SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements

Abstract

Summary: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem-loop structure, the SECIS element in the 3 untranslated region of (UTR) selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web-based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities.

Availability: SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/.

Fig. 1.

Eukaryotic SECIS element consensus sequence. Novel conserved residues are shown in magenta. Where a specific nucleotide is shown, it was observed in that position in 50% or more of the aligned sequences. Where a class of nucleotides is shown, that class was observed in that position in 70% or more of the aligned sequences. Y=U or C, K=G or U, N=any nucleotide, W=A or U, R=A or G, M=A or C. Quartet: four consecutive non-Watson–Crick base pairs. Base pairs forming the quartet were called abcd/a^′b^′c^′d^′ for the sake of clarity in the text. Position ‘z’ is the first nucleotide after the run of Ms, positions 2H3/2^′H3 are the second base pair of Helix 3 and 1ap the first nucleotide of the apical loop. The range of possible lengths for helix 1 is hard to determine because it depends on the local 2D structure of the mRNA 3^′UTR.