Photoaffinity Labeling of Escherichia coli Ribosomes: New Approaches and Results

Abstract

Affinity and photoaffinity labeling have proven to be powerful methods for the identification of functional sites within the Escherichia coli ribosome. Although results have been obtained for many of the known ribosomal ligands, including peptidyl-, aminoacyl-, and uncharged tRNA, mRNA, GTP, protein factors, and antibiotics, we pointed out in previous critical reviews of this area (Cooperman, 1978, 1980) that much of the published work was of questionable significance. The reasons for this were directly traceable to the demanding nature of the experiment. On the one hand, evaluating the significance of a labeling experiment often requires determining the extent of labeling of individual components (here defined as ribosomal proteins or limited regions of rRNA), as a function of such variables as reaction time, or, for photoaffinity labels, of light fluence, of affinity label concentration, and of the presence or absence of other ribosomal ligands, because it is not uncommon for labeling to be spread over a large number of components. On the other hand, the tediousness and/or limited reproducibility (with respect to yields) of the analytical techniques then available made such determinations quite difficult to carry out. Ribosomal proteins were typically prepared for analysis using one- and two-dimensional polyacrylamide gel electrophoresis (PAGE) and/or immunoprecipitation as separation techniques.