Abstract
BackgroundSelenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24.Methodology/Principal FindingsWe characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian (25 proteins) selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events), gene loss (10 events) and replacement of Sec with cysteine (12 events). We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2). Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes.Conclusions/SignificanceThis analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.
Highlights
Selenocysteine (Sec)-containing proteins have been identified in all domains of life [1,2,3]
The smallest selenoproteome (24 selenoprotein genes) was predicted in frog and in some mammals (Figure 1). 21 selenoproteins were found in all vertebrates: GPx1-4, TR1, TR3, Dio1, Dio2, Dio3, SelH, Selenoprotein I (SelI), SelK, SelM, SelN, SelO, SelP, MsrB1, SelS, SelT1, SelW1, Sep15
Our results suggest that SPS2b arose by reverse transcription following the monotreme/marsupial split and eventually replaced SPS2a in placental mammals
Summary
Selenocysteine (Sec)-containing proteins (selenoproteins) have been identified in all domains of life [1,2,3]. In these proteins Sec is encoded by UGA, a codon typically used for termination of protein synthesis. The function of approximately half of mammalian selenoproteins is not known. The mammalian selenoproteins can be broadly classified into two classes: housekeeping and stress-related [22]. Housekeeping selenoproteins are less affected by dietary selenium (Se) status and often serve functions critical to cell survival, whereas stress-related selenoproteins are not essential for survival and often show decreased expression in Se-deficient conditions. Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24
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