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Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins.

Donovan J, Copeland PR - BMC Evol. Biol. (2009)

Bottom Line: In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5.Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages.In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, Microbiology, and Immunology, Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey - Robert Wood Johnson Medical School, Piscataway, NJ, USA. donovaje@umdnj.edu

ABSTRACT

Background: The co-translational incorporation of selenocysteine into nascent polypeptides by recoding the UGA stop codon occurs in all domains of life. In eukaryotes, this event requires at least three specific factors: SECIS binding protein 2 (SBP2), a specific translation elongation factor (eEFSec), selenocysteinyl tRNA, and a cis-acting selenocysteine insertion sequence (SECIS) element in selenoprotein mRNAs. While the phylogenetic relationships of selenoprotein families and the evolution of selenocysteine usage are well documented, the evolutionary history of SECIS binding proteins has not been explored.

Results: In this report we present a phylogeny of the eukaryotic SECIS binding protein family which includes SBP2 and a related protein we herein term SBP2L. Here we show that SBP2L is an SBP2 paralogue in vertebrates and is the only form of SECIS binding protein in invertebrate deuterostomes, suggesting a key role in Sec incorporation in these organisms, but an SBP2/SBP2L fusion protein is unable to support Sec incorporation in vitro. An in-depth phylogenetic analysis of the conserved L7Ae RNA binding domain suggests an ancestral relationship with ribosomal protein L30. In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5.

Conclusion: Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages. In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.

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Identification of conserved motifs within SBP2 and SBP2L. (A) Global alignment of vertebrate SBP2 sequences (top) with detailed alignment of conserved motifs as indicated (bottom). (B) Global and detailed alignments of SBP2L as in (A).
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Figure 5: Identification of conserved motifs within SBP2 and SBP2L. (A) Global alignment of vertebrate SBP2 sequences (top) with detailed alignment of conserved motifs as indicated (bottom). (B) Global and detailed alignments of SBP2L as in (A).

Mentions: SBP2L and SBP2 are further distinguished by the presence of highly conserved sequence motifs that are unique to each protein. Figure 5 highlights these motifs in separate SBP2 and SBP2L multiple sequence alignments derived from the same species examined in Figure 4. In SBP2L, the conserved motifs include QTDF210-252, DSGY265-279, SEIS442-474, TPVS622-662, PISE844-868 and RIES1016-1032. In contrast there are only three sites of SBP2-specific conservation: DFPE216-226, QEPP380-405, which includes the poly-lysine tract that has been shown to be active as a nuclear localization signal [17], and IWKK816-839. Table 1 provides a summary of the occurrence of thee motifs in each species analyzed. Interestingly, none of these regions are annotated in the NCBI Conserved Domains Database, and PSI-BLAST analysis does not link them to any other protein families (data not shown), but the significant degree of identity across highly diverse species makes them important focal points for further investigation into the function and regulation of SBP2 and SBP2L. As shown in Figure 5 and Table 1, we observed variability in the occurrence of some of the motifs, notably the lack of DFPE216-226 in frog and the lack of TPVS622-662 in the sea squirts (C. intestinalis and C. savignyi) as well as a the hemichordate acorn worm (Saccoglossus kowalevskii). These results confirm the phylogeny shown in Figure 2 demonstrating that SBP2L is not limited to deuterostomes since we identified SBP2L motifs in a mollusk (L. gigantea), and an annelid worm (Capitella sp.I). Among the conserved motifs in SBP2L, TPVS622-662 is of interest because it lies between the SID and RBD, and the corresponding sequence in SBP2 is degenerate and has been found to be dispensable for Sec incorporation activity [18]. Considering that a dynamic interaction between the SID and RBD has been shown to be essential for Sec incorporation [2], it is likely that the interaction of the corresponding domains in SBP2L may be regulated by this conserved stretch of amino acids.


Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins.

Donovan J, Copeland PR - BMC Evol. Biol. (2009)

Identification of conserved motifs within SBP2 and SBP2L. (A) Global alignment of vertebrate SBP2 sequences (top) with detailed alignment of conserved motifs as indicated (bottom). (B) Global and detailed alignments of SBP2L as in (A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746813&req=5

Figure 5: Identification of conserved motifs within SBP2 and SBP2L. (A) Global alignment of vertebrate SBP2 sequences (top) with detailed alignment of conserved motifs as indicated (bottom). (B) Global and detailed alignments of SBP2L as in (A).
Mentions: SBP2L and SBP2 are further distinguished by the presence of highly conserved sequence motifs that are unique to each protein. Figure 5 highlights these motifs in separate SBP2 and SBP2L multiple sequence alignments derived from the same species examined in Figure 4. In SBP2L, the conserved motifs include QTDF210-252, DSGY265-279, SEIS442-474, TPVS622-662, PISE844-868 and RIES1016-1032. In contrast there are only three sites of SBP2-specific conservation: DFPE216-226, QEPP380-405, which includes the poly-lysine tract that has been shown to be active as a nuclear localization signal [17], and IWKK816-839. Table 1 provides a summary of the occurrence of thee motifs in each species analyzed. Interestingly, none of these regions are annotated in the NCBI Conserved Domains Database, and PSI-BLAST analysis does not link them to any other protein families (data not shown), but the significant degree of identity across highly diverse species makes them important focal points for further investigation into the function and regulation of SBP2 and SBP2L. As shown in Figure 5 and Table 1, we observed variability in the occurrence of some of the motifs, notably the lack of DFPE216-226 in frog and the lack of TPVS622-662 in the sea squirts (C. intestinalis and C. savignyi) as well as a the hemichordate acorn worm (Saccoglossus kowalevskii). These results confirm the phylogeny shown in Figure 2 demonstrating that SBP2L is not limited to deuterostomes since we identified SBP2L motifs in a mollusk (L. gigantea), and an annelid worm (Capitella sp.I). Among the conserved motifs in SBP2L, TPVS622-662 is of interest because it lies between the SID and RBD, and the corresponding sequence in SBP2 is degenerate and has been found to be dispensable for Sec incorporation activity [18]. Considering that a dynamic interaction between the SID and RBD has been shown to be essential for Sec incorporation [2], it is likely that the interaction of the corresponding domains in SBP2L may be regulated by this conserved stretch of amino acids.

Bottom Line: In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5.Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages.In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular Genetics, Microbiology, and Immunology, Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey - Robert Wood Johnson Medical School, Piscataway, NJ, USA. donovaje@umdnj.edu

ABSTRACT

Background: The co-translational incorporation of selenocysteine into nascent polypeptides by recoding the UGA stop codon occurs in all domains of life. In eukaryotes, this event requires at least three specific factors: SECIS binding protein 2 (SBP2), a specific translation elongation factor (eEFSec), selenocysteinyl tRNA, and a cis-acting selenocysteine insertion sequence (SECIS) element in selenoprotein mRNAs. While the phylogenetic relationships of selenoprotein families and the evolution of selenocysteine usage are well documented, the evolutionary history of SECIS binding proteins has not been explored.

Results: In this report we present a phylogeny of the eukaryotic SECIS binding protein family which includes SBP2 and a related protein we herein term SBP2L. Here we show that SBP2L is an SBP2 paralogue in vertebrates and is the only form of SECIS binding protein in invertebrate deuterostomes, suggesting a key role in Sec incorporation in these organisms, but an SBP2/SBP2L fusion protein is unable to support Sec incorporation in vitro. An in-depth phylogenetic analysis of the conserved L7Ae RNA binding domain suggests an ancestral relationship with ribosomal protein L30. In addition, we describe the emergence of a motif upstream of the SBP2 RNA binding domain that shares significant similarity with a motif within the pseudouridine synthase Cbf5.

Conclusion: Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages. In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 and SBP2L are paralogous in vertebrates.

Show MeSH