title: S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA.
abstract: Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.
authors: Dorota
authors: D
authors: Matelska
authors: Elzbieta
authors: E
authors: Purta
authors: Sylwia
authors: S
authors: Panek
authors: Michal J
authors: MJ
authors: Boniecki
authors: Janusz M
authors: JM
authors: Bujnicki
authors: Stanislaw
authors: S
authors: Dunin-Horkawicz
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D024202:Electrophoretic Mobility Shift Assay; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D038601:Ribosomal Protein S6 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D016963:Thermus thermophilus / Q000235:genetics / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D038601:Ribosomal Protein S6; D012269:Ribosomal Proteins; C041184:ribosomal protein S18
keywords: RNA secondary structure; RNA structure prediction; feedback regulation; ribosomal protein S6; ribosome
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