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.