The microbial selenoproteome of the Sargasso Sea

Abstract

Background: Selenocysteine (Sec) is a rare amino acid which occurs in proteins in major domains of life. It is encoded by TGA, which also serves as the signal for termination of translation, precluding identification of selenoprotein genes by available annotation tools. Information on full sets of selenoproteins (selenoproteomes) is essential for understanding the biology of selenium. Herein, we characterized the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome project.

Results: We identified 310 selenoprotein genes that clustered into 25 families, including 101 new selenoprotein genes that belonged to 15 families. Most of these proteins were predicted redox proteins containing catalytic selenocysteines. Several bacterial selenoproteins previously thought to be restricted to eukaryotes were detected by analyzing eukaryotic and bacterial SECIS elements, suggesting that eukaryotic and bacterial selenoprotein sets partially overlapped. The Sargasso Sea microbial selenoproteome was rich in selenoproteins and its composition was different from that observed in the combined set of completely sequenced genomes, suggesting that these genomes do not accurately represent the microbial selenoproteome. Most detected selenoproteins occurred sporadically compared to the widespread presence of their cysteine homologs, suggesting that many selenoproteins recently evolved from cysteine-containing homologs.

Conclusions: This study yielded the largest selenoprotein dataset to date, doubled the number of prokaryotic selenoprotein families and provided insights into forces that drive selenocysteine evolution.

Figure 1

A schematic diagram of the search algorithm. Details of the search process are provided in Materials and methods and are discussed in the text.

Figure 2

Multiple sequence alignments of new selenoproteins and their Cys homologs. The alignments show Sec-flanking regions in detected proteins. Both selenoprotein sequences detected in the Sargasso Sea database and their Cys-containing homologs present in indicated organisms are shown. Conserved residues are highlighted. Predicted Sec (U) and the corresponding Cys (C) residues in other homologs are shown in red and blue background, respectively. Sequence alignments were generated with ClustalW and shaded by BoxShade v3.21.

Figure 3

Predicted bacterial SECIS elements in representative sequences of some new selenoprotein families. Only sequences downstream of in-frame UGA codons are shown. In-frame UGA codons and conserved guanosines in the apical loop are shown in red. AhpD-like protein, AACY01418594; Arsenate reductase, AACY01238341; Glutaredoxin, AACY01002222; DsbA-like protein, AACY01178397; Hypothetical protein 1, AACY01574522; Rhodanase-related sulfurtransferase, AACY01016424; OsmC-like protein, AACY01145085; DsrE-like protein, AACY01486889.

Figure 4

Alignment of SECIS elements present in Sargasso Sea selenoproteins. The Sargasso Sea dataset includes 10 known selenoprotein families and 15 new families. SECIS elements in representative members of these families were manually aligned on the basis of primary sequence and secondary structure features.

Figure 5

Multiple alignments of deiodinase, GPx and SelW. Conserved residues are highlighted. Predicted Sec (U) in selenoproteins and the corresponding Cys (C) residues in homologs are shown in red and blue background, respectively. Sequence alignments were generated with ClustalW and shaded by BoxShade v3.21.

Figure 6

Phylogenetic analyses of deiodinase, GPx and SelW protein families. Selenoproteins are shown in red and Cys-containing homologs in green. The phylogenetic trees were generated by ClustalW and represented by Treeme.

Figure 7

Comparison of bacterial and eukaryotic SECIS elements in deiodinase, GPx and SelW protein sequences. (a) In bacterial SECIS elements, only sequences downstream of in-frame UGA codons are shown and the conserved features (in-frame UGA codon and conserved G in the apical loop) are highlighted in red. (b) In eukaryotic SECIS elements, conserved features (quartet, AA in the apical loop or bulge and an A preceding the quartet) are shown in blue. Bacterial elements are from deiodinase-like protein, AACY01143874; GPx, AACY01190440; and SelW-like protein, AACY01475618. Eukaryotic elements are from deiodinase, NM_000792, Homo sapiens; GPx, X68314, H. sapiens; SelW, AY221261, Danio rerio.