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Random Sequences Rapidly Evolve into de novo Promoters

Avihu H. Yona, Eric J. Alm, Jeff Gore
doi: https://doi.org/10.1101/111880
Avihu H. Yona
1Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Eric J. Alm
2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
3Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
4Center for Microbiome, Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Jeff Gore
1Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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  • For correspondence: gore@mit.edu
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Abstract

How do new promoters evolve? To follow evolution of de novo promoters, we put various random sequences upstream to the lac operon in Escherichia coli and evolved the cells in the presence of lactose. We found that a typical random sequence of ~100 bases requires only one mutation in order to enable growth on lactose by increasing resemblance to the canonical promoter motifs. We further found that ~10% of random sequences could serve as active promoters even without any period of evolutionary adaptation. Such a short mutational distance from a random sequence to an active promoter may improve evolvability yet may also lead to undesirable accidental expression. We found that across the E. coli genome accidental expression is minimized by avoiding codon combinations that resemble promoter motifs. Our results suggest that the promoter recognition machinery has been tuned to allow high accessibility to new promoters, and similar findings might also be observed in higher organisms or in other motif recognition machineries, like transcription factor binding sites or protein-protein interactions.

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Posted August 07, 2017.
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Random Sequences Rapidly Evolve into de novo Promoters
Avihu H. Yona, Eric J. Alm, Jeff Gore
bioRxiv 111880; doi: https://doi.org/10.1101/111880
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Random Sequences Rapidly Evolve into de novo Promoters
Avihu H. Yona, Eric J. Alm, Jeff Gore
bioRxiv 111880; doi: https://doi.org/10.1101/111880

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