Bacterial Roots and Branches of the HCN/CNG Family of Ion Channels: Phylogeny, Structure, and Implications for Eukaryotic HCN/CNG Structure and Function

Abstract

In gene, protein, and RNA families, it is typical for bacterial, archaeal, and eukaryotic members to form separate clusters. In this paper we report and analyze both phylogenetically and structurally a different pattern in the HCN/CNG family of ion channels, in which two subsets of bacterial members of the family clusters with eukaryotic members, rather than with the other bacterial members. The most parsimonious interpretation of the phylogeny is that this pattern is a consequence of horizontal gene transfer from a eukaryotic organism into a bacterium. We term the bacterial descendants of such transfer Eukaryotic-Like HCN/CNG's (ELHCN/CNG's). All of the ELHCN/CNG's have typical potassium channel selectivity filters. Thus in that sense they are more similar to HCN's than CNG's. However by more global similarity measures, they are roughly equally distant from the HCN's and CNG's, suggesting that the eukaryote-to-bacteria horizontal transfer was of a common ancestor to both the HCN's and CNG's. Our phylogenetic analysis further suggests that among the bacteria, subsequent spread of these two subsets was as much by horizontal transfer as by lineal descent. One possible mechanism for such transfer is amoeba, for which there is evidence that they engage in horizontal transfer with bacteria, and also facilitate horizontal transfer among bacteria. The ELHCN/CNG's may be useful biophysical and functional models for eukaryotic members of this family, especially because they share with the eukaryotic members a long C-linker between the inner helix of the permeation pathway and the ligand binding sites in the cyclic nucleotide binding domain. We present a model-built structure of one of the ELHCN/CNG's, which suggests a mechanism for coupling of ligand binding with channel opening.