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Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

Morgan N. Price, Kelly M. Wetmore, R. Jordan Waters, Mark Callaghan, Jayashree Ray, Jennifer V. Kuehl, Ryan A. Melnyk, Jacob S. Lamson, Yumi Suh, Zuelma Esquivel, Harini Sadeeshkumar, Romy Chakraborty, Benjamin E. Rubin, James Bristow, Matthew J. Blow, Adam P. Arkin, Adam M. Deutschbauer
doi: https://doi.org/10.1101/072470
Morgan N. Price
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Kelly M. Wetmore
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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R. Jordan Waters
2Joint Genome Institute, Lawrence Berkeley National Laboratory
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Mark Callaghan
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Jayashree Ray
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Jennifer V. Kuehl
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Ryan A. Melnyk
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Jacob S. Lamson
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Yumi Suh
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Zuelma Esquivel
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Harini Sadeeshkumar
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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Romy Chakraborty
3Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory
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Benjamin E. Rubin
4Division of Biological Sciences, University of California, San Diego
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James Bristow
2Joint Genome Institute, Lawrence Berkeley National Laboratory
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Matthew J. Blow
2Joint Genome Institute, Lawrence Berkeley National Laboratory
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  • For correspondence: MJBlow@lbl.gov APArkin@lbl.gov AMDeutschbauer@lbl.gov
Adam P. Arkin
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
5Department of Bioengineering, University of California, Berkeley
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  • For correspondence: MJBlow@lbl.gov APArkin@lbl.gov AMDeutschbauer@lbl.gov
Adam M. Deutschbauer
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
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  • For correspondence: MJBlow@lbl.gov APArkin@lbl.gov AMDeutschbauer@lbl.gov
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Abstract

Summary The function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted August 31, 2016.
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Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes
Morgan N. Price, Kelly M. Wetmore, R. Jordan Waters, Mark Callaghan, Jayashree Ray, Jennifer V. Kuehl, Ryan A. Melnyk, Jacob S. Lamson, Yumi Suh, Zuelma Esquivel, Harini Sadeeshkumar, Romy Chakraborty, Benjamin E. Rubin, James Bristow, Matthew J. Blow, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 072470; doi: https://doi.org/10.1101/072470
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Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes
Morgan N. Price, Kelly M. Wetmore, R. Jordan Waters, Mark Callaghan, Jayashree Ray, Jennifer V. Kuehl, Ryan A. Melnyk, Jacob S. Lamson, Yumi Suh, Zuelma Esquivel, Harini Sadeeshkumar, Romy Chakraborty, Benjamin E. Rubin, James Bristow, Matthew J. Blow, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 072470; doi: https://doi.org/10.1101/072470

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