Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

Abstract

BackgroundA long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects.ResultsThe venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis) of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27%) were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements) and class II (DNA transposons) mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large divergence between A. mexicanus and A. picadoi, and a closer kinship between A. mexicanus and C. godmani.ConclusionsOur comparative next-generation sequencing (NGS) analysis reveals taxon-specific trends governing the formulation of the venom arsenal. Knowledge of the venom proteome provides hints on the translation efficiency of toxin-coding transcripts, contributing thereby to a more accurate interpretation of the transcriptome. The application of NGS to the analysis of snake venom transcriptomes, may represent the tool for opening the door to systems venomics.

Venom evolution through gene duplications

“…To date, most venom transcriptomic studies have used expression data to discover novel toxins, and for this purpose, next-gen sequencing will likely replace the use of cDNA libraries in the near future (Durban et al, 2011;Hu et al, 2011;Whittington et al, 2009). The two next-gen instruments that dominate the current market are the Illumina HiSeq 2000 and the Roche 454 GS FLX+ System.…”

Disintegrins of Crotalus simus tzabcan venom: Isolation, characterization and evaluation of the cytotoxic and anti-adhesion activities of tzabcanin, a new RGD disintegrin

“…Because snake venom disintegrins are often derived from proteolytic processing of P-II metalloproteinases, a custom BLAST database of C. s. tzabcan P-II SVMPs was constructed from published data [36]. The sequences obtained for disintegrins in this study were then queried against this database, and exact matches were considered P-II derived disintegrins.…”

Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms

“…some studies have detected concordance between the abundance of both toxin gene transcripts and proteins in snake venom systems (22,23), many others have demonstrated that the toxin genes detected in venom glands do not correlate well with the composition of secreted venom (7,24), suggesting that some level of regulatory control acts on protein translation. However, most studies typically focused on comparisons at the toxin family level by using a single species, which could be misleading if mechanisms affecting translation act differentially on toxin paralogs and, therefore, result in different outcomes in different species.…”

“…However, the efficacy of these therapies is largely restricted to the snake species whose venom was used in manufacture. This limitation arises because variation in venom composition is ubiquitous at every level of snake taxonomy, including interspecifically and intraspecifically and even ontogenetically (6)(7)(8)(9). Importantly, the extent of this variation is not simply reflected by taxonomic distance (9)(10)(11) and, therefore, cannot be readily predicted.…”