PURPOSE: The evolutionary conservation of the retinitis pigmentosa GTPase regulator (RPGR) gene was examined across vertebrate and invertebrate lineages to elucidate its function.
METHODS: Orthologous RPGR sequences from vertebrates and invertebrates were selected. Multiple sequence alignments, phylogenetic analyses, synteny, and gene structure comparisons were carried out. Expression of the alternatively spliced constitutive (RPGRconst or RPGRex1-19) and RPGRORF15 isoforms was examined in developing and adult zebrafish.
RESULTS: Phylogenetic analyses and syntenic relationships were consistent with the selected sequences being true orthologues, although whole genome duplications in teleost fish resulted in a more complex picture. The splice form RPGRconst was present in all vertebrate and invertebrate species but the defining carboxyl (C)-terminal exon of RPGRORF15 was absent from all invertebrates. The regulator of chromosome condensation (RCC1)-like domain adopts a seven-bladed β-propeller structure, which was present in both major splice forms and strongly conserved across evolution. The repetitive acidic region of RPGRORF15 showed a high rate of in-frame deletions/insertions across nine primate species, compared with flanking sequences, consistent with an unstable and rapidly evolving region. In zebrafish, RPGRconst transcripts were most strongly expressed in early development, while the RPGRORF15 isoform showed highest expression in adult eye.
CONCLUSIONS: The regulator of chromosome condensation 1-like domain of RPGR was conserved in vertebrates and invertebrates, but RPGRORF15 was unique to vertebrates, consistent with a proposed role in the ciliary-based transport of cargoes such as rhodopsin, which is ∼10 times more abundant in vertebrate than invertebrate photoreceptors. The repetitive acidic region of RPGRORF15 shows a rapid rate of evolution, consistent with a mutation "hot spot."