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Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation

Nature Ecology & Evolution volume 2, pages 873–881 (2018)Cite this article

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Abstract

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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Fig. 1: Conceptual and experimental models.
Fig. 2: Bacterial growth and allelic content in the antibiotics array.
Fig. 3: Invasion experiments.
Fig. 4: MCPs alleviate trade-offs under strong selective pressures.
Fig. 5: Theoretical model.
Fig. 6: Numerical examples predicting the duration of plasmid-mediated heterozygosity under a range of fluctuating antibiotic conditions.

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain

    Jeronimo Rodriguez-Beltran, Javier DelaFuente & Alvaro San Millan

  2. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Mexico

    J. Carlos R. Hernandez-Beltran, Ayari Fuentes-Hernandez & Rafael Peña-Miller

  3. Departamento de Sanidad Animal and VISAVET, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain

    Jose A. Escudero

  4. Department of Zoology, University of Oxford, Oxford, UK

    R. Craig MacLean

  5. Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain

    Alvaro San Millan

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  1. Jeronimo Rodriguez-Beltran
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Contributions

J.R.B., A.S.M. and R.C.M. were responsible for the conceptualization of the study; J.R.B., A.S.M. and J.A.E. designed the methodology; R.P.M., J.C.R.H.B. and A.F.H. postulated and analysed the mathematical model; J.C.R.H.B., A.F.H., J.A.E., J.D. and J.R.B. performed experiments and contributed to data analysis; J.R.B. and A.S.M. analysed data and prepared the original draft of the manuscript and undertook the reviewing and editing; all authors supervised and approved the final version of the manuscript. A.S.M. was responsible for funding acquisition and supervision.

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Correspondence to Jeronimo Rodriguez-Beltran or Alvaro San Millan.

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Supplementary Figs. 1–10, Supplementary Tables 1–3.

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Supplementary Data 1

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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