Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors

Abstract

Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such "Cys-less" receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the "Cys-loop" proline is absolutely conserved, suggesting the more fitting name "Pro loop" for that motif, and "Pro-loop receptors" for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.

Fig 1. Phylogenetic tree of organisms whose genomes contain predicted Pro-loop receptors.

Colored branches represent taxons that were not discussed previously in the pLGIC literature (green: unicellular eukaryotes, orange: archaea, magenta: bacteria). Colored squares next to eukaryotic taxa indicate the types of pLGICs present (green: Cys-less, blue: cationic-type Cys-loop, red: anionic-type Cys-loop); the half green squares next to metazoan taxons indicate the presence of Cys-less pLGICs in some species. The tree is extracted from NCBI Taxonomy.

Fig 2. Subset of large multiple sequence alignment.

Contains 11 novel pLGIC sequences from bacteria, archaea, and eukaryotes. GLIC, nematode GluCl, mouse serotonin, and human GABA_A β3 receptors are included for comparison. Residues are colored by type according to the ClustalX scheme. Unconserved regions are hidden and indicated by blue, vertical lines. Species names are abbreviated in the figure. Bacteria: Gloeobacter violaceus, Crocosphaera watsonii, Synechococcus sp., archaea: Thaumarchaeota archaeon, Methanobacterium formicicum, Nitrososphaera viennensis, eukaryotes: Capsaspora owczarzarki, Monosiga brevicollis, Pythium ultimum, Stylonychia lemnae.

Fig 3. Location of the most conserved residues within the structure of a pLGIC subunit.

One subunit of the homomeric GABA_A β3 receptor shown as cartoon, colored from blue to red along the sequence. Conserved residues listed in Table 1 are shown as sticks and colored by residue type (orange: Pro, grey: Phe, green: Tyr, red: Asp, blue: Arg).

Fig 4. Prime numbering scheme for transmembrane helices M1 to M3.

A sequence alignment for a set of pLGICs is shown annotated with a prime numbering convention in each helix, starting on the cytoplasmic side. Sequences are labeled with their abbreviated gene and species names, or Uniprot identifier in the case of the predicted pLGIC from the protozoan Monosiga brevicollis. The figure shows the existing convention for M2, generalizes that proposed for M3 in nAChR α subunits [34], and proposes a new convention for M1. Triangles indicate 1’ positions as well as conserved residues that may help anchoring other sequences.

Fig 5. Inferred phylogenetic tree of the Pro-loop superfamily.

Branch colors represent a combination of taxonomy and sequence features: magenta: eubacteria, orange: archaea, pale green: Cys-less pLGICs of protists cyan: Cys-less pLGICs of metazoans, blue: cationic-type Cys-loop of metazoans, dark blue: cationic-type Cys-loop of protists, red: anionic-type Cys-loop of metazoans, dark red: anionic-type Cys-loop of protists, pale red: anionic-type Cys-less of metazoans. Circles indicate SH support above 90%. The gray arrow indicates two bacterial branches of poorly-defined position, which sometimes group with eukaryotic sequences.

Fig 6. Schematic, putative molecular phylogeny of the Pro-loop superfamily.

Each taxonomic category represents many species. Dashed lines indicate alternate hypotheses. Speciation events followed by short branches ending with gene loss depict the many unicellular lineages that have likely lost their Pro-loop receptors. In the case of metazoans, the cyan line indicates the clade of Cys-less Pro-loop receptors that survives in a few extant invertebrates. The red arrow indicates appearance of the Cys loop, presumably in an ancient unicellular eukaryote. Dashed red-blue lines describe the ancestral Cys-loop receptor, which may have been anionic or cationic-type.