In silico characterisation and chromosomal localisation of human RRH (peropsin)--implications for opsin evolution

Abstract

Background: The vertebrate opsins are proteins which utilise a retinaldehyde chromophore in their photosensory or photoisomerase roles in the visual/irradiance detection cycle. The majority of the opsins, such as rod and cone opsins, have a very highly conserved gene structure suggesting a common lineage. Exceptions to this are RGR-opsin and melanopsin, whose genes have very different intron insertion positions. The gene structure of another opsin, peropsin (retinal pigment epithelium-derived rhodopsin homologue, RRH) is unknown.

Results: By in silico analysis of the GenBank database we have determined that the human RRH comprises 7 exons spanning approximately 16.5 kb and is localised to chromosome 4q25 in the following gene sequence: cen-EGF-RRH-IF-qter - a position that excludes this gene as a candidate for the RP29 autosomal recessive retinitis pigmentosa locus. A comparison of opsin gene structures reveals that RRH and RGR share two common intron (introns 1 and 4) insertion positions which may reflect a shared ancestral gene.

Conclusion: The opsins comprise a diverse group of genes which appear to have arisen from three different lineages. These lineages comprise the "classical opsin superfamily" which includes the rod and cone opsins, pinopsin, VA-opsin, parapinopsin and encephalopsin; the RRH and RGR group; and the melanopsin line. A common lineage for RRH and RGR, together with their sites of expression in the RPE, indicates that peropsin may act as a retinal isomerase.

Figure 1

Exon-intron boundaries of RRH based on GenBank BK000958. Uppercase = exon; lowercase = intron. * Exon sizes exclude the 5' and 3' UTRs.

Figure 2

Mini-contig showing the arrangement of genes around the RRH locus. Clone names (with associated GenBank accession numbers) are given as are their sizes and regions of overlap in bp. The direction of transcription and location of translation initiation codons (atg) of the various genes are also indicated in bp.

Figure 3

Human RRH coding sequence and conceptual translation (peropsin) with transmembrane domains (boldface) as predicted by the rod opsin model of Palczewski et al. [48]. The six intron insertion sites in the RRH gene defined in Figure 1 are indicated by black filled circles. Equivalent intron insertion sites for the visual (rod and cone) opsins are indicated by red filled circles – intron positions 1–4 are common to all rod (RHO) and cone opsins, whilst intron 0 is only found in the LWS opsins (OPN1MW, OPN1LW) [13,17]. The shifted second intron of the pinopsin and VA-opsin families [21,22] are indicated as 2a and 2b respectively in red circles. Parapineal opsin [9] and encephalopsin (OPN3) [10] possess only introns 1, 3 and 4 of the rod and cone opsins. Equivalent intron insertion sites for RGR-opsin (RGR) [24] are indicated by open circles, whilst those for melanopsin (OPN4) [25] are indicated by yellow filled circles. Only intron insertion sites 1–7 for melanopsin are indicated due to the extreme length of the melanopsin C-terminus which makes positioning of introns 8 and 9 inaccurate since there is no overlap with any other opsin. Note that intron insertion sites 1 and 4 in RRH are equivalent to intron insertion sites 1 and 4 in RGR.

Figure 4

Maximum parsimony tree with bootstrap confidence levels based on nucleotide coding sequence of the various vertebrate opsin classes rooted with human melanopsin (see Materials and Methods). Cone opsin class nomenclature after Hunt et al. [16]. To the right of the tree is a schematic representation of the intron insertion sites in the various opsin genes based on Figure 3. Conserved intron positions between opsin classes are indicated by a dashed vertical line. The relative position of the second rod and cone opsin intron is indicated by an arrow head in the pinopsin and VA-opsin classes to show their shifted second intron positions (2a and 2b).