Evolution of satellite plasmids can stabilize the maintenance of newly acquired accessory genes in bacteria

Abstract

12Plasmids play a principal role in the spread of antibiotic resistance and other traits by horizontal 13 gene transfer in bacteria. However, newly acquired plasmids generally impose a fitness burden 14 on a cell, and they are lost from a population rapidly if there is not selection to maintain a unique 15 function encoded on the plasmid. Mutations that ameliorate this fitness cost can sometimes 16 eventually stabilize a plasmid in a new host, but they typically do so by inactivating some of its 17 novel accessory genes. In this study, we identified an additional evolutionary pathway that can 18 prolong the maintenance of newly acquired genes encoded on a plasmid. We discovered that 19 propagation of an RSF1010-based IncQ plasmid in Escherichia coli often generated 'satellite 20 plasmids' with spontaneous deletions of accessory genes and genes required for plasmid 21 replication. These smaller plasmid variants are nonautonomous genetic parasites. Their presence 22 Significance Statement 30Plasmids are multicopy DNA elements found in bacteria that replicate independently of a cell's 31 chromosome. The spread of plasmids carrying antibiotic-resistance genes to new bacterial 32 pathogens is a challenge for treating life-threatening infections. Often plasmids or their accessory 33 genes encoding unique functions are lost soon after transfer into a new cell because they impose 34 a fitness burden. We report that a family of transmissible plasmids can rapidly evolve 'satellite 35 plasmids' that replicate as genetic parasites of the original plasmid. Satellite plasmid formation 36 reduces the burden from the newly acquired genes, which may enable them to survive intact for 37 longer after transfer into a new cell and thereby contribute to the spread of antibiotic resistance 38 and other traits within bacterial populations. 39Recently acquired plasmids generally impose a fitness burden on a new host cell, which may 53 be due to the cost of expressing antibiotic resistance genes (6) or due to plasmid-encoded genes 54 interfering with host processes (7-9). Therefore, purifying selection can rapidly lead to the loss 55 of genes encoded on a plasmid from a new host unless there is positive selection for traits they 56 confer (10). Continuous conjugative transfer to spread a plasmid to new cells within a population 57 can counteract the purifying selection process to some extent, but there is also a fitness cost of 58 increasing the conjugation rate on donor cells (11). Compensatory mutations on the chromosome 59 and/or plasmid can sometimes ameliorate the cost of a plasmid and favor its persistence (12-17). 60However, it takes a long time, typically several hundred cell generations, with constant selection 61 5 for novel plasmid function to evolve and fix these types of compensatory mutations in laboratory 62 experiments (12, 18, 19). These conditions may be unrealistic in most natural settings. 63Most experimental work examining BHR plasmid stability has used IncP plasmids as a 64 model (13, 14, 17). Fewer studies have focu...