Literature summary extracted from

Mariotti, M.; Santesmasses, D.; Capella-Gutierrez, S.; Mateo, A.; Arnan, C.; Johnson, R.; D'Aniello, S.; Yim, S.H.; Gladyshev, V.N.; Serras, F.; Corominas, M.; Gabaldon, T.; Guigo, R.
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization (2015), Genome Res., 25, 1256-1267.

Cloned(Commentary)

EC Number	Cloned (Comment)	Organism
2.7.9.3	a single SPS gene, phylogenetic analysis	Ciona intestinalis
2.7.9.3	gene ptuf/SelD or SPS1, genetic structure analysis, SPS1-UGA might perhaps be translated by a readthrough mechanism not involving Sec insertion. In this respect, there is growing evidence for abundant stop codon readthrough in insects, with UGA being the most frequently observed readthrough codon in Drosophila	Drosophila melanogaster
2.7.9.3	gene seld-1, genetic structure analysis	Caenorhabditis elegans
2.7.9.3	gene SPS, phylogenetic analysis	Oikopleura dioica
2.7.9.3	gene SPS, phylogenetic analysis	Molgula tectiformis
2.7.9.3	gene SPS2, phylogenetic analysis	Botryllus schlosseri

Metals/Ions

EC Number	Metals/Ions	Comment	Organism
2.7.9.3	Mg2+	required	Escherichia coli
2.7.9.3	Mg2+	required	Homo sapiens
2.7.9.3	Mg2+	required	Drosophila melanogaster
2.7.9.3	Mg2+	required	Caenorhabditis elegans

Natural Substrates/ Products (Substrates)

EC Number	Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
2.7.9.3	ATP + selenide + H2O	Escherichia coli	-	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	Homo sapiens	-	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	Drosophila melanogaster	-	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	Caenorhabditis elegans	-	AMP + selenophosphate + phosphate	-	?

Organism

EC Number	Organism	UniProt	Comment	Textmining
2.7.9.3	Botryllus schlosseri	-	contains an active SPS2-Sec and an inactive SPS1-Gly isozyme	-
2.7.9.3	Caenorhabditis elegans	O62461	-	-
2.7.9.3	Ciona intestinalis	-	-	-
2.7.9.3	Drosophila melanogaster	O18373	gene ptuf/SelD or SPS1	-
2.7.9.3	Escherichia coli	-	-	-
2.7.9.3	Homo sapiens	Q99611	Sephs2	-
2.7.9.3	Molgula tectiformis	-	contains an active SPS-Sec and an inactive SPS-Gly isozyme	-
2.7.9.3	no activity in Acyrthosiphon pisum	-	selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared	-
2.7.9.3	no activity in Coleoptera	-	selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared	-
2.7.9.3	no activity in Drosophila willistoni	-	-	-
2.7.9.3	no activity in Endopterygota	-	selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared	-
2.7.9.3	no activity in Hymenoptera	-	selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared	-
2.7.9.3	no activity in Lepidoptera	-	selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared	-
2.7.9.3	Oikopleura dioica	-	-	-

Substrates and Products (Substrate)

EC Number	Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
2.7.9.3	ATP + selenide + H2O	-	Escherichia coli	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	-	Homo sapiens	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	-	Drosophila melanogaster	AMP + selenophosphate + phosphate	-	?
2.7.9.3	ATP + selenide + H2O	-	Caenorhabditis elegans	AMP + selenophosphate + phosphate	-	?

Synonyms

EC Number	Synonyms	Comment	Organism
2.7.9.3	SelD	-	Escherichia coli
2.7.9.3	SelD	-	Ciona intestinalis
2.7.9.3	SelD	-	Homo sapiens
2.7.9.3	SelD	-	Drosophila melanogaster
2.7.9.3	SelD	-	Oikopleura dioica
2.7.9.3	SelD	-	Molgula tectiformis
2.7.9.3	SelD	-	Botryllus schlosseri
2.7.9.3	seld-1	-	Caenorhabditis elegans
2.7.9.3	selenide water dikinase	-	Homo sapiens
2.7.9.3	selenide water dikinase	-	Drosophila melanogaster
2.7.9.3	selenide water dikinase	-	Caenorhabditis elegans
2.7.9.3	selenophosphate synthetase	-	Escherichia coli
2.7.9.3	selenophosphate synthetase	-	Ciona intestinalis
2.7.9.3	selenophosphate synthetase	-	Homo sapiens
2.7.9.3	selenophosphate synthetase	-	Drosophila melanogaster
2.7.9.3	selenophosphate synthetase	-	Caenorhabditis elegans
2.7.9.3	selenophosphate synthetase	-	Oikopleura dioica
2.7.9.3	selenophosphate synthetase	-	Molgula tectiformis
2.7.9.3	selenophosphate synthetase	-	Botryllus schlosseri
2.7.9.3	Sephs2	-	Homo sapiens
2.7.9.3	SPS	-	Escherichia coli
2.7.9.3	SPS	-	Ciona intestinalis
2.7.9.3	SPS	-	Caenorhabditis elegans
2.7.9.3	SPS	-	Oikopleura dioica
2.7.9.3	SPS	-	Molgula tectiformis
2.7.9.3	SPS	-	Botryllus schlosseri
2.7.9.3	SPS1	-	Drosophila melanogaster
2.7.9.3	Sps2	-	Homo sapiens

Cofactor

EC Number	Cofactor	Comment	Organism
2.7.9.3	ATP	-	Escherichia coli
2.7.9.3	ATP	-	Homo sapiens
2.7.9.3	ATP	-	Drosophila melanogaster
2.7.9.3	ATP	-	Caenorhabditis elegans

General Information

EC Number	General Information	Comment	Organism
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common, e.g. Drosophila melanogaster possesses three selenoprotein genes, while Drosophila willistoni has replaced Sec with Cys in them and lost the capacity to synthesize Sec. Unequal selective pressure on SPS1 and SPS2 genes after duplication, overview	Drosophila melanogaster
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. At the root of ascidians, the ancestral SPS2-Sec gene acquired a novel SPS-Gly transcript isoform through alternative exon usage at the 5'-end. Then, at the root of the ascidian lineage, Styelidae and Pyuridae, the SPS-Sec transcript of this dual SPS1/SPS2 gene (SPS-ae) retrotransposed to the genome creating a novel SPS2-Sec gene (GDR). This presumably triggered the loss of Sec from the parental gene, which, because both the SECIS and the UGA containing exon degenerated (SL), specialized only in the production of SPS1-Gly. Parallel gene duplications of SPS proteins in metazoa, phylogenetic analysis, overview	Ciona intestinalis
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. At the root of ascidians, the ancestral SPS2-Sec gene acquired a novel SPS-Gly transcript isoform through alternative exon usage at the 5'-end. Then, at the root of the ascidian lineage, Styelidae and Pyuridae, the SPS-Sec transcript of this dual SPS1/SPS2 gene (SPS-ae) retrotransposed to the genome creating a novel SPS2-Sec gene (GDR). This presumably triggered the loss of Sec from the parental gene, which, because both the SECIS and the UGA containing exon degenerated (SL), specialized only in the production of SPS1-Gly. Parallel gene duplications of SPS proteins in metazoa, phylogenetic analysis, overview	Oikopleura dioica
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. At the root of ascidians, the ancestral SPS2-Sec gene acquired a novel SPS-Gly transcript isoform through alternative exon usage at the 5'-end. Then, at the root of the ascidian lineage, Styelidae and Pyuridae, the SPS-Sec transcript of this dual SPS1/SPS2 gene (SPS-ae) retrotransposed to the genome creating a novel SPS2-Sec gene (GDR). This presumably triggered the loss of Sec from the parental gene, which, because both the SECIS and the UGA containing exon degenerated (SL), specialized only in the production of SPS1-Gly. Parallel gene duplications of SPS proteins in metazoa, phylogenetic analysis, overview	Molgula tectiformis
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. At the root of ascidians, the ancestral SPS2-Sec gene acquired a novel SPS-Gly transcript isoform through alternative exon usage at the 5'-end. Then, at the root of the ascidian lineage, Styelidae and Pyuridae, the SPS-Sec transcript of this dual SPS1/SPS2 gene (SPS-ae) retrotransposed to the genome creating a novel SPS2-Sec gene (GDR). This presumably triggered the loss of Sec from the parental gene, which, because both the SECIS and the UGA containing exon degenerated (SL), specialized only in the production of SPS1-Gly. Parallel gene duplications of SPS proteins in metazoa, phylogenetic analysis, overview	Botryllus schlosseri
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. In Caenorhabditis elegans, the entire pathway is maintained only to synthesize a single selenoprotein. Unequal selective pressure on SPS1 and SPS2 genes after duplication, overview	Caenorhabditis elegans
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. Phylogenetic profile of SPS and selenium utilization traits in prokaryotes, overview	Escherichia coli
2.7.9.3	evolution	selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. Unequal selective pressure on SPS1 and SPS2 genes after duplication, overview	Homo sapiens
2.7.9.3	additional information	SPS2, i.e. Sephs2, invertebrates is a selenoprotein	Homo sapiens
2.7.9.3	physiological function	Drosophila SPS1 (i.e., ptuf/SelD) lacks the ability to catalyze selenide-dependent ATP hydrolysis or to complement SelD deficiency in Escherichia coli. Drosophila SPS1 has been proposed to be involved in vitamin B6 metabolism and in redox homeostasis since it protects from damage induced by reactive oxygen species	Drosophila melanogaster