H. Moine et al., THE RNA-BINDING SITE OF S8 RIBOSOMAL-PROTEIN OF ESCHERICHIA-COLI - SELEX AND HYDROXYL RADICAL PROBING STUDIES, RNA, 3(3), 1997, pp. 255-268
The RNA binding site of ribosomal protein S8 of Escherichia coli is co
nfined to a small region within the stem of a hairpin in 16S rRNA (nt
588-605/633-651), and thus represents a model system for understanding
RNA/protein interaction rules. The S8 binding site on 165 rRNA was su
spected to contain noncanonical features difficult to prove with class
ical genetical or biochemical means. We performed in vitro iterative s
election of RNA aptamers that bind S8. For the different aptamers, the
interactions with the protein were probed with hydroxyl radicals. Apt
amers that were recognized according to the same structural rules as w
ild-type RNA, but with variations not found in nature, were identified
. These aptamers revealed features in the S8 binding site that had bee
n concealed during previous characterizations by the high base conserv
ation throughout evolution. Our data demonstrate that the core structu
re of the S8 binding site is composed of three interdependent bases (n
t 597/641/643), with an essential intervening adenine nucleotide (posi
tion 642). The other elements important for the binding site are a bas
e pair (598/640) above the three interdependent bases and a bulged bas
e at position 595, the identity of which is not important. Possible im
plications on the geometry of the S8 binding site are discussed with t
he help of a three-dimensional model.