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Toxins
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Evolution, Genomics and Proteomics of Venom
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Evolution, Genomics and Proteomics of Venom

A special issue of Toxins (ISSN 2072-6651). This special issue belongs to the section "Animal Venoms".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 26206

Special Issue Editors

Dr. Sebastien Dutertre

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Guest Editor
Institut des Biomolécules Max Mousseron (UMR 5247), Université Montpellier, CNRS, Place Eugène Bataillon, CEDEX 05, 34095 Montpellier, France
Interests: venoms; conotoxins; peptides; proteomics; transcriptomics; drug discovery
Special Issues, Collections and Topics in MDPI journals
Dr. Eivind A.B. Undheim

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Co-Guest Editor
1. Centre for Biodiversity Dynamics, Department of Biology, NTNU, N-7491 Trondheim, Norway
2. Centre for Ecological and Evolutionary Synthesis, Department of Bioscience, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
Interests: animal venoms and toxins; structure-function relationships; phylogenetics; molecular evolution of venoms; venom proteomics; venom transcriptomics; venoms-based drug discovery

Special Issue Information

Dear Colleagues,

Venoms are highly complex mixtures of biological compounds (“toxins”) which have evolved to serve a range of ecological roles, including the capture of prey and defense against aggressors. In most venoms, proteins and peptides comprise the majority of toxins, and proteomic approaches are therefore central to deciphering the biochemical complexity that underlies the functional diversity of venoms. However, understanding how this diversity has emerged requires a multifaceted methodology that also includes comparative evolutionary, transcriptomic, and genomic approaches. Together, these methods have facilitated the identification and characterization of venom-derived pharmacological tools and lead molecules for development as therapeutics, cosmetics, or agrochemicals. This Special Issue focuses on developments and utilization of transcriptomic, genomic, and/or proteomic and mass spectrometry approaches that lead to new knowledge on the biology, evolution, or potential application of venoms and toxins.

Dr. Sebastien Dutertre
Dr. Eivind A.B. Undheim
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a double-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Toxins is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • venom
  • toxin
  • proteomics
  • proteotranscriptomics
  • transcriptomics
  • genomics
  • top-down
  • bottom-up
  • mass spectrometry
  • mass spectrometry imaging

Published Papers (7 papers)

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Research

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10 pages, 1989 KiB  
Article
Proteomic Analysis of the Predatory Venom of Conus striatus Reveals Novel and Population-Specific κA-Conotoxin SIVC
by Fabrice Saintmont, Guillaume Cazals, Claudia Bich and Sebastien Dutertre
Toxins 2022, 14(11), 799; https://doi.org/10.3390/toxins14110799 - 17 Nov 2022
Cited by 1 | Viewed by 1731
Abstract
Animal venoms are a rich source of pharmacological compounds with ecological and evolutionary significance, as well as with therapeutic and biotechnological potentials. Among the most promising venomous animals, cone snails produce potent neurotoxic venom to facilitate prey capture and defend against aggressors. Conus [...] Read more.
Animal venoms are a rich source of pharmacological compounds with ecological and evolutionary significance, as well as with therapeutic and biotechnological potentials. Among the most promising venomous animals, cone snails produce potent neurotoxic venom to facilitate prey capture and defend against aggressors. Conus striatus, one of the largest piscivorous species, is widely distributed, from east African coasts to remote Polynesian Islands. In this study, we investigated potential intraspecific differences in venom composition between distinct geographical populations from Mayotte Island (Indian Ocean) and Australia (Pacific Ocean). Significant variations were noted among the most abundant components, namely the κA-conotoxins, which contain three disulfide bridges and complex glycosylations. The amino acid sequence of a novel κA-conotoxin SIVC, including its N-terminal acetylated variant, was deciphered using tandem mass spectrometry (MS/MS). In addition, the glycosylation pattern was found to be consisting of two HexNAc and four Hex for the Mayotte population, which diverge from the previously characterized two HexNAc and three Hex combinations for this species, collected elsewhere. Whereas the biological and ecological roles of these modifications remain to be investigated, population-specific glycosylation patterns provide, for the first time, a new level of intraspecific variations in cone snail venoms. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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14 pages, 1581 KiB  
Article
Comparative Venom Proteomics of Iranian, Macrovipera lebetina cernovi, and Cypriot, Macrovipera lebetina lebetina, Giant Vipers
by Parviz Ghezellou, Melissa Dillenberger, Seyed Mahdi Kazemi, Daniel Jestrzemski, Bernhard Hellmann and Bernhard Spengler
Toxins 2022, 14(10), 716; https://doi.org/10.3390/toxins14100716 - 20 Oct 2022
Cited by 4 | Viewed by 2409
Abstract
Envenoming by Macrovipera lebetina subspecies causes severe life-threatening difficulties for people living in North Africa and the Middle East. To better understand the pathophysiology of envenoming and improve patient management, knowledge about the venom components of the subspecies is essential. Here, the venom [...] Read more.
Envenoming by Macrovipera lebetina subspecies causes severe life-threatening difficulties for people living in North Africa and the Middle East. To better understand the pathophysiology of envenoming and improve patient management, knowledge about the venom components of the subspecies is essential. Here, the venom proteomes of Macrovipera lebetina lebetina from Cyprus and Macrovipera lebetina cernovi from Iran were characterized using RP-HPLC separation of the crude venom proteins, SDS-PAGE of fractionated proteins, and LC-MS/MS of peptides obtained from in-gel tryptic digestion of protein bands. Moreover, we also used high-resolution shot-gun proteomics to gain more reliable identification, where the whole venom proteomes were subjected directly to in-solution digestion before LC-HR-MS/MS. The data revealed that both venoms consisted of at least 18 protein families, of which snake venom Zn2+-dependent metalloprotease (SVMP), serine protease, disintegrin, phospholipase A2, C-type lectin-like, and L-amino acid oxidase, together accounted for more than 80% of the venoms’ protein contents. Although the two viper venoms shared mostly similar protein classes, the relative occurrences of these toxins were different in each snake subspecies. For instance, P-I class of SVMP toxins were found to be more abundant than P-III class in the venoms of M. l. cernovi compared to M. l. lebetina, which gives hints at a more potent myonecrotic effect and minor systemic hemorrhage following envenoming by M. l. cernovi than M. l. lebetina. Moreover, single-shot proteomics also revealed many proteins with low abundance (<1%) within the venoms, such as aminopeptidase, hyaluronidase, glutaminyl-peptide cyclotransferase, cystatin, phospholipase B, and vascular endothelial growth factor. Our study extends the in-depth understanding of the venom complexity of M. lebetina subspecies, particularly regarding toxin families associated with envenoming pathogenesis and those hard-detected protein classes expressed in trace amounts. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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19 pages, 2193 KiB  
Article
Investigation of Peptide Toxin Diversity in Ribbon Worms (Nemertea) Using a Transcriptomic Approach
by Anna E. Vlasenko, Vasiliy G. Kuznetsov and Timur Yu. Magarlamov
Toxins 2022, 14(8), 542; https://doi.org/10.3390/toxins14080542 - 08 Aug 2022
Cited by 1 | Viewed by 1792
Abstract
Nemertea is a phylum of nonsegmented worms (supraphylum: Spiralia), also known as ribbon worms. The members of this phylum contain various toxins, including peptide toxins. Here, we provide a transcriptomic analysis of peptide toxins in 14 nemertean species, including Cephalothrix cf. simula, [...] Read more.
Nemertea is a phylum of nonsegmented worms (supraphylum: Spiralia), also known as ribbon worms. The members of this phylum contain various toxins, including peptide toxins. Here, we provide a transcriptomic analysis of peptide toxins in 14 nemertean species, including Cephalothrix cf. simula, which was sequenced in the current study. The summarized data show that the number of toxin transcripts in the studied nemerteans varied from 12 to 82. The most represented groups of toxins were enzymes and ion channel inhibitors, which, in total, reached a proportion of 72% in some species, and the least represented were pore-forming toxins and neurotoxins, the total proportion of which did not exceed 18%. The study revealed that nemerteans possess a much greater variety of toxins than previously thought and showed that these animals are a promising object for the investigation of venom diversity and evolution, and in the search for new peptide toxins. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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15 pages, 1084 KiB  
Article
Proteo-Transcriptomic Characterization of Sirex nitobei (Hymenoptera: Siricidae) Venom
by Chenglong Gao, Lili Ren, Ming Wang, Zhengtong Wang, Ningning Fu, Huiying Wang, Xiaochen Wang, Tegen Ao, Wensheng Du, Zijin Zheng, Huadong Li and Juan Shi
Toxins 2021, 13(8), 562; https://doi.org/10.3390/toxins13080562 - 11 Aug 2021
Cited by 6 | Viewed by 2501
Abstract
The wood-boring woodwasp Sirex nitobei is a native pest in Asia, infecting and weakening the host trees in numerous ecological and commercial coniferous forest plantations. In China, hosts of S. nitobei are diverse, so the pest has spread to several provinces of China, [...] Read more.
The wood-boring woodwasp Sirex nitobei is a native pest in Asia, infecting and weakening the host trees in numerous ecological and commercial coniferous forest plantations. In China, hosts of S. nitobei are diverse, so the pest has spread to several provinces of China, resulting in considerable economic and ecological damage. During female oviposition, S. nitobei venom along with arthrospores of the symbiotic fungus Amylostereum areolatum or A. chaetica is injected into host trees, and the combination of these two biological factors causes the death of xylem host trees. The presence of venom alone causes only the yellowing and wilting of needles. In this study, we constructed the venom gland transcriptome of S. nitobei for the first time and a total of 15,036 unigenes were acquired. From the unigenes, 11,560 ORFs were identified and 537 encoding protein sequences with signal peptides at the N-terminus. Then, we used the venomics approach to characterize the venom composition of female S. nitobei and predicted 1095 proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. We focused on seven proteins that were both highly expressed in the venom gland transcriptome and predicted in the crude venom proteome. These seven proteins are laccase-2, laccase-3, a protein belonging to the Kazal family, chitooligosaccharidolytic β-N-acetylglucosaminidase, beta-galactosidase, icarapin-like protein, and waprin-Thr1-like protein. Using quantitative real-time PCR (qRT-PCR), we also proved that the genes related to these seven proteins are specifically expressed in the venom glands. Finally, we revealed the functional role of S. nitobei venom in the physiological response of host trees. It can not only promote the colonization of symbiotic fungus but contribute to the development of eggs and larvae. This study provides a deeper understanding of the molecular mechanism of the woodwasp–pine interaction. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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36 pages, 11448 KiB  
Article
Proteo-Trancriptomic Analyses Reveal a Large Expansion of Metalloprotease-Like Proteins in Atypical Venom Vesicles of the Wasp Meteorus pulchricornis (Braconidae)
by Jean-Luc Gatti, Maya Belghazi, Fabrice Legeai, Marc Ravallec, Marie Frayssinet, Stéphanie Robin, Djibril Aboubakar-Souna, Ramasamy Srinivasan, Manuele Tamò, Marylène Poirié and Anne-Nathalie Volkoff
Toxins 2021, 13(7), 502; https://doi.org/10.3390/toxins13070502 - 19 Jul 2021
Cited by 5 | Viewed by 3331
Abstract
Meteorus pulchricornis (Ichneumonoidea, Braconidae) is an endoparasitoid wasp of lepidopteran caterpillars. Its parasitic success relies on vesicles (named M. pulchricornis Virus-Like Particles or MpVLPs) that are synthesized in the venom gland and injected into the parasitoid host along with the venom during oviposition. [...] Read more.
Meteorus pulchricornis (Ichneumonoidea, Braconidae) is an endoparasitoid wasp of lepidopteran caterpillars. Its parasitic success relies on vesicles (named M. pulchricornis Virus-Like Particles or MpVLPs) that are synthesized in the venom gland and injected into the parasitoid host along with the venom during oviposition. In order to define the content and understand the biogenesis of these atypical vesicles, we performed a transcriptome analysis of the venom gland and a proteomic analysis of the venom and purified MpVLPs. About half of the MpVLPs and soluble venom proteins identified were unknown and no similarity with any known viral sequence was found. However, MpVLPs contained a large number of proteins labelled as metalloproteinases while the most abundant protein family in the soluble venom was that of proteins containing the Domain of Unknown Function DUF-4803. The high number of these proteins identified suggests that a large expansion of these two protein families occurred in M. pulchricornis. Therefore, although the exact mechanism of MpVLPs formation remains to be elucidated, these vesicles appear to be “metalloproteinase bombs” that may have several physiological roles in the host including modifying the functions of its immune cells. The role of DUF4803 proteins, also present in the venom of other braconids, remains to be clarified. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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18 pages, 6685 KiB  
Article
Tentacle Morphological Variation Coincides with Differential Expression of Toxins in Sea Anemones
by Lauren M. Ashwood, Michela L. Mitchell, Bruno Madio, David A. Hurwood, Glenn F. King, Eivind A. B. Undheim, Raymond S. Norton and Peter J. Prentis
Toxins 2021, 13(7), 452; https://doi.org/10.3390/toxins13070452 - 29 Jun 2021
Cited by 11 | Viewed by 4464
Abstract
Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple [...] Read more.
Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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Review

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26 pages, 2145 KiB  
Review
Old World Vipers—A Review about Snake Venom Proteomics of Viperinae and Their Variations
by Maik Damm, Benjamin-Florian Hempel and Roderich D. Süssmuth
Toxins 2021, 13(6), 427; https://doi.org/10.3390/toxins13060427 - 17 Jun 2021
Cited by 34 | Viewed by 8822
Abstract
Fine-tuned by millions of years of evolution, snake venoms have frightened but also fascinated humanity and nowadays they constitute potential resources for drug development, therapeutics and antivenoms. The continuous progress of mass spectrometry techniques and latest advances in proteomics workflows enabled toxinologists to [...] Read more.
Fine-tuned by millions of years of evolution, snake venoms have frightened but also fascinated humanity and nowadays they constitute potential resources for drug development, therapeutics and antivenoms. The continuous progress of mass spectrometry techniques and latest advances in proteomics workflows enabled toxinologists to decipher venoms by modern omics technologies, so-called ‘venomics’. A tremendous upsurge reporting on snake venom proteomes could be observed. Within this review we focus on the highly venomous and widely distributed subfamily of Viperinae (Serpentes: Viperidae). A detailed public literature database search was performed (2003–2020) and we extensively reviewed all compositional venom studies of the so-called Old-World Vipers. In total, 54 studies resulted in 89 venom proteomes. The Viperinae venoms are dominated by four major, four secondary, six minor and several rare toxin families and peptides, respectively. The multitude of different venomics approaches complicates the comparison of venom composition datasets and therefore we differentiated between non-quantitative and three groups of quantitative workflows. The resulting direct comparisons within these groups show remarkable differences on the intra- and interspecies level across genera with a focus on regional differences. In summary, the present compilation is the first comprehensive up-to-date database on Viperinae venom proteomes and differentiating between analytical methods and workflows. Full article
(This article belongs to the Special Issue Evolution, Genomics and Proteomics of Venom)
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