1
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Yeung HY, Ramiro IBL, Andersen DB, Koch TL, Hamilton A, Bjørn-Yoshimoto WE, Espino S, Vakhrushev SY, Pedersen KB, de Haan N, Hipgrave Ederveen AL, Olivera BM, Knudsen JG, Bräuner-Osborne H, Schjoldager KT, Holst JJ, Safavi-Hemami H. Fish-hunting cone snail disrupts prey's glucose homeostasis with weaponized mimetics of somatostatin and insulin. Nat Commun 2024; 15:6408. [PMID: 39164229 PMCID: PMC11336141 DOI: 10.1038/s41467-024-50470-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/04/2024] [Indexed: 08/22/2024] Open
Abstract
Venomous animals have evolved diverse molecular mechanisms to incapacitate prey and defend against predators. Most venom components disrupt nervous, locomotor, and cardiovascular systems or cause tissue damage. The discovery that certain fish-hunting cone snails use weaponized insulins to induce hypoglycemic shock in prey highlights a unique example of toxins targeting glucose homeostasis. Here, we show that, in addition to insulins, the deadly fish hunter, Conus geographus, uses a selective somatostatin receptor 2 (SSTR2) agonist that blocks the release of the insulin-counteracting hormone glucagon, thereby exacerbating insulin-induced hypoglycemia in prey. The native toxin, Consomatin nG1, exists in several proteoforms with a minimized vertebrate somatostatin-like core motif connected to a heavily glycosylated N-terminal region. We demonstrate that the toxin's N-terminal tail closely mimics a glycosylated somatostatin from fish pancreas and is crucial for activating the fish SSTR2. Collectively, these findings provide a stunning example of chemical mimicry, highlight the combinatorial nature of venom components, and establish glucose homeostasis as an effective target for prey capture.
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Affiliation(s)
- Ho Yan Yeung
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
- Department of Biochemistry, University of Utah, 15 N Medical Drive, Salt Lake City, UT, 84112, USA
| | - Iris Bea L Ramiro
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Daniel B Andersen
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
- Department of Biochemistry, University of Utah, 15 N Medical Drive, Salt Lake City, UT, 84112, USA
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Alexander Hamilton
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Department of Clinical Sciences in Malmö, Islet Cell Exocytosis, Lund University, Malmö, Sweden
| | - Walden E Bjørn-Yoshimoto
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Samuel Espino
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Kasper B Pedersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Noortje de Haan
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2333, ZA, Leiden, The Netherlands
| | - Agnes L Hipgrave Ederveen
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2333, ZA, Leiden, The Netherlands
| | - Baldomero M Olivera
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Jakob G Knudsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, DK-2100, Copenhagen, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Jens Juul Holst
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.
- Department of Biochemistry, University of Utah, 15 N Medical Drive, Salt Lake City, UT, 84112, USA.
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.
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2
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Ratibou Z, Inguimbert N, Dutertre S. Predatory and Defensive Strategies in Cone Snails. Toxins (Basel) 2024; 16:94. [PMID: 38393171 PMCID: PMC10892987 DOI: 10.3390/toxins16020094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Cone snails are carnivorous marine animals that prey on fish (piscivorous), worms (vermivorous), or other mollusks (molluscivorous). They produce a complex venom mostly made of disulfide-rich conotoxins and conopeptides in a compartmentalized venom gland. The pharmacology of cone snail venom has been increasingly investigated over more than half a century. The rising interest in cone snails was initiated by the surprising high human lethality rate caused by the defensive stings of some species. Although a vast amount of information has been uncovered on their venom composition, pharmacological targets, and mode of action of conotoxins, the venom-ecology relationships are still poorly understood for many lineages. This is especially important given the relatively recent discovery that some species can use different venoms to achieve rapid prey capture and efficient deterrence of aggressors. Indeed, via an unknown mechanism, only a selected subset of conotoxins is injected depending on the intended purpose. Some of these remarkable venom variations have been characterized, often using a combination of mass spectrometry and transcriptomic methods. In this review, we present the current knowledge on such specific predatory and defensive venoms gathered from sixteen different cone snail species that belong to eight subgenera: Pionoconus, Chelyconus, Gastridium, Cylinder, Conus, Stephanoconus, Rhizoconus, and Vituliconus. Further studies are needed to help close the gap in our understanding of the evolved ecological roles of many cone snail venom peptides.
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Affiliation(s)
- Zahrmina Ratibou
- CRIOBE, UAR CNRS-EPHE-UPVD 3278, University of Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan, France;
| | - Nicolas Inguimbert
- CRIOBE, UAR CNRS-EPHE-UPVD 3278, University of Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860 Perpignan, France;
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3
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Jimenez EC. Peptide antagonists of NMDA receptors: Structure-activity relationships for potential therapeutics. Peptides 2022; 153:170796. [PMID: 35367253 DOI: 10.1016/j.peptides.2022.170796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 12/19/2022]
Abstract
The N-methyl-D-aspartate (NMDA) receptors are heteromeric cation channels involved in memory, learning, and synaptic plasticity. The dysfunction associated with NMDA receptors results in neurodegenerative conditions. The conantokins comprise a family of Conus venom peptides that induce sleep upon intracranial injection into young mice and are known to be NMDA receptor antagonists. This work comprehensibly documents the conantokins that have been characterized to date, focusing on the biochemistry, solution structures in the presence or absence of divalent cations, functions as selective NMDA receptor antagonists, and structure-activity relationships. Furthermore, the applications of conantokins as potential therapeutics for certain neurological conditions, including neuropathic pain, epilepsy, and ischaemia that are linked to NMDA receptor dysfunction are reviewed.
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Affiliation(s)
- Elsie C Jimenez
- Department of Physical Sciences, College of Science, University of the Philippines Baguio, Baguio City 2600, Philippines.
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4
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Laugesen SH, Chou DHC, Safavi-Hemami H. Unconventional insulins from predators and pathogens. Nat Chem Biol 2022; 18:688-697. [PMID: 35761080 DOI: 10.1038/s41589-022-01068-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022]
Abstract
Insulin and its related peptides are found throughout the animal kingdom, in which they serve diverse functions. This includes regulation of glucose homeostasis, neuronal development and cognition. The surprising recent discovery that venomous snails evolved specialized insulins to capture fish demonstrated the nefarious use of this hormone in nature. Because of their streamlined role in predation, these repurposed insulins exhibit unique characteristics that have unraveled new aspects of the chemical ecology and structural biology of this important hormone. Recently, insulins were also reported in other venomous predators and pathogenic viruses, demonstrating the broader use of insulin by one organism to manipulate the physiology of another. In this Review, we provide an overview of the discovery and biomedical application of repurposed insulins and other hormones found in nature and highlight several unique insights gained from these unusual compounds.
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Affiliation(s)
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University, Stanford, CA, USA
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA. .,School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.
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5
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Fouda MMA, Abdel-Wahab M, Mohammadien A, Germoush MO, Sarhan M. Proteomic analysis of Red Sea Conus taeniatus venom reveals potential biological applications. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20210023. [PMID: 34712278 PMCID: PMC8525892 DOI: 10.1590/1678-9199-jvatitd-2021-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Diverse and unique bioactive neurotoxins known as conopeptides or conotoxins
are produced by venomous marine cone snails. Currently, these small and
stable molecules are of great importance as research tools and platforms for
discovering new drugs and therapeutics. Therefore, the characterization of
Conus venom is of great significance, especially for
poorly studied species. Methods: In this study, we used bioanalytical techniques to determine the venom
profile and emphasize the functional composition of conopeptides in
Conus taeniatus, a neglected worm-hunting cone snail.
Results: The proteomic analysis revealed that 84.0% of the venom proteins were between
500 and 4,000 Da, and 16.0% were > 4,000 Da. In C.
taeniatus venom, 234 peptide fragments were identified and
classified as conotoxin precursors or non-conotoxin proteins. In this
process, 153 conotoxin precursors were identified and matched to 23
conotoxin precursors and hormone superfamilies. Notably, the four conotoxin
superfamilies T (22.87%), O1 (17.65%), M (13.1%) and O2 (9.8%) were the most
abundant peptides in C. taeniatus venom, accounting for
63.40% of the total conotoxin diversity. On the other hand, 48 non-conotoxin
proteins were identified in the venom of C. taeniatus.
Moreover, several possibly biologically active peptide matches were
identified, and putative applications of the peptides were assigned. Conclusion: Our study showed that the composition of the C.
taeniatus-derived proteome is comparable to that of other
Conus species and contains an effective mix of toxins,
ionic channel inhibitors and antimicrobials. Additionally, it provides a
guidepost for identifying novel conopeptides from the venom of C.
taeniatus and discovering conopeptides of potential
pharmaceutical importance.
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Affiliation(s)
- Maged M A Fouda
- Department of Biology, College of Science, Jouf University, Saudi Arabia.,Zoology Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | | | - Amal Mohammadien
- Department of Biology, College of Science, Taeif University, Saudi Arabia.,Zoology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Mousa O Germoush
- Department of Biology, College of Science, Jouf University, Saudi Arabia
| | - Moustafa Sarhan
- Zoology Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
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6
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Tae HS, Gao B, Jin AH, Alewood PF, Adams DJ. Globular and ribbon isomers of Conus geographus α-conotoxins antagonize human nicotinic acetylcholine receptors. Biochem Pharmacol 2021; 190:114638. [PMID: 34062129 DOI: 10.1016/j.bcp.2021.114638] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
The short disulfide-rich α-conotoxins derived from the venom of Conus snails comprise a conserved CICII(m)CIII(n)CIV cysteine framework (m and n, number of amino acids) and the majority antagonize nicotinic acetylcholine receptors (nAChRs). Depending on disulfide connectivity, α-conotoxins can exist as either globular (CI-CIII, CII-CIV), ribbon (CI-CIV, CII-CIII) or bead (CI-CII, CIII-CIV) isomers. In the present study, C. geographus α-conotoxins GI, GIB, G1.5 and G1.9 were chemically synthesized as globular and ribbon isomers and their activity investigated at human nAChRs expressed in Xenopus oocytes using the two-electrode voltage clamp recording technique. Both the globular and ribbon isomers of the 3/5 (m/n) α-conotoxins GI and GIB selectively inhibit heterologous human muscle-type α1β1δε nAChRs, whereas G1.5, a 4/7 α-conotoxin, selectively antagonizes neuronal (non-muscle) nAChR subtypes particularly human α3β2, α7 and α9α10 nAChRs. In contrast, globular and ribbon isomers of G1.9, a novel C-terminal elongated 4/8 α-conotoxin exhibited no activity at the human nAChR subtypes studied. This study reinforces earlier observations that 3/5 α-conotoxins selectively target the muscle nAChR subtypes, although interestingly, GIB is also active at α7 and α9 α10 nAChRs. The 4/7 α-conotoxins target human neuronal nAChR subtypes whereas the pharmacology of the 4/8 α-conotoxin remains unknown.
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Affiliation(s)
- Han-Shen Tae
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou 571199, China
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
| | - David J Adams
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW 2522, Australia.
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7
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Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. Nat Commun 2021; 12:3117. [PMID: 34035261 PMCID: PMC8149454 DOI: 10.1038/s41467-021-23216-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Hox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria. In vertebrates insulin is a direct transcriptional target of Pdx: the same is true in Pacific oysters and the authors show insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue, showing this gene interaction dates back to the origin of Bilateria.
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8
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Bao N, Lecaer JP, Nghia ND, Vinh PTK. Isolation and structural identification of a new T1-conotoxin with unique disulfide connectivities derived from Conus bandanus. J Venom Anim Toxins Incl Trop Dis 2020; 26:e20190095. [PMID: 32425993 PMCID: PMC7216822 DOI: 10.1590/1678-9199-jvatitd-2019-0095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/15/2020] [Indexed: 08/30/2023] Open
Abstract
Background: Conopeptides are neuropharmacological peptides derived from the venomous
salivary glands of cone snails. Among 29 superfamilies based on conserved
signal sequences, T-superfamily conotoxins, which belong to the smallest
group, include four different frameworks that contain four cysteines
denominated I, V, X and XVI. In this work, the primary structure and the
cysteine connectivity of novel conotoxin of Conus bandanus
were determined by tandem mass spectrometry using collision-induced
dissociation. Methods: The venom glands of C. bandanus snails were dissected,
pooled, and extracted with 0.1% trifluoroacetic acid in three steps and
lyophilized. The venom was fractionated and purified in an HPLC system with
an analytical reversed-phase C18 column. The primary peptide
structure was analyzed by MALDI TOF MS/MS using collision-induced
dissociation and confirmed by Edman's degradation. The peptide’s cysteine
connectivity was determined by rapid partial reduction-alkylation
technique. Results: The novel conotoxin,
NGC1C2(I/L)VREC3C4, was
firstly derived from de novo sequencing by MS/MS. The
presence of isoleucine residues in this conotoxin was confirmed by the Edman
degradation method. The conotoxin, denominated Bn5a, belongs to the
T1-subfamily of conotoxins. However, the disulfide bonds
(C1-C4/C2-C3) of Bn5a were
not the same as found in other T1-subfamily conopeptides but shared common
connectivities with T2-subfamily conotoxins. The T1-conotoxin of C.
bandanus proved the complexity of the disulfide bond pattern of
conopeptides. The homological analysis revealed that the novel conotoxin
could serve as a valuable probe compound for the human-nervous-system
norepinephrine transporter. Conclusion: We identified the first T1-conotoxin, denominated Bn5a, isolated from
C. bandanus venom. However, Bn5a conotoxin exhibited
unique C1-C4/C2-C3 disulfide
connectivity, unlike other T1-conotoxins
(C1-C3/C2-C4). The
structural and homological analyses herein have evidenced novel conotoxin
Bn5a that may require further investigation.
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Affiliation(s)
- Nguyen Bao
- Faculty of Food Technology, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Khanh Hoa, Vietnam
| | - Jean-Pière Lecaer
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, FRC3115, UPR 2301, F-91198 Gif-sur-Yvette, France
| | - Ngo Dang Nghia
- Institute of Biotechnology and Environment, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Khanh Hoa, Vietnam
| | - Phan Thi Khanh Vinh
- Faculty of Food Technology, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Khanh Hoa, Vietnam
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The α 1-adrenoceptor inhibitor ρ-TIA facilitates net hunting in piscivorous Conus tulipa. Sci Rep 2019; 9:17841. [PMID: 31780714 PMCID: PMC6882899 DOI: 10.1038/s41598-019-54186-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/07/2019] [Indexed: 11/08/2022] Open
Abstract
Cone snails use separately evolved venoms for prey capture and defence. While most use a harpoon for prey capture, the Gastridium clade that includes the well-studied Conus geographus and Conus tulipa, have developed a net hunting strategy to catch fish. This unique feeding behaviour requires secretion of "nirvana cabal" peptides to dampen the escape response of targeted fish allowing for their capture directly by mouth. However, the active components of the nirvana cabal remain poorly defined. In this study, we evaluated the behavioural effects of likely nirvana cabal peptides on the teleost model, Danio rerio (zebrafish). Surprisingly, the conantokins (NMDA receptor antagonists) and/or conopressins (vasopressin receptor agonists and antagonists) found in C. geographus and C. tulipa venom failed to produce a nirvana cabal-like effect in zebrafish. In contrast, low concentrations of the non-competitive adrenoceptor antagonist ρ-TIA found in C. tulipa venom (EC50 = 190 nM) dramatically reduced the escape response of zebrafish larvae when added directly to aquarium water. ρ-TIA inhibited the zebrafish α1-adrenoceptor, confirming ρ-TIA has the potential to reverse the known stimulating effects of norepinephrine on fish behaviour. ρ-TIA may act alone and not as part of a cabal, since it did not synergise with conopressins and/or conantokins. This study highlights the importance of using ecologically relevant animal behaviour models to decipher the complex neurobiology underlying the prey capture and defensive strategies of cone snails.
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10
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Sudewi AA, Susilawathi NM, Mahardika BK, Mahendra AN, Pharmawati M, Phuong MA, Mahardika GN. Selecting Potential Neuronal Drug Leads from Conotoxins of Various Venomous Marine Cone Snails in Bali, Indonesia. ACS OMEGA 2019; 4:19483-19490. [PMID: 31763573 PMCID: PMC6868881 DOI: 10.1021/acsomega.9b03122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Many conotoxins, natural peptides of marine cone snails, have been identified to target neurons. Here, we provide data on pharmacological families of the conotoxins of 11 species of cone snails collected in Bali. The identified definitive pharmacological families possibly targeting neuronal tissues were α (alpha), ι (iota), κ (kappa), and ρ (rho). These classes shall target nicotinic acetylcholine receptors, voltage-gated Na channels, voltage-gated K channels, and α1-adrenoceptors, respectively. The VI/VII-O3 conotoxins might be prospected as an inhibitor of N-methyl-d-aspartate. Con-ikot-ikot could be applied as an α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor blocker medicine. The definitive pharmacology classes of conotoxins as well as those yet to be elucidated need to be further established and verified.
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Affiliation(s)
- Anak A.
R. Sudewi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Ni M. Susilawathi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Bayu K. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
| | - Agung N. Mahendra
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Made Pharmawati
- Faculty
of Mathematic and Natural Sciences, Udayana
University of Bali, Kampus
Bukit Jimbaran, Badung 80361, Bali, Indonesia
| | - Mark A. Phuong
- Department
of Ecology and Evolutionary Biology, University
of California, Los Angeles, Los
Angeles 90095, California, United States
| | - Gusti N. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
- The Indonesian
Biodiversity Research Center, Jl. Sudirman, Denpasar 80225, Bali, Indonesia
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11
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Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. Toxins (Basel) 2019; 11:toxins11110623. [PMID: 31661832 PMCID: PMC6891753 DOI: 10.3390/toxins11110623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components such as chymotrypsin and L-rhamnose-binding lectin. The large majority of conotoxins appeared to be from new gene superfamilies, three of which are highly different from previously reported venom peptide toxins. Their low conotoxin diversity and the type of insulin found suggested that these species, for which no ecological information are available, have a worm or molluscan diet associated with a narrow dietary breadth. Our results indicate that Profundiconus venom is highly distinct from that of other cone snails, and therefore important for examining venom evolution in the Conidae family.
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12
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Conotoxin Diversity in the Venom Gland Transcriptome of the Magician's Cone, Pionoconus magus. Mar Drugs 2019; 17:md17100553. [PMID: 31569823 PMCID: PMC6835573 DOI: 10.3390/md17100553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Differential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appeared to be more expressed in the former whereas the O2 superfamily was more expressed in the latter.
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15
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Surm JM, Smith HL, Madio B, Undheim EA, King GF, Hamilton BR, Burg CA, Pavasovic A, Prentis PJ. A process of convergent amplification and tissue‐specific expression dominates the evolution of toxin and toxin‐like genes in sea anemones. Mol Ecol 2019; 28:2272-2289. [DOI: 10.1111/mec.15084] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/09/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim M. Surm
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Hayden L. Smith
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
| | - Bruno Madio
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Eivind A.B. Undheim
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
| | - Glenn F. King
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Brett R. Hamilton
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
- Centre for Microscopy and Microanalysis University of Queensland Saint Lucia Queensland Australia
| | - Chloé A. Burg
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Ana Pavasovic
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
| | - Peter J. Prentis
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
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16
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Yao G, Peng C, Zhu Y, Fan C, Jiang H, Chen J, Cao Y, Shi Q. High-Throughput Identification and Analysis of Novel Conotoxins from Three Vermivorous Cone Snails by Transcriptome Sequencing. Mar Drugs 2019; 17:md17030193. [PMID: 30917600 PMCID: PMC6471451 DOI: 10.3390/md17030193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
The venom of each Conus species consists of a diverse array of neurophysiologically active peptides, which are mostly unique to the examined species. In this study, we performed high-throughput transcriptome sequencing to extract and analyze putative conotoxin transcripts from the venom ducts of 3 vermivorous cone snails (C. caracteristicus, C. generalis, and C. quercinus), which are resident in offshore waters of the South China Sea. In total, 118, 61, and 48 putative conotoxins (across 22 superfamilies) were identified from the 3 Conus species, respectively; most of them are novel, and some possess new cysteine patterns. Interestingly, a series of 45 unassigned conotoxins presented with a new framework of C-C-C-C-C-C, and their mature regions were sufficiently distinct from any other known conotoxins, most likely representing a new superfamily. O- and M-superfamily conotoxins were the most abundant in transcript number and transcription level, suggesting their critical roles in the venom functions of these vermivorous cone snails. In addition, we identified numerous functional proteins with potential involvement in the biosynthesis, modification, and delivery process of conotoxins, which may shed light on the fundamental mechanisms for the generation of these important conotoxins within the venom duct of cone snails.
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Affiliation(s)
- Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yabing Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Chongxu Fan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Jisheng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Ying Cao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
| | - Manuel J. Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias; Universidad de Cádiz; Puerto Real Spain
| | - Juan E. Uribe
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
- Department of Invertebrate Zoology, Smithsonian Institution; National Museum of Natural History; Washington District of Columbia USA
- Grupo de Evolución, Sistemática y Ecología Molecular; Universidad del Magdalena; Santa Marta Colombia
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
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18
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Bernáldez-Sarabia J, Figueroa-Montiel A, Dueñas S, Cervantes-Luévano K, Beltrán JA, Ortiz E, Jiménez S, Possani LD, Paniagua-Solís JF, Gonzalez-Canudas J, Licea-Navarro A. The Diversified O-Superfamily in Californiconus californicus Presents a Conotoxin with Antimycobacterial Activity. Toxins (Basel) 2019; 11:toxins11020128. [PMID: 30791616 PMCID: PMC6410186 DOI: 10.3390/toxins11020128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022] Open
Abstract
Californiconus californicus, previously named Conus californicus, has always been considered a unique species within cone snails, because of its molecular, toxicological and morphological singularities; including the wide range of its diet, since it is capable of preying indifferently on fish, snails, octopus, shrimps, and worms. We report here a new cysteine pattern conotoxin assigned to the O1-superfamily capable of inhibiting the growth of Mycobacterium tuberculosis (Mtb). The conotoxin was tested on a pathogen reference strain (H37Rv) and multidrug-resistant strains, having an inhibition effect on growth with a minimal inhibitory concentration (MIC) range of 3.52–0.22 μM, similar concentrations to drugs used in clinics. The peptide was purified from the venom using reverse phase high-performance liquid chromatography (RP-HPLC), a partial sequence was constructed by Edman degradation, completed by RACE and confirmed with venom gland transcriptome. The 32-mer peptide containing eight cysteine residues was named O1_cal29b, according to the current nomenclature for this type of molecule. Moreover, transcriptomic analysis of O-superfamily toxins present in the venom gland of the snail allowed us to assign several signal peptides to O2 and O3 superfamilies not described before in C. californicus, with new conotoxins frameworks.
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Affiliation(s)
- Johanna Bernáldez-Sarabia
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Andrea Figueroa-Montiel
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Salvador Dueñas
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Karla Cervantes-Luévano
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Jesús A Beltrán
- Departamento de Ciencias Computacionales, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Ernesto Ortiz
- Departamento de Medicina Molecular y Bioprocesos, IBT, UNAM, Cuernavaca, Morelos, C.P. 62210, Mexico.
| | - Samanta Jiménez
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
| | - Lourival D Possani
- Departamento de Medicina Molecular y Bioprocesos, IBT, UNAM, Cuernavaca, Morelos, C.P. 62210, Mexico.
| | - Jorge F Paniagua-Solís
- Teraclon IDF, S.L., Parque Tecnológico de Madrid, Tres Cantos, Madrid, C.P. 28760, Espana.
| | | | - Alexei Licea-Navarro
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Ensenada, BC C.P. 22860, Mexico.
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19
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Dutt M, Dutertre S, Jin AH, Lavergne V, Alewood PF, Lewis RJ. Venomics Reveals Venom Complexity of the Piscivorous Cone Snail, Conus tulipa. Mar Drugs 2019; 17:md17010071. [PMID: 30669642 PMCID: PMC6356538 DOI: 10.3390/md17010071] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 01/30/2023] Open
Abstract
The piscivorous cone snail Conus tulipa has evolved a net-hunting strategy, akin to the deadly Conus geographus, and is considered the second most dangerous cone snail to humans. Here, we present the first venomics study of C. tulipa venom using integrated transcriptomic and proteomic approaches. Parallel transcriptomic analysis of two C. tulipa specimens revealed striking differences in conopeptide expression levels (2.5-fold) between individuals, identifying 522 and 328 conotoxin precursors from 18 known gene superfamilies. Despite broad overlap at the superfamily level, only 86 precursors (11%) were common to both specimens. Conantokins (NMDA antagonists) from the superfamily B1 dominated the transcriptome and proteome of C. tulipa venom, along with superfamilies B2, A, O1, O3, con-ikot-ikot and conopressins, plus novel putative conotoxins precursors T1.3, T6.2, T6.3, T6.4 and T8.1. Thus, C. tulipa venom comprised both paralytic (putative ion channel modulating α-, ω-, μ-, δ-) and non-paralytic (conantokins, con-ikot-ikots, conopressins) conotoxins. This venomic study confirms the potential for non-paralytic conotoxins to contribute to the net-hunting strategy of C. tulipa.
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Affiliation(s)
- Mriga Dutt
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4068, Australia.
| | - Sébastien Dutertre
- Institut des Biomolecules Max Mousseron, UMR 5247, Université Montpellier-CNRS, 34093 Montpellier, France.
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4068, Australia.
| | | | - Paul Francis Alewood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4068, Australia.
| | - Richard James Lewis
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4068, Australia.
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20
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Gao B, Peng C, Zhu Y, Sun Y, Zhao T, Huang Y, Shi Q. High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail ( Conus quercinus) by Transcriptome Sequencing. Int J Mol Sci 2018; 19:ijms19123901. [PMID: 30563163 PMCID: PMC6321112 DOI: 10.3390/ijms19123901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The primary objective of this study was to realize the large-scale discovery of conotoxin sequences from different organs (including the venom duct, venom bulb and salivary gland) of the vermivorous Oak cone snail, Conus quercinus. Using high-throughput transcriptome sequencing, we identified 133 putative conotoxins that belong to 34 known superfamilies, of which nine were previously reported while the remaining 124 were novel conotoxins, with 17 in new and unassigned conotoxin groups. A-, O1-, M-, and I2- superfamilies were the most abundant, and the cysteine frameworks XIII and VIII were observed for the first time in the A- and I2-superfamilies. The transcriptome data from the venom duct, venom bulb and salivary gland showed considerable inter-organizational variations. Each organ had many exclusive conotoxins, and only seven of all the inferred mature peptides were common in the three organs. As expected, most of the identified conotoxins were synthesized in the venom duct at relatively high levels; however, a number of conotoxins were also identified in the venom bulb and the salivary gland with very low transcription levels. Therefore, various organs have different conotoxins with high diversity, suggesting greater contributions from several organs to the high-throughput discovery of new conotoxins for future drug development.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Herbs, College of Pharmacy, Hainan Medical University, Haikou 571199, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yabing Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yuhui Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Tian Zhao
- Chemistry Department, College of Art and Science, Boston University, Boston, MA 02215, USA.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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21
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Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M. Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins (Basel) 2018; 10:toxins10120503. [PMID: 30513724 PMCID: PMC6315676 DOI: 10.3390/toxins10120503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/12/2018] [Accepted: 11/22/2018] [Indexed: 12/24/2022] Open
Abstract
Cone snails (genus Conus) are venomous marine snails that inject prey with a lethal cocktail of conotoxins, small, secreted, and cysteine-rich peptides. Given the diversity and often high affinity for their molecular targets, consisting of ion channels, receptors or transporters, many conotoxins have become invaluable pharmacological probes, drug leads, and therapeutics. Transcriptome sequencing of Conus venom glands followed by de novo assembly and homology-based toxin identification and annotation is currently the state-of-the-art for discovery of new conotoxins. However, homology-based search techniques, by definition, can only detect novel toxins that are homologous to previously reported conotoxins. To overcome these obstacles for discovery, we have created ConusPipe, a machine learning tool that utilizes prominent chemical characters of conotoxins to predict whether a certain transcript in a Conus transcriptome, which has no otherwise detectable homologs in current reference databases, is a putative conotoxin. By using ConusPipe on RNASeq data of 10 species, we report 5148 new putative conotoxin transcripts that have no homologues in current reference databases. 896 of these were identified by at least three out of four models used. These data significantly expand current publicly available conotoxin datasets and our approach provides a new computational avenue for the discovery of novel toxin families.
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Affiliation(s)
- Qing Li
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Maren Watkins
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Samuel D Robinson
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Helena Safavi-Hemami
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
- USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.
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22
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Nuclear Magnetic Resonance seq (NMRseq): A New Approach to Peptide Sequence Tags. Toxins (Basel) 2018; 10:toxins10110437. [PMID: 30373307 PMCID: PMC6266860 DOI: 10.3390/toxins10110437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 10/25/2018] [Indexed: 12/03/2022] Open
Abstract
Structural analysis of peptides with nuclear magnetic resonance (NMR) spectroscopy generally relies on knowledge of the primary sequence to enable assignment of the resonances prior to determination of the three-dimensional structure. Resonance assignment without knowledge of the sequence is complicated by redundancy in amino acid type, making complete de novo sequencing using NMR spectroscopy unlikely to be feasible. Despite this redundancy, we show here that NMR spectroscopy can be used to identify short sequence tags that can be used to elucidate full-length peptide sequences via database searching. In the current study, we have used this approach to identify conotoxins from the venom of the cone snail Conus geographus and determined the three-dimensional structure of a member of the I3 superfamily. This approach is most likely to be useful for the characterization of disulfide-rich peptides, such as those that were chosen for this study, as they generally have well-defined structures, which enhances the quality of the NMR spectra. In contrast to other sequencing methods, the lack of sample manipulation, such as protease digestion, allows for subsequent bioassays to be carried out using the native sample used for sequence identification.
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Abalde S, Tenorio MJ, Afonso CML, Zardoya R. Conotoxin Diversity in Chelyconus ermineus (Born, 1778) and the Convergent Origin of Piscivory in the Atlantic and Indo-Pacific Cones. Genome Biol Evol 2018; 10:2643-2662. [PMID: 30060147 PMCID: PMC6178336 DOI: 10.1093/gbe/evy150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/27/2022] Open
Abstract
The transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born, 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals. Three different regions (distal, medium, and proximal with respect to the venom bulb) of the venom duct were analyzed independently. Diversity (in terms of number of distinct members) of conotoxin precursor superfamilies increased toward the distal region whereas transcripts detected toward the proximal region showed higher expression levels. Only the superfamilies A and I3 showed statistically significant differential expression across regions of the venom duct. Sequences belonging to the alpha (motor cabal) and kappa (lightning-strike cabal) subfamilies of the superfamily A were mainly detected in the proximal region of the venom duct. The mature peptides of the alpha subfamily had the α4/4 cysteine spacing pattern, which has been shown to selectively target muscle nicotinic-acetylcholine receptors, ultimately producing paralysis. This function is performed by mature peptides having a α3/5 cysteine spacing pattern in piscivorous cone species from the Indo-Pacific region, thereby supporting a convergent evolution of piscivory in cones.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cadiz, Puerto Real, Spain
| | - Carlos M L Afonso
- Fisheries, Biodiversity and Conervation Group, Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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24
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Zhang H, Fu Y, Wang L, Liang A, Chen S, Xu A. Identifying novel conopepetides from the venom ducts of Conus litteratus through integrating transcriptomics and proteomics. J Proteomics 2018; 192:346-357. [PMID: 30267875 DOI: 10.1016/j.jprot.2018.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/17/2022]
Abstract
The venom ducts of marine cone snails secrete highly complex mixtures of cysteine-rich active peptides, which are generally known as conotoxins or conopeptides and provide a potential fertile resource for pharmacological neuroscience research and the discovery of new drugs. Previous studies have devoted substantial effort to the identification of novel conopeptides, and the 109 cone snail species have yielded 7000 known conopeptides to date. Here, we used de novo deep transcriptome sequencing analyses combined with traditional Sanger sequencing and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) to identify 30 distinct conopeptide precursors. Twenty of these were previously reported and the other 10 were novel conopeptide precursors. The study provides the first identification of the Con-ikot-ikot, NSF-bt05, O3 and I1 gene superfamilies in C. litteratus. A new putative superfamily was identified. In addition, the following cysteine frameworks were first identified in this study: CC-C-C-C-C-C-C-C-C-C-C-C-CC-C-C-C-C-C and C-C-C-C-C-CC-C. Several isomerases involved in post-translational modification of conopeptides were identified as well. The discovery of new conopeptides in C. litteratus will enhance our understanding of the conopeptide diversity in this particular clade of cone snails. We also found the existence of intraspecific variations in vermivorous species. Finally, the analysis strategy offers a relatively reliable workflow for screening for peptide drug candidates. SIGNIFICANCE: These novel conopeptides provide a potential resource for the development of new channel-targeting drugs. The intraspecific variation in C. litteratus enhance our understanding of the conopeptide diversity in this particular clade of cone snails. The identified three cysteine residues, which might participate in the formation of disulfide bonds, provide a clue to get the connectivity of cysteine frameworks. Finally, the analysis strategy offers a relatively reliable workflow for screening for peptide drug candidates.
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Affiliation(s)
- Han Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Yonggui Fu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China
| | - Anwen Liang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Shenzhen Research Institute, Sun Yat-Sen University, People's Republic of China.
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China.
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25
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Chou CH, Huang HY, Huang WC, Hsu SD, Hsiao CD, Liu CY, Chen YH, Liu YC, Huang WY, Lee ML, Chen YC, Huang HD. The aquatic animals' transcriptome resource for comparative functional analysis. BMC Genomics 2018; 19:103. [PMID: 29764375 PMCID: PMC5954267 DOI: 10.1186/s12864-018-4463-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/. Electronic supplementary material The online version of this article (10.1186/s12864-018-4463-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsi-Yuan Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, 320, Taiwan
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Hung Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Yun Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Lin Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Chang Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
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26
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Gao B, Peng C, Yang J, Yi Y, Zhang J, Shi Q. Cone Snails: A Big Store of Conotoxins for Novel Drug Discovery. Toxins (Basel) 2017; 9:E397. [PMID: 29215605 PMCID: PMC5744117 DOI: 10.3390/toxins9120397] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
Marine drugs have developed rapidly in recent decades. Cone snails, a group of more than 700 species, have always been one of the focuses for new drug discovery. These venomous snails capture prey using a diverse array of unique bioactive neurotoxins, usually named as conotoxins or conopeptides. These conotoxins have proven to be valuable pharmacological probes and potential drugs due to their high specificity and affinity to ion channels, receptors, and transporters in the nervous systems of target prey and humans. Several research groups, including ours, have examined the venom gland of cone snails using a combination of transcriptomic and proteomic sequencing, and revealed the existence of hundreds of conotoxin transcripts and thousands of conopeptides in each Conus species. Over 2000 nucleotide and 8000 peptide sequences of conotoxins have been published, and the number is still increasing quickly. However, more than 98% of these sequences still lack 3D structural and functional information. With the rapid development of genomics and bioinformatics in recent years, functional predictions and investigations on conotoxins are making great progress in promoting the discovery of novel drugs. For example, ω-MVIIA was approved by the U.S. Food and Drug Administration in 2004 to treat chronic pain, and nine more conotoxins are at various stages of preclinical or clinical evaluation. In short, the genus Conus, the big family of cone snails, has become an important genetic resource for conotoxin identification and drug development.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou 571199, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Jiaan Yang
- Micro Pharmtech, Ltd., Wuhan 430075, China.
| | - Yunhai Yi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Junqing Zhang
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou 571199, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics 2017; 14:931-939. [DOI: 10.1080/14789450.2017.1377613] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Samuel D. Robinson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
| | | | | | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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28
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Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H. Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus. Genome Biol Evol 2017; 9:2211-2225. [PMID: 28922871 PMCID: PMC5604253 DOI: 10.1093/gbe/evx157] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
The genus Conus comprises approximately 700 species of venomous marine cone snails that are highly efficient predators of worms, snails, and fish. In evolutionary terms, cone snails are relatively young with the earliest fossil records occurring in the Lower Eocene, 55 Ma. The rapid radiation of cone snail species has been accompanied by remarkably high rates of toxin diversification. To shed light on the molecular mechanisms that accompany speciation, we investigated the toxin repertoire of two sister species, Conus andremenezi and Conus praecellens, that were until recently considered a single variable species. A total of 196 and 250 toxin sequences were identified in the venom gland transcriptomes of C. andremenezi and C. praecellens belonging to 25 and 29 putative toxin gene superfamilies, respectively. Comparative analysis with closely (Conus tribblei and Conus lenavati) and more distantly related species (Conus geographus) suggests that speciation is associated with significant diversification of individual toxin genes (exogenes) whereas the expression pattern of toxin gene superfamilies within lineages remains largely conserved. Thus, changes within individual toxin sequences can serve as a sensitive indicator for recent speciation whereas changes in the expression pattern of gene superfamilies are likely to reflect more dramatic differences in a species' interaction with its prey, predators, and competitors.
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Affiliation(s)
- Qing Li
- Eccles Institute of Human Genetics, University of Utah
| | - Neda Barghi
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Institute für Populationsgenetik, Vetmeduni, Vienna, 1210, Austria
| | - Aiping Lu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Alexander E. Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | | | - Arturo O. Lluisma
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - Gisela P. Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah
- USTAR Center for Genetic Discovery, University of Utah
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29
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Huang Y, Peng C, Yi Y, Gao B, Shi Q. A Transcriptomic Survey of Ion Channel-Based Conotoxins in the Chinese Tubular Cone Snail (Conus betulinus). Mar Drugs 2017; 15:md15070228. [PMID: 28718820 PMCID: PMC5532670 DOI: 10.3390/md15070228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023] Open
Abstract
Conotoxins in the venom of cone snails (Conus spp.) are a mixture of active peptides that work as blockers, agonists, antagonists, or inactivators of various ion channels. Recently we reported a high-throughput method to identify 215 conotoxin transcripts from the Chinese tubular cone snail, C. betulinus. Here, based on the previous datasets of four transcriptomes from three venom ducts and one venom bulb, we explored ion channel-based conotoxins and predicted their related ion channel receptors. Homologous analysis was also performed for the most abundant ion channel protein, voltage-gated potassium (Kv; with Kv1.1 as the representative), and the most studied ion channel receptor, nicotinic acetylcholine receptor (nAChR; with α2-nAChR as the representative), in different animals. Our transcriptomic survey demonstrated that ion channel-based conotoxins and related ion channel proteins/receptors transcribe differentially between the venom duct and the venom bulb. In addition, we observed that putative κ-conotoxins were the most common conotoxins with the highest transcription levels in the examined C. betulinus. Furthermore, Kv1.1 and α2-nAChR were conserved in their functional domains of deduced protein sequences, suggesting similar effects of conotoxins via the ion channels in various species, including human beings. In a word, our present work suggests a high-throughput way to develop conotoxins as potential drugs for treatment of ion channel-associated human diseases.
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Affiliation(s)
- Yu Huang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yunhai Yi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou 571199, China.
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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30
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Dutertre S, Nicke A, Tsetlin VI. Nicotinic acetylcholine receptor inhibitors derived from snake and snail venoms. Neuropharmacology 2017. [PMID: 28623170 DOI: 10.1016/j.neuropharm.2017.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nicotinic acetylcholine receptor (nAChR) represents the prototype of ligand-gated ion channels. It is vital for neuromuscular transmission and an important regulator of neurotransmission. A variety of toxic compounds derived from diverse species target this receptor and have been of elemental importance in basic and applied research. They enabled milestone discoveries in pharmacology and biochemistry ranging from the original formulation of the receptor concept, the first isolation and structural analysis of a receptor protein (the nAChR) to the identification, localization, and differentiation of its diverse subtypes and their validation as a target for therapeutic intervention. Among the venom-derived compounds, α-neurotoxins and α-conotoxins provide the largest families and still represent indispensable pharmacological tools. Application of modified α-neurotoxins provided substantial structural and functional details of the nAChR long before high resolution structures were available. α-bungarotoxin represents not only a standard pharmacological tool and label in nAChR research but also for unrelated proteins tagged with a minimal α-bungarotoxin binding motif. A major advantage of α-conotoxins is their smaller size, as well as superior selectivity for diverse nAChR subtypes that allows their development into ligands with optimized pharmacological and chemical properties and potentially novel drugs. In the following, these two groups of nAChR antagonists will be described focusing on their respective roles in the structural and functional characterization of nAChRs and their development into research tools. In addition, we provide a comparative overview of the diverse α-conotoxin selectivities that can serve as a practical guide for both structure activity studies and subtype classification. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Sébastien Dutertre
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier - CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Annette Nicke
- Walther Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-Universität, Nußbaumstr. 26, 80336 Munich, Germany.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str.16/10, Moscow 117999, Russian Federation
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31
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Franklin JB, Rajesh RP, Vinithkumar NV, Kirubagaran R. Identification of short single disulfide-containing contryphans from the venom of cone snails using de novo mass spectrometry-based sequencing methods. Toxicon 2017; 132:50-54. [PMID: 28400262 DOI: 10.1016/j.toxicon.2017.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Jayaseelan Benjamin Franklin
- Andaman and Nicobar Centre for Ocean Science and Technology, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Dollygunj, Port Blair 744103, India.
| | | | - Nambali Valsalan Vinithkumar
- Andaman and Nicobar Centre for Ocean Science and Technology, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Dollygunj, Port Blair 744103, India
| | - Ramalingam Kirubagaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Pallikaranai, Chennai 600100, India
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32
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The Venom Repertoire of Conus gloriamaris (Chemnitz, 1777), the Glory of the Sea. Mar Drugs 2017; 15:md15050145. [PMID: 28531118 PMCID: PMC5450551 DOI: 10.3390/md15050145] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/15/2022] Open
Abstract
The marine cone snail Conus gloriamaris is an iconic species. For over two centuries, its shell was one of the most prized and valuable natural history objects in the world. Today, cone snails have attracted attention for their remarkable venom components. Many conotoxins are proving valuable as research tools, drug leads, and drugs. In this article, we present the venom gland transcriptome of C. gloriamaris, revealing this species' conotoxin repertoire. More than 100 conotoxin sequences were identified, representing a valuable resource for future drug discovery efforts.
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Richter S, Helm C, Meunier FA, Hering L, Campbell LI, Drukewitz SH, Undheim EAB, Jenner RA, Schiavo G, Bleidorn C. Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system. BMC Evol Biol 2017; 17:64. [PMID: 28259138 PMCID: PMC5336659 DOI: 10.1186/s12862-017-0904-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present the first molecular characterization of glycerotoxin (GLTx), a potent neurotoxin found in the venom of the bloodworm Glycera tridactyla (Glyceridae, Annelida). Within the animal kingdom, GLTx shows a unique mode of action as it can specifically up-regulate the activity of Cav2.2 channels (N-type) in a reversible manner. The lack of sequence information has so far hampered a detailed understanding of its mode of action. RESULTS Our analyses reveal three ~3.8 kb GLTx full-length transcripts, show that GLTx represents a multigene family, and suggest it functions as a dimer. An integrative approach using transcriptomics, quantitative real-time PCR, in situ hybridization, and immunocytochemistry shows that GLTx is highly expressed exclusively in four pharyngeal lobes, a previously unrecognized part of the venom apparatus. CONCLUSIONS Our results overturn a century old textbook view on the glycerid venom system, suggesting that it is anatomically and functionally much more complex than previously thought. The herein presented GLTx sequence information constitutes an important step towards the establishment of GLTx as a versatile tool to understand the mechanism of synaptic function, as well as the mode of action of this novel neurotoxin.
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Affiliation(s)
- Sandy Richter
- Institute of Biology - Molecular Evolution and Systematics of Animals, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
- Department of Life Sciences, Natural History Museum, Cromwell Rd, London, SW7 5BD UK
| | - Conrad Helm
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| | - Frederic A. Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, 4072 QLD Australia
| | - Lars Hering
- Institute of Biology - Department of Zoology, University of Kassel, Heinrich-Plett-Straße 40, D-34132 Kassel, Germany
| | - Lahcen I. Campbell
- Department of Life Sciences, Natural History Museum, Cromwell Rd, London, SW7 5BD UK
- The European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Stephan H. Drukewitz
- Institute of Biology - Molecular Evolution and Systematics of Animals, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
| | - Eivind A. B. Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Brisbane, 4072 QLD Australia
| | - Ronald A. Jenner
- Department of Life Sciences, Natural History Museum, Cromwell Rd, London, SW7 5BD UK
| | - Giampietro Schiavo
- Sobell Department of Motor Neuroscience & Movement Disorders, UCL Institute of Neurology, University College London, Queen Square, London, WC1N 3BG UK
| | - Christoph Bleidorn
- Institute of Biology - Molecular Evolution and Systematics of Animals, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Calle José Gutierrez Abascal 2, 28006 Madrid, Spain
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34
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Robinson SD, Safavi-Hemami H. Insulin as a weapon. Toxicon 2016; 123:56-61. [DOI: 10.1016/j.toxicon.2016.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/08/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
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35
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Vijayasarathy M, Basheer SM, Franklin JB, Balaram P. Contryphan Genes and Mature Peptides in the Venom of Nine Cone Snail Species by Transcriptomic and Mass Spectrometric Analysis. J Proteome Res 2016; 16:763-772. [DOI: 10.1021/acs.jproteome.6b00776] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Soorej M. Basheer
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Jayaseelan Benjamin Franklin
- Andaman
and Nicobar Centre for Ocean Science and Technology, Earth System
Sciences Organisation-National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair 744103, India
| | - Padmanabhan Balaram
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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36
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Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM. Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. Mol Biol Evol 2016; 33:2924-2934. [PMID: 27524826 PMCID: PMC5062327 DOI: 10.1093/molbev/msw174] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A specialized insulin was recently found in the venom of a fish-hunting cone snail, Conus geographus Here we show that many worm-hunting and snail-hunting cones also express venom insulins, and that this novel gene family has diversified explosively. Cone snails express a highly conserved insulin in their nerve ring; presumably this conventional signaling insulin is finely tuned to the Conus insulin receptor, which also evolves very slowly. By contrast, the venom insulins diverge rapidly, apparently in response to biotic interactions with prey and also possibly the cones' own predators and competitors. Thus, the inwardly directed signaling insulins appear to experience predominantly purifying sele\ction to target an internal receptor that seldom changes, while the outwardly directed venom insulins frequently experience directional selection to target heterospecific insulin receptors in a changing mix of prey, predators and competitors. Prey insulin receptors may often be constrained in ways that prevent their evolutionary escape from targeted venom insulins, if amino-acid substitutions that result in escape also degrade the receptor's signaling functions.
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Affiliation(s)
- Helena Safavi-Hemami
- Department of Biology, University of Utah, Salt Lake City, UT Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Aiping Lu
- School of Life Sciences and Technology, Institute of Protein Research, Tongji University, Shanghai, China
| | - Qing Li
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Science, Leninsky Prospect, Moscow, Russia
| | - Jason Biggs
- University of Guam Marine Laboratory, Agana, Guam
| | | | - Jon Seger
- Department of Biology, University of Utah, Salt Lake City, UT
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT
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37
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Phuong MA, Mahardika GN, Alfaro ME. Dietary breadth is positively correlated with venom complexity in cone snails. BMC Genomics 2016; 17:401. [PMID: 27229931 PMCID: PMC4880860 DOI: 10.1186/s12864-016-2755-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/19/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. RESULTS We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. CONCLUSIONS The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Jl Sesetan-Markisa 6, Denpasar, Bali, 80225, Indonesia
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
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Peng C, Yao G, Gao BM, Fan CX, Bian C, Wang J, Cao Y, Wen B, Zhu Y, Ruan Z, Zhao X, You X, Bai J, Li J, Lin Z, Zou S, Zhang X, Qiu Y, Chen J, Coon SL, Yang J, Chen JS, Shi Q. High-throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcriptome sequencing. Gigascience 2016; 5:17. [PMID: 27087938 PMCID: PMC4832519 DOI: 10.1186/s13742-016-0122-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 04/07/2016] [Indexed: 01/06/2023] Open
Abstract
Background The venom of predatory marine cone snails mainly contains a diverse array of unique bioactive peptides commonly referred to as conopeptides or conotoxins. These peptides have proven to be valuable pharmacological probes and potential drugs because of their high specificity and affinity to important ion channels, receptors and transporters of the nervous system. Most previous studies have focused specifically on the conopeptides from piscivorous and molluscivorous cone snails, but little attention has been devoted to the dominant vermivorous species. Results The vermivorous Chinese tubular cone snail, Conus betulinus, is the dominant Conus species inhabiting the South China Sea. The transcriptomes of venom ducts and venom bulbs from a variety of specimens of this species were sequenced using both next-generation sequencing and traditional Sanger sequencing technologies, resulting in the identification of a total of 215 distinct conopeptides. Among these, 183 were novel conopeptides, including nine new superfamilies. It appeared that most of the identified conopeptides were synthesized in the venom duct, while a handful of conopeptides were identified only in the venom bulb and at very low levels. Conclusions We identified 215 unique putative conopeptide transcripts from the combination of five transcriptomes and one EST sequencing dataset. Variation in conopeptides from different specimens of C. betulinus was observed, which suggested the presence of intraspecific variability in toxin production at the genetic level. These novel conopeptides provide a potentially fertile resource for the development of new pharmaceuticals, and a pathway for the discovery of new conotoxins. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0122-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Peng
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Ge Yao
- Research Institute of Pharmaceutical Chemistry, Beijing, 102205 China
| | - Bing-Miao Gao
- School of Pharmaceutical Sciences, Hainan Medical University, Haikou, 571199 China
| | - Chong-Xu Fan
- Research Institute of Pharmaceutical Chemistry, Beijing, 102205 China
| | - Chao Bian
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | | | - Ying Cao
- Research Institute of Pharmaceutical Chemistry, Beijing, 102205 China
| | - Bo Wen
- BGI-Shenzhen, Shenzhen, 518083 China
| | | | - Zhiqiang Ruan
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | | | - Xinxin You
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | - Jie Bai
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | - Jia Li
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | | | | | - Xinhui Zhang
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | - Ying Qiu
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | - Jieming Chen
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China
| | - Steven L Coon
- Molecular Genomics Laboratory, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jiaan Yang
- Micro Pharmatech Ltd, Wuhan, 430075 China
| | - Ji-Sheng Chen
- Research Institute of Pharmaceutical Chemistry, Beijing, 102205 China
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen, 518083 China ; Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083 China ; BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China
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39
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Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides. Proc Natl Acad Sci U S A 2016; 113:3227-32. [PMID: 26957604 DOI: 10.1073/pnas.1525790113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Formation of correct disulfide bonds in the endoplasmic reticulum is a crucial step for folding proteins destined for secretion. Protein disulfide isomerases (PDIs) play a central role in this process. We report a previously unidentified, hypervariable family of PDIs that represents the most diverse gene family of oxidoreductases described in a single genus to date. These enzymes are highly expressed specifically in the venom glands of predatory cone snails, animals that synthesize a remarkably diverse set of cysteine-rich peptide toxins (conotoxins). Enzymes in this PDI family, termed conotoxin-specific PDIs, significantly and differentially accelerate the kinetics of disulfide-bond formation of several conotoxins. Our results are consistent with a unique biological scenario associated with protein folding: The diversification of a family of foldases can be correlated with the rapid evolution of an unprecedented diversity of disulfide-rich structural domains expressed by venomous marine snails in the superfamily Conoidea.
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40
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Macrander J, Broe M, Daly M. Multi-copy venom genes hidden in de novo transcriptome assemblies, a cautionary tale with the snakelocks sea anemone Anemonia sulcata (Pennant, 1977). Toxicon 2015; 108:184-8. [PMID: 26464059 DOI: 10.1016/j.toxicon.2015.09.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/29/2015] [Indexed: 12/20/2022]
Abstract
Using a partial transcriptome of the snakelocks anemone (Anemonia sulcata) we identify toxin gene candidates that were incorrectly assembled into several Trinity components. Our approach recovers hidden diversity found within some toxin gene families that would otherwise go undetected when using Trinity, a widely used program for venom-focused transcriptome reconstructions. Unidentified hidden transcripts may significantly impact conclusions made regarding venom composition (or other multi-copy conserved genes) when using Trinity or other de novo assembly programs.
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Affiliation(s)
- Jason Macrander
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA.
| | - Michael Broe
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
| | - Marymegan Daly
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
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41
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Olivera BM, Seger J, Horvath MP, Fedosov AE. Prey-Capture Strategies of Fish-Hunting Cone Snails: Behavior, Neurobiology and Evolution. BRAIN, BEHAVIOR AND EVOLUTION 2015; 86:58-74. [PMID: 26397110 DOI: 10.1159/000438449] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The venomous fish-hunting cone snails (Conus) comprise eight distinct lineages evolved from ancestors that preyed on worms. In this article, we attempt to reconstruct events resulting in this shift in food resource by closely examining patterns of behavior, biochemical agents (toxins) that facilitate prey capture and the combinations of toxins present in extant species. The first sections introduce three different hunting behaviors associated with piscivory: 'taser-and-tether', 'net-engulfment' and 'strike-and-stalk'. The first two fish-hunting behaviors are clearly associated with distinct groups of venom components, called cabals, which act in concert to modify the behavior of prey in a specific manner. Derived fish-hunting behavior clearly also correlates with physical features of the radular tooth, the device that injects these biochemical components. Mapping behavior, biochemical components and radular tooth features onto phylogenetic trees shows that fish-hunting behavior emerged at least twice during evolution. The system presented here may be one of the best examples where diversity in structure, physiology and molecular features were initially driven by particular pathways selected through behavior.
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42
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Himaya SWA, Jin AH, Dutertre S, Giacomotto J, Mohialdeen H, Vetter I, Alewood PF, Lewis RJ. Comparative Venomics Reveals the Complex Prey Capture Strategy of the Piscivorous Cone Snail Conus catus. J Proteome Res 2015; 14:4372-81. [PMID: 26322961 DOI: 10.1021/acs.jproteome.5b00630] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Venomous marine cone snails produce a unique and remarkably diverse range of venom peptides (conotoxins and conopeptides) that have proven to be invaluable as pharmacological probes and leads to new therapies. Conus catus is a hook-and-line fish hunter from clade I, with ∼20 conotoxins identified, including the analgesic ω-conotoxin CVID (AM336). The current study unravels the venom composition of C. catus with tandem mass spectrometry and 454 sequencing data. From the venom gland transcriptome, 104 precursors were recovered from 11 superfamilies, with superfamily A (especially κA-) conotoxins dominating (77%) their venom. Proteomic analysis confirmed that κA-conotoxins dominated the predation-evoked milked venom of each of six C. catus analyzed and revealed remarkable intraspecific variation in both the intensity and type of conotoxins. High-throughput FLIPR assays revealed that the predation-evoked venom contained a range of conotoxins targeting the nAChR, Cav, and Nav ion channels, consistent with α- and ω-conotoxins being used for predation by C. catus. However, the κA-conotoxins did not act at these targets but induced potent and rapid immobilization followed by bursts of activity and finally paralysis when injected intramuscularly in zebrafish. Our venomics approach revealed the complexity of the envenomation strategy used by C. catus, which contains a mix of both excitatory and inhibitory venom peptides.
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Affiliation(s)
- S W A Himaya
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Sébastien Dutertre
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia.,Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier-CNRS , Place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | - Jean Giacomotto
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Hoshyar Mohialdeen
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, 4072 Queensland, Australia
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43
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Abstract
Over the last three decades, transcriptomic studies of venom gland cells have continuously evolved, opening up new possibilities for exploring the molecular diversity of animal venoms, a prerequisite for the discovery of new drug candidates and molecular phylogenetics. The molecular complexity of animal venoms is much greater than initially thought. In this review, we describe the different technologies available for transcriptomic studies of venom, from the original individual cloning approaches to the more recent global Next Generation Sequencing strategies. Our understanding of animal venoms is evolving, with the discovery of complex and diverse bio-optimized cocktails of compounds, including mostly peptides and proteins, which are now beginning to be studied by academic and industrial researchers.
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44
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Abstract
Peptide neurotoxins from cone snails called conotoxins are renowned for their therapeutic potential to treat pain and several neurodegenerative diseases. Inefficient assay-guided discovery methods have been replaced by high-throughput bioassays integrated with advanced MS and next-generation sequencing, ushering in the era of 'venomics'. In this review, we focus on the impact of venomics on the understanding of cone snail biology as well as the application of venomics to accelerate the discovery of new conotoxins. We also discuss the continued importance of medicinal chemistry approaches to optimize conotoxins for clinical use, with a descriptive case study of MrIA featured.
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45
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Optimized deep-targeted proteotranscriptomic profiling reveals unexplored Conus toxin diversity and novel cysteine frameworks. Proc Natl Acad Sci U S A 2015; 112:E3782-91. [PMID: 26150494 DOI: 10.1073/pnas.1501334112] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cone snails are predatory marine gastropods characterized by a sophisticated venom apparatus responsible for the biosynthesis and delivery of complex mixtures of cysteine-rich toxin peptides. These conotoxins fold into small highly structured frameworks, allowing them to potently and selectively interact with heterologous ion channels and receptors. Approximately 2,000 toxins from an estimated number of >70,000 bioactive peptides have been identified in the genus Conus to date. Here, we describe a high-resolution interrogation of the transcriptomes (available at www.ddbj.nig.ac.jp) and proteomes of the diverse compartments of the Conus episcopatus venom apparatus. Using biochemical and bioinformatic tools, we found the highest number of conopeptides yet discovered in a single Conus specimen, with 3,305 novel precursor toxin sequences classified into 9 known superfamilies (A, I1, I2, M, O1, O2, S, T, Z), and identified 16 new superfamilies showing unique signal peptide signatures. We were also able to depict the largest population of venom peptides containing the pharmacologically active C-C-CC-C-C inhibitor cystine knot and CC-C-C motifs (168 and 44 toxins, respectively), as well as 208 new conotoxins displaying odd numbers of cysteine residues derived from known conotoxin motifs. Importantly, six novel cysteine-rich frameworks were revealed which may have novel pharmacology. Finally, analyses of codon usage bias and RNA-editing processes of the conotoxin transcripts demonstrate a specific conservation of the cysteine skeleton at the nucleic acid level and provide new insights about the origin of sequence hypervariablity in mature toxin regions.
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46
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Structure and function of μ-conotoxins, peptide-based sodium channel blockers with analgesic activity. Future Med Chem 2015; 6:1677-98. [PMID: 25406007 DOI: 10.4155/fmc.14.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
μ-Conotoxins block voltage-gated sodium channels (VGSCs) and compete with tetrodotoxin for binding to the sodium conductance pore. Early efforts identified µ-conotoxins that preferentially blocked the skeletal muscle subtype (NaV1.4). However, the last decade witnessed a significant increase in the number of µ-conotoxins and the range of VGSC subtypes inhibited (NaV1.2, NaV1.3 or NaV1.7). Twenty µ-conotoxin sequences have been identified to date and structure-activity relationship studies of several of these identified key residues responsible for interactions with VGSC subtypes. Efforts to engineer-in subtype specificity are driven by in vivo analgesic and neuromuscular blocking activities. This review summarizes structural and pharmacological studies of µ-conotoxins, which show promise for development of selective blockers of NaV1.2, and perhaps also NaV1.1,1.3 or 1.7.
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47
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García-Ortega LF, Martínez O. How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq. PLoS One 2015; 10:e0130262. [PMID: 26107654 PMCID: PMC4479379 DOI: 10.1371/journal.pone.0130262] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/19/2015] [Indexed: 01/02/2023] Open
Abstract
RNA-seq experiments estimate the number of genes expressed in a transcriptome as well as their relative frequencies. However, an undetermined number of genes can remain undetected due to their low expression relative to the sample size (sequence depth). Estimation of the true number of genes expressed in a transcriptome is essential in order to determine which genes are exclusively expressed in specific tissues or under particular conditions. A reliable estimate of the true number of expressed genes is also required to accurately measure transcriptome changes and to predict the sequencing depth needed to increase the proportion of detected genes. This problem is analogous to ecological sampling problems such as estimating the number of species at a given site. Here we present a non-parametric estimator for the number of undetected genes as well as for the extra sample size needed to detect a given proportion of the undetected genes. Our estimators are superior to ones already published by having smaller standard errors and biases. We applied our method to a set of 32 publicly available RNA-seq experiments, including the evaluation of 311 individually sequenced libraries. We found that in the majority of the cases more than one thousand genes are undetected, and that on average approximately 6% of the expressed genes per accession remain undetected. This figure increases to approximately 10% if individual sequencing libraries are analyzed. Our method is also applicable to metagenomic experiments. Using our method, the number of undetected genes as well as the sample size needed to detect them can be calculated, leading to more accurate and complete gene expression studies.
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Affiliation(s)
- Luis Fernando García-Ortega
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
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48
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Christensen SB, Bandyopadhyay PK, Olivera BM, McIntosh JM. αS-conotoxin GVIIIB potently and selectively blocks α9α10 nicotinic acetylcholine receptors. Biochem Pharmacol 2015; 96:349-56. [PMID: 26074268 DOI: 10.1016/j.bcp.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/05/2015] [Indexed: 11/18/2022]
Abstract
Although acetylcholine is widely utilized in vertebrate nervous systems, nicotinic acetylcholine receptors (nAChRs), including the α9α10 subtype, also are expressed in a wide variety of non-neuronal cells. These cell types include cochlear hair cells, adrenal chromaffin cells and immune cells. α9α10 nAChRs present in these cells may respectively play roles in protection from noise-induced hearing loss, response to stress and neuroprotection. Despite these critical functions, there are few available selective ligands to confirm mechanistic hypothesis regarding the role of α9α10 nAChRs. Conus, has been a rich source of ligands for receptors and ion channels. Here, we identified Conus geographus venom as a lead source for a novel α9α10 antagonist. The active component was isolated and the encoding gene cloned. The peptide signal sequence and cysteine arrangement had the signature of the σ-conotoxin superfamily. Previously isolated σ-conotoxin GVIIIA, also from Conus geographus, targets the 5-HT3 receptor. In contrast, αS-GVIIIB blocked the α9α10 nAChR with an IC50 of 9.8 nM, yet was inactive at the 5-HT3 receptor. Pharmacological characterization of αS-GVIIIB shows that it is over 100-fold selective for the α9α10 nAChR compared to other nAChR subtypes. Thus, the S-superfamily represents a novel conotoxin scaffold for flexibly targeting a variety of receptor subtypes. Functional competition studies utilized distinct off-rate kinetics of conotoxins to identify the α10/α9 nAChR interface as the site of αS-GVIIIB binding; this adds to the importance of the (+) face of the α10 rather than the (+) face of the α9 nAChR subunit as critical to binding of α9α10-targeted conotoxins.
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Affiliation(s)
- Sean B Christensen
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | | | | | - J Michael McIntosh
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA; George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT 84108, USA; Department of Psychiatry, University of Utah, Salt Lake City, UT 84112, USA.
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49
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Bioinformatics-Aided Venomics. Toxins (Basel) 2015; 7:2159-87. [PMID: 26110505 PMCID: PMC4488696 DOI: 10.3390/toxins7062159] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/12/2022] Open
Abstract
Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.
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50
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Barghi N, Concepcion GP, Olivera BM, Lluisma AO. Comparison of the Venom Peptides and Their Expression in Closely Related Conus Species: Insights into Adaptive Post-speciation Evolution of Conus Exogenomes. Genome Biol Evol 2015; 7:1797-814. [PMID: 26047846 PMCID: PMC4494072 DOI: 10.1093/gbe/evv109] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/24/2022] Open
Abstract
Genes that encode products with exogenous targets, which comprise an organism's "exogenome," typically exhibit high rates of evolution. The genes encoding the venom peptides (conotoxins or conopeptides) in Conus sensu lato exemplify this class of genes. Their rapid diversification has been established and is believed to be linked to the high speciation rate in this genus. However, the molecular mechanisms that underlie venom peptide diversification and ultimately emergence of new species remain poorly understood. In this study, the sequences and expression levels of conotoxins from several specimens of two closely related worm-hunting species, Conus tribblei and Conus lenavati, were compared through transcriptome analysis. Majority of the identified putative conopeptides were novel, and their diversity, even in each specimen, was remarkably high suggesting a wide range of prey targets for these species. Comparison of the interspecific expression patterns of conopeptides at the superfamily level resulted in the discovery of both conserved as well as species-specific expression patterns, indicating divergence in the regulatory network affecting conotoxin gene expression. Comparison of the transcriptomes of the individual snails revealed that each specimen produces a distinct set of highly expressed conopeptides, reflecting the capability of individual snails to fine-tune the composition of their venoms. These observations reflect the role of sequence divergence and divergence in the control of expression for specific conopeptides in the evolution of the exogenome and hence venom composition in Conus.
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Affiliation(s)
- Neda Barghi
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
| | - Gisela P Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | | | - Arturo O Lluisma
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines Philippine Genome Center, University of the Philippines, Quezon City, Philippines
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