The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes

Abstract

Background: Many drugs of natural origin are hydrophobic and can pass through cell membranes. Hydrophobic molecules must be susceptible to active efflux systems if they are to be maintained at lower concentrations in cells than in their environment. Multi-drug resistance (MDR), often mediated by intrinsic membrane proteins that couple energy to drug efflux, provides this function. All eukaryotic genomes encode several gene families capable of encoding MDR functions, among which the ABC transporters are the largest. The number of candidate MDR genes means that study of the drug-resistance properties of an organism cannot be effectively carried out without taking a genomic perspective.

Results: We have annotated sequences for all 60 ABC transporters from the Caenorhabditis elegans genome, and performed a phylogenetic analysis of these along with the 49 human, 30 yeast, and 57 fly ABC transporters currently available in GenBank. Classification according to a unified nomenclature is presented. Comparison between genomes reveals much gene duplication and loss, and surprisingly little orthology among analogous genes. Proteins capable of conferring MDR are found in several distinct subfamilies and are likely to have arisen independently multiple times.

Conclusions: ABC transporter evolution fits a pattern expected from a process termed 'dynamic-coherence'. This is an unusual result for such a highly conserved gene family as this one, present in all domains of cellular life. Mechanistically, this may result from the broad substrate specificity of some ABC proteins, which both reduces selection against gene loss, and leads to the facile sorting of functions among paralogs following gene duplication.

Figure 1

Structural diversity of ABC transporters. Illustration of the various domain organizations found among members of the ABC transporter family in C. elegans. TM indicates a transmembrane domain typically containing six predicted membrane-spanning helices. ABC indicates an ATP-binding cassette domain. The color codes for each structure are used throughout the figures to show the lack of concordance between structural categories and families defined on the basis of sequence similarity.

Figure 2

Tree of human ATP-binding cassette domains. The evolution of the ABCB subfamily from within the ABCC subfamily, and the structural diversity of subfamily B is shown here. Each cluster of ABC domains within each subfamily, except for subfamily B, is collapsed to form a single, representative, branch; n-term: amino-terminal ABC; c-term: carboxy-terminal ABC. The phylogeny of ATP-binding cassettes from human ABC transporters was produced according the following procedure. Predicted amino-acid sequences were aligned using ClustalX [54]. Aligned sequences were used to generate matrices of mean distances among proteins, and these matrices were used to generate a phylogenetic tree according to the neighbor-joining algorithm [55], refined using the SPR branch-swapping technique under the minimum evolution criterion, implemented by PAUP*4.0b10 [56]. Bootstrapping [57] was used to determine the relative support for the various branches of the tree (1,000 replicates), and nodes with less than 50% support were collapsed to form polytomies. The structures of the proteins in which the domains are embedded are indicated according to the color scheme in Figure 1. It should be noted that branch lengths in the figures are not to scale and do not represent distances between protein sequences. The original alignment files are available as Additional data files 1-8.

Figure 3

Phylogenetic tree of ABCA proteins in three eukaryote genomes. A phylogeny derived and displayed according to the procedure outlined in the legend to Figure 2, except that complete protein sequences were used, not just those of the ATP-binding cassettes. The genome of origin for each protein is indicated by prefixes before each gene name, according the following scheme: Ce, C. elegans; Dm, D. melanogaster; Hs, H. sapiens; Sc, S. cerevisiae.

Figure 4

Phylogenetic tree of ABCB proteins in four eukaryote genomes. A phylogeny derived and displayed according to the procedure outlined in the legend to Figure 3. Shown here is the division between the half transporters, which are most of the ABCB genes in mammals, and the full-transporters (called P-glycoproteins (P-gps)) that have evolved from them. Four lineages of P-gps (exemplified by genes F22E10.1-4, T21E8.1-3, C47A10.1 and C54D1.1) have been lost in both flies and mammals, and of the two remaining P-gp lineages, one has been lost in each of the fly and human lines of descent. Subsequent duplications within the single remaining P-gp lineage in both flies and mammals have not been sufficient to keep pace with continuing P-gp duplications in the worm genome.

Figure 5

Phylogenetic tree of ABCC proteins in four eukaryote genomes. A phylogeny derived and displayed according to the procedure outlined in the legend of Figure 3.

Figure 6

Phylogenetic trees of ABCD, ABCE, and ABCF proteins in four eukaryote genomes. Phylogenies derived and displayed according to the procedure outlined in the legend of Figure 3.

Figure 7

Phylogenetic trees of ABCG and ABCH proteins in four eukaryote genomes. Phylogenies derived and displayed according to the procedure outlined in the legend of Figure 3.