RNA



The location of protein S8 and surrounding elements of 16S rRNA in the 70S ribosome from combined use of directed hydroxyl radical probing and X-ray crystallography


LAURA  LANCASTER a1, GLORIA M.  CULVER a1p1, GULNARA ZH.  YUSUPOVA a1, JAMIE H.  CATE a1p2, MARAT M.  YUSUPOV a1 and HARRY F.  NOLLER a1c1
a1 Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, California 95064, USA

Abstract

Ribosomal protein S8, which is essential for the assembly of the central domain of 16S rRNA, is one of the most thoroughly studied RNA-binding proteins. To map its surrounding RNA in the ribosome, we carried out directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to nine different positions on the surface of protein S8 in 70S ribosomes. Hydroxyl radical-induced cleavage was observed near the classical S8-binding site in the 620 stem, and flanking the other S8-footprinted regions of the central domain at the three-helix junction near position 650 and the 825 and 860 stems. In addition, cleavage near the 5′ terminus of 16S rRNA, in the 300 region of its 5′ domain, and in the 1070 region of its 3′-major domain provide information about the proximity to S8 of RNA elements not directly involved in its binding. These data, along with previous footprinting and crosslinking results, allowed positioning of protein S8 and its surrounding RNA elements in a 7.8-[Angstrom capital A, ring] map of the Thermus thermophilus 70S ribosome. The resulting model is in close agreement with the extensive body of data from previous studies using protein–protein and protein–RNA crosslinking, chemical and enzymatic footprinting, and genetics.

(Received February 11 2000)
(Revised February 23 2000)
(Accepted March 6 2000)


Key Words: ribosome structure; RNA–protein interaction; rRNA; S8.

Correspondence:
c1 Reprint requests to: Harry F. Noller, Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, California 95064, USA; e-mail: harry@nuvolari.ucsc.edu.
p1 Present address: Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
p2 Present address: Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.