An antibiotic-binding motif of an RNA fragment derived from the A-site-related region of Escherichia coli 16S rRNA.
A small RNA derived from the decoding region of Escherichia coli 16S rRNA can bind to antibiotics of aminoglycosides (neomycin and paromomycin) that act on the small ribosomal subunit [Purohit,P. and Stern,S. (1994) Nature, 370, 659-662]. In the present study, the P-site subdomain was removed from this decoding region RNA to construct a 27mer RNA (designated as ASR-27), which includes the A-site-related region (positions 1402-1412 and 1488-1497) of 16S rRNA. Footprint experiments with dimethyl sulfate as a chemical probe indicated that the ASR-27 RNA can interact with the neomycin family in the same manner as the decoding region RNA. A mutagenesis analysis of the ASR-27 RNA revealed that paromomycin binding of ASR-27 involves the C1407.G1494 and C1409-G1491 base pairs, and the internal loop comprising A1408 and the nucleotides in positions 1492-1493, located between the two C.G base pairs. In addition, a G or U in position 1495, and base pairing between positions 1405 and 1496 are also involved. These structural features were found in a viral RNA element, the Rev-binding site of human immunodeficiency virus type-1, which may explain why neomycin can bind to this viral RNA.
Miyaguchi
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H
Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Japan.
Narita
H
H
Sakamoto
K
K
Yokoyama
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S
D000617:Aminoglycosides; D000900:Anti-Bacterial Agents / Q000378:metabolism*; D015694:Gene Products, rev / Q000378:metabolism; D015497:HIV-1 / Q000378:metabolism; D016296:Mutagenesis; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D054321:rev Gene Products, Human Immunodeficiency Virus
D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D015694:Gene Products, rev; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D054321:rev Gene Products, Human Immunodeficiency Virus