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Unique Scorpion Toxin with a Putative Ancestral Fold Provides Insight Into Evolution of the Inhibitor Cystine Knot Motif

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Unique Scorpion Toxin with a Putative Ancestral Fold Provides Insight Into Evolution of the Inhibitor Cystine Knot Motif Unique scorpion toxin with a putative ancestral fold provides insight into evolution of the inhibitor cystine knot motif Jennifer J. Smitha, Justine M. Hillb, Michelle J. Littlec, Graham M. Nicholsonc, Glenn F. Kinga,1, and Paul F. Alewooda,1 aInstitute for Molecular Bioscience and bSchool of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD 4072, Australia; and cNeurotoxin Research Group, School of Medical and Molecular Biosciences, University of Technology, Sydney NSW 2007, Australia Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved May 10, 2011 (received for review March 7, 2011) The three-disulfide inhibitor cystine knot (ICK) motif is a fold Here we describe the discovery of a scorpion-venom peptide common to venom peptides from spiders, scorpions, and aquatic that represents an example of a unique fourth scorpion toxin fold. cone snails. Over a decade ago it was proposed that the ICK motif Moreover, this structure is an example of a native peptide that is an elaboration of an ancestral two-disulfide fold coined the adopts the previously hypothetical DDH fold. Thus, the current disulfide-directed β-hairpin (DDH). Here we report the isolation, work provides support for the hypothesis that the DDH fold is characterization, and structure of a novel toxin [U1-liotoxin-Lw1a the evolutionary precursor of the ICK motif. (U1-LITX-Lw1a)] from the venom of the scorpion Liocheles waigien- sis that is the first example of a native peptide that adopts the DDH Results fold. U1-LITX-Lw1a not only represents the discovery of a missing Mass Profile of the Liocheles waigiensis Venom Peptidome. Research link in venom protein evolution, it is the first member of a fourth on scorpion venoms has focused primarily on members of the structural fold to be adopted by scorpion-venom peptides. Addi- medically important Buthidae family. There have been far fewer tionally, we show that U1-LITX-Lw1a has potent insecticidal activity studies on nonbuthids, and very little research has been performed across a broad range of insect pest species, thereby providing a on Australian scorpions despite their evolutionary significance. unique structural scaffold for bioinsecticide development. We therefore decided to examine the venom of the nonbuthid Australian scorpion L. waigiensis (Scorpiones: Scorpionoidea: molecular evolution ∣ NMR ∣ protein structure Liochelidae) as this species had not been studied previously. MS analysis of L. waigiensis venom revealed 200 distinct masses >10 corpions are one of the most ancient venomous animals, with ranging from 1 kDa to kDa. The majority (88%) of observa- Sthe oldest fossil scorpion dating to the Silurian Period around ble masses were smaller than 5 kDa (Fig. 1B), indicating that the 430 million years ago (1). Scorpion venoms are consequently venom is dominated by small peptides. Mass profiling of the ve- the product of millions of years of evolutionary fine-tuning, re- nom using both nanoelectrospray and MALDI-TOF instruments sulting in the chemically and pharmacologically complex mixture proved to be complementary, with only approximately 30% of the present in extant venoms (2). The predominant components of total masses (57 of 192) observed using both methods (Fig. 1B). scorpion venoms are bioactive peptides, many of which have potential application in the pharmaceutical (3) and agrochemical Isolation and Sequencing of a Unique Peptide. A unique peptide of (4) industries. mass 4,171.91 Da was purified from L. waigiensis venom using Over the past 60 years, approximately 730 scorpion-venom reversed-phase (rp) HPLC (Fig. 1A). Because its molecular target peptides have been isolated from 56 species (5). The vast majority remains to be determined, the peptide was named U1-liotoxin- of scorpion toxins characterized to date contain a common core Lw1a (U1-LITX-Lw1a) based on the recently introduced nomen- topology comprising one or two short α-helices connected to a clature for venom peptides (14). Reduction of the purified triple-stranded antiparallel β-sheet stabilized by three or four peptide followed by alkylation with iodoacetamide led to a mass disulfide bonds (6). This fold, known as the cystine-stabilized increase of 232 Da, indicating the presence of two disulfide bonds. The reduced and alkylated peptide was subjected to α/β (CSα/β) motif, is one of only three structural scaffolds that N-terminal sequencing that, combined with tandem mass spectro- have been found in disulfide-containing scorpion-venom pep- metry (MS/MS) analysis, revealed the primary structure of the tides. The topologically unrelated cystine-stabilized α-helix-loop- 36-residue peptide as DFPLSKEYESCVRPRKCKPPLKCNKA- helix (CSα/α) fold consists of two short α-helices connected by a QICVDPNKGW. β-turn; only seven scorpion peptides have been discovered that adopt this fold (7). The third fold found in scorpion-venom pep- U -LITX-Lw1a Is Expressed as a Prepropeptide. The DNA sequences tides is the inhibitor cystine knot (ICK) motif (8) that dominates 1 of clones from 5′ RACE analysis of a venom-gland cDNA library the venom peptidome of spiders (9) and is also present in pep- revealed the presence of a unique transcript upstream of the tides from evolutionarily unrelated organisms (10). The CSα/β scorpion neurotoxins evolved by recruitment into the venom and subsequent neofunctionalization of CSα/β defen- Author contributions: J.J.S., M.J.L., G.M.N., and P.F.A. designed research; J.J.S., J.M.H., sins (11). The CSα/β defensins are antimicrobial peptides that are M.J.L., and G.F.K. performed research; J.J.S., M.J.L., G.M.N., G.F.K., and P.F.A. analyzed data; widely distributed in plants, fungi, nematodes, and the arthropod and J.J.S., G.M.N., G.F.K., and P.F.A. wrote the paper. classes Insecta and Arachnida. The conservation of gene struc- The authors declare no conflict of interest. ture between scorpion CSα/β defensins, which are found in the This article is a PNAS Direct Submission. haemolymph, and the CSα/β venom neurotoxins supports a para- Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 2KYJ). The NMR chemical shifts have been logous relationship between these two classes of peptides (12). deposited in the BioMagResBank, www.bmrb.wisc.edu (accession no. 16963). In contrast, little is known about the evolutionary origins of the 1To whom correspondence may be addressed. E-mail: [email protected] or CSα/α and ICK folds. It was previously suggested that the three- [email protected]. disulfide ICK fold is an elaboration of a simpler, ancestral two- This article contains supporting information online at www.pnas.org/lookup/suppl/ disulfide fold coined the disulfide-directed β-hairpin (DDH) (13). doi:10.1073/pnas.1103501108/-/DCSupplemental. 10478–10483 ∣ PNAS ∣ June 28, 2011 ∣ vol. 108 ∣ no. 26 www.pnas.org/cgi/doi/10.1073/pnas.1103501108 Downloaded by guest on October 1, 2021 A Structure of U1-LITX-Lw1a. The three-dimensional structure of 1.8 90 U1-LITX-Lw1a was determined using homonuclear NMR meth- 1.6 80 ods. Statistics highlighting the high precision and stereochemical 1.4 70 quality of the ensemble of 20 U1-LITX-Lw1a structures are * shown in Table S1. The highest-ranked member of the ensemble 1.2 60 oS vl e has a MolProbity score of 2.54, placing it in the 45th percentile 1.0 50 n t relative to all other structures ranked by MolProbity. 0.8 B 40 % (arbritrary units) The structure of U1-LITX-Lw1a is remarkable for a scorpion- 0.6 30 α β α α 214nm venom peptide. It does not contain the CS / ,CS / , or ICK A 0.4 20 motif common to other disulfide-rich scorpion toxins but instead 0.2 10 contains a unique two-disulfide scaffold (Fig. 2). The only ele- 0.0 ments of secondary structure are two short but well-defined two- 10 20 30 40 50 60 70 80 90 100 110 stranded β-sheets. The N-terminal β-sheet comprises β-strands 1 Retention time (min) and 2 (residues 4–5 and 16–17, respectively), whereas the C-term- B inal β-sheet is composed of β-strands 3 and 4 (residues 22–23 and 80 250 29–30, respectively) (Fig. 2). Nanospray 200 uC MALDI-TOF Remarkably, a search for structural homologs of U1-LITX- 60 m u (105) (144) l Lw1a using DALI (17) yielded a total of 29 unique matches with 150 a vit ≥2 40 e a statistically significant Z score . Of these structural homo- 100 ot ot logs, 28 contain an ICK motif, including 23 spider toxins and one at 48 57 87 20 50 l cone snail toxin. Notably, however, all of these structurally homo- Number of masses 0 0 logous toxins contain at least one additional disulfide bond. <1 ICK toxins have proliferated in spider venoms to the point >10 1 to 22 to 33 to 44 to 55 to 66 to 77 to 88 to 9 9 to 10 where they now dominate most spider-venom peptidomes (18). Mass (kDa) The marked insensitivity of this structural scaffold to changes in Fig. 1. Analysis of the venom peptidome of L. waigiensis.(A) rpHPLC intercystine resides has enabled spiders to develop diverse phar- chromatogram of crude venom from the scorpion L. waigiensis. The aceto- macologies using the same disulfide framework. Fig. 4 shows an nitrile gradient is shown as a solid line, and the peak marked with an asterisk overlay of U1-LITX-Lw1a on the structure of ICK spider toxins corresponds to the U1-LITX-Lw1a peptide. (B, Left) Histogram showing the with different pharmacologies, including toxins with high affinity abundance of peptide toxins in the venom of L.
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