The protein network of bacterial motility

Motility is achieved in most bacterial species by the flagellar apparatus. It consists of dozens of different proteins with thousands of individual subunits. The published literature about bacterial chemotaxis and flagella documented 51 protein–protein interactions (PPIs) so far. We have screened whole genome two‐hybrid arrays of Treponema pallidum and Campylobacter jejuni for PPIs involving known flagellar proteins and recovered 176 and 140 high‐confidence interactions involving 110 and 133 proteins, respectively. To explore the biological relevance of these interactions, we tested an Escherichia coli gene deletion array for motility defects (using swarming assays) and found 159 gene deletion strains to have reduced or no motility. Comparing our interaction data with motility phenotypes from E. coli , Bacillus subtilis , and Helicobacter pylori , we found 23 hitherto uncharacterized proteins involved in motility. Integration of phylogenetic information with our interaction and phenotyping data reveals a conserved core of motility proteins, which appear to have recruited many additional species‐specific components over time. Our interaction data also predict 18 110 interactions for 64 flagellated bacteria. Synopsis Motility is achieved in most bacterial species by a complex machine called the flagellar apparatus. This mechanical nanomachine consists of dozens of different proteins, most of which are present in multiple, sometimes thousands of copies (as in the case of the filament protein FliC). The bacterial flagellum rotates at a rotation frequency of 300 Hz, has an energy conversion rate of nearly 100%, and is able to self assemble (Berg, 2003 ; Macnab, 1999 , 2003 ; Kojima and Blair, 2004 ). Systematic analysis of hundreds of completely sequenced bacterial genomes has predicted many additional motility genes. Most of these predicted motility genes lie in known flagellar operons or gene clusters, although often their actual roles in motility remain unknown. A major goal of this study was to find novel flagellar components among the many proteins of still unknown function. In addition, we attempted an integrative systems biology approach to assemble a comprehensive picture of the flagellar protein complex in different bacterial species. In this study, we first identified genes essential for bacterial motility by systematically testing the swarming capability of 3985 gene deletion strains of Escherichia coli (Baba et al , 2006 ) and identified 159 mutants