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Genomic analysis of a key innovation in an experimental Escherichia coli population

Nature volume 489, pages 513–518 (2012)Cite this article

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Abstract

Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit+), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population’s history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

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Figure 1: Phylogeny of Ara–3 population.
Figure 2: Tandem amplification in Cit + genomes.
Figure 3: Expression levels from native citT , native rnk and evolved rnk-citT regulatory regions during aerobic metabolism.
Figure 4: New rnk-citT module confers Cit + phenotype in potentiated background.
Figure 5: Refinement of Cit + phenotype by increased number of rnk-citT modules.
Figure 6: Evidence for epistatic interactions in potentiation of Cit + phenotype.
Figure 7: Mutations that produced Cit + phenotype in 14 replay experiments.

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Acknowledgements

We thank N. Hajela, M. Kauth and S. Sleight for assistance, J. Meyer and J. Plucain for discussion, and C. Turner for comments on the paper. Sequencing services were provided by the MSU Research Technology Support Facility. We acknowledge support from the US National Science Foundation (DEB-1019989 to R.E.L.) including the BEACON Center for the Study of Evolution in Action (DBI-0939454), the US National Institutes of Health (K99-GM087550 to J.E.B.), the Defense Advanced Research Projects Agency (HR0011-09-1-0055 to R.E.L.), a Rudolf Hugh Fellowship (to Z.D.B.), a DuVall Family Award (to Z.D.B.), a Ronald M. and Sharon Rogowski Fellowship (to Z.D.B.) and a Barnett Rosenberg Fellowship (to Z.D.B).

Author information

Authors and Affiliations

  1. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, 48824, Michigan, USA

    Zachary D. Blount & Richard E. Lenski

  2. BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, 48824, Michigan, USA

    Zachary D. Blount, Jeffrey E. Barrick & Richard E. Lenski

  3. Department of Chemistry and Biochemistry, The University of Texas, Austin, 78712, Texas, USA

    Jeffrey E. Barrick

  4. Institute for Cellular and Molecular Biology, The University of Texas, Austin, 78712, Texas, USA

    Jeffrey E. Barrick

  5. Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada,

    Carla J. Davidson

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Contributions

J.E.B. and Z.D.B performed genome sequencing and analyses. J.E.B. performed phylogenetic analyses and developed code for sequence analyses. Z.D.B. performed growth curves, molecular experiments and sequenced specific genes. C.J.D. performed gene expression experiments. R.E.L. conceived and directs the long-term experiment. Z.D.B., J.E.B., C.J.D. and R.E.L. analysed data, wrote the paper and prepared figures.

Corresponding authors

Correspondence to Zachary D. Blount or Richard E. Lenski.

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The authors declare no competing financial interests.

Additional information

All genome data have been deposited in the NCBI Sequence Read Archive database (SRA026813). Other data have been deposited in the DRYAD database (http://dx.doi.org/10.5061/dryad.8q6n4). R.E.L. will make strains available to qualified recipients, subject to a material transfer agreement that can be found at http://www.technologies.msu.edu/inventors/mta-cda/mta/mta-forms.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5, Supplementary Tables 1, 3-15 and legend for Supplementary Table 2 (see separate file for Supplementary Table 2). (PDF 971 kb)

Supplementary Table 2

This table shows the mutations found in 29 sequenced genomes from population Ara–3. When opened, this file generates a summary table showing all mutations in html format; separate tables that show mutations for each individual genome in html format; and machine-readable data files for each genome. (ZIP 381 kb)

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Blount, Z., Barrick, J., Davidson, C. et al. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489, 513–518 (2012). https://doi.org/10.1038/nature11514

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