Paper
Abstract Background The mammalian retina contains high amounts of metals/metalloid-selenium. Their dyshomeostases are associated with certain retinal diseases. We carried out this bioinformatics study to identify the relationships between putative retinal metal/selenium binding proteins, their molecular functions and biological processes. Methods Identification of putative mouse metal/selenium binding proteins was based on known binding motifs, domains, patterns, and profiles. Annotations were obtained from Uniprot keyword “metal binding”, “metal ion co-factors”, “selenium proteins”. Protein functions were estimated by associative frequency with key words in UniProt annotations. The raw data of 5 mouse proteomics PRIDE datasets (available to date) were downloaded and processed with Mascot against the mouse taxa of Uniprot (SwissProt/Trembl) and MaxQuant (version 1.6.10.43) for qualitative and quantitative datasets, respectively. Clinically relevant variants were evaluated using archive and aggregates information in ClinVar. Results The 438 proteins common to all the retina proteomics datasets were used to identify over-represented Gene Ontology categories. The putative mouse retinal metal/metalloid binding proteins identified are mainly involved in: 1) metabolic processes (enzymes), 2) homeostasis, 3) transport (vesicle mediated, transmembrane, along microtubules), 4) cellular localisation, 5) regulation of signalling and exocytosis, 6) organelle organisation, 7) (de)phosphorylation and 8) complex assembly. Twenty-one proteins were identified as involved in response to light stimulus and/or visual system development. An association of metal ion binding proteins rhodopsin, photoreceptor specific nuclear receptor, calcium binding protein 4 with disease-related mutations in inherited retinal conditions was identified, where the mutations affected an area within or in close proximity to the metal binding site or domain. Conclusion These findings suggest a functional role for the putative metal/metalloid binding site in retinal proteins in certain retinal disorders.