Acquire and rewire: mobile genetic elements co-opt the bacterial core genome

Rebeca Carvalho, James Hall, João Botelho

It is assumed that bacterial genomes are streamlined, with genes encoding core functions integrated with one another and with aligned fitness interests. Such genes can gain little from horizontal transfer, as any recipient would already carry its own copy better adapted to resident networks. These restrictions motivated the ‘complexity hypothesis’, which predicts that core genes are rarely transferred. Yet homologues of core genes are repeatedly found outside their native chromosomal context, carried by mobile genetic elements such as plasmids and phage-plasmids, and by domesticated replicons such as chromids. Explaining this pattern requires us to ask whether a copy rides a mobile, self-interested element or a domesticated, host-aligned one. On domesticated, vertically inherited carriers, a second copy plausibly serves the host, through dosage, niche-specific benefit or functional specialization. On mobile, selfish elements, it may instead serve the element, by promoting behaviors that favor onward transmission. Because they enter cells that already have a host-encoded copy, we propose that mobile variants can act through dosage or through effects disproportionate to their abundance, for example by co-assembling with the chromosomal product. Here, we discuss the evolutionary drivers and consequences of extrachromosomal core genes and argue that these overlooked copies deserve systematic study.