Model of ribosome heterogeneity in E. coli. (A) Two distinct pathways for releasing stalled ribosomes during nutrient-limited stress. The first pathway is the stringent stress response, where ribosomes stalled on mRNA bind deacylated tRNA at the A site, thereby facilitating the association of RelA (Protein Data Bank (PDB): 5KPV). This interaction induces the production of (p)ppGpp, an alarmone that ultimately results in elevated transcription of rrnH carried out by RNA polymerase (PDB: 5MY1) and RpoS (PDB: 6UUC) complex within the cell. Consequently, the population of stress-response proteins is upregulated as a direct consequence of nutrient-limiting conditions. The alternative pathway is induced upon degradation of RelB in the RelB–RelE complex, which releases RelE (PDB: 4V7J) to bind at the A site of stalled ribosomes in the absence of aa-tRNA. RelE cleaves mRNA at the second nucleotide of the A site codon, leading to the association of small protein B (SmpB) and the tmRNA complex (PDB: 7AC7), which ultimately releases stalled ribosomes from the mRNA. (RNAP, RNA polymerase) (B) In the cartoon diagram, different colour patches indicate that the ribosomes are composed of different variants of 16S and 23S rRNAs. Model A illustrates mRNA translation by a heterogeneous population of ribosomes, each carrying different rRNA derived from various rDNA operons. Model B illustrates mRNA translation by a homogeneous population of ribosomes originating from a single rDNA operon. The shapes shown in the mRNA cartoons depict the PTrMs present in 5’ and 3’ untranslated regions (UTRs). (Key: LSU: large subunit, SSU: small subunit)
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