RT Journal Article SR Electronic T1 Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes JF bioRxiv FD Cold Spring Harbor Laboratory SP 072470 DO 10.1101/072470 A1 Morgan N. Price A1 Kelly M. Wetmore A1 R. Jordan Waters A1 Mark Callaghan A1 Jayashree Ray A1 Jennifer V. Kuehl A1 Ryan A. Melnyk A1 Jacob S. Lamson A1 Yumi Suh A1 Zuelma Esquivel A1 Harini Sadeeshkumar A1 Romy Chakraborty A1 Benjamin E. Rubin A1 James Bristow A1 Matthew J. Blow A1 Adam P. Arkin A1 Adam M. Deutschbauer YR 2016 UL http://biorxiv.org/content/early/2016/08/31/072470.abstract AB 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.