FIG. 1.

Phylogenetic analysis of a selection of experimentally studied bacterial histidine kinases that are related to a group of fungal genes (one exception: the bacterial sequences from Streptomyces are from a published sequence from a genome project in progress and not yet experimentally studied). The bacterial proteins shown in this tree include a cluster of proteins most related to the fungal homologs (proposed orthologs) and selected experimentally studied proteins from a subfamily of histidine kinases that help illustrate the orthologous group. The tree was rooted by a more divergent member of the extended sensor histidine kinase family, P. aeruginosa PhoQ. The tree was constructed using the neighbor-joining method of PHYLIP (for methodology, see the unpublished PHYLIP documentation that is freely available: http://www.ibb.waw.pl/docs/PHYLIPdoc/main.html). Horizontal branch lengths in the tree correspond to the degree of relatedness of each protein. The number of times out of 100 that a given node of the tree was present in 100 bootstrapped replicates of the analysis is also indicated at each node to provide a statistical evaluation of the branching order in the tree. Brackets contain a description of phenotypes affected by disruption or overexpression of each gene, including changes in compounds secreted. Those proteins that were investigated and then were shown to play a role in virulence are in bold (i.e., all those investigated for their role in pathogenicity to date that have been shown to be virulence factors). We propose that the proteins shown here from Pseudomonas, Azotobacter, and Streptomyces, as well as the enteric ExpS and BarA proteins, are orthologous (i.e., diverged due to organism speciation), while the fungal genes are xenologous (obtained through horizontal gene transfer from an ancestor of the Streptomyces to an ancestor of these fungi and then subsequently diverged). Analysis using iPSORT (http://HypothesisCreator.net/iPSORT/) for the prediction of mitochondrial targeting sequences indicated that the fungal histidine kinases do not function in the mitochondria and they are apparently not encoded in the mitochondrial genome and thus are not similar to bacterial kinases due to the bacterial origin of mitochondria.