Tags

Type your tag names separated by a space and hit enter

Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition.
J Mol Biol. 1996 Aug 30; 261(4):550-67.JM

Abstract

S15 is a primary ribosomal protein that interacts specifically with a three-way junction in the central domain of 16 S rRNA, whose binding induces a conformational change in the RNA. In the accompanying paper, we demonstrated that S15 binds with high affinity to a 61 nucleotide RNA corresponding to the minimal rRNA binding site. Here, the sequence and structural determinants for the RNA in the Bacillus stearothermophilus S15-rRNA interaction have been probed using site-directed mutagenesis, chemical modification interference, and iodine footprinting of phosphorothioate RNA. Mutations and RNA modifications that interfere with protein binding cluster in two distinct regions, one containing an internal loop and the other containing a three-way junction. The internal loop, defined by two A.G base-pairs and a bulged guanosine, is not important for the specific interaction, however, BS15 interacts with a phylogenetically conserved G.U base-pair above this internal loop. Near the three-way junction in helix 22, a bulged adenosine and two base-pairs adjacent to the junction also provide important determinants for BS15 binding. Chemical modification interference also suggests that four highly phylogenetically conserved nucleotides in the three-way junction may form non-canonical G.G and U.A base-pairs that are required for the BS15-rRNA interaction. Ethylation modification interference suggests that BS15 binding is accompanied by a conformational change in the RNA involving orientation of helices 20 and 22 at an acute angle with respect to one another. Projection of the data provided by mutagenesis, chemical modification interference analysis, and iodine footprinting onto a three-dimensional model illustrates that BS15 is likely to interact with the minor groove along an extended face of helix 22.

Links

Publisher Full Text

Authors+Show Affiliations

Batey RT
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.
Williamson JR
No affiliation info available

MeSH

Base SequenceDiethyl PyrocarbonateEthylnitrosoureaGeobacillus stearothermophilusHydrazinesIodineModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedNucleic Acid ConformationNucleotidesProtein BindingRNA, BacterialRNA, Ribosomal, 16SRibosomal ProteinsThionucleotides

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

8794876

Citation

Batey, R T., and J R. Williamson. "Interaction of the Bacillus Stearothermophilus Ribosomal Protein S15 With 16 S rRNA: II. Specificity Determinants of RNA-protein Recognition." Journal of Molecular Biology, vol. 261, no. 4, 1996, pp. 550-67.
Batey RT, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition. J Mol Biol. 1996;261(4):550-67.
Batey, R. T., & Williamson, J. R. (1996). Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition. Journal of Molecular Biology, 261(4), 550-67.
Batey RT, Williamson JR. Interaction of the Bacillus Stearothermophilus Ribosomal Protein S15 With 16 S rRNA: II. Specificity Determinants of RNA-protein Recognition. J Mol Biol. 1996 Aug 30;261(4):550-67. PubMed PMID: 8794876.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition. AU - Batey,R T, AU - Williamson,J R, PY - 1996/8/30/pubmed PY - 1996/8/30/medline PY - 1996/8/30/entrez SP - 550 EP - 67 JF - Journal of molecular biology JO - J Mol Biol VL - 261 IS - 4 N2 - S15 is a primary ribosomal protein that interacts specifically with a three-way junction in the central domain of 16 S rRNA, whose binding induces a conformational change in the RNA. In the accompanying paper, we demonstrated that S15 binds with high affinity to a 61 nucleotide RNA corresponding to the minimal rRNA binding site. Here, the sequence and structural determinants for the RNA in the Bacillus stearothermophilus S15-rRNA interaction have been probed using site-directed mutagenesis, chemical modification interference, and iodine footprinting of phosphorothioate RNA. Mutations and RNA modifications that interfere with protein binding cluster in two distinct regions, one containing an internal loop and the other containing a three-way junction. The internal loop, defined by two A.G base-pairs and a bulged guanosine, is not important for the specific interaction, however, BS15 interacts with a phylogenetically conserved G.U base-pair above this internal loop. Near the three-way junction in helix 22, a bulged adenosine and two base-pairs adjacent to the junction also provide important determinants for BS15 binding. Chemical modification interference also suggests that four highly phylogenetically conserved nucleotides in the three-way junction may form non-canonical G.G and U.A base-pairs that are required for the BS15-rRNA interaction. Ethylation modification interference suggests that BS15 binding is accompanied by a conformational change in the RNA involving orientation of helices 20 and 22 at an acute angle with respect to one another. Projection of the data provided by mutagenesis, chemical modification interference analysis, and iodine footprinting onto a three-dimensional model illustrates that BS15 is likely to interact with the minor groove along an extended face of helix 22. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/8794876/Interaction_of_the_Bacillus_stearothermophilus_ribosomal_protein_S15_with_16_S_rRNA:_II__Specificity_determinants_of_RNA_protein_recognition_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(96)90482-9 DB - PRIME DP - Unbound Medicine ER -