Bacterial protein factories slow down when key RNA modifications are removed
Researchers discovered that enzymes controlling ribosomal RNA modifications don't work independently—removing multiple enzymes simultaneously cripples bacterial protein synthesis at cold temperatures. The findings could reshape strategies for developing antibiotics that target ribosomal function, a major drug discovery pathway worth billions annually.
Originaltitel: Translational impacts of enzymes that modify ribosomal RNA around the peptidyl transferase centre
<p>Large ribosomal RNAs (rRNAs) are modified heavily post-transcriptionally in functionally important regions but, paradoxically, individual knockouts (KOs) of the modification enzymes have minimal impact on <em>Escherichia coli</em> growth. Furthermore, we recently constructed a strain with combined KOs of five modification enzymes (RluC, RlmKL, RlmN, RlmM and RluE) of the ‘critical region’ of the peptidyl transferase centre (PTC) in 23S rRNA that exhibited only a minor growth defect at 37°C (although major at 20°C). However, our combined KO of modification enzymes RluC and RlmE (not RluE) resulted in conditional lethality (at 20°C). Although the growth rates for both multiple-KO strains were characterized, the molecular explanations for such deficits remain unclear. Here, we pinpoint biochemical defects in these strains. <em>In vitro</em> fast kinetics at 20°C and 37°C with ribosomes purified from both strains revealed, counterintuitively, the slowing of translocation, not peptide bond formation or peptidyl release. Elongation rates of protein synthesis <em>in vivo</em>, as judged by the kinetics of β-galactosidase induction, were also slowed. For the five-KO strain, the biggest deficit at 37°C was in 70S ribosome assembly, as judged by a dominant 50S peak in ribosome sucrose gradient profiles at 5 mM Mg<sup>2+</sup>. Reconstitution of this 50S subunit from purified five-KO rRNA and ribosomal proteins supported a direct role in ribosome biogenesis of the PTC region modifications <em>per se</em>, rather than of the modification enzymes. These results clarify the importance and roles of the enigmatic rRNA modifications.</p>