E. coli possesses seven operons that produce the rRNA required for ribosome assembly. Each operon is regulated in response to changes in the environment. The stringent response refers to regulation triggered by amino acid starvation. When an uncharged tRNA binds to the A site of a ribosome, it initiates a series of events that leads to the production of ppGpp, an alarmone derived from guanosine diphosphate (GDP). RelA, an enzyme associated with ribosomes, catalyzes the synthesis of ppGpp. Elevated levels of ppGpp inhibit rRNA synthesis, as well as tRNA synthesis and some mRNA synthesis, except for the mRNA required for amino acid biosynthesis. ppGpp also binds RNA pol and alters promoter 2.

Operons for ribosomal proteins (rproteins) can be inhibited by an excess of their own protein products. A specific r-protein from each operon represses translation of the polycistronic mRNA by binding to the Shine-Dalgarno (SD) sequence located upstream of the first initiating AUG codon. This physical impediment prevents the small ribosomal subunit from binding to the SD sequence, thus inhibiting the synthesis of all r-proteins in the operon. The same r-protein also has a higher affinity for rRNA than for mRNA. When the concentration of rRNA decreases, the r-protein becomes available to bind to its own mRNA and inhibit translation. This coordinated regulation ensures the balanced synthesis of r-proteins and transcription of rRNA.

In eukaryotes, the regulation of gene expression is more complex due to the higher degree of genome complexity and the presence of a nuclear membrane. While transcription remains the primary site of regulation, eukaryotes do not possess operons and must employ alternative strategies to coordinate the regulation of genes involved in specific responses. Eukaryotic gene expression is also regulated at various levels other than transcription, such as alternative mRNA splicing and polyadenylation, control of mRNA stability, and control of translational efficiency. Additionally, regulation at the protein level occurs through mechanisms that modulate stability, processing, or targeting of the protein.
Stringent response: E. coli has seven operons that synthesize the rRNA needed for ribosome assembly, and each is regulated in response to changes in environmental conditions. Regulation in response to amino acid starvation is known as the stringent response. The binding of an uncharged transfer RNA (tRNA) to the A site of a ribosome (see p. 452) triggers a series of events that leads to the production of the alarmone guanosine tetraphosphate (ppGpp). The synthesis of this unusual derivative of guanosine diphosphate (GDP) is catalyzed by stringent factor (RelA), an enzyme physically associated with ribosomes. Elevated levels of ppGpp result in inhibition of rRNA synthesis (Fig. 33.7). [Note: In addition to rRNA synthesis, tRNA synthesis and some mRNA synthesis (for example, for ribosomal proteins) are also inhibited. However, synthesis of mRNA for enzymes required for amino acid biosynthesis is not inhibited. ppGpp binds RNA pol and alters promoter 2.
Regulatory ribosomal proteins: Operons for ribosomal proteins (rproteins) can be inhibited by an excess of their own protein products. For each operon, one specific r-protein functions in the repression of selection through use of different sigma factors for the polymerase (see p. 435).] translation of the polycistronic mRNA from that operon (Fig. 33.8). The r-protein does so by binding to the Shine-Dalgarno (SD) sequence located on the mRNA just upstream of the first initiating AUG codon (see p. 448) and acting as a physical impediment to the binding of the small ribosomal subunit to the SD sequence. Thus, one r-protein inhibits synthesis of all the r-proteins of the operon. This same r-protein also binds to rRNA and with a higher affinity than for mRNA. If the concentration of rRNA falls, the r-protein then is available to bind its own mRNA and inhibit its translation. This coordinated regulation keeps the synthesis of r-proteins in balance with the transcription of rRNA, so that each is present in appropriate amounts for the formation of ribosomes.
IV. REGULATION OF EUKARYOTIC GENE EXPRESSION
The higher degree of complexity of eukaryotic genomes, as well as the presence of a nuclear membrane, necessitates a wider range of regulatory processes. As with the prokaryotes, transcription is the primary site of regulation. Again, the theme of trans-acting factors binding to cis-acting elements is seen. Operons, however, are not found in eukaryotes, which must use alternate strategies to solve the problem of how to coordinately regulate all the genes required for a specific response. In eukaryotes, gene expression is also regulated at multiple levels other than transcription. For example, the major modes of posttranscriptional regulation at the mRNA level are alternative mRNA splicing and polyadenylation, control of mRNA stability, and control of translational efficiency. Additional regulation at the protein level occurs by mechanisms that modulate stability, processing, or targeting of the protein.
A. Coordinate regulation