Biology subjects

Rossine, F.

Publications and source records attributed to Rossine, F..

3 recordsLinked to original sources

bioRxiv2026

SOS-mediated prophage induction constrains resistance evolution to DNA-damaging antibiotics

Most naturally occurring bacteria are lysogens, encoding one or more temperate phages (prophages) integrated into their genome. As prophages are induced by the bacterial SOS response, DNA-damaging antibiotics can trigger SOS-mediated prophage induction, where prophages undergo lytic replication and lyse their host, even at sub-inhibitory concentrations. This prophage-antibiotic synergy therefore sensitizes lysogenic hosts to DNA-damaging antibiotics. However, the mechanism by which prophage-induced sensitization affects the evolution of resistance against these agents is unclear. Here we show that ciprofloxacin-resistant lysogens arise less frequently but exhibit higher levels of resistance following selection. Whole-genome sequencing showed that increased lysogen resistance arose from selection towards mutations in drug targets, efflux pathways, and stress response regulators that reduce antibiotic efficacy or alter SOS induction. Consistent with this result, resistant lysogens exhibited a dampened SOS response, suggesting that prophage induction imposes an additional selective filter on their hosts by eliminating mutants that experience sufficient DNA damage to activate the SOS response. By contrast, prophage carriage had no effect on sensitivity or resistance evolution for antibiotics where DNA damage occurs downstream of the primary mechanism of action. Together, these findings indicate that prophage induction acts as an evolutionary bottleneck that restricts many resistance trajectories while favoring the emergence of rarer, large-effect mutations, potentially accelerating the evolution of high-level resistance.

microbiology↗

bioRxiv2025

Intracellular competition shapes plasmid population dynamics

Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-replicating genetic elements that underlie much of the evolutionary flexibility of bacteria. Evolving plasmids face selective pressures on their hosts, but also compete within the cell for replication, making them an ideal system for studying the joint dynamics of multilevel selection. While theory indicates that within-cell selection should matter for plasmid evolution, experimental measurement of within-cell plasmid fitness and its consequences has remained elusive. Here we measure the within-cell fitness of competing plasmids and characterize drift and selective dynamics. We achieve this by the controlled splitting of synthetic plasmid dimers to create balanced competition experiments. We find that incompatible plasmids co-occur for longer than expected due to methylation-based plasmid eclipsing. During this period of co-occurrence, less transcriptionally active plasmids display a within-cell selective advantage over their competing plasmids, leading to preferential fixation of silent plasmids. When the transcribed gene is beneficial to the cell, for example an antibiotic resistance gene, there is a cell-plasmid fitness tradeoff mediated by the dominance of the beneficial trait. Surprisingly, more dominant plasmid-encoded traits are less likely to fix but more likely to initially invade than less dominant traits. Taken together, our results show that plasmid evolution is driven by dynamics at two levels, with a transient, but critical, contribution of within-cell fitness.

evolutionary biology↗

bioRxiv2025

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

Mobile genetic elements (MGEs) are diverse, self-replicating DNA molecules that can reside within cellular hosts and integrate into one another. This co-occurrence imposes distinct evolutionary pressures. Plasmids often contain insertion sequences (ISs). However, the multi-copy nature of plasmids should hinder IS introduction and spread, disfavoring inheritance of nascent plasmid variants through genetic drift. Mechanisms by which ISs overcome these barriers remain unidentified. Here we find that the RNA-guided nuclease TnpB enables such a mechanism to bias its inheritance in plasmids. We show that TnpB, the likely ancestor to Cas12, enables a gene drive to spread the IS within multicopy plasmids and functions as a primitive anti-self defense system in conjugative plasmids. The gene drive between TnpB-bearing ISs and plasmids promotes the spread of both MGEs beyond the ability of either individually. The nested existence between MGEs is not an incidental result of selfish spread, but a driver of it.

microbiology↗