Identification of dynamic sequences in the central domain of 7SL RNA

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Abstract
The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random linker insertion approach and twelve mutant genes carrying alterations in the central domain of 7SL RNA were characterized. Mutant RNAs were produced by in vitro transcription of the various templates and their electrophoretic behaviour was determined. Bases between positions 98 and 133 as well as 206 and 251 proved to be necessary for the 7SL RNA to be able to exist in alternative conformations, while changes at the positions 85 to 97, 144 to 166 and 252 to 266 did not abolish this property. The dynamic sequences are located in the "central T" in the secondary structure of the 7SL RNA. They are phylogenetically conserved and include bases which are homologeous to 5S ribosomal RNA. A dynamic core structure composed of the dynamic parts of the 7SL RNA is suggested. An attempt was made to define the different conformers present in the wild-type 7SL RNA. These alternative configurations could play a functional role during the initial stage of protein translocation across the membrane of the endoplasmic reticulum.