Regulation of Gene Expression in Prokaryotes:- Synthesis of Ribosomal Proteins Is Coordinated with rRNA Synthesis
In bacteria, an increased cellular demand for protein synthesis is met by increasing the number of ribosomes rather than altering the activity of individual ribosomes. In general, the number of ribosomes increases as the cellular growth rate increases. At high growth rates, ribosomes make up approximately 45% of the cell’s dry weight. The proportion of cellular resources devoted to making ribosomes is so large, and the function of ribosomes so important, that cells must coordinate the syn thesis of the ribosomal components: the ribosomal proteins (r-proteins) and RNAs (rRNAs). This regulation is distinct from the mechanisms described so far, because it occurs largely at the level of translation. The 52 genes that encode the r-proteins occur in at least 20 operons, each with 1 to 11 genes. Some of these operons also contain the genes for the subunits of DNA primase , RNA polymerase , and protein synthesis elongation factors (see Fig. 1)—revealing the close coupling of replication, transcription, and protein synthesis during cell growth. The r-protein operons are regulated primarily through a translational feedback mechanism. One r-protein encoded by each operon also functions as a translational repressor, which binds to the mRNA transcribed from that operon and blocks translation of all the genes the messenger encodes (Fig. 1). In general, the r-protein that plays the role of repressor also binds directly to an rRNA. Each translational re pressor r-protein binds with higher affinity to the ap propriate rRNA than to its mRNA, so the mRNA is bound and translation repressed only when the level of the r-protein exceeds that of the rRNA. This ensures that translation of the mRNAs encoding r-proteins is re pressed only when synthesis of these r-proteins exceeds that needed to make functional ribosomes. In this way, the rate of r-protein synthesis is kept in balance with rRNA availability. The mRNA binding site for the translational re pressor is near the translational start site of one of the genes in the operon, usually the first gene (Fig. 1). In other operons this would affect only that one gene, because in bacterial polycistronic mRNAs most genes have independent translation signals. In the r-protein operons, however, the translation of one gene depends on the translation of all the others. The mechanism of this translational coupling is not yet understood in de tail. However, in some cases the translation of multiple genes appears to be blocked by folding of the mRNA into an elaborate three-dimensional structure that is stabilized both by internal base-pairing and by binding of the translational repressor protein. When the translational repressor is absent, ribosome binding and translation of one or more of the genes disrupts the folded structure of the mRNA and allows all the genes to be translated.
Because the synthesis of r-proteins is coordinated with the available rRNA, the regulation of ribosome pro duction reflects the regulation of rRNA synthesis. In E. coli, rRNA synthesis from the seven rRNA operons responds to cellular growth rate and to changes in the availability of crucial nutrients, particularly amino acids. The regulation coordinated with amino acid concentrations is known as the stringent response (Fig. 2). When amino acid concentrations are low, rRNA synthesis is halted. Amino acid starvation leads to the binding of uncharged tRNAs to the ribosomal A site; this triggers a sequence of events that begins with the binding of an enzyme called stringent factor (RelA protein) to the ribosome. When bound to the ribosome, stringent factor catalyzes formation of the unusual nucleotide guanosine tetraphosphate it adds pyrophosphate to the 3position of GTP, in the reaction
GTP+ATP→ pppGpp + AMP
then a phosphohydrolase cleaves off one phosphate to form ppGpp. The abrupt rise in ppGpp level in response to amino acid starvation results in a great reduction in rRNA synthesis, mediated at least in part by the binding of ppGpp to RNA polymerase.
FIGURE 1 Translational feedback in some ribosomal protein operons. The r-proteins that act as translational repressors are shaded pink. Each translational repressor blocks the translation of all genes in that operon by binding to the indicated site on the mRNA. Genes that encode subunits of RNA polymerase are shaded yellow; genes that encode elongation factors are blue. The r-proteins of the large (50S) ribosomal subunit are designated L1 to L34; those of the small (30S) subunit, S1 to S21.
FIGURE 2 Stringent response in E. coli. This response to amino acid starvation is triggered by binding of an uncharged tRNA in the ribosomal A site. A protein called stringent factor binds to the ribosome and catalyzes the synthesis of pppGpp, which is converted by a phosphohydrolase to ppGpp. The signal ppGpp reduces transcription of some genes and increases that of others, in part by binding to the β subunit of RNA polymerase and altering the enzyme’s promoter specificity. Synthesis of rRNA is reduced when ppGpp levels increase.
The nucleotide ppGpp, along with cAMP, belongs to a class of modified nucleotides that act as cellular second messengers . In E. coli, these two nucleotides serve as starvation signals; they cause large changes in cellular metabolism by increasing or de creasing the transcription of hundreds of genes. In eu karyotic cells, similar nucleotide second messengers also have multiple regulatory functions. The coordination of cellular metabolism with cell growth is highly complex, and further regulatory mechanisms undoubtedly remain to be discovered.
