Fig. 7

Model for protection of the genome against rampant retrotransposition. a. Wild-type host background. Under normal cellular conditions, the bacterial nucleoid is condensed, DNA replication is tightly controlled, and intron RNPs (red RNA lariat bound by gray intron-encoded protein) are bound by ribosomes (blue), which function to limit retrotransposition. Ribosome-bound RNPs encounter steric clashes (black X) with proteins at crowded DNA replication forks, inhibiting retrotransposition, with limited access to primers for cDNA synthesis (Low). In contrast, retrohoming into the homing site (black dot) in double-stranded DNA is unaffected by the presence of ribosomes with retrohoming being efficient, consistent with freedom from crowded replication forks (High). b. Mutant host backgrounds. Mutating certain host genes (blue insertion on the chromosome) increases retrotransposition frequency. (1) Disrupted amino acid biosynthesis pathways or misregulated stringent response (spoT::ISS1, rpoE::ISS1, hisH::ISS1) leads to restructuring of the nucleoid into a conformation more favorable for retrotransposition. (2) Stalled replication forks (increased single-stranded gaps) due to the activation of the stringent response or disruption of DNA recombination and repair functionalities (coiA::ISS1, recT::ISS1) become prime targets for retrotransposition. (3) Dysfunctional ribosome binding (rlmH::ISS1) allows intron RNPs to more freely invade DNA replication forks (Higher), whereas retrohoming remains unchanged (High). For illustrative purposes only, various effects of mutants (numbered 1, 2, and 3) are shown together on the same figure