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J Bioinform Syst Biol
2022 Feb 03;51:1-25. doi: 10.26502/jbsb.5107030.
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Characterization of Two Novel EF-Hand Proteins Identifies a Clade of Putative Ca2+-Binding Protein Specific to the Ambulacraria.
Soto-Acabá A
,
Ortiz-Pineda PA
,
Medina-Feliciano JG
,
Salem-Hernández J
,
García-Arrarás JE
.
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In recent years, transcriptomic databases have become one of the main sources for protein discovery. In our studies of nervous system and digestive tract regeneration in echinoderms, we have identified several transcripts that have attracted our attention. One of these molecules corresponds to a previously unidentified transcript (Orpin) from the sea cucumber Holothuria glaberrima that appeared to be upregulated during intestinal regeneration. We have now identified a second highly similar sequence and analyzed the predicted proteins using bioinformatics tools. Both sequences have EF-hand motifs characteristic of calcium-binding proteins (CaBPs) and N-terminal signal peptides. Sequence comparison analyses such as multiple sequence alignments and phylogenetic analyses only showed significant similarity to sequences from other echinoderms or from hemichordates. Semi-quantitative RT-PCR analyses revealed that transcripts from these sequences are expressed in various tissues including muscle, haemal system, gonads, and mesentery. However, contrary to previous reports, there was no significant differential expression in regenerating tissues. Nonetheless, the identification of unique features in the predicted proteins and their presence in the holothurian draft genome suggest that these might comprise a novel subfamily of EF-hand containing proteins specific to the Ambulacraria clade.
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