The molecular evolution of the p120-catenin subfamily and its functional associations

Abstract

Background: p120-catenin (p120) is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1-3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor.

Methodology/principal findings: To clarify functional relationships between these proteins and how they relate to the classical cadherins, we have examined the proteomes of 14 diverse vertebrate and metazoan species. The data reveal a single ancient δ-catenin-like p120 family member present in the earliest metazoans and conserved throughout metazoan evolution. This single p120 family protein is present in all protostomes, and in certain early-branching chordate lineages. Phylogenetic analyses suggest that gene duplication and functional diversification into "p120-like" and "δ-catenin-like" proteins occurred in the urochordate-vertebrate ancestor. Additional gene duplications during early vertebrate evolution gave rise to the seven vertebrate p120 family members. Kaiso family members (i.e., Kaiso, ZBTB38 and ZBTB4) are found only in vertebrates, their origin following that of the p120-like gene lineage and coinciding with the evolution of vertebrate-specific mechanisms of epigenetic gene regulation by CpG island methylation.

Conclusions/significance: The p120 protein family evolved from a common δ-catenin-like ancestor present in all metazoans. Through several rounds of gene duplication and diversification, however, p120 evolved in vertebrates into an essential, ubiquitously expressed protein, whereas loss of the more selectively expressed δ-catenin, p0071 and ARVCF are tolerated in most species. Together with phylogenetic studies of the vertebrate cadherins, our data suggest that the p120-like and δ-catenin-like genes co-evolved separately with non-neural (E- and P-cadherin) and neural (N- and R-cadherin) cadherin lineages, respectively. The expansion of p120 relative to δ-catenin during vertebrate evolution may reflect the pivotal and largely disproportionate role of the non-neural cadherins with respect to evolution of the wide range of somatic morphology present in vertebrates today.

Figure 1. Domain structure of the p120-catenin family.

(A) The vertebrate members of the p120-catenin family of proteins all contain a central Armadillo repeat domain consisting of 9 tandemly linked imperfect 42 amino-acid repeats (blue boxes). The four “Core” members also contain an amino-terminally located coiled-coil domain (green boxes). In the case of p120 and ARVCF, alternative splicing in this region gives rise to two major isoforms, which either contain (isoform 1) or not (isoform 3) this coiled-coil region. All “Core” members, except p120, also have a carboxy-terminally located PDZ ligand domain (purple boxes). (B) The invertebrate members of the p120-catenin family similarly possess centrally located Armadillo repeats, though in the case of Amphioxis this region contains 6 rather than 9 repeats. N-terminal regions show more diversity with no distinct domain structure (D. melanogaster, Amphioxis, Ciona δ-catenin-like), Fibronectin type III domains (orange circles, C. elegans), or a coiled-coil domain (Ciona p120-like). Similar to vertebrate members, the C. elegans family member also contains a carboxy-terminally located PDZ ligand domain (purple box).

Figure 2. The evolutionary history of the p120-catenin family of proteins.

(A) Maximum likelihood analysis on an alignment constructed using entire protein sequences, (B) Bayesian inference analysis on an alignment constructed using entire protein sequences, (C) Maximum likelihood analysis on an alignment constructed using the nine Arm domains, and (D) Bayesian inference analysis on an alignment constructed using the nine Arm domains. Color-coded clades correspond to the seven family members found in vertebrates (p120, ARVCF, p0071, δ-catenin, plakophilins 1–3) and each clade contains only sequences from vertebrates. Numbers near internodes indicate bootstrap (for maximum likelihood analyses)/posterior probability (for Bayesian inference analyses) clade support values. Clade support values <50% are not shown. PK1-3: plakophilins 1–3.

Figure 3. The evolutionary history of the Kaiso family of proteins.

The majority-rule consensus tree from a Bayesian inference analysis on an alignment constructed using entire protein sequences is shown. Numbers near internodes indicate posterior probability (for Bayesian inference analyses)/bootstrap (for maximum likelihood analyses) clade support values. Clade support values <50% are not shown.

Figure 4. Presence/Absence of families involved in cell-cell adhesion and signalling.

Phylogenetic distribution of p120-family proteins, kaiso-family proteins, junctional proteins, and proteins collectively required for a functional wnt pathway. A filled box indicates the presence of an orthologue from the corresponding protein family. Color coding for the phylogenetic tree is as follows: pre-metazoan in green, metazoan in blue, bilateral metazoans in red.