Location of Ribosomal Protein Binding Sites on 16S Ribosomal RNA

Abstract

The distribution of ribosomal protein binding sites on the 16S ribosomal RNA molecule has been analyzed by limited ribonuclease hydrolysis of RNA-protein complexes, as well as by the interaction of individual proteins with RNA fragments purified from partial enzymatic digests. Of the six 30S subunit proteins known to interact directly with 16S RNA, proteins S4, S8, S15, S20, and, probably, S13 bind within a fragment produced by T1 RNase (12S RNA) that comprises some 900 nucleotides and covers almost the entire 5'-terminal half of the 16S molecule. A fragment of 500-00 nucleotides (8S RNA) that is contiguous with 12S RNA and arises from the 3'-terminal portion of the 16S molecule is believed to contain the binding site for protein S7. Protein S15 interacts specifically with a sequence of about 135 nucleotides (4S RNA) that derives from 12S RNA after more extensive hydrolysis. Protein S4, but none of the other ribosomal proteins, binds to a 500-nucleotide fragment (9S RNA), generated by pancreatic RNase, that lies at the 5'-terminus of 16S RNA and is completely overlapped by the 12S fragment. A preliminary map of the binding sites is presented.Reconstitution of the 30S ribosomal subunit of Escherichia coli proceeds by the sequential and cooperative addition of 20 or 21 different proteins to 16S RNA (1). In the initial stages of the assembly sequence, six ribosomal proteins directly interact with independent binding sites on the RNA molecule (1-4). The specific structural features that permit ribosomal RNA to recognize and bind these proteins are not known.We ratio is increased to 1:5, hydrolysis is more extensive; fragments of about 10 S and 4 S are generated from the 12S RNA, as demonstrated by nucleotide sequence analysis, and the 8S RNA is degraded to small oligonucleotides. Fragments with the same sedimentation rates result when enzymatic digestion is performed after individual ribosomal proteins have been attached to the 16S RNA (Fig. 1, dashed curves).The action of pancreatic ribonuclease A on 16S RNA is also limited under similar conditions, and the presence of bound protein again affords the RNA no additional protection. At an enzyme to substrate ratio of 1:20, the principal component in the digest sediments at about 11 S; an increase of the ratio to 1: 5 results in fragments with apparent sedimentation coefficients of 9 S and 4 S.The resistance of large RNA segments to RNase digestion in these experiments is attributable to the high concentration of Mg++ ions in the incubation buffer; reduction of the Mg++ concentration alone renders the 16S RNA more labile to degradation, whereas removal of mofnovalent cations has no effect on fragment size. Since the RNA chain possesses a high degree of secondary structure and a compact conformation at the Mg++ concentrations used (6), RNase attack is most likely limited by decreased accessibility of the 16S molecule to the enzyme. (Fig. lb), while no protein S4 radioactivity is observed in the 8S peak. Under the same conditions, S8, S13, S15, and S20, four oth...

Heterologous protein—RNA interactions in bacterial ribosomes

“…The former confirmed the earlier heterologous binding result for S4 [4]. Given the complexities of the RNA binding sites for S4 [7,13,171 and L24 [ 14,151 , these results probably reflect a high degree of conservation of RNA sequence, and, indeed for 16 S RNA of Proteus vulgaris this has been indicated [25]. Undoubtedly, therefore, these bacterial RNA's are the best candidates for further structural investigations of protein-RNA interactions.…”

The identification of the RNA binding site for a 50 s ribosomal protein by a new technique

“…The sites on the 16 S RNA to which certain proteins from the 30 S ribosomal particle become attached have been localised within the primary sequence of the RNA [6,7]. This was done by binding the proteins to specific fragments of the RNA [6] or by isolating regions of the RNA protected against nuclease digestion by the presence of a protein [7]. Analogous studies of some components of the 50 S ribosomal particle have revealed that three proteins participate in binding the 5 S RNA to a region somewhere within the 3'-two-thirds of the 23 S RNA [8][9][10].…”

“…Some progress has been made in this direction recently. The sites on the 16 S RNA to which certain proteins from the 30 S ribosomal particle become attached have been localised within the primary sequence of the RNA [6,7]. This was done by binding the proteins to specific fragments of the RNA [6] or by isolating regions of the RNA protected against nuclease digestion by the presence of a protein [7].…”

The primary structure of ribosomal protein S4 from Escherichia coli

“…The protein chains of many mutant S4 proteins are shorter or longer than wild type S4; b) Protein S4 binds specifically to E. coli 181 and the protein-RNA interaction has been studied in some detail [14,15,17,18].…”