The Structure of Ribosomal RNA and Its Organization Relative to Ribosomal Protein

The chapter describes how the sequence information has been used to derive convincing secondary structure models for the RNA from both subunits of the E. coli ribosome, and compares the various models that are proposed. It shows how extrapolation of these data to ribosomal RNA molecules of widely differing size classes leads to the clear conclusion that the secondary structures, as well as significant regions in the primary sequences, have been conserved to a large extent throughout evolution. The chapter deals with the three dimensional organization of the ribosomal RNA and its arrangement with respect to the ribosomal proteins, concentrating once again on the E. coli ribosome. In particular, it includes a review of the application of cross-linking techniques (bath RNA to protein and intra-RNA) to this problem. In general, rather than presenting an exhaustive survey of the literature, the chapter has selected topics or examples to illustrate those problems or points of interest that one considers to be most relevant to the central objective in this field of research— namely, the elucidation of the three-dimensional structure of the ribosomal RNA in situ in the ribosome.