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Pseudogene repair driven by selection pressure applied in experimental evolution

Nature Microbiology volume 4, pages 386–389 (2019)Cite this article

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Abstract

Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product non-functional. Pseudogenes are found in many genomes and are not always eliminated, even if they are potentially ‘wasteful’. This raises a fundamental question about their prevalence. Here we report pseudogene efeU repair that restores the iron uptake system of Escherichia coli under a designed selection pressure during adaptive laboratory evolution.

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Fig. 1: The fragmentation and repair of efeU.
Fig. 2: Mutations in efeU acquired during ALE.

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Code availability

All code used to analyse the data is available at https://github.com/SBRG/mutation_analysis.

Data availability

DNA sequencing data from this study are available from the Sequence Read Archive database (SRA accession PRJNA505542). RNA sequencing data from this study are available from the Gene Expression Omnibus database under the accession number GSE122779.

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Acknowledgements

This work was funded by the Novo Nordisk Foundation under grant number NNF10CC1016517.

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Authors and Affiliations

  1. Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

    Amitesh Anand, Connor A. Olson, Laurence Yang, Anand V. Sastry, Edward Catoiu, Kumari Sonal Choudhary, Patrick V. Phaneuf, Troy E. Sandberg, Sibei Xu, Ying Hefner, Richard Szubin, Adam M. Feist & Bernhard O. Palsson

  2. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark

    Adam M. Feist & Bernhard O. Palsson

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  1. Amitesh Anand
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Contributions

A.A., A.M.F. and B.O.P. designed the study. A.A., C.A.O., S.X., Y.H. and R.S. performed the experiments. A.A., L.Y., A.V.S., C.A.O., E.C. and T.E.S. analysed the data. K.S.C. and P.V.P. contributed analysis tools. A.A. and B.O.P. wrote the manuscript.

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Correspondence to Bernhard O. Palsson.

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The authors declare no competing interests.

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Supplementary Information

Supplementary Figures 1–5, Supplementary Tables 1–6 and Supplementary References.

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Anand, A., Olson, C.A., Yang, L. et al. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol 4, 386–389 (2019). https://doi.org/10.1038/s41564-018-0340-2

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