Chromosomal position of ribosomal protein genes impacts long term evolution of Vibrio cholerae.

Larotonda, L. I.; Mornico, D.; Khanna, V.; Bernal-Bayard, J.; Ghigo, J. M.; Kennedy-Val, M.-E.; Comerci, D. J.; Mazel, D.; SOLER-BISTUE, A.

doi:10.1101/2022.05.06.490600

bioRxiv · 10.1101/2022.05.06.490600

Chromosomal position of ribosomal protein genes impacts long term evolution of Vibrio cholerae.

Larotonda, L. I.·Mornico, D.·Khanna, V.·Bernal-Bayard, J.·Ghigo, J. M.·Kennedy-Val, M.-E.·Comerci, D. J.·Mazel, D.·SOLER-BISTUE, A.

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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- 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 ribosomal protein genomic position, we evolved strains bearing S10 at its current oriC-proximal location or derivatives where the locus far from it, at the chromosomal termini. All populations increased their growth rate along the experiment regardless S10 genomic location. However, the growth rate advantage of an oriC-proximal location persisted along experimental evolution indicating that suppressor mutations cannot compensate S10 genomic position. An increment in biofilm forming capacity was another common trait observed along the experiment. Deep sequencing of populations showed on average 1 mutation fixed each 100 generations, mainly at genes linked to flagellum biosynthesis regulation, lipopolysaccharide synthesis, chemotaxis, biofilm and quorum sensing. We selected fast-growing clones displaying a [~]10% growth rate increment. We found that they harbored inactivating mutations at, among other sites, the flagellum master regulators flrAB. The introduction of these mutations into naive V. cholerae strains resulted in a [~]10% increase of 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.

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Larotonda, L. I., Mornico, D., Khanna, V., Bernal-Bayard, J., Ghigo, J. M., Kennedy-Val, M.-E., Comerci, D. J., Mazel, D., SOLER-BISTUE, A.. 2022-05-06. Chromosomal position of ribosomal protein genes impacts long term evolution of Vibrio cholerae.. https://doi.org/10.1101/2022.05.06.490600

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