Evolution and origin of HRS, a protein interacting with Merlin, the Neurofibromatosis 2 gene product

Abstract

Hepatocyte growth factor receptor tyrosine kinase substrate (HRS) is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2) gene product, and this interaction may be important for Merlin's tumor suppressor activity. Understanding the evolution, origin, and structure of HRS may provide new insight into Merlin function. We show that HRS homologs are present across a wide range of Metazoa with the yeast Vps27 protein as their most distant ancestor. The phylogenetic tree of the HRS family coincides with species evolution and divergence, suggesting a unique function for HRS. Sequence alignment shows that various protein domains of HRS, including the VHS domain, the FYVE domain, the UIM domain, and the clathrin-binding domain, are conserved from yeast to multicellular organisms. The evolutionary transition from unicellular to multicellular organisms was accompanied by the appearance of a binding site for Merlin, which emerges in the early Metazoa after its separation from flatworms. In addition to the region responsible for growth suppression, the Merlin-binding and STAM-binding domains of HRS are conserved among multicellular organisms. The residue equivalent to tyrosine-377, which is phosphorylated in the human HRS protein, is highly conserved throughout the HRS family. Three additional conserved boxes lacking assigned functions are found in the HRS proteins of Metazoa. While boxes 1 and 3 may constitute the Eps-15-and Snx1-binding sites, respectively, box 2, containing the residue equivalent to tyrosine-377, is likely to be important for HRS phosphorylation. While several functional domains are conserved throughout the HRS family, the STAM-binding, Merlin-binding, and growth suppression domains evolved in the early Metazoa around the time the Merlin protein emerged. As these domains appear during the transition to multicellularity, their functional roles may be related to cell-cell interaction.

Keywords: HRS; Merlin; endosomal protein; hepatocyte growth factor receptor tyrosine kinase substrate.

Figure 1.

Phylogenetic tree for HRS protein family. The names of proteins are given in Table 1. Length of branch is shown above and the bootstrap value, of a branch bellow the line. The scale for branch length is given in the upper right corner. Cn-vps27 protein is an outgroup.

Figure 2.

Alignment of the VHS-domain. The depth of three-level shadow is directly proportional to the degree of evolutionary conservation. The bar above the alignment shows the position of VHS domain. *—Intermediate enumerator. ##C—an alternative splicing site of Drosophila gene; the symbols bellow the alignment show the degree conservation of alignment positions (abbreviated as in GeneDoc program).

Figure 3.

FYVE-domain alignment. The abbreviations as in Figure 1. The FYVE domain of Cryptococcus neoformans is shown by blue letters; phosphorylation site, with yellow.

Figure 4.

UIM-domain alignment. Abbreviations as in Figure 1. Amino-acids belonging to UIM domain are blue shadowed. Ubiquitin interacting aminoacids are denoted by orange letters. UIM domain of Vps27 protein differ from UIM domains of HRS protein and is denoted by red letters.

Figure 5.

STAM domain alignment. Abbreviations as in Figure 1. Conserved residues of NF2 interacting domain denoted by pink color and the conserved residues of growth suppression domain by orange color. The phosphoserine (539 position of alignment) in Cryptococcus neoformans sequence denoted with yellow letter.

Figure 6.

Clathrin binding domain alignment. Abbreviations as at Figure 1.