Ribosome-mRNA contact sites at different stages of translation initiation as revealed by cross-linking of model mRNAs

Binding of mRNA to the Bacterial Translation Initiation Complex

Translation initiation is a key step for regulating the synthesis of several proteins. In bacteria, translation initiation involves the interaction of the mRNA with the ribosomal small subunit. Additionally, translation initiation factors 1, 2, and 3, and the initiator tRNA, also assemble on the ribosomal small subunit and are essential for efficiently recruiting an mRNA for protein biosynthesis. In the following chapter, we describe fluorescence-based methods for studying the interaction of mRNA with the bacterial initiation complex. Model mRNAs with a covalently attached fluorescent probe showed an increase in fluorescence intensity when bound to the bacterial initiation complex. Utilizing the increase in fluorescence intensity upon mRNA binding to the bacterial initiation complex, we determined the equilibrium binding constants and the association and dissociation rate constants. These methods are important for quantitatively analyzing the effects of mRNA secondary structure and the role of the initiation factors in recruitment of mRNA by the bacterial initiation complex.

Cross-linking of nucleic acids to proteins. Modified poly(A) as mRNA for Escherichia coli ribosomes

Poly(adenylic acid) was modified by methylchlorotetrolic ester in a reproducible and defined content of the derivatized bases. The nucleic acid derivative is protein reactive and was coupled to 70S ribosomes from Escherichia coli, in order to identify proteins along the mRNA pathway. The binding of the label becomes specific under the direction of tRNA(Lys) and is then almost exclusively located on the small subunit. The proteins S1, S12, S18 and S21 were labeled, as shown by an antibody assay. The yield of the affinity label was 5.4%, as calculated from the labeled nucleic acid. This compares favourably with the yields from photolabile compounds.

Ribosomal localization of the mRNA in the 30S initiation complex as revealed by UV crosslinking

Translation initiation complexes consisting of 30S ribosomal subunits, 32P-labelled mRNA (002 mRNA), fMet-tRNA and the three initiation factors were subjected to UV-crosslinking to determine the protein and rRNA neighbors of the bound mRNA by immunochemical methods and by nucleic acid hybridization techniques. The mRNA was found to be crosslinked to a specific region of the 16S rRNA spanning from nucleotide 418 to 615 and to ribosomal proteins S1 and S21 (the main targets), S3, S10, S12 and S14; a low level of crosslinking was also detected with S2, S7, S13, S18 and S19.