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SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.

Mariotti M, Lobanov AV, Guigo R, Gladyshev VN - Nucleic Acids Res. (2013)

Bottom Line: Seblastian is able to both identify known selenoproteins and predict new selenoproteins.By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues.An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.

View Article: PubMed Central - PubMed

Affiliation: Division of Genetics, Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA and Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.

ABSTRACT
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3' UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.

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AhpC selenoproteins. Two selenoprotein candidates in our Seblastian predictions were found in M.brevicollis and E.huxleyi, here framed in orange. The figure shows them aligned with other AhpC selenoproteins predicted using Selenoprofiles in eukaryotes (top) and prokaryotes (bottom). Some metazoan cysteine homologues are also shown on the top. The Sec is found in the highlighted redox box UXXC, present also in vertebrates as CXXC. For the full alignment and further details regarding the search for AhpC proteins, see Supplementary Material S6.
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gkt550-F4: AhpC selenoproteins. Two selenoprotein candidates in our Seblastian predictions were found in M.brevicollis and E.huxleyi, here framed in orange. The figure shows them aligned with other AhpC selenoproteins predicted using Selenoprofiles in eukaryotes (top) and prokaryotes (bottom). Some metazoan cysteine homologues are also shown on the top. The Sec is found in the highlighted redox box UXXC, present also in vertebrates as CXXC. For the full alignment and further details regarding the search for AhpC proteins, see Supplementary Material S6.

Mentions: The best scoring candidate was found in the choanoflagellate Monosiga brevicollis and showed homology to AhpC. This is a thioredoxin-like protein family (like many known selenoproteins), and its distant homolog was previously detected as a selenoprotein in Bacteria. Recently, an AhpC-like selenoprotein was also predicted in some sponges (17), but it was thought to be limited to this lineage. Using Selenoprofiles, we built a profile alignment with the AhpC selenoproteins in Bacteria, choanoflagellates and Porifera, including also a number of metazoan cysteine homologues. We used our new profile to scan a collection of eukaryotic and prokaryotic genomes and detected AhpC selenoproteins in a wide range of lineages, including protists and basal metazoans. In Figure 4, we present an alignment of the Sec-containing domain of AhpC selenoproteins, along with some metazoan cysteine homologues. Among the Selenoprofiles AhpC predictions, we also found our second best scoring Seblastian candidate, in the Emiliana huxleyi genome.Figure 4.


SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.

Mariotti M, Lobanov AV, Guigo R, Gladyshev VN - Nucleic Acids Res. (2013)

AhpC selenoproteins. Two selenoprotein candidates in our Seblastian predictions were found in M.brevicollis and E.huxleyi, here framed in orange. The figure shows them aligned with other AhpC selenoproteins predicted using Selenoprofiles in eukaryotes (top) and prokaryotes (bottom). Some metazoan cysteine homologues are also shown on the top. The Sec is found in the highlighted redox box UXXC, present also in vertebrates as CXXC. For the full alignment and further details regarding the search for AhpC proteins, see Supplementary Material S6.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753652&req=5

gkt550-F4: AhpC selenoproteins. Two selenoprotein candidates in our Seblastian predictions were found in M.brevicollis and E.huxleyi, here framed in orange. The figure shows them aligned with other AhpC selenoproteins predicted using Selenoprofiles in eukaryotes (top) and prokaryotes (bottom). Some metazoan cysteine homologues are also shown on the top. The Sec is found in the highlighted redox box UXXC, present also in vertebrates as CXXC. For the full alignment and further details regarding the search for AhpC proteins, see Supplementary Material S6.
Mentions: The best scoring candidate was found in the choanoflagellate Monosiga brevicollis and showed homology to AhpC. This is a thioredoxin-like protein family (like many known selenoproteins), and its distant homolog was previously detected as a selenoprotein in Bacteria. Recently, an AhpC-like selenoprotein was also predicted in some sponges (17), but it was thought to be limited to this lineage. Using Selenoprofiles, we built a profile alignment with the AhpC selenoproteins in Bacteria, choanoflagellates and Porifera, including also a number of metazoan cysteine homologues. We used our new profile to scan a collection of eukaryotic and prokaryotic genomes and detected AhpC selenoproteins in a wide range of lineages, including protists and basal metazoans. In Figure 4, we present an alignment of the Sec-containing domain of AhpC selenoproteins, along with some metazoan cysteine homologues. Among the Selenoprofiles AhpC predictions, we also found our second best scoring Seblastian candidate, in the Emiliana huxleyi genome.Figure 4.

Bottom Line: Seblastian is able to both identify known selenoproteins and predict new selenoproteins.By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues.An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.

View Article: PubMed Central - PubMed

Affiliation: Division of Genetics, Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA and Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.

ABSTRACT
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3' UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.

Show MeSH