Chromosomal position of ribosomal protein genes impacts long term evolution ofVibrio cholerae

Abstract

It is unclear how gene order within the chromosome influences bacterial evolution. The genomic location of genes encoding the flow of genetic information is biased towards the replication origin (oriC) in fast-growing bacteria. To study the role of chromosomal location on cell physiology we relocated the S10-spec-α locus (S10), harboring half of ribosomal protein genes, to different chromosomal positions in the fast-growing pathogen V. cholerae. We found that growth rate, fitness and infectivity inversely correlated the distance between S10 and oriC. To gain insight into the evolutionary effect of RP genomic position, we evolved strains bearing S10 at its current oriC-proximal location or derivatives harboring the locus far from it (i.e. 1.5Mbp). Populations deep sequencing on average 1 mutation fixed each 100 generations, mainly at genes linked to flagellum regulation, lipopolysaccharide synthesis, chemotaxis, biofilm and quorum sensing. Along the experiment, populations showed an increment in biofilm forming capacity. All populations increased their growth rate. However, growth rate advantage of populations bearing S10 at an oriC-proximal persisted along the experiment over those where the main ribosomal protein gene cluster locates at an oriC-distal position. This indicates that suppressor mutations cannot compensate S10 genomic location. We selected fast-growing clones displaying a ∼10% growth rate increment finding that they harbored inactivating mutations at, among other sites, flagellum master regulators flrAB regardless S10 genomic location. The introduction of these mutations on naïve V. cholerae strains resulted in a ∼10% increase in growth rate. Our study therefore demonstrates that the location of ribosomal protein genes conditions the evolutionary trajectory of growth rate in the long term. While genomic content is highly plastic in prokaryotes, gene order is an underestimated factor that conditions cellular physiology and lineage evolution. The lack of suppression enables artificial gene relocation for genetic circuit reprogramming.