Role of mRNA-rRNA Interactions in Translation

The Scripps Research Institute, La Jolla CA

Investigators

Abstract

Mauro The focus of this research is a newly discovered mechanism of translational control in which the nucleic acid component of ribosomes (rRNA) appears to regulate translation by base pairing to complementary segments contained within particular mRNAs. The working hypothesis is that base pairing interactions between mRNAs and rRNA may affect ribosome recruitment, competition, or translation efficiency. Studies are proposed to determine when base pairing occurs between mRNAs and rRNA and to describe the mechanisms by which these interactions affect translation. They will also evaluate the extent to which these interactions contribute to the overall pattern of protein expression in a cell. Initial studies will focus on the mRNAs that encode ribosomal protein S15 and homeodomain protein Gtx. Photochemical cross-linking and inhibition of reverse transcriptase (toeprinting) will be used to analyze how full-length mRNAs, that contain segments complementary to 18S rRNA, physically interact with the 18S rRNA contained within intact 40S ribosomal subunits. In addition, polysome profiles will be examined and ribosome spacing will be measured to distinguish between interactions that are independent of translation and interactions that occur while ribosomes scan or translate the mRNA. A number of other mRNAs that contain segments complementary to different regions of the rRNA will also be analyzed to address accessibility of different segments of the rRNA and to determine the extent to which the results obtained with the S15 and Gtx mRNAs are sufficient to describe a general mechanism. In addition, the binding of complementary sequences to rRNA will be examined to determine if these interactions affect the rate of translation of other mRNAs by competing for common sites on the rRNA or by altering the ribosomal subunit. Studies of eukaryotic gene expression often rely on measurements of mRNA levels. Yet, for many protein-coding genes, this is a poor predictor of protein production because many posttranscriptional events, including mRNA processing, stability, and translation, are subject to regulation. This research should increase our understanding of a mechanism of translational control that has not been extensively investigated before, while providing basic information about ribosome structure and accessibility to mRNA. The results of these studies may also identify RNA motifs with potential applications as regulatory sequences in gene therapy.