Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 β-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.
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We thank R. León-Sampedro for valuable technical assistance with bioinformatic analyses. This work was supported by the Instituto de Salud Carlos III (Plan Estatal de I + D + i 2013–2016): grants CP15-00012, PI16-00860 and CIBER (CB06/02/0053), co-financed by the European Development Regional Fund (ERDF) ‘A way to achieve Europe’. R.P.M. and R.C.M. are supported by a Newton Advanced Fellowship awarded by the Royal Society (NA140196). R.P.M. and A.F.H. are funded by UNAM-PAPIIT (IA201017 and IA201016). R.C.M. was supported by a Wellcome Trust Senior Research Fellowship (WT106918AIA). J.C.R.H.B. is a doctoral student from Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM) and received fellowship 596191 from CONACYT. J.A.E. is supported by the Atracción de Talento programme of the Comunidad de Madrid (2016-T1/BIO-1105). A.S.M. is supported by a Miguel Servet Fellowship from the Instituto de Salud Carlos III (MS15/00012) cofinanced by The European Social Fund (ESF) ‘Investing in your future’ and ERDF.
The authors declare no competing interests.
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Supplementary Figs. 1–10, Supplementary Tables 1–3.
Plots representing raw data of the bacterial growth and allelic content in the antibiotic array related to Figs. 2 and 4. The title on each plot denotes the population colonizing the antibiotic array, as well as the antibiotic selection route applied. Optical density (left side) and GFP/RFP ratio (right side) are colour-coded as indicated in the respective legends. The red square denotes the populations that were used to inoculate a fresh antibiotic array on the following day.
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Rodriguez-Beltran, J., Hernandez-Beltran, J.C.R., DelaFuente, J. et al. Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation. Nat Ecol Evol 2, 873–881 (2018). https://doi.org/10.1038/s41559-018-0529-z
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