factor, polypyrimidine tract binding protein (PTB). Deletion of 25 nts from the 3'terminus of the 5'untranslated region resulted in reduced binding with PTB protein and also showed significant decrease in IRES activity compared to the wild type. We have also demonstrated putative contact points of PTB on the IRF2-5'UTR using primer extension inhibition assay. Majority of the PTB toe-prints were found to be restricted to the 3'end of the IRES. Additionally, Circular Dichroism (CD) spectra analysis suggested change in the conformation of the RNA upon PTB binding. Further, binding studies using S10 extract from HeLa cells, partially silenced for PTB gene expression, resulted in reduced binding by other trans-acting factors. Finally, we have demonstrated that addition of recombinant PTB enhances ribosome assembly on IRF2 IRES suggesting possible role of PTB in mediating internal initiation of translation of IRF2 RNA.
  
  
  CONCLUSIONS
  It appears that PTB binding to multiple sites within IRF2 5'UTR leads to a conformational change in the RNA that facilitate binding of other trans-acting factors to mediate internal initiation of translation.
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India.
authors.forename: Debojyoti
authors.initials: D
authors.lastname: Dhar
authors.forename: Musturi
authors.initials: M
authors.lastname: Venkataramana
authors.forename: Anand
authors.initials: A
authors.lastname: Ponnuswamy
authors.forename: Saumitra
authors.initials: S
authors.lastname: Das
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D002942:Circular Dichroism; D004722:Endoribonucleases / Q000737:chemistry; D017353:Gene Deletion; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D050836:Interferon Regulatory Factor-2 / Q000378:metabolism*; D038941:Polypyrimidine Tract-Binding Protein / Q000737:chemistry / Q000502:physiology*; D014176:Protein Biosynthesis; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D006163:Ribonuclease T1 / Q000737:chemistry; D015533:Transcriptional Activation
chemical_list: D020121:5' Untranslated Regions; C494229:IRF2 protein, human; D050836:Interferon Regulatory Factor-2; D038941:Polypyrimidine Tract-Binding Protein; D004722:Endoribonucleases; C032825:ribonuclease V(1); D006163:Ribonuclease T1