Figure 1. Collision course averted in RNA phage growth. (a) Synthesis of phage minus-strand RNA requires the template to be copied in the opposite direction from which ribosomes move on the same RNA during translation. To avoid collision, translational repression makes the RNA translationally dormant, so that replication can proceed unimpeded. (b) Synthesis of phage RNA plus strands by replicase proceeds in the same direction as ribosome movement.

Figure 2. T4 gene 32 autoregulation. A pseudoknot in the mRNA at the 5¢ end is the nucleation point for binding to the mRNA of gene 32 protein monomers, depicted as filled half-circles. The horizontal hatchmarks in the pseudoknot represent hydrogen bonds in the two stems of this structure. Binding of gene 32 protein is cooperative and proceeds downstream until the ribosome-binding site (rbs) and the start codon (AUG) are coated with gene 32 protein, thereby blocking access of ribosomes to the translation start of the gene 32 coding region.

Figure 3. The principle of SELEX (systematic evolution of ligands by exponential enrichment). A random pool of RNAs (typically with a diversity of 10¹⁴), generated by mixed nucleotide incorporation during oligonucleotide synthesis, is designed with fixed sequences attached at both ends (shown as small rectangles). This RNA pool is bound to a protein target, immobilized (e.g. on a nitrocellulose filter), and unbound RNAs are washed away. Bound RNAs are eluted and amplified by reverse transcriptase polymerase chain reaction (RT-PCR), using the fixed sequences at the ends to bind appropriate primers. The products of this reaction are transcribed (e.g. by T7 RNA polymerase), creating an enriched pool for another round of binding to target. This cycle is repeated in multiple rounds (as many as 12 or more), to yield a collection of RNAs with high affinity for the target protein.

Figure 4. (a) Regulation of the E. coli r-protein ‘streptomycin’ operon. Ribosomal protein S7 acts as a translational repressor of this operon, binding to target sites near the translation starts for itself and for EF-G synthesis, blocking ribosome access. Because synthesis of EF-G is translationally coupled to synthesis of EF-Tu, blocking EF-G synthesis also blocks EF-Tu synthesis. Binding of the S7 repressor also destabilizes the mRNA upstream of the binding site (encoding S12), thus preventing S12 synthesis as well. P, promoter; rbs, ribosome-binding site; AUG, translation start codon. (b) and (c), example of molecular mimicry. Model of secondary structure of E. coli r-protein L1 binding sites on 23S rRNA (b) and on mRNA from the operon containing the genes encoding L11 and L1 (c). Nucleotide sequences in red indicate homology; numbering denotes nucleotide positions in their respective primary sequences. Parts (b) and (c) are based on Thomas and Nomura (1987) Nucleic Acids Research 15: 3085–3096.

Figure 5. Regulation of transferrin receptor mRNA stability by iron-responsive element–iron-regulatory protein (IRE–IRP) interactions in the 3¢ untranslated region. Five IREs (A–E) and other structural features are depicted. The regulatory region consists of two areas that are separated by the large loop on the right and that may be brought into closer proximity by long range RNA–RNA interactions. IRP binding in the absence of iron (a) protects the mRNA from an initial endonucleolytic clip, which occurs (presumably in a region between IREC and IRED) when the transcript is not protected in the presence of iron (b). ORF, open reading frame. Reproduced with permission from Hentze and Kuhn (1996) Proceedings of the National Academy of Sciences of the USA 93: 8175–8182. Copyright © 1996 National Academy of Sciences, USA.