Structure and activity of the internal ribosome entry site within the human p27 Kip1 5'-untranslated region

The cyclin dependent kinase inhibitor p27(Kip1) is a key cell cycle regulatory protein that is often downregulated in cancer cells. The cellular levels of p27(Kip1) are regulated, in part, through translational control mechanisms. The 5'-UTR of the p27(Kip1) mRNA is known to harbor an IRES that may facilitate expression of p27(Kip1) under conditions of stress such as loss of cell adhesion or growth factor and nutrient deprivation. The results presented here further characterize the p27(Kip1) 5'-UTR and its IRES activity. We confirm that the major transcription start site of the p27(Kip1) gene produces an mRNA with a 5'-UTR of approximately 472 nucleotides. Other minor transcripts are also observed but the 472 nucleotide 5'-UTR displays the highest IRES activity. A structural model for the 472 nucleotide 5'-UTR was derived from nuclease digestion patterns coupled with MFOLD secondary structural prediction software. These results indicate that the 5'-UTR has significant secondary structure but also contains a large single-stranded loop that extends from nucleotides -31 to -66 relative to the start codon. Mapping of the ribosome entry window indicates that the ribosome is recruited to this single-stranded loop. The single-stranded loop also includes a U-rich sequence that has previously been shown to bind several proteins, including HuR. This is significant because HuR has previously been shown to inhibit p27(Kip1) IRES activity and cause downregulation of endogenous p27(Kip1) protein levels. Thus HuR may inhibit IRES activity by blocking the ribosome entry site.