With a stepwise degradation and terminal labeling procedure the 3′-terminal sequence of E. coli 16S ribosomal RNA is shown to be Pyd-A-C-C-U-C-C-U-U-AOH. It is suggested that this region of the RNA is able to interact with mRNA and that the 3′-terminal U-U-AOH is involved in the termination of protein synthesis through base-pairing with terminator codons. The sequence A-C-C-U-C-C could recognize a conserved sequence found in the ribosome binding sites of various coliphage mRNAs; it may thus be involved in the formation of the mRNA·30S subunit complex.

https://www.pnas.org/content/pnas/71/4/1342.full.pdf

The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites

The sequence of the 3'-terminus of 16S RNA from different bacteria has been determined. Complementarity relationships between this sequence and a purine-rich tract in the ribosome binding site of different bacterial mRNAs suggest that the 3'-end of 16S RNA determines the intrinsic capacity of ribosomes to translate a particular cistron.

Determinant of cistron specificity in bacterial ribosomes

Chemical footprinting shows that several classes of antibiotics (streptomycin, tetracycline, spectinomycin, edeine, hygromycin and the neomycins) protect concise sets of highly conserved nucleotides in 16S ribosomal RNA when bound to ribosomes These findings have strong implications for the mechanism of action of these antibiotics and for the assignment of functions to specific structural features of 16S rRNA

Interaction of antibiotics with functional sites in 16S ribosomal RNA

https://www.cell.com/cell/pdf/0092-8674(78)90039-9.pdf

How do eucaryotic ribosomes select initiation regions in messenger RNA

Publisher Summary This chapter examines the range of the variation of secondary structure among the 16-S-like rRNAs. This brings into a larger structural context a recent detailed analysis of the individual helical elements and provides a basis for an accurate alignment of the corresponding regions of different primary structures. Computer-assisted comparative is used in the analysis of aligned sequences to describe the pattern of phylogenetic conservation for each nucleotide position in 16-S rRNA. A search for matching patterns among unpaired positions in the RNA chain then produces a list of candidates for potential base–base tertiary interactions. The completion of nucleotide sequences for 34 16-S-like rRNAs includes 4 eubacteria, 4 chloroplasts, 12 mitochondria, 4 archaebacteria, and 10 eukaryotes. Secondary structure models for these molecules have been developed in the course of refinement of the E. coli model, and have been used to arrive at improved sequence alignments for the 16-S-like rRNAs. Schematic drawings of (1) eubacterial, (2) archaebacterial, (3) eukaryotic cytoplasmic, (4) plant mitochondrial, (5) fungal mitochondrial, and (6) mammalian mitochondrial structures are shown in the chapter.

Comparative Anatomy of 16-S-like Ribosomal RNA

Treatment of sensitive Escherichia coli cells with colicin E3 leads to inactivation of 30S ribosomal subunits In vitro reconstitution of 30S subunits indicates that the E3-induced defect lies solely in the 16S RNA 16S RNA from E3-treated cells lacks several T1 RNase oligonucleotides of normal 16S RNA, including the one from the 3′-end of the 16S RNA, as analyzed by the fingerprint technique of Sanger An RNA fragment about 50 nucleotides long has been isolated from E3-treated cells This RNA contains the original 3′-terminal oligonucleotide and other oligonucleotides missing in the E3-16S RNA The results show that colicin E3 treatment causes the cleavage of 16S RNA at a specific position near the 3′-terminus

https://www.pnas.org/content/pnas/68/5/964.full.pdf

J. E. Dahlberg

Papers

Specific Inactivation of 16S Ribosomal RNA Induced by Colicin E3 In Vivo