Stichodactyla helianthus' de novo transcriptome assembly: Discovery of a new actinoporin isoform

Abstract

Transcriptomic profiling of venom producing tissues from different animals is an effective approach for discovering new toxins useful in biotechnological and pharmaceutical applications, as well in evolutionary comparative studies of venomous animals. Stichodactyla helianthus is a Caribbean sea anemone which produces actinoporins as part of its toxic venom. This family of pore forming toxins is multigenic and at least two different isoforms, encoded by separate genes, are produced by S. helianthus. These isoforms, sticholysins I and II, share 93% amino acid identity but differ in their pore forming activity and act synergistically. This observation suggests that other actinoporin isoforms, if present in the venomous mixture, could offer an advantageous strategy to modulate whole venom activity. Using high-throughput sequencing we generated a de novo transcriptome of S. helianthus and determined the relative expression of assembled transcripts using RNA-Seq to better characterize components of this species' venom, focusing on actinoporin diversity. Applying this approach, we have discovered at least one new actinoporin variant from S. helianthus in addition to several other putative venom components.

Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms

“…While there has been a recent increase in transcriptomic and proteotranscriptomic analyses of cnidarian venoms (e.g., [ 7 , 8 , 22 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 ]), the phylum as a whole, which contains over 13,000 species, remains highly understudied. Cnidaria is split into three taxonomic groups: Anthozoa (sea anemones, corals, zoanthids, etc.…”

Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data

“…Despite having multiple assembly or expression approaches currently available for comparative venom transcriptome studies, we chose Trinity and RSEM because they are widely used in these types of analyses ( Haney et al, 2014 ; Zhang et al, 2014 ; Júnior et al, 2016 ; Macrander, Broe & Daly, 2016 ; Durban et al, 2017 ; Verdes, Simpson & Holford, 2018 ; Rivera-de Torre, Martínez-del-Pozo & Garb, 2018 ). Venomix is capable of producing similar outputs regardless of assembly or quantification program when the input files are formatted properly.…”

“…Among these, programs founded in machine learning appear to be the most abundant tools currently available; these use a combination of lineage specific annotation datasets ( Kaplan, Morpurgo & Linial, 2007 ; Fan et al, 2011 ; Wong et al, 2013 ) and identifiers based on residue frequency and protein domains of interest ( Gupta et al, 2013 ). Although taxonomic and tissue specific application of these programs vary, the pipelines follow a similar mechanical path ( Haney et al, 2014 ; Zhang et al, 2014 ; Júnior et al, 2016 ; Macrander, Broe & Daly, 2016 ; Durban et al, 2017 ; Verdes, Simpson & Holford, 2018 ; Rivera-de Torre, Martínez-del-Pozo & Garb, 2018 ). First, they begin with millions of raw reads assembled de novo using Trinity ( Grabherr et al, 2011 ) or similar ( Archer et al, 2014 ).…”

Pore-Forming Proteins from Cnidarians and Arachnids as Potential Biotechnological Tools

“…Like most animal venoms, sea anemones’ venoms can be largely classified as non-proteinaceous toxins, neurotoxins, enzymes, or cytolysins [3,4,6]. Among the latter, actinoporins are a family of α-PFTs produced by sea anemones as part of their venomous arsenal.…”

“…Additional amplification of the venom gland-expressed gene can generate variants that produce a toxic protein product or compound. Due to this duplication–neofunctionalization mechanism, it is common to find venom toxins genetically structured as multigene families [2,4,5,6].…”