Evolutionary analyses of polymeric immunoglobulin receptor (pIgR) in the mammals reveals an outstanding mutation rate in the lagomorphs

Abstract

Background: The transcytosis of polymeric immunoglobulins, IgA and IgM, across the epithelial barrier to the luminal side of mucosal tissues is mediated by the polymeric immunoglobulin receptor (pIgR). At the luminal side the extracellular ligand binding region of pIgR, the secretory component (SC), is cleaved and released bound to dimeric IgA (dIgA), protecting it from proteolytic degradation, or in free form, protecting the mucosa form pathogens attacks. The pIgR was first cloned for rabbit in early 1980's and since then has been described for all vertebrates, from fish to mammals. The existence of more than one functional pIgR alternative-spliced variant in the European rabbit, the complete pIgR as other mammals and a shorter pIgR lacking two SC exons, raised the question whether other lagomorphs share the same characteristics and how has the PIGR gene evolved in these mammals.

Results: To investigate these questions, we sequenced expressed pIgR genes for other leporid genus, Lepus spp., and obtained and aligned pIgR sequences from representative species of all mammalian orders. The obtained mammalian phylogeny, as well as the Bayesian inference of evolutionary rates and genetic distances, show that Lagomorpha pIgR is evolving at a higher substitution rate. Codon-based analyses of positive selection show that mammalian pIgR is evolving under strong positive selection, with strong incidence in the domains excised from the rabbit short pIgR isoform. We further confirmed that the hares also express the two rabbit pIgR isoforms.

Conclusions: The Lagomorpha pIgR unique evolutionary pattern may reflect a group specific adaptation. The pIgR evolution may be linked to the unusual expansion of IgA genes observed in lagomorphs, or to neofunctionalization in this group. Further studies are necessary to clarify the driving forces behind the unique lagomorph pIgR evolution.

Keywords: european rabbit; evolution; fc receptors; immune system; positive selection.

Figure 1

Phylogenetic tree of mammalian pIgR gene. Maximum likelihood (ML) method and the GTR+G+I model of nucleotide substitution were used to obtain the pIgR phylogenetic tree. Mammalian orders are highlighted in different colors. Bootstrap values are indicated near most relevant branches. For Lagomorpha sequences the last letter in the name identifies the long and short isoform that we sequenced, L identifies the long isoform and C the short isoform.

Figure 2

Alignment of leporid and human pIgR amino acid sequences. Shown are the pIgR amino acid sequences for the two European rabbit subspecies (O.c. cuniculus and O.c. algirus), the two studied hare species (L. europaeus and L. timidus) and Human (H. sapiens); for leporids, 1L identifies the long isoform and 1C the short isoform. The deletion of Ig like domains 2 and 3 in the leporids short isoforms is indicated between > and <. The PSC’s identified for the mammalian pIgR are highlighted in red rectangles. Protein domains are shaded in different colors: Ig like domains in two alternating blue accents, the linker spacer in grey, the transmembrane domain in yellow and the cytoplasmic tail in orange. The Ig like domain 1 CDRs are within red boxes. Conserved Cys residues are marked with * above the alignment. N-glycosilation sites are marked above the alignment: # indicates European rabbit glycosylation sites (51) and $ shows the rabbit and hare glycosylation site.

Figure 3

Branch-specific evolutionary rates (substitutions/site/million years) for PIGR estimated using BEAST v1.10.4 (34). The median of the high posterior density distribution is mapped onto the mammalian phylogenetic tree. The thickness and color of branches vary according to the inferred rate. The mammalian orders are indicated in different colors in a vertical bar to the right of the tree.

Figure 4

Sliding window along the pIgR nucleotide sequences showing the nucleotide diversity for Leporidae and Ochotonidae for (A) all sites and for (B) nonsynonymous sites. All Lagomorph sequences used in this study, except the Leporidae short transcripts, were used in this analysis. The analysis was performed in DnaSP version 6.12 with a window length of 250 nucleotides and a step size of 12 nucleotides. The pIgR domains are indicated.