Comparative genome analysis of cortactin and HS1: the significance of the F-actin binding repeat domain

Abstract

Background: In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related protein (Arp)2/3 mediated actin polymerization. It shares a high amino acid sequence and structural similarity to hematopoietic lineage cell-specific protein 1 (HS1) although their functions differ considerable. In this manuscript we describe the genomic organization of these two genes in a variety of species by a combination of cloning and database searches. Based on our analysis, we predict the genesis of the actin-binding repeat domain during evolution.

Results: Cortactin homologues exist in sponges, worms, shrimps, insects, urochordates, fishes, amphibians, birds and mammalians, whereas HS1 exists in vertebrates only, suggesting that both genes have been derived from an ancestor cortactin gene by duplication. In agreement with this, comparative genome analysis revealed very similar exon-intron structures and sequence homologies, especially over the regions that encode the characteristic highly conserved F-actin-binding repeat domain. Cortactin splice variants affecting this F-actin-binding domain were identified not only in mammalians, but also in amphibians, fishes and birds. In mammalians, cortactin is ubiquitously expressed except in hematopoietic cells, whereas HS1 is mainly expressed in hematopoietic cells. In accordance with their distinct tissue specificity, the putative promoter region of cortactin is different from HS1.

Conclusions: Comparative analysis of the genomic organization and amino acid sequences of cortactin and HS1 provides inside into their origin and evolution. Our analysis shows that both genes originated from a gene duplication event and subsequently HS1 lost two repeats, whereas cortactin gained one repeat. Our analysis genetically underscores the significance of the F-actin binding domain in cytoskeletal remodeling, which is of importance for the major role of HS1 in apoptosis and for cortactin in cell migration.

Figure 1

Exon map of cortactin and HS1 from different species. Exon/intron boundaries found in the genomic databases by performing BLAST searches with the cortactin cDNA of different species to their genomic DNA, are indicated as vertical boxes in different colors. A lack of boxes means that the boundaries were not found. The genomic organization of some species could not be fully elucidated, because cDNA/genomic sequences were not completely available. The actin binding repeat domain of the cortactin protein is represented by red boxes and the SH3 domain by the purple box. The vertical green stripe indicates the sequence coding for the Arp2/3 binding domain. Pro = proline rich region. The y in the proline rich region represents tyrosine phosphorylation sites. Hs, human; Pt, chimpanzee; Mm, mouse; Rn, rat.

Figure 2

A schematic view over 800 bp of the proximal promoters. Distribution of putative binding sites where represented for the transcription factors SP1 (red), GATA1 or GATA2 (green), AP-1 (dark blue), E2F (yellow), cEts (purple), C/EBPa or C/EBPb (light blue) and the TATAA box (gray) and CCAAT box (white) in the promoter regions of cortactin, human (HsCort), chimpanzee (PtCort), mouse (MmCort), mosquito (AgCort), Drosophila (Dmcort), and HS1, human (HsHS1), chimpanzee (PtHS1), mouse (MmHS1) and rat (RnHS1). The mRNA starting point (assigned +1) is indicated by an arrow.

Figure 3

Phylogenetic relationship of cortactin and HS1 genes. Evolutionary comparison of the N-terminal of cortactin and HS1 proteins including repeat 3 (corresponding to nucleotide 1–190 of human cortactin), represented in a phylogenetic tree based on a cluster alogorithmic alignment generated using GeneBee ClustalW 1.83 program. The number of repeats in the full length actin binding domain for the indicated species are depicted between brackets. Hs, human; Pt, chimpanzee; Mm, mouse; Rn, rat; Gg, chicken; Xl, frog Xenopus laevis ; Dr, zebrafish; Tr, pufferfish Takifugu rubripes ; Tn, pufferfish Tetraodon nigroviridis ; Dm, fruit fly Drosophila ; Ag, mosquito; Sp, sea urchin; Sd, sponge.

Figure 4

Model for the origin of cortactin and HS1 during evolution. Exon/intron boundaries from the exons encoding the actin binding repeat domain are represented in yellow. The actin binding repeat domain of the cortactin protein is represented by red boxes.