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Background  Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after splicing. These molecules can invade DNA site-specifically, through a process known as retrohoming, or can invade ectopic sites through retrotransposition. Retrotransposition, in particular, can be strongly influenced by both environmental and cellular factors.    Results  To investigate host factors that influence retrotransposition, we performed random insertional mutagenesis using the IS S1  transposon to generate a library of over 1000 mutants in  Lactococcus lactis , the native host of the Ll.LtrB group II intron. By screening this library, we identified 92 mutants with increased retrotransposition frequencies (RTP-ups). We found that mutations in amino acid transport and metabolism tended to have increased retrotransposition frequencies. We further explored a subset of these RTP-up mutants, the most striking of which is a mutant in the ribosomal RNA methyltransferase  rlmH,  which exhibited a reproducible 20-fold increase in retrotransposition frequency. In vitro and in vivo experiments revealed that ribosomes in the  rlmH  mutant were defective in the m3Ψ modification and exhibited reduced binding to the intron RNA.    Conclusions  Taken together, our results reinforce the importance of the native host organism in regulating group II intron retrotransposition. In particular, the evidence from the  rlmH  mutant suggests a role for ribosome modification in limiting rampant retrotransposition.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13100-021-00237-z.

Methylation of rRNA as a host defense against rampant group II intron retrotransposition