RNA-structural mimicry in Escherichia coli ribosomal protein L4-dependent regulation of the S10 operon.
Ribosomal protein L4 regulates the 11-gene S10 operon in Escherichia coli by acting, in concert with transcription factor NusA, to cause premature transcription termination at a Rho-independent termination site in the leader sequence. This process presumably involves L4 interaction with the leader mRNA. Here, we report direct, specific, and independent binding of ribosomal protein L4 to the S10 mRNA leader in vitro. Most of the binding energy is contributed by a small hairpin structure within the leader region, but a 64-nucleotide sequence is required for the bona fide interaction. Binding to the S10 leader mRNA is competed by the 23 S rRNA L4 binding site. Although the secondary structures of the mRNA and rRNA binding sites appear different, phosphorothioate footprinting of the L4-RNA complexes reveals close structural similarity in three dimensions. Mutational analysis of the mRNA binding site is compatible with the structural model. In vitro binding of L4 induces structural changes of the S10 leader RNA, providing a first clue for how protein L4 may provoke transcription termination.
Stelzl
Ulrich
U
Memorial Sloan Kettering Cancer Center, Cellular Biochemistry and Biophysics Program, New York, New York 10021, USA. u.stelzl@mdc-berlin.de
Zengel
Janice M
JM
Tovbina
Marina
M
Walker
Marquis
M
Nierhaus
Knud H
KH
Lindahl
Lasse
L
Patel
Dinshaw J
DJ
D020121:5' Untranslated Regions / Q000378:metabolism; D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D003101:Collodion / Q000494:pharmacology; D004252:DNA Mutational Analysis; D004305:Dose-Response Relationship, Drug; D004926:Escherichia coli / Q000378:metabolism*; D015971:Gene Expression Regulation, Enzymologic; D007455:Iodine / Q000494:pharmacology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic
D020121:5' Untranslated Regions; D012333:RNA, Messenger; D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; C056368:ribosomal protein L4; D003101:Collodion; D007455:Iodine