Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs

Abstract

BackgroundInsertions of spliceosomal introns are very rare events during evolution of vertebrates and the mechanisms governing creation of novel intron(s) remain obscure. Largely, gene structures of melanocortin (MC) receptors are characterized by intron-less architecture. However, recently a few exceptions have been reported in some fishes. This warrants a systematic survey of MC receptors for understanding intron insertion events during vertebrate evolution.Methodology/Principal FindingsWe have compiled an extended list of MC receptors from different vertebrate genomes with variations in fishes. Notably, the closely linked MC2Rs and MC5Rs from a group of ray-finned fishes have three and one intron insertion(s), respectively, with conserved positions and intron phase. In both genes, one novel insertion was in the highly conserved DRY motif at the end of helix TM3. Further, the proto-splice site MAG↑R is maintained at intron insertion sites in these two genes. However, the orthologs of these receptors from zebrafish and tetrapods are intron-less, suggesting these introns are simultaneously created in selected fishes. Surprisingly, these novel introns are traceable only in four fish genomes. We found that these fish genomes are severely compacted after the separation from zebrafish. Furthermore, we also report novel intron insertions in P2Y receptors and in CHRM3. Finally, we report ultrasmall introns in MC2R genes from selected fishes.Conclusions/SignificanceThe current repository of MC receptors illustrates that fishes have no MC3R ortholog. MC2R, MC5R, P2Y receptors and CHRM3 have novel intron insertions only in ray-finned fishes that underwent genome compaction. These receptors share one intron at an identical position suggestive of being inserted contemporaneously. In addition to repetitive elements, genome compaction is now believed to be a new hallmark that promotes intron insertions, as it requires rapid DNA breakage and subsequent repair processes to gain back normal functionality.

Thermosensitive ion channel TRPV1 is endogenously expressed in the sperm of a fresh water teleost fish (Labeo rohita) and regulates sperm motility

“…Recently, we have reported that TRPV1 is a highly conserved protein throughout the evolution. 23 Endogenous expression and involvement of TRPV1 in the sperm cells from different species is in full agreement with its conservation at the protein as well as in the genome level.…”

A Novel Model for Development, Organization, and Function of Gonadotropes in Fish Pituitary

“…Whereas the exon–intron division is a relatively well-conserved feature of closely related genes, addition or deletion of introns occurs at a frequency of ca. 1 intron/gene every 100 million years ( 38 – 40 ), and such events are common in many fish ( 41 , 42 ). The fact that much of the other observed differences in mRNA size could be attributed to changes in the length of non-coding sequences, and not changes within the open reading frame, may also serve to explain the high tolerance to these significant insertions/deletions since these regions are less subject to functional constraints.…”

“…Since we included the first intron of both genes in our constructs, we also tested for similarities within these sequences. In the lhb introns, a specific sequence of putative binding motifs was found in both zebrafish and tilapia, although the motifs were more densely distributed in the tilapia, corresponding to the trend toward a more compact genome in tilapia than in zebrafish ( 42 ).…”

Fish pigmentation and the melanocortin system

“…In fish, the number, affinity, specificity, tissue distribution and the physiological roles are far from defined and appear to be species-specific. For example, pufferfish (Tetraodon nigroviridis) has only four receptors lacking Mc3r (Schiöth et al, 2005), while zebrafish has six receptors with two copies of Mc5r (Kumar et al, 2011). The larger number of Mcr paralogs found in some teleost species probably originated in the extra round of whole genome duplication that occurred during early teleost evolution…”