Molecular evolution of the LNX gene family

Abstract

BackgroundLNX (Ligand of Numb Protein-X) proteins typically contain an amino-terminal RING domain adjacent to either two or four PDZ domains - a domain architecture that is unique to the LNX family. LNX proteins function as E3 ubiquitin ligases and their domain organisation suggests that their ubiquitin ligase activity may be targeted to specific substrates or subcellular locations by PDZ domain-mediated interactions. Indeed, numerous interaction partners for LNX proteins have been identified, but the in vivo functions of most family members remain largely unclear.ResultsTo gain insights into their function we examined the phylogenetic origins and evolution of the LNX gene family. We find that a LNX1/LNX2-like gene arose in an early metazoan lineage by gene duplication and fusion events that combined a RING domain with four PDZ domains. These PDZ domains are closely related to the four carboxy-terminal domains from multiple PDZ domain containing protein-1 (MUPP1). Duplication of the LNX1/LNX2-like gene and subsequent loss of PDZ domains appears to have generated a gene encoding a LNX3/LNX4-like protein, with just two PDZ domains. This protein has novel carboxy-terminal sequences that include a potential modular LNX3 homology domain. The two ancestral LNX genes are present in some, but not all, invertebrate lineages. They were, however, maintained in the vertebrate lineage, with further duplication events giving rise to five LNX family members in most mammals. In addition, we identify novel interactions of LNX1 and LNX2 with three known MUPP1 ligands using yeast two-hybrid asssays. This demonstrates conservation of binding specificity between LNX and MUPP1 PDZ domains.ConclusionsThe LNX gene family has an early metazoan origin with a LNX1/LNX2-like protein likely giving rise to a LNX3/LNX4-like protein through the loss of PDZ domains. The absence of LNX orthologs in some lineages indicates that LNX proteins are not essential in invertebrates. In contrast, the maintenance of both ancestral LNX genes in the vertebrate lineage suggests the acquisition of essential vertebrate specific functions. The revelation that the LNX PDZ domains are phylogenetically related to domains in MUPP1, and have common binding specificities, suggests that LNX and MUPP1 may have similarities in their cellular functions.

Lnx2 ubiquitin ligase is essential for exocrine cell differentiation in the early zebrafish pancreas

“…In zebrafish, three LNX1/2 homologs (lnx1, lnx2a, and lnx2b) have been identified (18), and Lnx2b affects dorso-ventral patterning by modulation of Dharma (Bozozok, Nieuwkoid) stability (18,19). In eutherian mammals, LNX-2b has been lost by pseudogenization, contributing several exons to the noncoding Xist RNA (36,37). We show here that zebrafish Lnx2a, like human LNX1, can mediate Numb ubiquitylation and degradation.…”

PDZRN4 acts as a suppressor of cell proliferation in human liver cancer cell lines

“…LNX1 and LNX2 share a common domain structure consisting of one RING and four PDZ domains . LNX3 and LNX4 are structurally similar, both of them contain one RING domain and two PDZ domains, which are probably derived from LNX1 or LNX2 because of the loss of one PDZ domain . Previous studies have shown that, LNX1 and LNX2 function as E3‐dependent ubiquitin ligases in the degradation of cell fate determinant Numb, which asymmetrically distributed in dividing neuro‐epithelial cells that undergo asymmetric cell divisions and can inhibit the ability of Notch to suppress neuronal differentiation .…”

“…10 LNX3 and LNX4 are structurally similar, 11 both of them contain one RING domain and two PDZ domains, which are probably derived from LNX1 or LNX2 because of the loss of one PDZ domain. 12 Previous studies have shown that, LNX1 and LNX2 function as E3-dependent ubiquitin ligases in the degradation of cell fate determinant Numb, which asymmetrically distributed in dividing neuro-epithelial cells that undergo asymmetric cell divisions and can inhibit the ability of Notch to suppress neuronal differentiation. 13,10,[14][15][16] LNX3, also named PDZRN3, plays an essential role in the differentiation of myoblasts into myotubes, and depletion of PDZRN3 will inhibit the formation of myotubes.…”

Ubiquitin ligase LNX1 is a major regulator of glycine recapture by the presynaptic transporter GlyT2

“…Our data using interaction assays, imaging and glycine transport assays reveal that LNX1 interacts with the c-terminus of GlyT2 in neurons and ubiquitinates a c-terminal cluster of lysines of this transporter to control its expression and activity. LNX1 (Ligand of Numb Protein-X) or PDZRN (PDZ and RING) is part of the LNX family of proteins, which consists of five members (LNX1-5) that present a structure containing both an n-terminus RINGfinger domain and one to four PDZ domains in tandem in the c-terminus [56][57][58] . This modular domain organization, unique to the LNX family, suggests that LNX members have a facility for ubiquitinating substrates containing protein binding motifs (PBM), which are recognized specifically through the different PDZ domains.…”