Co-evolution dynamics of defense systems and anti-defense proteins in Enterobacteriaceae

Abstract

Bacterial defense systems (DEFs) undergo rapid evolutionary changes, yet the specific contributions of chromosomal versus mobile genetic element (MGE) environments to these dynamics remain unclear. Here, we analyzed 7,059 Enterobacteriaceae genomes using a phylogenetic birth-death model to quantify gene gain, loss, expansion, and reduction. We reveal that while DEF turnover rates diverge from the background dynamics of their carrying elements, they remain statistically consistent across different genomic environments. Although turnover patterns vary among specific defense families, DEFs generally exhibit a conserved bias toward gain and reduction, regardless of their genomic location. Moreover, anti-defense proteins display accelerated loss, expansion, and reduction rates relative to their cognate defense systems. Variability in turnover rates among defense types is primarily driven by expansion and reduction. We also identified that on prophages, both DEFs and anti-DEFs undergo co-loss with 300 Clusters of Orthologous Genes (COGs). Overall, these results suggest that defense systems possess intrinsic turnover dynamics independent of their genomic environment, and that on prophages, they are often co-spread with their anti-defense proteins on evolutionary timescales. ImportanceBacterial defense systems (DEF) and anti-defense proteins (anti-DEF) are highly dynamic; while it is known that mobile genetic elements (MGEs) facilitate the spread of these systems, we lack a quantitative understanding of how the genomic environment shapes their evolutionary fate. Here, we dissected the birth-death dynamics of DEF and anti-DEF across Enterobacteriaceae, showing that DEF on MGEs, particularly prophages, follows a gain-biased but reduction-prone trajectory. This suggests that MGEs act as rapid shuttles for acquiring new immunity families, which subsequently undergo frequent copy-number reductions due to the evolutionary cost of the mobile elements. Furthermore, we uncovered a tight evolutionary coupling between DEF and anti-DEF, which undergo co-loss with many Clusters of Orthologous Genes (COGs). By quantifying gene turnover rates, our study provides an explanation for the heterogeneity of bacterial immunity: it is driven by the high-frequency acquisition of MGE-borne defenses, while their long-term persistence relies on translocation to the more stable chromosomal environment.