Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes

Abstract

Gene duplication is a key mechanism for the adaptive evolution and neofunctionalization of gene families. Large multigene families often exhibit complex evolutionary histories as a result of frequent gene duplication acting in concordance with positive selection pressures. Alterations in the domain structure of genes, causing changes in the molecular scaffold of proteins, can also result in a complex evolutionary history and has been observed in functionally diverse multigene toxin families. Here, we investigate the role alterations in domain structure have on the tempo of evolution and neofunctionalization of multigene families using the snake venom metalloproteinases (SVMPs) as a model system. Our results reveal that the evolutionary history of viperid (Serpentes: Viperidae) SVMPs is repeatedly punctuated by domain loss, with the single loss of the cysteine-rich domain, facilitating the formation of P-II class SVMPs, occurring prior to the convergent loss of the disintegrin domain to form multiple P-I SVMP structures. Notably, the majority of phylogenetic branches where domain loss was inferred to have occurred exhibited highly significant evidence of positive selection in surface-exposed amino acid residues, resulting in the neofunctionalization of P-II and P-I SVMP classes. These results provide a valuable insight into the mechanisms by which complex gene families evolve and detail how the loss of domain structures can catalyze the accelerated evolution of novel gene paralogues. The ensuing generation of differing molecular scaffolds encoded by the same multigene family facilitates gene neofunctionalization while presenting an evolutionary advantage through the retention of multiple genes capable of encoding functionally distinct proteins.

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

“…These gene families were selected based on the results of the proteomic analyses, which identified the presence of these toxin types in the venom of the majority of the sampled species. The remaining toxin family identified and analyzed, the short-coding disintegrins (DIS), were discarded from phylogenetic analysis due to their apparent convergent evolution from SVMPs (18,36). For each toxin family, nonredundant nucleotide sequences from each of the six transcriptomes were aligned with published gene homologs isolated from the venom systems of other viperid snakes, using the MUSCLE algorithm (37).…”

“…Typically, toxins are encoded by relatively few (approximately 5-10) multilocus gene families, with each family capable of producing related isoforms generated by gene duplication events occurring over evolutionary time (1,14,15). The birth and death model of gene evolution (16) is frequently invoked as the mechanism giving rise to venom gene paralogs, with evidence that natural selection acting on surface exposed residues of the resulting gene duplicates facilitates subfunctionalization/neofunctionalization of the encoded proteins (15,(17)(18)(19). The result of these processes is a complex suite of toxins that act synergistically to cause rapid prey death.…”

Dynamic evolution of venom proteins in squamate reptiles

“…Consequently, we utilised positive selection tests to investigate whether adaptive evolution could be detected in any of the non-toxin branches present within each of the gene trees. Notably, despite the limitations of the approach in this specific instance (in particular the fact that the analysis only detects evidence of excess selection in the branches of interest over background levels -the latter of which are likely to be high, as most toxin genes evolve by positive selection [21][22][23] ), we detected significant evidence of adaptive evolution acting on two independent non-toxin branches present in the lectin gene tree ( Fig. 4; Supplementary Table S3).…”

“…Here we propose that the same process may be responsible for some instances of reverse recruitment, with a gene expressed in the venom gland being duplicated (which occurs frequently in a number of toxin families [21][22][23][24][25][26] ) and undergoing adaptive evolution to neofunctionalise the encoded protein for physiological expression (Fig. 6).…”

Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales

“…Polymorphisms at a much larger genomic scale, such as gene duplications and deletions (Stranger et al 2007), also can alter the expression level of a particular protein (Nguyen et al 2006). The correlation between gene copy-number differences and changes in gene expression has been documented previously (Cheng et al 2005;Freeman et al 2006;Nair et al 2008), including in venoms (Margres et al 2015b), and venom protein families are believed to be the result of gene duplication and positive selection (Casewell et al 2011) via the birth-anddeath model of protein evolution (Fry et al 2008). The significant expression variation we detected therefore could be the result of variation in copy number, assuming that variation in copy number would affect low-expression (and presumably low-copy) genes more than high-expression, high-copy genes (e.g., the difference between 10 and 12 copies for a particular protein may not be significant, but the difference between 2 and 4 copies may be).…”