Does 5S RNA function by a switch between two secondary structures?

Abstract

THE structure of 5S RNA has been a lively field for experiment and speculation, with no definitive resolution of the problem in sight (see refs 1 and 2 for reviews). Fox and Woese3 suggested comparative sequence analysis of prokaryotic 5S RNAs as a method for locating base paired regions, an appealing procedure because of its similarity to the method used to substantiate the cloverleaf model for tRNA. Its logic states that if all known 5S RNA sequences contain complementary bases at a site, a double helix probably exists there in the functional form. We propose that comparative sequence analysis suggests two different functional structures for prokaryotic 5S RNA. One of them has been introduced by Fox and Woese3, and its set condary structure is based on four conserved helices: the ‘molecular stalk’ (Escherichia coli residues 1–10 and 119–110), the weak ‘tuned helix’ (18–23/65–60), the ‘common arm base’ (31–34/51–48) and the ‘prokaryotic loop’ (82-86/94-90). The base paired structure that results is consistent with enzymatic digestion14 and chemical modification1,5 results on native 5S RNA, if allowance is made for protection of residues by tertiary bonding as well as secondary structure. This ‘model’, however, does not explain the apparent conservation of a double helix (33–39/88–82 in E. coli) (Table 1) which is sterically inconsistent with two of the helices listed (the common arm base and the prokaryotic loop). Fox and Woese3 noted this conservation but considered it unimportant because of the variable helix length and the conflict with the other two helices.