The "Jack-of-all-Trades" Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium

Abstract

The γ-proteobacteria are a group of diverse bacteria including pathogenic Escherichia, Salmonella, Vibrio, and Pseudomonas species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as Salmonella and E. coli. Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.

Keywords: bacterial flagella; electron cryotomography; horizontal gene transfer; molecular evolution; subtomogram averaging.

FIGURE 1

The Enterobacteriaceae have β-like motors. (A) An unrooted global flagellar phylogeny. γ-proteobacteria are highlighted in green: the enteric Enterobacteriaceae γ-proteobacteria (Salmonella enterica and Escherichia coli) are not clustered with the other γ-proteobacteria, but are clustered within the β-proteobacteria (purple). Fully annotated version of this tree is presented in Supplementary Figure S1. (B) An organismal phylogeny focused on γ- (green) and β-proteobacteria (purple), rooted with an ε-proteobacterium, Campylobacter jejuni. The Enterobacteriaceae are highlighted in green. Fully annotated version of this tree is presented in Supplementary Figure S4. (C) The flagellar phylogeny of the γ- (green) and β-proteobacteria (purple). Note the shift in position of the Enterobacteriaceae (highlighted in green) from the γ-proteobacterial clade to within the β-proteobacterial clade. Rooted with Campylobacter jejuni. Fully annotated version of this tree is presented in Supplementary Figure S5. (D) The Bordetella bronchiseptica flagellar gene cluster is arranged in one continuous genetic locus.

FIGURE 2

Horizontal transfer of flagellar genes is confirmed by cryo electron tomography and subtomogram averaging. Subtomogram averages of the “donor” (Bordetella bronchiseptica) and “acceptor” (Plesiomonas shigelloides) strains confirms that the γ-proteobacterium, Salmonella enterica, has a flagellar motor that is structurally similar to the β-proteobacterium, B. bronchiseptica, and structurally distinct from the two motors of its close relative, the γ-proteobacterium P. shigelloides. The organism phylogeny (left) and flagellar phylogeny (right) are inconsistent as the γ-proteobacterium, Salmonella enterica, has a β-proteobacterial motor. Middle: Subtomogram averages of B. bronchiseptica (EMD-4999), S. enterica (EMD-3154), P. shigelloides polar motor (EMD-10057) and P. shigelloides lateral motor (EMD-10000). Note the faint C-ring density in the lateral motor. Subtomogram average boxes are 100 × 100 nm. Unsymmetrized structures are shown in Supplementary Figure S7.