Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes

Abstract

Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named Snake Venom Metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an ‘SVMP-like’ function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary non-catalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, while the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on non-homologous genes, yielding alternate biochemical components.

Divergent Specialization of Simple Venom Gene Profiles among Rear-Fanged Snake Genera (Helicops and Leptodeira, Dipsadinae, Colubridae)

“…We created a custom database of non-toxin and toxin nucleotide sequences by downloading venom gland transcriptomes of Crotalus adamanteus [ 60 ], Crotalus horridus [ 74 ], Micrurus fulvius [ 75 ], Boiga irregularis [ 21 ], Hypsiglena sp. [ 21 ], and Spilotes sulphureus [ 26 ], the annotated genome of Ophiophagus hannah [ 76 ], and sequences of snake venom matrix metalloproteinase [ 77 ] from NCBI GenBank. A combination of these species has been used previously to identify putative rear-fanged snake venom components and represent a diversity of venomous snakes [ 26 ].…”

The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence

“…Another recent described diagnostic trait for Tachymenini is the presence of the class of venom toxins known as svMMPs (snake venom matrix metalloproteinase) in their venom gland transcriptomes and venom proteomes (Bayona‐Serrano et al, 2020). Although this class of toxin is also found in Xenodontini and Conophiini, the evolution from endogenous counterparts (seMMP‐9) through sequential domain losses were different and convergent in these three tribes.…”

Duvernoy’s Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes

“…This dichotomy between recognized importance and continued neglect is underscored by the fact that, when studied, colubrid venoms are a source of incredible toxin diversity and even novel toxins (and toxin families). Transcriptomic and proteomic studies of colubrid venoms have also unlocked important new insights into the ecology, evolution, and natural history of the snakes themselves (e.g., [ 38 , 39 , 40 , 69 ]). Without an understanding of these key, overlooked components, the broader picture of venom evolution as a whole will remain incomplete.…”

“…RFS are increasingly being recognized as important pieces largely missing from the broader context of venom evolution, variation, and ecological significance [ 25 , 26 , 31 , 34 , 35 , 36 , 37 ]. When modern transcriptomic and/or proteomic methods have been applied, RFS have been shown to harbor tremendous toxin diversity, including novel phenotypes (e.g., [ 38 ]), prey-specific toxins (e.g., [ 39 , 40 ]), and novel components not previously considered venoms (e.g., [ 41 ]).…”