Rapid and efficient identification of cysteine-rich peptides by random screening of a venom gland cDNA library from the hexathelid spider Macrothele gigas

From genome to proteome: Comprehensive identification of venom toxins from the Chinese funnel-web spider (Macrothelidae: Macrothele yani)

Macrothelidae is a family of mygalomorph spiders containing the extant genera Macrothele and Vacrothele. China is an important center of diversity for Macrothele with 65 % of the known species occurring there. Previous work on Macrothele was able to uncover several important toxin compounds including Raventoxin which may have applications in biomedicine and agricultural chemistry. Despite the importance of Macrothele spiders, high-quality reference genomes are still lacking, which hinders our understanding and application of the toxin compounds. In this study, we assembled the genome of the Macrothele yani to help fill gaps in our understanding of toxin biology in this lineage of spiders to encourage the future study and applications of these compounds. The final assembled genome was 6.79 Gb in total length, had a contig N50 of 21.44 Mb, and scaffold N50 of 156.16 Mb. Hi-C scaffolding assigned 98.19 % of the genome to 46 pseudo-chromosomes with a BUSCO score of 95.7 % for the core eukaryotic gene set. The assembled genome was found to contain 75.62 % repetitive DNA and a total of 39,687 protein-coding genes were annotated making it the spider genome with highest number of genes. Through integrated analysis of venom gland transcriptomics and venom proteomics, a total of 194 venom toxins were identified, including 38 disulfide-rich peptide neurotoxins, among which 12 were ICK knottin peptides. In summary, we present the first high-quality genome assembly at the chromosomal level for any Macrothelidae spider, filling an important gap in our knowledge of these spiders. Such high-quality genomic data will be invaluable as a reference in resolving Araneae spider phylogenies and in screening different spider species for novel compounds applicable to numerous medical and agricultural applications.

Transcriptome analysis reveals the peptide toxins diversity of Macrothele palpator venom

Spider venom is a large pharmacological repertoire of different bioactive peptide toxins. However, obtaining crude venom from some spiders is challenging. Thus, studying individual toxins through venom purification is a daunting task. In this study, we constructed the cDNA library and transcriptomic sequencing from the Macrothele palpator venom glands. Subsequently, 718 high-quality expressed sequence tags (ESTs) were identified, and grouped into three categories, including 449 toxin-like (62.53 %), 136 cellular component (18.94 %) and 133 non-matched (18.52 %) based on the gene function annotation. Additionally, 112 non-redundant toxin-like peptides were classified into 13 families (families A-M) based on their sequence homology and cysteine framework. Bioinformatics analysis revealed a high sequence similarity between families A-J and the toxins from Macrothele gigas in the NR database. In contrast, families K-M had a generally low sequence homology with known spider peptide toxins and unpredictable biological functions. Taken together, this study adds many new members to the spider toxin superfamily and provides a basis for identifying various potential biological tools in M. palpator venom.

Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses

This review gives an overview on the development of research on spider venoms with a focus on structure and function of venom components and techniques of analysis. Major venom component groups are small molecular mass compounds, antimicrobial (also called cytolytic, or cationic) peptides (only in some spider families), cysteine-rich (neurotoxic) peptides, and enzymes and proteins. Cysteine-rich peptides are reviewed with respect to various structural motifs, their targets (ion channels, membrane receptors), nomenclature, and molecular binding. We further describe the latest findings concerning the maturation of antimicrobial, and cysteine-rich peptides that are in most known cases expressed as propeptide-containing precursors. Today, venom research, increasingly employs transcriptomic and mass spectrometric techniques. Pros and cons of venom gland transcriptome analysis with Sanger, 454, and Illumina sequencing are discussed and an overview on so far published transcriptome studies is given. In this respect, we also discuss the only recently described cross contamination arising from multiplexing in Illumina sequencing and its possible impacts on venom studies. High throughput mass spectrometric analysis of venom proteomes (bottom-up, top-down) are reviewed.

The Dual Prey-Inactivation Strategy of Spiders-In-Depth Venomic Analysis of Cupiennius salei

Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to a major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.

The peptide toxin δ-hexatoxin-MrIX inhibits fast inactivation of NaVs in mouse cerebellar granule cells

Spider venom is rich in peptide toxins that could be used to explore the structure and function of voltage-gated sodium channels (Na_Vs). This study has characterized a 44-amino acid peptide toxin, δ-hexatoxin-MrIX (δ-HXTX-MrIX), from the venom of the spider Macrothele raveni. δ-hexatoxin-MrIX potently inhibited the fast inactivation of Na_Vs in mouse cerebellar granule cells (CGCs) with an EC₅₀ of 35.3 ± 5.9 nM. The toxin shifted both the steady-state activation and the steady-state inactivation curves of CGC Na_Vs to the hyperpolarized direction. δ-hexatoxin-MrIX also acted on Na_V1.3 and Na_V1.4 channels heterologously expressed in HEK293T cells, as well as on Na_Vs in acutely isolated cockroach DUM neurons. However, the Na_V1.5, Na_V1.7 and Na_V1.8 channels were resistant to δ-hexatoxin-MrIX. The toxin inhibited the fast inactivation of Na_V1.3 and Na_V1.4 with high affinity (EC₅₀ values of 82.0 ± 3.0 nM and 24.0 ± 4.7 nM, respectively), but the saturating dose of toxin showed distinct efficacy on these two types of channels. δ-hexatoxin-MrIX is a peptide toxin acting on CGC Na_Vs and could be used as a pharmacological tool to explore the role of Na_Vs in granule cell maturation during cerebellum development.

Insecticidal activity of a recombinant knottin peptide from Loxosceles intermedia venom and recognition of these peptides as a conserved family in the genus

Loxosceles intermedia venom comprises a complex mixture of proteins, glycoproteins and low molecular mass peptides that act synergistically to immobilize envenomed prey. Analysis of a venom-gland transcriptome from L. intermedia revealed that knottins, also known as inhibitor cystine knot peptides, are the most abundant class of toxins expressed in this species. Knottin peptides contain a particular arrangement of intramolecular disulphide bonds, and these peptides typically act upon ion channels or receptors in the insect nervous system, triggering paralysis or other lethal effects. Herein, we focused on a knottin peptide with 53 amino acid residues from L. intermedia venom. The recombinant peptide, named U₂ -sicaritoxin-Li1b (Li1b), was obtained by expression in the periplasm of Escherichia coli. The recombinant peptide induced irreversible flaccid paralysis in sheep blowflies. We screened for knottin-encoding sequences in total RNA extracts from two other Loxosceles species, Loxosceles gaucho and Loxosceles laeta, which revealed that knottin peptides constitute a conserved family of toxins in the Loxosceles genus. The insecticidal activity of U₂ -SCTX-Li1b, together with the large number of knottin peptides encoded in Loxosceles venom glands, suggests that studies of these venoms might facilitate future biotechnological applications of these toxins.

A Comparative Analysis of the Venom Gland Transcriptomes of the Fishing Spiders Dolomedes mizhoanus and Dolomedes sulfurous

Dolomedes sulfurous and Dolomedes mizhoanus are predaceous arthropods catching and feeding on small fish. They live in the same area and have similar habits. Their venoms exhibit some similarities and differences in biochemical and electrophysiological properties. In the present work, we first performed a transcriptomic analysis by constructing the venom gland cDNA library of D. sulfurous and 127 novel putative toxin sequences were consequently identified, which were classified into eight families. This venom gland transcriptome was then compared with that of D. mizhoanus, which revealed that the putative toxins from both spider venoms might have originated from the same gene ancestors although novel toxins were evolved independently in the two spiders. The putative toxins from both spiders contain 6-12 cysteine residues forming seven cysteine patterns. As revealed by blast search, the two venoms are rich in neurotoxins targeting ion channels with pharmacological and therapeutic significance. This study provides insight into the venoms of two closely related species of spider, which will be of use for future investigations into the structure and function of their toxins.

Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)

The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.

Scorpion and spider venom peptides: gene cloning and peptide expression

This communication reviews most of the important findings related to venom components isolated from scorpions and spiders, mainly by means of gene cloning and expression. Rather than revising results obtained by classical biochemical studies that report structure and function of venom components, here the emphasis is placed on cloning and identification of genes present in the venomous glands of these arachnids. Aspects related to cDNA library construction, specific or random ESTs cloning, transcriptome analysis, high-throughput screening, heterologous expression and folding are briefly discussed, showing some numbers of species and components already identified, but also shortly mentioning limitations and perspectives of research for the future in this field.

Expression of a spider venom peptide in transgenic tobacco confers insect resistance

Spider venom contains a mixture of peptide toxins, some able to kill insects specifically to those considered as important pest. In this study, a peptide toxin produced by the Macrothele gigas spider, Magi 6, was cloned and expressed in tobacco plants, as this toxin has been shown to constitute an effective insecticide. For this purpose, a genetic construction for the cDNA that codifies for Magi 6 was subcloned in a plant expression vector using the 35S promoter and the 5'-end leader from tobacco mosaic virus, in order to transform tobacco leaf disks. The resulting plants demonstrated the presence of Magi 6 gene in the tobacco genome using PCR, and transcription of the cDNA was verified by means of RT-PCR. The expression of the Magi 6 peptide in tobacco was demonstrated by Western blot, which exhibited the expected size, thus suggesting a correct processing of the signal peptide. No morphological alterations in the different transgenic lines were observed, nor any change in plant growth. Subsequently, experiments were carried out challenging detached leaves or whole plants with the herbivorous insect Spodoptera frugiperda. The bioassays indicated that the transgenic lines were significantly more resistant than the wild type plants. This work demonstrated that the expression of Magi 6 peptide in transgenic plants conferred resistance to insect attack and opens the possibility of employing this peptide to improve the resistance of diverse plants.

An insecticidal peptide from the theraposid Brachypelma smithi spider venom reveals common molecular features among spider species from different genera

The soluble venom of the Mexican theraposid spider Brachypelma smithi was screened for insecticidal peptides based on toxicity to house crickets. An insecticidal peptide, named Bs1 (which stands for Brachypelma smithi toxin 1) was obtained in homogeneous form after the soluble venom was fractionated using reverse-phase and cation-exchange chromatography. It contains 41 amino acids cross-linked by three disulfide bridges. Its sequence is similar to an insecticidal peptide isolated from the theraposid spider Ornithoctonus huwena from China, and another from the hexathelid spider Macrothelegigas from Japan, indicating that they are phylogenetically related. A cDNA library was prepared from the venomous glands of B. smithi and the gene that code for Bs1 was cloned. Sequence analysis of the nucleotides of Bs1 showed similarities to that of the hexathelid spider from Japan proving additional evidence for close genetic relationship between these spider peptides. The mRNAs of these toxins code for signal peptides that are processed at the segment rich in acidic and basic residues. Their C-terminal amino acids are amidated. However, they contain only a glycine residue at the most C-terminal position, without the presence of additional basic amino acid residues, normally required for post-translation processing of other toxins reported in the literature. The possible mechanism of action of Bs1 was investigated using several ion channels as putative receptors. Bs1 had minor, but significant effects on the Para/tipE insect ion channel, which could indirectly correlate with the observed lethal activity to crickets.

Venomics: unravelling the complexity of animal venoms with mass spectrometry

Animal venoms and toxins are now recognized as major sources of bioactive molecules that may be tomorrow's new drug leads. Their complexity and their potential as drug sources have been demonstrated by application of modern analytical technologies, which have revealed venoms to be vast peptide combinatorial libraries. Structural as well as pharmacological diversity is immense, and mass spectrometry is now one of the major investigative tools for the structural investigation of venom components. Recent advances in its use in the study of venom and toxins are reviewed. The application of mass spectrometry techniques to peptide toxin sequence determination by de novo sequencing is discussed in detail, in the light of the search for novel analgesic drugs. We also present the combined application of LC-MALDI separation with mass fingerprinting and ISD fragmentation for the determination of structural and pharmacological classes of peptides in complex spider venoms. This approach now serves as the basis for the full investigation of complex spider venom proteomes, in combination with cDNA analysis.

Classification of spider neurotoxins using structural motifs by primary structure features. Single residue distribution analysis and pattern analysis techniques

In recent years the data on the novel structures of spider toxins have been greatly increasing. The sequence data should be classified. We introduced two primary structure analysis techniques-single residue distribution analysis (SRDA) and pattern analysis for classifying spider polypeptide toxins with molecular weight less than 10kDa. For multiple sequence alignment, we also introduced three novel sequence representation formats named as a simple record, motif record and a pattern record, which can be useful for large-scale analysis of structures. About 300 sequences of spider toxins were analyzed and nine primary structure motifs were identified. New classification of spider toxins was proposed on the basis of previously described principal structural motif (PSM) and extra structural motif (ESM) [Kozlov, S.A., Malyavka, A.A., McCutchen, B., Lu, A., Schepers, E., Herrmann, R., Grishin, E.V., 2005. A novel strategy for the identification of toxin-like structures in spider venom. Proteins 59 (1), 131-140]. Five main structural classes were revealed, and for putative ion channel inhibitors from the most numerous classes 1, 2, and 3, five-digital personal ID numbers were introduced. A reference table with simple, motif and pattern representation sequence formats was created for all analyzed structures.

Molecular components and toxicity of the venom of the solitary wasp, Anoplius samariensis

The solitary spider wasp, Anoplius samariensis, is known to exhibit a unique long-term, non-lethal paralysis in spiders that it uses as a food source for its larvae. However, neither detailed venom components nor paralytic compounds have ever been characterized. In this study, we examined the components in the low molecular weight fraction of the venom and the paralytic activity of the high molecular weight fraction. The major low molecular weight components of the venom were identified as gamma-aminobutyric acid and glutamic acid by micro-liquid chromatography/electrospray ionization mass spectrometry and nuclear magnetic resonance spectrometry analysis. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass analysis revealed that the A. samariensis venom contained the various proteins with weights of 4-100 kDa. A biological assay using Joro spiders (Nephila clavata) clearly showed that the high molecular weight fraction of the venom prepared by ultrafiltration exerted as potent non-lethal long-term paralysis as the whole venom, whereas the low molecular weight fraction was devoid of any paralytic activity. These results indicated that several venomous proteins in the high molecular weight fraction are responsible for the paralytic activity. Furthermore, we determined the primary structure of one component designated As-fr-19, which was a novel multiple-cysteine peptide with high sequence similarity to several sea anemone and snake toxins including dendrotoxins, rather than any insect toxic peptides identified so far. Taken together, our data showed the unprecedented molecular and toxicological profiles of wasp venoms.

Effects of spider Macrothele raven venom on cell proliferation and cytotoxicity in HeLa cells

AIM

To examine the effect of venom from the spider Macrothele raven on cell proliferation and cytotoxicity in human cervical carcinoma, HeLa cells.

METHODS

Morphological and biochemical signs of apoptosis appeared using acridine orange-ethidium bromide (AO/EB) staining. Marked morphological changes in HeLa cells after treatment with spider venom were observed using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Cell proliferation and cytotoxicity were determined by [methyl-3H] thymidine assay ([3H]TdR) and lactate dehydrogenase (LDH) release, respectively. DNA fragmentation and cell cycle distribution were monitored using flow cytometry. In addition, Western blot analysis was used to evaluate the level of caspase-3 expression. In vivo examination of the inhibition of the size of tumors in nude mice treated with spider venom was measured.

RESULTS

Marked morphological changes were observed using AO/EB staining, SEM and TEM assay. Spider venom at concentrations of 10-40 mg/L caused dose- and time-dependent inhibition of HeLa cell proliferation. The ratio of apoptosis and necrosis increased. The activity of caspase-3 was upregulated after spider venom treatment. In vivo study of tumor size revealed that tumors significantly decreased in size from controls to tumors treated for 3 weeks with spider venom (P<0.05).

CONCLUSION

The inhibition of HeLa cells by the venom of the spider Macrothele raveni was carried out in three ways: induction of apoptosis, necrosis of toxicity damage and direct lysis. Spider venom is a novel anti-tumor material both in vitro and in vivo.