Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: Application of a method called SERF

Two-thirds of the 54 proteins of the Escherichia coli ribosome interact dir ectly with the rRNAs, but the rRNA binding sites of only a very few protein s are known. We present a method (selection of random RNA fragments; SERF) that can identify the minimal binding region for proteins within ribonucleo -protein complexes such as the ribosome, The power of the method is exempli fied with the ribosomal proteins L4 and L6. Binding sequences are identifie d for both proteins and characterized by phosphorothioate footprinting. Sur prisingly, the binding region of L4, a 53-nt rRNA fragment of domain I of 2 3S rRNA, can simultaneously and independently bind L24, one of the two asse mbly initiator proteins of the large subunit.