Discontinuous distribution of IRBP homologues across the tree of life. (a) Schematic of the vertebrate visual cycle indicating physical separation of light-mediated retinoid sensing in photoreceptor (PR) cells and retinoid regeneration in retinal pigment epithelium (RPE) cells. Interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3) is required to transport retinoids between the two types of cells. b Histogram of BLASTp e-values obtained after searching the RefSeq protein database for IRBP homologues. Single domain homologues in invertebrate eukaryotes are classified and colored by species name or species group. Above is the species tree of the eukaryotes whose genomes were queried in this study. The grey-branched species lack detectable IRBP homologues in their genomes. The e values of the 10 closest bacterial homologues for IRBP are shown to the left. (C) Sequence comparison between individual domains of human IRBP and its top-score bacterial homologue. (D) Structural comparison of D4 from bovine IRBP (PDB: 7JTI) (4) and predicted structure of a bacterial trigonum generated by AlphaFold2 (5). credit: Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2214815120
A group of molecular and chemical biologists at the University of California, San Diego, has identified potential evidence for horizontal gene transfer between domains leading to eye development in vertebrates. In their study, it was reported in Proceedings of the National Academy of SciencesChinmay Kalluraya, Alexander Weitzel, Brian Tsu, and Matthew Daugherty used the IQ-TREE software to trace the evolutionary history of genes associated with vision.
Since scientists have proven that humans, along with other animals, evolved due to evolutionary processes, one problem has arisen – how can evolution explain the evolution of something as complex as the eyeball? Even Charles Darwin is said to have been baffled by the question. Recently, some groups have used this apparent conundrum as a way to completely discredit the theory of evolution. In this new effort, the team in California sought to answer the question definitively.
Their work began with the idea that vertebrate vision may have started with light-sensitive genes passed on from microbes. To see if this was the case, the team sent potential human gene candidates into the IQ-TREE program to search for similar gene sequences in other organisms, specifically, microbes.
They found a promising candidate, a gene called IRBP. In humans, it encodes a protein used in the eye as part of the process of converting light into electrical impulses that are eventually sent to the brain via the optic nerve. The research team notes that the gene is an essential component of vision in all vertebrates. IRBP is also found in microbes, specifically in bacterial peptides, a class of enzymes known to recycle proteins.
The researchers note that although IRBP and the protein it encodes are present in all vertebrates, it is not present in most invertebrates. They suggest that this indicates that the IRBP gene may have been transferred from a microbe more than 500 million years ago into ancient vertebrates, which led to the evolution of light sensitivity and, over time, to organs such as eyeballs.
more information:
Chinmay A. Kalluraya et al, Bacterial origin of a key innovation in vertebrate eye evolution, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2214815120
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