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Orientation of the tRNA anticodon in the ribosomal P-site: Quantitative footprinting with U33-modified, anticodon stem and loop domains

Published online by Cambridge University Press:  01 September 1999

S. SALMAN ASHRAF
Affiliation:
Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA Present address: Novalon Pharmaceutical Corporation, 4222 Emperor Boulevard, Suite 560, Durham, North Carolina 27703-8466, USA.
RICHARD GUENTHER
Affiliation:
Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
PAUL F. AGRIS
Affiliation:
Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
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Abstract

Binding of transfer RNA (tRNA) to the ribosome involves crucial tRNA–ribosomal RNA (rRNA) interactions. To better understand these interactions, U33-substituted yeast tRNAPhe anticodon stem and loop domains (ASLs) were used as probes of anticodon orientation on the ribosome. Orientation of the anticodon in the ribosomal P-site was assessed with a quantitative chemical footprinting method in which protection constants (Kp) quantify protection afforded to individual 16S rRNA P-site nucleosides by tRNA or synthetic ASLs. Chemical footprints of native yeast tRNAPhe, ASL-U33, as well as ASLs containing 3-methyluridine, cytidine, or deoxyuridine at position 33 (ASL-m3U33, ASL-C33, and ASL-dU33, respectively) were compared. Yeast tRNAPhe and the ASL-U33 protected individual 16S rRNA P-site nucleosides differentially. Ribosomal binding of yeast tRNAPhe enhanced protection of C1400, but the ASL-U33 and U33-substituted ASLs did not. Two residues, G926 and G1338 with Kps ≈ 50–60 nM, were afforded significantly greater protection by both yeast tRNAPhe and the ASL-U33 than other residues, such as A532, A794, C795, and A1339 (Kps ≈ 100–200 nM). In contrast, protections of G926 and G1338 were greatly and differentially reduced in quantitative footprints of U33-substituted ASLs as compared with that of the ASL-U33. ASL-m3U33 and ASL-C33 protected G530, A532, A794, C795, and A1339 as well as the ASL-U33. However, protection of G926 and G1338 (Kps between 70 and 340 nM) was significantly reduced in comparison to that of the ASL-U33 (43 and 61 nM, respectively). Though protections of all P-site nucleosides by ASL-dU33 were reduced as compared to that of the ASL-U33, a proportionally greater reduction of G926 and G1338 protections was observed (Kps = 242 and 347 nM, respectively). Thus, G926 and G1338 are important to efficient P-site binding of tRNA. More importantly, when tRNA is bound in the ribosomal P-site, G926 and G1338 of 16S rRNA and the invariant U33 of tRNA are positioned close to each other.

Type
Research Article
Information
RNA , Volume 5 , Issue 9 , September 1999 , pp. 1191 - 1199
Copyright
© 1999 RNA Society

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