Panel A: Specialized translation in V. vulnificus mediated by I-rDNA operon products. I-ribosomes (orange) selectively translate a specific mRNA (orange) cohort characterized by sequestration of start codons within secondary structures. In contrast, standard mRNAs (blue) are translated by canonical ribosomes (grey). Panel B: Reversible ribosome remodeling in S. cerevisiae under environmental stress. Salt or pH stress triggers Tsr2-mediated dissociation of eS26, generating eS26-deficient ribosomes (orange). While canonical ribosomes (grey) favor mRNAs with strong Kozak sequences (blue), eS26-deficient variants lack this selectivity, facilitating the preferential translation of mRNAs with weak Kozak motifs (orange). Panel C: Homeostatic regulation of bS21 in F. johnsoniae. In most Bacteroides, mRNAs (blue) lack Shine-Dalgarno (SD) sequences. The ribosomal protein bS21 (orange) functions by sequestering the anti-SD sequence. Efficient translation of b21 mRNA, which contains an SD sequence, requires bS21-deficient ribosomes, creating a feedback loop that maintains stoichiometric levels of bS21 across the ribosomal pool.
Validated cases of ribosome specialization. (A) In V. vulnificus, the I-rDNA operon produces ribosomes (I-ribosomes, in orange), which are required for the translation of a subset of mRNAs (in orange), whose start codon (AUG) is embedded in secondary structure (Song et al., 2019). Other mRNAs (in blue) do not require the I-ribosomes. Ribosomes produced from the other operons are in gray. (B) In S. cerevisiae, exposure to high salt or pH leads to the reversible, Tsr2-mediated dissociation of eS26 from ribosomes (Ferretti et al., 2018; Ferretti et al., 2017; Yang and Karbstein, 2022), to yield eS26-deficient ribosomes (in orange). These do not recognize part of the Kozak sequence. mRNAs without a strong Kozak sequence (orange) are not well translated by canonical ribosomes (in gray), which prefer Kozak-containing mRNAs (blue with the highlighted Kozak sequence). However, eS26-deficient ribosomes do not discriminate against weak Kozak mRNAs, enabling a relative increase in the production of their encoded proteins. (C) In F. johnsoniae and other Bacteroides, most mRNAs (in blue) do not have SD sequences and adding a SD sequence does not promote translation. This is because bS21 (shown in orange on the ribosome) sequesters the anti-SD. Ribosomes lacking bS21 do recognize the SD sequence. Because the b21 mRNA has a SD sequence, which—together with bS21-deficient ribosomes—is required for its efficient translation, this establishes a feedback loop to ensure all ribosomes contain bS21 (Jha et al., 2021; McNutt et al., 2023).