Exon Shuffling and Origin of Scorpion Venom Biodiversity

Abstract

Scorpion venom is a complex combinatorial library of peptides and proteins with multiple biological functions. A combination of transcriptomic and proteomic techniques has revealed its enormous molecular diversity, as identified by the presence of a large number of ion channel-targeted neurotoxins with different folds, membrane-active antimicrobial peptides, proteases, and protease inhibitors. Although the biodiversity of scorpion venom has long been known, how it arises remains unsolved. In this work, we analyzed the exon-intron structures of an array of scorpion venom protein-encoding genes and unexpectedly found that nearly all of these genes possess a phase-1 intron (one intron located between the first and second nucleotides of a codon) near the cleavage site of a signal sequence despite their mature peptides remarkably differ. This observation matches a theory of exon shuffling in the origin of new genes and suggests that recruitment of different folds into scorpion venom might be achieved via shuffling between body protein-coding genes and ancestral venom gland-specific genes that presumably contributed tissue-specific regulatory elements and secretory signal sequences.

Keywords: exon shuffling; exon-intron structure; molecular diversity; scorpion venom.

Figure 1

The fold diversity of scorpion venom components. (A) Representative structure of three different types of peptides: MMTX (PDB: 2RTZ) (CSαβ fold), λ-MeuTx-1 (ICK fold) [7], and the α-helical Meucin-24 (PDB: 2KFE); (B) Representative structures of scorpion venom-derived proteases and protease inhibitors: The chymotrypsin-like protease MmChTP whose structure was modelled on SWISS-MODEL (www.expasy.org) using the template of a mannose-binding lectin-associated serine proteinase-3 (PDB: 4KKD); the Kunitz-type protease inhibitor LmKTT-1a (PDB: 2M01).

Figure 2

Representative gene structures of scorpion venom-derived neurotoxins and antimicrobial peptides. UTR, untranslated region; SP, signal peptide; MP, mature peptide; PP, propeptide. Functional classes: KCT, potassium channel toxin; SCT, sodium channel toxin; CCT, chloride channel toxin; DFN, defensin; RyR, ryanodine receptor; AMP, antimicrobial peptide. MM, Mesobuthus martensii; ME, M. eupeus; CE, Centruroides exilicauda; and OC, Opistophthalmus carinatus.

Figure 3

Representative gene structures of scorpion venom-derived proteases (MmChTP and CsEChTP) and protease inhibitors (MmPI-1, MmPI-2a, MmPI-2b, and CsEPI-1). MM, M. martensii; CE, C. exilicauda.

Figure 4

The hypothetical evolutionary model for the origin of scorpion venom biodiversity. Exon shuffling is proposed as a major evolutionary mechanism mediating the origin of venom proteins from ancestral body proteins, in which a venom gland-specific ancestral gene is considered as a donor providing two necessary elements for venom gland-specific expression: a promoter and a secretory signal.