Figure 2. Experimental evolution of Vibrio fischeri produced multiple alleles in the sensor kinase BinK.
(A). Phylogenetic relationship, symbiotic capacity, and mutations accrued during squid experimental evolution of ecologically diverse Vibrio fischeri strains. Strain relationships were inferred under maximum likelihood using whole genomes with RealPhy (Bertels et al., 2014) and with node supports calculated from 1,000 bootstraps. Graphic symbols for ecological niches represent the source of isolation. Intrinsic squid symbiotic capacities of the five experimentally evolved strains, as determined by the minimum inoculum concentration required for successful colonization of 90% of squid with a 3 hr (ES114, EM17, and WH1) or over-night (H905 and MJ11) inoculum, are represented by color spectrum. Consensus genomes for each of the parallel V. fischeri populations evolved through E. scolopes are shown on the right, with variants indicated by circles. Mutation details are shown in Table 2. The mutations that were selected in host-passaged populations improved symbiotic capacity rather than general vigor. (B) BinK mutations arising in squid-evolved populations of MJ11 occurred in the HAMP and HATPaseC domains. A homo-dimer structural model for BinK using TMPRed and hybrid histidine kinase domain modelling (Anantharaman and Aravind, 2000; Stewart and Chen, 2010) predicts that the accessory sensory Cache1 domain localizes to the periplasm whereas the remaining four functional domains (accessory HAMP, and conserved HisKA, HATPaseC, and REC phosphorelay domains) are cytoplasmic (shown as gray band). A position-specific scoring matrix (PSSM) analysis for each of the squid-evolved BinK positions indicates whether a given amino acid is more (positive) or less (negative) likely to be functionally neutral. Scores for the substitutions incurred at these sites are shown in bold. Please refer to Figure 2—figure supplement 1 for a phylogenetic assessment of BinK orthology across Aliivibrio and V. fischeri strains.
Figure 2—figure supplement 1. BinK orthology, conserved domains and squid-adapted binK alleles.
