Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice to yield mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein, with multiple activities including reverse transcriptase. This activity is responsible for copying the intron RNA into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8 Å resolution and in its protein-depleted form at 4.5 Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship of the reverse transcriptase catalytic domain to telomerase, whereas the active center for splicing resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.

SignificanceMycobacteria as well as other bacteria remodel their ribosomes in response to zinc depletion by replacing zinc-binding ribosomal proteins with zinc-free paralogues, releasing zinc for other metabolic processes. In this study, we show that the remodeled ribosome acquires a structurally stable but functionally inactive and aminoglycoside-resistant state in zinc-starved Mycobacterium smegmatis. Conversely, M. smegmatis cells that are growth arrested in zinc-rich conditions have unstable ribosomes and reduced survival. We further provide evidence for ribosome remodeling in Mycobacterium tuberculosis in host tissues, suggesting that ribosome hibernation occurs during TB infections. Our findings could offer insights into mechanisms of persistence and antibiotic tolerance of mycobacterial infections.

The authors wish to note, "The availability of the high-resolution structures of the complete 55 S mitoribosome recently published in Amunts et al. (1) and Greber et al. (2) have shown that our cryo-EM map is consistent with their high-resolution coordinates. However, a comparison with these two studies shows that at our resolution of 7 Å, some of our placements, particularly of the mito-specific MRPs, were in error. While this comparison highlights the difficulty of interpretation of multiple nonhomologous MRPs at our modest resolution, it also shows that the fold of the nucleic acid component of the RNP complex, the 12S rRNA, could be traced. We will be updating our previously published coordinates in light of the new papers." www.pnas.org/cgi