Pseudogene repair driven by selection pressure applied in experimental evolution

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.

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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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.

Corresponding author

Correspondence to Bernhard O. Palsson.

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The authors declare no competing interests.

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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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