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Haufe Y, Kuruva V, Samanani Z, Lokaj G, Kamnesky G, Shadamarshan P, Shahoei R, Katz D, Sampson JM, Pusch M, Brik A, Nicke A, Leffler AE. Basic Residues at Position 11 of α-Conotoxin LvIA Influence Subtype Selectivity between α3β2 and α3β4 Nicotinic Receptors via an Electrostatic Mechanism. ACS Chem Neurosci 2023; 14:4311-4322. [PMID: 38051211 DOI: 10.1021/acschemneuro.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Understanding the determinants of α-conotoxin (α-CTX) selectivity for different nicotinic acetylcholine receptor (nAChR) subtypes is a prerequisite for the design of tool compounds to study nAChRs. However, selectivity optimization of these small, disulfide-rich peptides is difficult not only because of an absence of α-CTX/nAChR co-structures but also because it is challenging to predict how a mutation to an α-CTX will alter its potency and selectivity. As a prototypical system to investigate selectivity, we employed the α-CTX LvIA that is 25-fold selective for the α3β2 nAChR over the related α3β4 nAChR subtype, which is a target for nicotine addiction. Using two-electrode voltage clamp electrophysiology, we identified LvIA[D11R] that is 2-fold selective for the α3β4 nAChR, reversing the subtype preference. This effect is specifically due to the change in charge and not shape of LvIA[D11R], as substitution of D11 with citrulline retains selectivity for the α3β2 nAChR. Furthermore, LvIA[D11K] shows a stronger reversal, with 4-fold selectivity for the α3β4 nAChR. Motivated by these findings, using site-directed mutagenesis, we found that β2[K79A] (I79 on β4), but not β2[K78A] (N78 on β4), largely restores the potency of basic mutants at position 11. Finally, to understand the structural basis of this effect, we used AlphaFold2 to generate models of LvIA in complex with both nAChR subtypes. Both models confirm the plausibility of an electrostatic mechanism to explain the data and also reproduce a broad range of potency and selectivity structure-activity relationships for LvIA mutants, as measured using free energy perturbation simulations. Our work highlights how electrostatic interactions can drive α-CTX selectivity and may serve as a strategy for optimizing the selectivity of LvIA and other α-CTXs.
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Affiliation(s)
- Yves Haufe
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Veeresh Kuruva
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ziyana Samanani
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Gonxhe Lokaj
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Guy Kamnesky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - PranavKumar Shadamarshan
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Rezvan Shahoei
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Dana Katz
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Jared M Sampson
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Michael Pusch
- Istituto di Biofisica, CNR, Via De Marini 6, Genova 16149, Italy
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Annette Nicke
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Abba E Leffler
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
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Fedosov A, Tucci CF, Kantor Y, Farhat S, Puillandre N. Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production. J Mol Evol 2023; 91:837-853. [PMID: 37962577 PMCID: PMC10730640 DOI: 10.1007/s00239-023-10139-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Venomous marine gastropods of the family Conidae are among the most diversified predators in marine realm-in large due to their complex venoms. Besides being a valuable source of bioactive neuropeptides conotoxins, cone-snails venoms are an excellent model for molecular evolution studies, addressing origin of key innovations. However, these studies are handicapped by scarce current knowledge on the tissues involved in venom production, as it is generally assumed the sole prerogative of the venom gland (VG). The role of other secretory glands that are present in all Conus species (salivary gland, SG) or only in some species (accessory salivary gland, ASG) remains poorly understood. Here, for the first time, we carry out a detailed analysis of the VG, SG, and ASG transcriptomes in the vermivorous Conus virgo. We detect multiple transcripts clusters in both the SG and ASG, whose annotations imply venom-related functions. Despite the subsets of transcripts highly-expressed in the VG, SG, and ASG being very distinct, SG expresses an L-, and ASG-Cerm08-, and MEFRR- superfamily conotoxins, all previously considered specific for VG. We corroborate our results with the analysis of published SG and VG transcriptomes from unrelated fish-hunting C. geographus, and C. striatus, possibly fish-hunting C. rolani, and worm-hunting Conus quercinus. In spite of low expression levels of conotoxins, some other specific clusters of putative venom-related peptides are present and may be highly expressed in the SG of these species. Further functional studies are necessary to determine the role that these peptides play in envenomation. In the meantime, our results show importance of routine multi-tissue sampling both for accurate interpretation of tissue-specific venom composition in cone-snails, and for better understanding origin and evolution of venom peptides genes.
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Affiliation(s)
- Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Carmen Federica Tucci
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 35020, Legnaro, Italy
| | - Yuri Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninski Prospect, Moscow, 119071, Russian Federation
| | - Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005, Paris, France
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Zheng JW, Lu Y, Yang YF, Huang D, Li DW, Wang X, Gao Y, Yang WD, Guan Y, Li HY. Systematic dissection of genomic features determining the vast diversity of conotoxins. BMC Genomics 2023; 24:598. [PMID: 37814244 PMCID: PMC10561478 DOI: 10.1186/s12864-023-09689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Conus, a highly diverse species of venomous predators, has attracted significant attention in neuroscience and new drug development due to their rich collection of neuroactive peptides called conotoxins. Recent advancements in transcriptome, proteome, and genome analyses have facilitated the identification of conotoxins within Conus' venom glands, providing insights into the genetic features and evolutionary patterns of conotoxin genes. However, the underlying mechanism behind the extraordinary hypervariability of conotoxins remains largely unknown. RESULTS We analyzed the transcriptomes of 34 Conus species, examining various tissues such as the venom duct, venom bulb, and salivary gland, leading to the identification of conotoxin genes. Genetic variation analysis revealed that a subset of these genes (15.78% of the total) in Conus species underwent positive selection (Ka/Ks > 1, p < 0.01). Additionally, we reassembled and annotated the genome of C. betulinus, uncovering 221 conotoxin-encoding genes. These genes primarily consisted of three exons, with a significant portion showing high transcriptional activity in the venom ducts. Importantly, the flanking regions and adjacent introns of conotoxin genes exhibited a higher prevalence of transposon elements, suggesting their potential contribution to the extensive variability observed in conotoxins. Furthermore, we detected genome duplication in C. betulinus, which likely contributed to the expansion of conotoxin gene numbers. Interestingly, our study also provided evidence of introgression among Conus species, indicating that interspecies hybridization may have played a role in shaping the evolution of diverse conotoxin genes. CONCLUSIONS This study highlights the impact of adaptive evolution and introgressive hybridization on the genetic diversity of conotoxin genes and the evolution of Conus. We also propose a hypothesis suggesting that transposable elements might significantly contribute to the remarkable diversity observed in conotoxins. These findings not only enhance our understanding of peptide genetic diversity but also present a novel approach for peptide bioengineering.
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Affiliation(s)
- Jian-Wei Zheng
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- College of Food Science and Engineering, Foshan University of Science and Technology, Foshan, 528231, China
| | - Yang Lu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yu-Feng Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Dan Huang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Da-Wei Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Xiang Wang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yang Gao
- Gulou Hospital, Nanjing University, Nanjing, China
| | - Wei-Dong Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Hong-Ye Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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Wiere S, Sugai C, Espiritu MJ, Aurelio VP, Reyes CD, Yuzon N, Whittal RM, Tytgat J, Peigneur S, Bingham JP. Research into the Bioengineering of a Novel α-Conotoxin from the Milked Venom of Conus obscurus. Int J Mol Sci 2022; 23:12096. [PMID: 36292948 PMCID: PMC9602734 DOI: 10.3390/ijms232012096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
The marine cone snail produces one of the fastest prey strikes in the animal kingdom. It injects highly efficacious venom, often causing prey paralysis and death within seconds. Each snail has hundreds of conotoxins, which serve as a source for discovering and utilizing novel analgesic peptide therapeutics. In this study, we discovered, isolated, and synthesized a novel α3/5-conotoxins derived from the milked venom of Conus obscurus (α-conotoxin OI) and identified the presence of α-conotoxin SI-like sequence previously found in the venom of Conus striatus. Five synthetic analogs of the native α-conotoxin OI were generated. These analogs incorporated single residue or double residue mutations. Three synthetic post-translational modifications (PTMs) were synthetically incorporated into these analogs: N-terminal truncation, proline hydroxylation, and tryptophan bromination. The native α-conotoxin OI demonstrated nanomolar potency in Poecilia reticulata and Homosapiens muscle-type nicotinic acetylcholine receptor (nAChR) isoforms. Moreover, the synthetic α-[P9K] conotoxin OI displayed enhanced potency in both bioassays, ranging from a 2.85 (LD50) to 18.4 (IC50) fold increase in comparative bioactivity. The successful incorporation of PTMs, with retention of both potency and nAChR isoform selectivity, ultimately pushes new boundaries of peptide bioengineering and the generation of novel α-conotoxin-like sequences.
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Affiliation(s)
- Sean Wiere
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Christopher Sugai
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Michael J. Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR 97123, USA
| | - Vincent P. Aurelio
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Chloe D. Reyes
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Nicole Yuzon
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Randy M. Whittal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, 3000 Leuven, Belgium
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, 3000 Leuven, Belgium
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
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Koch TL, Ramiro IBL, Flórez Salcedo P, Engholm E, Jensen KJ, Chase K, Olivera BM, Bjørn-Yoshimoto WE, Safavi-Hemami H. Reconstructing the Origins of the Somatostatin and Allatostatin-C Signaling Systems Using the Accelerated Evolution of Biodiverse Cone Snail Toxins. Mol Biol Evol 2022; 39:msac075. [PMID: 35383850 PMCID: PMC9048919 DOI: 10.1093/molbev/msac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Somatostatin and its related peptides (SSRPs) form an important family of hormones with diverse physiological roles. The ubiquitous presence of SSRPs in vertebrates and several invertebrate deuterostomes suggests an ancient origin of the SSRP signaling system. However, the existence of SSRP genes outside of deuterostomes has not been established, and the evolutionary history of this signaling system remains poorly understood. Our recent discovery of SSRP-like toxins (consomatins) in venomous marine cone snails (Conus) suggested the presence of a related signaling system in mollusks and potentially other protostomes. Here, we identify the molluscan SSRP-like signaling gene that gave rise to the consomatin family. Following recruitment into venom, consomatin genes experienced strong positive selection and repeated gene duplications resulting in the formation of a hyperdiverse family of venom peptides. Intriguingly, the largest number of consomatins was found in worm-hunting species (>400 sequences), indicating a homologous system in annelids, another large protostome phylum. Consistent with this, comprehensive sequence mining enabled the identification of SSRP-like sequences (and their corresponding orphan receptor) in annelids and several other protostome phyla. These results established the existence of SSRP-like peptides in many major branches of bilaterians and challenge the prevailing hypothesis that deuterostome SSRPs and protostome allatostatin-C are orthologous peptide families. Finally, having a large set of predator-prey SSRP sequences available, we show that although the cone snail's signaling SSRP-like genes are under purifying selection, the venom consomatin genes experience rapid directional selection to target receptors in a changing mix of prey.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | - Iris Bea L. Ramiro
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | | | - Ebbe Engholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Knud Jørgen Jensen
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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Abalde S, Dutertre S, Zardoya R. A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae). Toxins (Basel) 2021; 13:toxins13090642. [PMID: 34564647 PMCID: PMC8472973 DOI: 10.3390/toxins13090642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/20/2022] Open
Abstract
Venoms are complex mixtures of proteins that have evolved repeatedly in the animal kingdom. Cone snail venoms represent one of the best studied venom systems. In nature, this venom can be dynamically adjusted depending on its final purpose, whether to deter predators or hunt prey. Here, the transcriptome of the venom gland and the proteomes of the predation-evoked and defensive venoms of the molluscivorous cone snail Cylinder ammiralis were catalogued. A total of 242 venom-related transcripts were annotated. The conotoxin superfamilies presenting more different peptides were O1, O2, T, and M, which also showed high expression levels (except T). The three precursors of the J superfamily were also highly expressed. The predation-evoked and defensive venoms showed a markedly distinct profile. A total of 217 different peptides were identified, with half of them being unique to one venom. A total of 59 peptides ascribed to 23 different protein families were found to be exclusive to the predatory venom, including the cono-insulin, which was, for the first time, identified in an injected venom. A total of 43 peptides from 20 protein families were exclusive to the defensive venom. Finally, comparisons of the relative abundance (in terms of number of peptides) of the different conotoxin precursor superfamilies showed that most of them present similar abundance regardless of the diet.
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
- Department of Zoology, Swedish Museum of Natural History, Frescativägen 40, 114 18 Stockholm, Sweden
- Correspondence:
| | | | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain;
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Katz D, DiMattia MA, Sindhikara D, Li H, Abraham N, Leffler AE. Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations. Mar Drugs 2021; 19:367. [PMID: 34202022 PMCID: PMC8306581 DOI: 10.3390/md19070367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Nicotinic acetylcholine receptor (nAChR) subtypes are key drug targets, but it is challenging to pharmacologically differentiate between them because of their highly similar sequence identities. Furthermore, α-conotoxins (α-CTXs) are naturally selective and competitive antagonists for nAChRs and hold great potential for treating nAChR disorders. Identifying selectivity-enhancing mutations is the chief aim of most α-CTX mutagenesis studies, although doing so with traditional docking methods is difficult due to the lack of α-CTX/nAChR crystal structures. Here, we use homology modeling to predict the structures of α-CTXs bound to two nearly identical nAChR subtypes, α3β2 and α3β4, and use free-energy perturbation (FEP) to re-predict the relative potency and selectivity of α-CTX mutants at these subtypes. First, we use three available crystal structures of the nAChR homologue, acetylcholine-binding protein (AChBP), and re-predict the relative affinities of twenty point mutations made to the α-CTXs LvIA, LsIA, and GIC, with an overall root mean square error (RMSE) of 1.08 ± 0.15 kcal/mol and an R2 of 0.62, equivalent to experimental uncertainty. We then use AChBP as a template for α3β2 and α3β4 nAChR homology models bound to the α-CTX LvIA and re-predict the potencies of eleven point mutations at both subtypes, with an overall RMSE of 0.85 ± 0.08 kcal/mol and an R2 of 0.49. This is significantly better than the widely used molecular mechanics-generalized born/surface area (MM-GB/SA) method, which gives an RMSE of 1.96 ± 0.24 kcal/mol and an R2 of 0.06 on the same test set. Next, we demonstrate that FEP accurately classifies α3β2 nAChR selective LvIA mutants while MM-GB/SA does not. Finally, we use FEP to perform an exhaustive amino acid mutational scan of LvIA and predict fifty-two mutations of LvIA to have greater than 100X selectivity for the α3β2 nAChR. Our results demonstrate the FEP is well-suited to accurately predict potency- and selectivity-enhancing mutations of α-CTXs for nAChRs and to identify alternative strategies for developing selective α-CTXs.
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Affiliation(s)
- Dana Katz
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Michael A. DiMattia
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Dan Sindhikara
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Hubert Li
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | | | - Abba E. Leffler
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
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8
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Rajaian Pushpabai R, Wilson Alphonse CR, Mani R, Arun Apte D, Franklin JB. Diversity of Conopeptides and Conoenzymes from the Venom Duct of the Marine Cone Snail Conus bayani as Determined from Transcriptomic and Proteomic Analyses. Mar Drugs 2021; 19:202. [PMID: 33916793 PMCID: PMC8066144 DOI: 10.3390/md19040202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/01/2023] Open
Abstract
Marine cone snails are predatory gastropods characterized by a well-developed venom apparatus and highly evolved hunting strategies that utilize toxins to paralyze prey and defend against predators. The venom of each species of cone snail has a large number of pharmacologically active peptides known as conopeptides or conotoxins that are usually unique in each species. Nevertheless, venoms of only very few species have been characterized so far by transcriptomic approaches. In this study, we used transcriptome sequencing technologies and mass spectrometric methods to describe the diversity of venom components expressed by a worm-hunting species, Conus bayani. A total of 82 conotoxin sequences were retrieved from transcriptomic data that contain 54 validated conotoxin sequences clustered into 21 gene superfamilies including divergent gene family, 17 sequences clustered to 6 different conotoxin classes, and 11 conotoxins classified as unassigned gene family. Seven new conotoxin sequences showed unusual cysteine patterns. We were also able to identify 19 peptide sequences using mass spectrometry that completely overlapped with the conotoxin sequences obtained from transcriptome analysis. Importantly, herein we document the presence of 16 proteins that include five post-translational modifying enzymes obtained from transcriptomic data. Our results revealed diverse and novel conopeptides of an unexplored species that could be used extensively in biomedical research due to their therapeutic potentials.
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Affiliation(s)
- Rajesh Rajaian Pushpabai
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; (R.R.P.); (C.R.W.A.); (R.M.)
| | - Carlton Ranjith Wilson Alphonse
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; (R.R.P.); (C.R.W.A.); (R.M.)
| | - Rajasekar Mani
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; (R.R.P.); (C.R.W.A.); (R.M.)
| | - Deepak Arun Apte
- Department of Marine Conservation, Bombay Natural History Society, Hornbill House, Dr. Sálim Ali Chowk, SBS Road, Mumbai 400 001, Maharashtra, India;
| | - Jayaseelan Benjamin Franklin
- Department of Marine Conservation, Bombay Natural History Society, Hornbill House, Dr. Sálim Ali Chowk, SBS Road, Mumbai 400 001, Maharashtra, India;
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9
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Armstrong DA, Jin AH, Braga Emidio N, Lewis RJ, Alewood PF, Rosengren KJ. Chemical Synthesis and NMR Solution Structure of Conotoxin GXIA from Conus geographus. Mar Drugs 2021; 19:md19020060. [PMID: 33530397 PMCID: PMC7912261 DOI: 10.3390/md19020060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
Conotoxins are disulfide-rich peptides found in the venom of cone snails. Due to their exquisite potency and high selectivity for a wide range of voltage and ligand gated ion channels they are attractive drug leads in neuropharmacology. Recently, cone snails were found to have the capability to rapidly switch between venom types with different proteome profiles in response to predatory or defensive stimuli. A novel conotoxin, GXIA (original name G117), belonging to the I3-subfamily was identified as the major component of the predatory venom of piscivorous Conus geographus. Using 2D solution NMR spectroscopy techniques, we resolved the 3D structure for GXIA, the first structure reported for the I3-subfamily and framework XI family. The 32 amino acid peptide is comprised of eight cysteine residues with the resultant disulfide connectivity forming an ICK+1 motif. With a triple stranded β-sheet, the GXIA backbone shows striking similarity to several tarantula toxins targeting the voltage sensor of voltage gated potassium and sodium channels. Supported by an amphipathic surface, the structural evidence suggests that GXIA is able to embed in the membrane and bind to the voltage sensor domain of a putative ion channel target.
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Affiliation(s)
- David A. Armstrong
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Richard J. Lewis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Paul F. Alewood
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - K. Johan Rosengren
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia;
- Correspondence:
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Huynh PN, Harvey PJ, Gajewiak J, Craik DJ, Michael McIntosh J. Critical residue properties for potency and selectivity of α-Conotoxin RgIA towards α9α10 nicotinic acetylcholine receptors. Biochem Pharmacol 2020; 181:114124. [PMID: 32593612 PMCID: PMC7572646 DOI: 10.1016/j.bcp.2020.114124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022]
Abstract
The α9α10 nicotinic acetylcholine receptor (nAChR) has been characterized as an effective anti-pain target that functions through a non-opioid mechanism. However, as a pentameric ion channel comprised of two different subunits, the specific targeting of α9α10 nAChRs has proven challenging. Previously the 13-amino-acid peptide, RgIA, was shown to block α9α10 nAChRs with high potency and specificity. This peptide, characterized from the venom of the carnivorous marine snail, Conus regius, produced analgesia in several rodent models of chronic pain. Despite promising pre-clinical data in behavioral assays, the number of specific α9α10 nAChR antagonists remains small and the physiological mechanisms of analgesia remain cryptic. In this study, we implement amino-acid substitutions to definitively characterize the chemical properties of RgIA that contribute to its activity against α9α10 nAChRs. Using this mutational approach, we determined the vital role of biochemical side-chain properties and amino acids in the second loop that are amenable to substitutions to further engineer next-generation analogs for the blockade of α9α10 nAChRs.
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Affiliation(s)
- Peter N Huynh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
| | - Peta J Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joanna Gajewiak
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - J Michael McIntosh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; George E. Whalen Veterans Affairs Medical Center, Salt Lake City, UT 84112, USA; Department of Psychiatry, University of Utah, Salt Lake City, UT 84112, USA
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11
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Li X, Chen W, Zhangsun D, Luo S. Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus. Mar Drugs 2020; 18:md18090464. [PMID: 32937857 PMCID: PMC7551347 DOI: 10.3390/md18090464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/02/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
The venom of various Conus species is composed of a rich variety of unique bioactive peptides, commonly referred to as conotoxins (conopeptides). Most conopeptides have specific receptors or ion channels as physiologically relevant targets. In this paper, high-throughput transcriptome sequencing was performed to analyze putative conotoxin transcripts from the venom duct of a vermivorous cone snail species, Conus litteratus native to the South China Sea. A total of 128 putative conotoxins were identified, most of them belonging to 22 known superfamilies, with 43 conotoxins being regarded as belonging to new superfamilies. Notably, the M superfamily was the most abundant in conotoxins among the known superfamilies. A total of 15 known cysteine frameworks were also described. The largest proportion of cysteine frameworks were VI/VII (C-C-CC-C-C), IX (C-C-C-C-C-C) and XIV (C-C-C-C). In addition, five novel cysteine patterns were also discovered. Simple sequence repeat detection results showed that di-nucleotide was the major type of repetition, and the codon usage bias results indicated that the codon usage bias of the conotoxin genes was weak, but the M, O1, O2 superfamilies differed in codon preference. Gene cloning indicated that there was no intron in conotoxins of the B1- or J superfamily, one intron with 1273-1339 bp existed in a mature region of the F superfamily, which is different from the previously reported gene structure of conotoxins from other superfamilies. This study will enhance our understanding of conotoxin diversity, and the new conotoxins discovered in this paper will provide more potential candidates for the development of pharmacological probes and marine peptide drugs.
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12
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Ning J, Ren J, Xiong Y, Wu Y, Zhangsun M, Zhangsun D, Zhu X, Luo S. Identification of Crucial Residues in α-Conotoxin EI Inhibiting Muscle Nicotinic Acetylcholine Receptor. Toxins (Basel) 2019; 11:toxins11100603. [PMID: 31623211 PMCID: PMC6832962 DOI: 10.3390/toxins11100603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/31/2022] Open
Abstract
α-Conotoxins (α-CTxs) are small disulfide-rich peptides from venom of Conus species that target nicotinic acetylcholine receptors (nAChRs). The muscle-type nAChRs have been recognized as a potential target for several diseases, such as myogenic disorders, muscle dystrophies, and myasthenia gravis. EI, an α4/7-CTx, mainly blocks α1β1δε nAChRs and has an extra N-terminal extension of three amino acids. In this study, the alanine scanning (Ala-scan) mutagenesis was applied in order to identify key residues of EI for binding with mouse α1β1δε nAChR. The Ala-substituted analogues were tested for their abilities of modulating muscle and neuronal nAChRs in Xenopus laevis oocytes using two-electrode voltage clamp (TEVC) recordings. Electrophysiological results indicated that the vital residues for functional activity of EI were His-7, Pro-8, Met-12, and Pro-15. These changes exhibited a significant decrease in potency of EI against mouse α1β1δε nAChR. Interestingly, replacing the critical serine (Ser) at position 13 with an alanine (Ala) residue resulted in a 2-fold increase in potency at the α1β1δε nAChR, and showed loss of activity on α3β2 and α3β4 nAChRs. Selectivity and potency of [S13A] EI was improved compared with wild-type EI (WT EI). In addition, the structure–activity relationship (SAR) of EI revealed that the “Arg1–Asn2–Hyp3” residues at the N-terminus conferred potency at the muscle-type nAChRs, and the deletion analogue △1–3 EI caused a total loss of activity at the α1β1δε nAChR. Circular dichroism (CD) spectroscopy studies demonstrated that activity loss of truncated analogue △1–3 EI for α1β1δε nAChR is attributed to disturbance of the secondary structure. In this report, an Ala-scan mutagenesis strategy is presented to identify crucial residues that are significantly affecting potency of E1 for mouse α1β1δε nAChR. It may also be important in remodeling of some novel ligands for inhibiting muscle-type nAChRs.
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Affiliation(s)
- Jiong Ning
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Jie Ren
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Yang Xiong
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Yong Wu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Manqi Zhangsun
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
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13
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Peigneur S, Devi P, Seldeslachts A, Ravichandran S, Quinton L, Tytgat J. Structure-Function Elucidation of a New α-Conotoxin, MilIA, from Conus milneedwardsi. Mar Drugs 2019; 17:md17090535. [PMID: 31527432 PMCID: PMC6780063 DOI: 10.3390/md17090535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/16/2022] Open
Abstract
The a-Conotoxins are peptide toxins that are found in the venom of marine cone snails and they are potent antagonists of various subtypes of nicotinic acetylcholine receptors (nAChRs). Because nAChRs have an important role in regulating transmitter release, cell excitability, and neuronal integration, nAChR dysfunctions have been implicated in a variety of severe pathologies. We describe the isolation and characterization of α-conotoxin MilIA, the first conopeptide from the venom of Conus milneedwardsi. The peptide was characterized by electrophysiological screening against several types of cloned nAChRs that were expressed in Xenopus laevis oocytes. MilIA, which is a member of the α3/5 family, is an antagonist of muscle type nAChRs with a high selectivity for muscle versus neuronal subtype nAChRs. Several analogues were designed and investigated for their activity in order to determine the key epitopes of MilIA. Native MilIA and analogues both showed activity at the fetal muscle type nAChR. Two single mutations (Met9 and Asn10) allowed for MilIA to strongly discriminate between the two types of muscle nAChRs. Moreover, one analogue, MilIA [∆1,M2R, M9G, N10K, H11K], displayed a remarkable enhanced potency when compared to native peptide. The key residues that are responsible for switching between muscle and neuronal nAChRs preference were elucidated. Interestingly, the same analogue showed a preference for α9α10 nAChRs among the neuronal types.
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Affiliation(s)
- Steve Peigneur
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, O & N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium.
| | - Prabha Devi
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, O & N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium.
- CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India.
| | - Andrea Seldeslachts
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, O & N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium.
| | | | - Loïc Quinton
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, 4000 Liège, Belgium.
| | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, O & N2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium.
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14
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Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails. Syst Biol 2019; 68:781-796. [PMID: 30816949 PMCID: PMC6934442 DOI: 10.1093/sysbio/syz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, 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
| | - Ristiyanti M Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Km.46, Jl. Raya Bogor, Cibinong, Bogor, West Java 16911, Indonesia
| | - Romanus Edy Prabowo
- Aquatic Biology Laboratory, Faculty of Biology, Universitas Jenderal Soedirman, Jalan dr. Suparno 63 Grendeng, Purwokerto, Indonesia, 53122
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Philipp W H Vogt
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 1259 Trumansburg Road, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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15
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Wen J, Hung A. Effects of C-Terminal Carboxylation on α-Conotoxin LsIA Interactions with Human α7 Nicotinic Acetylcholine Receptor: Molecular Simulation Studies. Mar Drugs 2019; 17:md17040206. [PMID: 30987002 PMCID: PMC6521072 DOI: 10.3390/md17040206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 01/25/2023] Open
Abstract
α-Conotoxins selectively bind to nicotinic acetylcholine receptors (nAChRs), which are therapeutic targets due to their important role in signaling transmission in excitable cells. A previous experimental study has demonstrated that carboxylation of the C-terminal of α-conotoxin LsIA reduces its potency to inhibit human α7 nAChR relative to naturally amidated LsIA. However, little is known about the contribution of conformational changes in the receptor and interactions, induced by C-terminal amidation/carboxylation of conotoxins, to selective binding to nAChRs, since most conotoxins and some disulfide-rich peptides from other conotoxin subfamilies possess a naturally amidated C-terminal. In this study, we employ homology modeling and molecular dynamics (MD) simulations to propose the determinants for differential interactions between amidated and carboxylated LsIAs with α7 nAChR. Our findings indicate an overall increased number of contacts favored by binding of amidated LsIA versus its carboxylated counterpart. Toxin-receptor pairwise interactions, which may play a role in enhancing the potency of the former, include ARG10-TRP77, LEU141 and CYS17-GLN79 via persistent hydrogen bonds and cation-π interactions, which are weakened in the carboxylated form due to a strong intramolecular salt-bridge formed by ARG10 and carboxylated C-terminus. The binding of amidated LsIA also induces enhanced movements in loop C and the juxtamembrane Cys-loop that are closely associated with receptor function. Additionally, the impacts of binding of LsIA on the overall structure and inter-subunit contacts were examined using inter-residue network analysis, suggesting a clockwise tilting of the α7 C and F loops upon binding to carboxylated LsIA, which is absent for amidated LsIA binding. The predicted molecular mechanism of LsIA binding to the α7 receptor may provide new insights into the important role of the C-terminal in the binding potency of conotoxins at neuronal nAChRs for pharmacological purposes.
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Affiliation(s)
- Jierong Wen
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC3001, Australia.
| | - Andrew Hung
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC3001, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails In Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs 2019; 17:E145. [PMID: 30832207 PMCID: PMC6471681 DOI: 10.3390/md17030145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both in amino acid sequence and length, and in posttranslational modifications, particularly the formation of multiple disulfide linkages. Most of the functionally characterized conopeptides target ion channels of animal nervous systems, which has led to research on their therapeutic applications. Many facets of the underlying molecular mechanisms responsible for the specificity and virulence of conopeptides, however, remain poorly understood. In this review, we will explore the chemical diversity of conopeptides from a computational perspective. First, we discuss current approaches used for classifying conopeptides. Next, we review different computational strategies that have been applied to understanding and predicting their structure and function, from machine learning techniques for predictive classification to docking studies and molecular dynamics simulations for molecular-level understanding. We then review recent novel computational approaches for rapid high-throughput screening and chemical design of conopeptides for particular applications. We close with an assessment of the state of the field, emphasizing important questions for future lines of inquiry.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Biosecurity and Public Health Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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18
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Ren J, Zhu X, Xu P, Li R, Fu Y, Dong S, Zhangsun D, Wu Y, Luo S. d-Amino Acid Substitution of α-Conotoxin RgIA Identifies its Critical Residues and Improves the Enzymatic Stability. Mar Drugs 2019; 17:md17030142. [PMID: 30823399 PMCID: PMC6472032 DOI: 10.3390/md17030142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/17/2019] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
α-Conotoxin RgIA is a selective and potent competitive antagonist of rat α9α10 nicotinic acetylcholine receptors (nAChR), but it is much less potent towards human α9α10 nAChR. Furthermore, RgIA is susceptible to proteolytic degradation due to containing four arginine residues. These disadvantages greatly limit its use for clinical applications. The purpose of this research was to identify critical stereocenters of RgIA and discover more stable analogues, enhancing its bioavailability by using the d-amino acid scan method. The activity of each variant was investigated against rat and human α9α10 nAChRs, which were expressed in Xenopus oocytes. Experimental assays showed that 14 out of 15 analogues had a substantial reduction in potency towards rat α9α10 nAChR. Noticeably, analogue 13 retained full biological activity compared with RgIA. Meanwhile, two other analogues, 14 and 15, of which l-Args were substituted with d-Args, exhibited a significantly increased potency towards human α9α10 nAChR, although these analogues showed decreased activities against rat α9α10 nAChR. Additionally, these three analogues exhibited a high resistance against enzymatic degradation in human serum and simulated intestinal fluid (SIF). Collectively, our findings suggest that a d-amino acid scan is a useful strategy for investigating how the side-chain chirality of amino acids affects the structure and function of peptides and may facilitate the development of more stable analogues to increase therapeutic potential.
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Affiliation(s)
- Jie Ren
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Pan Xu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Rui Li
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Ying Fu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Shuai Dong
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Yong Wu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Gao B, Peng C, Chen Q, Zhang J, Shi Q. Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species. PLoS One 2018; 13:e0193053. [PMID: 30059499 PMCID: PMC6066214 DOI: 10.1371/journal.pone.0193053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/02/2018] [Indexed: 12/15/2022] Open
Abstract
Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, 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, China
| | - Qin Chen
- School of Agricultural and Forestry Science and Technology, Hainan Radio & TV University, Haikou, China
| | - Junqing Zhang
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, 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, China
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24
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Ren J, Li R, Ning J, Zhu X, Zhangsun D, Wu Y, Luo S. Effect of Methionine Oxidation and Substitution of α-Conotoxin TxID on α3β4 Nicotinic Acetylcholine Receptor. Mar Drugs 2018; 16:md16060215. [PMID: 29925760 PMCID: PMC6025358 DOI: 10.3390/md16060215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/05/2018] [Accepted: 06/15/2018] [Indexed: 12/24/2022] Open
Abstract
α-Conotoxin TxID was discovered from Conus textile by gene cloning, which has 4/6 inter-cysteine loop spacing and selectively inhibits α3β4 nicotinic acetylcholine receptor (nAChR) subtype. However, TxID is susceptible to modification due to it containing a methionine (Met) residue that easily forms methionine sulfoxide (MetO) in oxidative environment. In this study, we investigated how Met-11 and its derivatives affect the activity of TxID using a combination of electrophysiological recordings and molecular modelling. The results showed most TxID analogues had substantially decreased activities on α3β4 nAChR with more than 10-fold potency loss and 5 of them demonstrated no inhibition on α3β4 nAChR. However, one mutant, [M11I]TxID, displayed potent inhibition at α3β4 nAChR with an IC50 of 69 nM, which only exhibited 3.8-fold less compared with TxID. Molecular dynamics simulations were performed to expound the decrease in the affinity for α3β4 nAChR. The results indicate replacement of Met with a hydrophobic moderate-sized Ile in TxID is an alternative strategy to reduce the impact of Met oxidation, which may help to redesign conotoxins containing methionine residue.
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Affiliation(s)
- Jie Ren
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Rui Li
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Jiong Ning
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Yong Wu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China.
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Abstract
To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and nontoxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100× coverage) and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are composed of one to six exons and are typically short in length (mean = ∼85 bp). Second, we expanded our understanding of the following genetic features of conotoxin evolution: 1) positive selection, where exons coding the mature toxin region were often three times more divergent than their adjacent noncoding regions, 2) expression regulation, with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome (24-63%), and 3) extensive gene turnover, where Conidae species varied from 120 to 859 conotoxin gene copies. Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. Overall, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Denpasar, Bali, Indonesia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Lu J, Zhang K, Wang S, Sun T, Yu S, Dai Q, Liu Z. Cloning, expression and functional characterization of a D-superfamily conotoxin Lt28.1 with previously undescribed cysteine pattern. Peptides 2017; 94:64-70. [PMID: 28666820 DOI: 10.1016/j.peptides.2017.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 12/17/2022]
Abstract
As a class of peptides with 10 cysteine residues (-C-CC-C-CC-C-C-C-C-), D-superfamily conotoxins (D-conotoxins) can specifically act on nicotinic acetylcholine receptors (nAChRs). According to the conserved signal peptides of D-conotoxins, seven D-conotoxin precursor sequences with a previously undescribed Cys arrangement (-C-C-C-CC-C-C-C-C-C-) were identified by PCR-RACE methodology in the present study. The alignment of sequences revealed that signal peptide regions were same as D-VxXXA from Conus vexillum, and their mature peptides were almost different from the D-conotoxins. Analyses of the evolutionary tree demonstrated that they had low homology to those reported conotoxins with 10 cysteine residues (less than 35%) and lied in a separate branch in the evolutionary tree. Furthermore, a previously undescribed D-superfamily conotoxin Lt28.1 was further expressed in Pichia pastoris and then functionally characterized. The results showed that the recombinant Lt28.1 targeted α9α10 nAChRs but not other nAChRs subtypes. These findings defined a new branch of D-superfamily and expanded our knowledge of targets and potential application of D-conotoxins.
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Affiliation(s)
- Jianbo Lu
- Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Kejun Zhang
- Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Shuo Wang
- Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Ting Sun
- Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Shuo Yu
- Beijing Institute of Biotechnology, Beijing 100071, PR China
| | - Qiuyun Dai
- Beijing Institute of Biotechnology, Beijing 100071, PR China.
| | - Zhuguo Liu
- Beijing Institute of Biotechnology, Beijing 100071, PR China.
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dao FY, Yang H, Su ZD, Yang W, Wu Y, Hui D, Chen W, Tang H, Lin H. Recent Advances in Conotoxin Classification by Using Machine Learning Methods. Molecules 2017; 22:molecules22071057. [PMID: 28672838 PMCID: PMC6152242 DOI: 10.3390/molecules22071057] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 11/16/2022] Open
Abstract
Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer's disease, Parkinson's disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine. Generally, conotoxin types are confirmed when their sequence, structure, and function are experimentally validated. However, it is time-consuming and costly to acquire the structure and function information by using biochemical experiments. Therefore, it is important to develop computational tools for efficiently and effectively recognizing conotoxin types based on sequence information. In this work, we reviewed the current progress in computational identification of conotoxins in the following aspects: (i) construction of benchmark dataset; (ii) strategies for extracting sequence features; (iii) feature selection techniques; (iv) machine learning methods for classifying conotoxins; (v) the results obtained by these methods and the published tools; and (vi) future perspectives on conotoxin classification. The paper provides the basis for in-depth study of conotoxins and drug therapy research.
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Affiliation(s)
- Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zhen-Dong Su
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Wuritu Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
- Development and Planning Department, Inner Mongolia University, Hohhot 010021, China.
| | - Yun Wu
- College of Computer and Information Engineering, Xiamen University of Technology, Xiamen 361024, China.
| | - Ding Hui
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
- Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China.
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou 646000, China.
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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Barghi N, Concepcion GP, Olivera BM, Lluisma AO. High conopeptide diversity in Conus tribblei revealed through analysis of venom duct transcriptome using two high-throughput sequencing platforms. Mar Biotechnol (NY) 2015; 17:81-98. [PMID: 25117477 PMCID: PMC4501261 DOI: 10.1007/s10126-014-9595-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 07/24/2014] [Indexed: 06/03/2023]
Abstract
The venom of each species of Conus contains different kinds of pharmacologically active peptides which are mostly unique to that species. Collectively, the ~500-700 species of Conus produce a large number of these peptides, perhaps exceeding 140,000 different types in total. To date, however, only a small fraction of this diversity has been characterized via transcriptome sequencing. In addition, the sampling of this chemical diversity has not been uniform across the different lineages in the genus. In this study, we used high-throughput transcriptome sequencing approach to further investigate the diversity of Conus venom peptides. We chose a species, Conus tribblei, as a representative of a poorly studied clade of Conus. Using the Roche 454 and Illumina platforms, we discovered 136 unique and novel putative conopeptides belonging to 30 known gene superfamilies and 6 new conopeptide groups, the greatest diversity so far observed from a transcriptome. Most of the identified peptides exhibited divergence from the known conopeptides, and some contained cysteine frameworks observed for the first time in cone snails. In addition, several enzymes involved in posttranslational modification of conopeptides and also some proteins involved in efficient delivery of the conopeptides to prey were identified as well. Interestingly, a number of conopeptides highly similar to the conopeptides identified in a phylogenetically distant species, the generalist feeder Conus californicus, were observed. The high diversity of conopeptides and the presence of conopeptides similar to those in C. californicus suggest that C. tribblei may have a broad range of prey preferences.
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Affiliation(s)
- Neda Barghi
- Marine Science Institute, University of the Philippines, Quezon City, Philippines
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Wu Y, Wang L, Zhou M, Jiang X, Zhu X, Chen Y, Luo S, You Y, Ren Z, Xu A. Soluble expression, purification and functional identification of the framework XV conotoxins derived from different Conus species. Peptides 2014; 56:77-83. [PMID: 24703966 DOI: 10.1016/j.peptides.2014.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/15/2022]
Abstract
The conotoxin cysteine framework XV (-C-C-CC-C-C-C-C-), which was named Lt15a, was firstly identified from the cDNA library of Conus litteratus. After that, 18 new framework XV conotoxin sequences were cloned from nine Conus species. Like other conopeptides, the XV-conotoxins have the conserved signal peptide and propeptide, and there are also some conserved residues in their mature peptide. All the framework XV conotoxins were apparently converged into two branches, because of the indel and point mutations occurred in their mature peptides. By fused with thioredoxin and 6×His tag, six XV-conotoxins were successfully expressed in Escherichia coli and purified. Different framework XV conotoxins have distinct biological activities on mice and frogs, and that may be related to the diversity of the toxin sequences. All the six XV-conotoxins had no obvious effects on the sodium currents of DRG neuron cells of Sprague-Dawley (SD) rats. The identification of this framework of conotoxins enriches our understanding of the structural and functional diversity of conotoxin.
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Affiliation(s)
- Yun Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Maojun Zhou
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Xiuhua Jiang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Xiaoyan Zhu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Shaonan Luo
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yuwen You
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenghua Ren
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, National Engineering Research Center of South China Sea Marine Biotechnology, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China; Beijing University of Chinese Medicine, 11 Dong Shan Huan Road, Beijing 100029, People's Republic of China.
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Zamora-Bustillos R, Rivera-Reyes R, Aguilar MB, Michel-Morfín E, Landa-Jaime V, Falcón A, Heimer EP. Identification, by RT-PCR, of eight novel I₂-conotoxins from the worm-hunting cone snails Conus brunneus, Conus nux, and Conus princeps from the eastern Pacific (Mexico). Peptides 2014; 53:22-9. [PMID: 24486530 DOI: 10.1016/j.peptides.2014.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Marine snails of the genus Conus (∼500 species) are tropical predators that produce venoms for capturing prey, defense and competitive interactions. These venoms contain 50-200 different peptides ("conotoxins") that generally comprise 7-40 amino acid residues (including 0-5 disulfide bridges), and that frequently contain diverse posttranslational modifications, some of which have been demonstrated to be important for folding, stability, and biological activity. Most conotoxins affect voltage- and ligand-gated ion channels, G protein-coupled receptors, and neurotransmitter transporters, generally with high affinity and specificity. Due to these features, several conotoxins are used as molecular tools, diagnostic agents, medicines, and models for drug design. Based on the signal sequence of their precursors, conotoxins have been classified into genetic superfamilies, whereas their molecular targets allow them to be classified into pharmacological families. The objective of this work was to identify and analyze partial cDNAs encoding precursors of conotoxins belonging to I superfamily from three vermivorous species of the Mexican Pacific coast: C. brunneus, C. nux and C. princeps. The precursors identified contain diverse numbers of amino acid residues (C. brunneus, 65 or 71; C. nux, 70; C. princeps, 72 or 73), and all include a highly conserved signal peptide, a C-terminal propeptide, and a mature toxin. All the latter have one of the typical Cys frameworks of the I-conotoxins (C-C-CC-CC-C-C). The prepropeptides belong to the I2-superfamily, and encode eight different hydrophilic and acidic mature toxins, rather similar among them, and some of which have similarity with I2-conotoxins targeting voltage- and voltage-and-calcium-gated potassium channels.
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Affiliation(s)
- R Zamora-Bustillos
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro 76230, Mexico; Laboratorio de Genética Molecular, Instituto Tecnológico de Conkal, Conkal, Yucatán 97345, Mexico
| | - R Rivera-Reyes
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro 76230, Mexico
| | - M B Aguilar
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro 76230, Mexico.
| | - E Michel-Morfín
- Departamento de Estudios para el Desarrollo Sustentable de Zonas Costeras. CUCSUR-Universidad de Guadalajara, San Patricio-Melaque, Jalisco 48980, Mexico
| | - V Landa-Jaime
- Departamento de Estudios para el Desarrollo Sustentable de Zonas Costeras. CUCSUR-Universidad de Guadalajara, San Patricio-Melaque, Jalisco 48980, Mexico; Posgrado en Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Nayarit, Mexico
| | - A Falcón
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro 76230, Mexico
| | - E P Heimer
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus UNAM Juriquilla, Querétaro 76230, Mexico
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Robinson SD, Safavi-Hemami H, McIntosh LD, Purcell AW, Norton RS, Papenfuss AT. Diversity of conotoxin gene superfamilies in the venomous snail, Conus victoriae. PLoS One 2014; 9:e87648. [PMID: 24505301 PMCID: PMC3914837 DOI: 10.1371/journal.pone.0087648] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/28/2013] [Indexed: 12/31/2022] Open
Abstract
Animal venoms represent a vast library of bioactive peptides and proteins with proven potential, not only as research tools but also as drug leads and therapeutics. This is illustrated clearly by marine cone snails (genus Conus), whose venoms consist of mixtures of hundreds of peptides (conotoxins) with a diverse array of molecular targets, including voltage- and ligand-gated ion channels, G-protein coupled receptors and neurotransmitter transporters. Several conotoxins have found applications as research tools, with some being used or developed as therapeutics. The primary objective of this study was the large-scale discovery of conotoxin sequences from the venom gland of an Australian cone snail species, Conus victoriae. Using cDNA library normalization, high-throughput 454 sequencing, de novo transcriptome assembly and annotation with BLASTX and profile hidden Markov models, we discovered over 100 unique conotoxin sequences from 20 gene superfamilies, the highest diversity of conotoxins so far reported in a single study. Many of the sequences identified are new members of known conotoxin superfamilies, some help to redefine these superfamilies and others represent altogether new classes of conotoxins. In addition, we have demonstrated an efficient combination of methods to mine an animal venom gland and generate a library of sequences encoding bioactive peptides.
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Affiliation(s)
- Samuel D. Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- * E-mail: (SDR); (HSH)
| | - Helena Safavi-Hemami
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- * E-mail: (SDR); (HSH)
| | - Lachlan D. McIntosh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
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Aguilar MB, Ortiz E, Kaas Q, López-Vera E, Becerril B, Possani LD, de la Cotera EPH. Precursor De13.1 from Conus delessertii defines the novel G gene superfamily. Peptides 2013; 41:17-20. [PMID: 23340018 DOI: 10.1016/j.peptides.2013.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/10/2013] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
Abstract
Peptide de13a was previously purified from the venom of the worm-hunting cone snail Conus delessertii from the Yucatán Channel, México. This peptide has eight cysteine (Cys) residues in the unique arrangement C-C-C-CC-C-C-C, which defines the cysteine framework XIII ("-" represents one or more non-Cys residues). Remarkably, δ-hydroxy-lysine residues have been found only in conotoxin de13a, which also contains an unusually high proportion of hydroxylated amino acid residues. Here, we report the cDNA cloning of the complete precursor De13.1 of a related peptide, de13b, which has the same Cys framework and inter-Cys spacings as peptide de13a, and shares high protein/nucleic acid sequence identity (87%/90%) with de13a, suggesting that both peptides belong to the same conotoxin gene superfamily. Analysis of the signal peptide of precursor De13.1 reveals that this precursor belongs to a novel conotoxin gene superfamily that we chose to name gene superfamily G. Thus far superfamily G only includes two peptides, each of which contains the same, distinctive Cys framework and a high proportion of amino acid residues with hydroxylated side chains.
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Affiliation(s)
- Manuel B Aguilar
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro 76230, Mexico.
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Olivera BM, Watkins M, Bandyopadhyay P, Imperial JS, de la Cotera EPH, Aguilar MB, Vera EL, Concepcion GP, Lluisma A. Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes. Ann N Y Acad Sci 2012; 1267:61-70. [PMID: 22954218 PMCID: PMC3488454 DOI: 10.1111/j.1749-6632.2012.06603.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An impressive biodiversity (>10,000 species) of marine snails (suborder Toxoglossa or superfamily Conoidea) have complex venoms, each containing approximately 100 biologically active, disulfide-rich peptides. In the genus Conus, the most intensively investigated toxoglossan lineage (∼500 species), a small set of venom gene superfamilies undergo rapid sequence hyperdiversification within their mature toxin regions. Each major lineage of Toxoglossa has its own distinct set of venom gene superfamilies. Two recently identified venom gene superfamilies are expressed in the large Turridae clade, but not in Conus. Thus, as major venomous molluscan clades expand, a small set of lineage-specific venom gene superfamilies undergo accelerated evolution. The juxtaposition of extremely conserved signal sequences with hypervariable mature peptide regions is unprecedented and raises the possibility that in these gene superfamilies, the signal sequences are conserved as a result of an essential role they play in enabling rapid sequence evolution of the region of the gene that encodes the active toxin.
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Abstract
ConoServer (http://www.conoserver.org) is a database specializing in the sequences and structures of conopeptides, which are toxins expressed by marine cone snails. Cone snails are carnivorous gastropods, which hunt their prey using a cocktail of toxins that potently subvert nervous system function. The ability of these toxins to specifically target receptors, channels and transporters of the nervous system has attracted considerable interest for their use in physiological research and as drug leads. Since the founding publication on ConoServer in 2008, the number of entries in the database has nearly doubled, the interface has been redesigned and new annotations have been added, including a more detailed description of cone snail species, biological activity measurements and information regarding the identification of each sequence. Automatically updated statistics on classification schemes, three-dimensional structures, conopeptide-bearing species and endoplasmic reticulum signal sequence conservation trends, provide a convenient overview of current knowledge on conopeptides. Transcriptomics and proteomics have began generating massive numbers of new conopeptide sequences, and two dedicated tools have been recently implemented in ConoServer to standardize the analysis of conopeptide precursor sequences and to help in the identification by mass spectrometry of toxins whose sequences were predicted at the nucleic acid level.
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Affiliation(s)
| | | | | | | | - David J. Craik
- *To whom correspondence should be addressed. Tel: +61 7 3346 2019; Fax: +61 7 3346 2101;
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Ye M, Hong J, Zhou M, Huang L, Shao X, Yang Y, Sigworth FJ, Chi C, Lin D, Wang C. A novel conotoxin, qc16a, with a unique cysteine framework and folding. Peptides 2011; 32:1159-65. [PMID: 21524672 PMCID: PMC3547678 DOI: 10.1016/j.peptides.2011.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/08/2011] [Accepted: 04/09/2011] [Indexed: 10/18/2022]
Abstract
A novel conotoxin, qc16a, was identified from the venom of vermivorous Conus quercinus. qc16a has only 11 amino acid residues, DCQPCGHNVCC, with a unique cysteine pattern. Its disulfide connectivity was determined to be I-IV, II-III. The NMR structure shows that qc16a adopts a ribbon conformation with a simple beta-turn motif formed by residues Gly6, His7 and Asn8. qc16a causes depression symptom in mice when injected intracranially. Point mutation results showed that Asp1, His7 and Asn8 are all essential for the activity of qc16a. Electrophysiologically, qc16a has no strong effect on the whole-cell currents of neurons and the currents of Drosophila Shaker channels, human BK channels and Na(V)1.7 channels. Its specific target still remains to be identified.
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Affiliation(s)
- Mingyu Ye
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jing Hong
- College of Biological Science and Technology, Fuzhou University, Fuzhou 350108, China
| | - Mi Zhou
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lijun Huang
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiaoxia Shao
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Youshan Yang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Fred J. Sigworth
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chengwu Chi
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Donghai Lin
- The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- To whom correspondence should be addressed: Chunguang Wang, Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China, Tel: 86-21-65984347, Fax: 86-21-65988403; ; or Donghai Lin, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, Tel: 86-592-2186078, Fax: 86-592-2186078;
| | - Chunguang Wang
- Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China
- To whom correspondence should be addressed: Chunguang Wang, Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China, Tel: 86-21-65984347, Fax: 86-21-65988403; ; or Donghai Lin, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, Tel: 86-592-2186078, Fax: 86-592-2186078;
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39
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Peng C, Chen W, Sanders T, Chew G, Liu J, Hawrot E, Chi C. Chemical synthesis and characterization of two α4/7-conotoxins. Acta Biochim Biophys Sin (Shanghai) 2010; 42:745-53. [PMID: 20801929 DOI: 10.1093/abbs/gmq074] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
α-Conotoxins are small disulfide-constrained peptides that act as potent and selective antagonists on specific subtypes of nicotinic acetylcholine receptors (nAChRs). We previously cloned two α-conotoxins, Mr1.1 from the molluscivorous Conus marmoreus and Lp1.4 from the vermivorous Conus leopardus. Both of them have the typical 4/7-type framework of the subfamily of α-conotoxins that act on neuronal nAChRs. In this work, we chemically synthesized these two toxins and characterized their functional properties. The synthetic Mr1.1 could primarily inhibit acetylcholine (ACh)-evoked currents reversibly in the oocyte-expressed rat α7 nAChR, whereas Lp1.4 was an unexpected specific blocker of the mouse fetal muscle α1β1γδ receptor. Although their inhibition affinities were relatively low, their unique receptor recognition profiles make them valuable tools for toxin-receptor interaction studies. Mr1.1 could also suppress the inflammatory response to pain in vivo, suggesting that it should be further investigated with respect to its molecular role in analgesia and its mechanism or therapeutic target for the treatment of pain.
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Affiliation(s)
- Can Peng
- Institute of Protein Research, Tongji University, Shanghai, China
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40
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Liu Z, Yu Z, Liu N, Zhao C, Hu J, Dai Q. cDNA cloning of conotoxins with framework XII from several Conus species. Acta Biochim Biophys Sin (Shanghai) 2010; 42:656-61. [PMID: 20732855 DOI: 10.1093/abbs/gmq066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In our efforts for cloning novel I(2)-superfamily conotoxins using the signal peptide sequence, we identified a novel conotoxin Lt12.4 from Conus litteratus. This gene has a framework XII (-C-C-C-C-CC-C-C-), which is distinct from the cysteine pattern I(2)-superfamily conotoxin (-C-C-CC-CC-C-C-). Subsequently, we found the signal peptide sequence of Lt12.4 by 5'-RACE. Using this new sequence, we identified another five novel conotoxins with this cysteine pattern from four Conus species (Conus eburneus, Conus imperialis, Conus marmoreus, and C. litteratus). These novel conotoxins have the same cysteine pattern as the reported Gla-TxX and Gla-MII, and may contain Gla residues. Furthermore, they have the highly conserved signal peptide and hypervariable mature peptide sequences, and widely exist in Conus species. Therefore, it could be defined as a new superfamily of E-conotoxins.
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Affiliation(s)
- Zhuguo Liu
- Beijing Institute of Biotechnology, China
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41
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Armishaw CJ. Synthetic α-conotoxin mutants as probes for studying nicotinic acetylcholine receptors and in the development of novel drug leads. Toxins (Basel) 2010; 2:1471-99. [PMID: 22069647 PMCID: PMC3153239 DOI: 10.3390/toxins2061471] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/27/2010] [Accepted: 06/11/2010] [Indexed: 11/19/2022] Open
Abstract
α-Conotoxins are peptide neurotoxins isolated from venomous marine cone snails that are potent and selective antagonists for different subtypes of nicotinic acetylcholine receptors (nAChRs). As such, they are valuable probes for dissecting the role that nAChRs play in nervous system function. In recent years, extensive insight into the binding mechanisms of α-conotoxins with nAChRs at the molecular level has aided in the design of synthetic analogs with improved pharmacological properties. This review examines the structure-activity relationship studies involving α-conotoxins as research tools for studying nAChRs in the central and peripheral nervous systems and their use towards the development of novel therapeutics.
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Affiliation(s)
- Christopher J Armishaw
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St Lucie, FL 34987, USA.
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42
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Safavi-Hemami H, Bulaj G, Olivera BM, Williamson NA, Purcell AW. Identification of Conus peptidylprolyl cis-trans isomerases (PPIases) and assessment of their role in the oxidative folding of conotoxins. J Biol Chem 2010; 285:12735-46. [PMID: 20147296 PMCID: PMC2857115 DOI: 10.1074/jbc.m109.078691] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 02/09/2010] [Indexed: 11/06/2022] Open
Abstract
Peptidylprolyl cis-trans isomerases (PPIases) are ubiquitous proteins that catalyze the cis-trans isomerization of prolines. A number of proteins, such as Drosophila rhodopsin and the human immunodeficiency viral protein HIV-1 Gag, have been identified as endogenous substrates for PPIases. However, very little is known about the interaction of PPIases with small, disulfide-rich peptides. Marine cone snails synthesize a wide array of cysteine-rich peptides, called conotoxins, many of which contain one or more prolines or hydroxyprolines. To identify whether PPIase-associated cis-trans isomerization of these residues affects the oxidative folding of conotoxins, we identified, sequenced, and expressed three functionally active isoforms of PPIase from the venom gland of Conus novaehollandiae, and we characterized their ability to facilitate oxidative folding of conotoxins in vitro. Three conotoxins, namely mu-GIIIA, mu-SIIIA, and omega-MVIIC, derived from two distinct toxin gene families were assayed. Conus PPIase significantly increased the rate of appearance of the native form of mu-GIIIA, a peptide containing three hydroxyprolines. In contrast, the presence of PPIase had no effect on the folding of mu-SIIIA and omega-MVIIC, peptides containing no or one proline residue, respectively. We further showed that an endoplasmic reticulum-resident PPIase isoform facilitated folding of mu-GIIIA more efficiently than two cytosolic isoforms. This is the first study to demonstrate PPIase-assisted folding of conotoxins, small disulfide-rich peptides with unique structural properties.
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Affiliation(s)
- Helena Safavi-Hemami
- From the
Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3010 Victoria, Australia and
| | | | | | - Nicholas A. Williamson
- From the
Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3010 Victoria, Australia and
| | - Anthony W. Purcell
- From the
Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3010 Victoria, Australia and
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Zamora-Bustillos R, Aguilar MB, Falcón A. Identification, by molecular cloning, of a novel type of I2-superfamily conotoxin precursor and two novel I2-conotoxins from the worm-hunter snail Conus spurius from the Gulf of México. Peptides 2010; 31:384-93. [PMID: 19836429 DOI: 10.1016/j.peptides.2009.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/03/2009] [Accepted: 10/06/2009] [Indexed: 11/24/2022]
Abstract
cDNA was prepared from the venom duct of a single Conus spurius specimen collected near the coast of Campeche, México. From it, PCR products were generated aiming to clone I-conotoxin precursors. Thirty clones were sequenced and predicted to encode ten distinct precursors: seven of I(2)-conotoxins and three of I(2)-like-conotoxins. These precursors contain three different, mature toxins, sr11a, sr11b and sr11c, of which two are novel and one (sr11a) has been previously purified and characterized from the venom of this species. The precursors include a 26- (I(2)) or 23- residue signal peptide (I(2)-like), a 31-residue "pro" region (I(2)-like), and a 32-residue mature toxin region (I(2) and I(2)-like). In addition, all the precursors have a 13-residue "post" region which contains a gamma-carboxylation recognition sequence that directs the gamma-carboxylation of Glu-9 and Glu-10 of toxin sr11a and, possibly, Glu-13 of toxin sr11b and Glu-9 of toxin sr11c. This is the first time that a "post" region has been found in precursors of I-conotoxins that also contain a "pro" region. The "post" peptide is enzymatically processed to yield the amidated mature toxin sr11a, which implies that gamma-carboxylation occurs before amidation. Phylogenetic analysis at the whole precursor level indicates that the I(2)-like-conotoxins of C. spurius are more related to I(2)-conotoxins than to I(1)- and I(3)-conotoxins from other species, and that they might represent a new subgroup of the I(2)-superfamily. The three I-conotoxins from C. spurius have charge differences at seven to nine positions, suggesting that they might have different molecular target types or subtypes.
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Affiliation(s)
- Roberto Zamora-Bustillos
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro 76230, Mexico
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44
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Puillandre N, Watkins M, Olivera BM. Evolution of Conus peptide genes: duplication and positive selection in the A-superfamily. J Mol Evol 2010; 70:190-202. [PMID: 20143226 DOI: 10.1007/s00239-010-9321-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 01/08/2010] [Indexed: 02/03/2023]
Abstract
A remarkable diversity of venom peptides is expressed in the genus Conus (known as "conotoxins" or "conopeptides"). Between 50 and 200 different venom peptides can be found in a single Conus species, each having its own complement of peptides. Conopeptides are encoded by a few gene superfamilies; here we analyze the evolution of the A-superfamily in a fish-hunting species clade, Pionoconus. More than 90 conopeptide sequences from 11 different Conus species were used to build a phylogenetic tree. Comparison with a species tree based on standard genes reveals multiple gene duplication events, some of which took place before the Pionoconus radiation. By analysing several A-conopeptides from other Conus species recorded in GenBank, we date the major duplication events after the divergence between fish-hunting and non-fish-hunting species. Furthermore, likelihood approaches revealed strong positive selection; the magnitude depends on which A-conopeptide lineage and amino-acid locus is analyzed. The four major A-conopeptide clades defined are consistent with the current division of the superfamily into families and subfamilies based on the Cys pattern. The function of three of these clades (the κA-family, the α4/7-subfamily, and α3/5-subfamily) has previously been characterized. The function of the remaining clade, corresponding to the α4/4-subfamily, has not been elucidated. This subfamily is also found in several other fish-hunting species clades within Conus. The analysis revealed a surprisingly diverse origin of α4/4 conopeptides from a single species, Conus bullatus. This phylogenetic approach that defines different genetic lineages of Conus venom peptides provides a guidepost for identifying conopeptides with potentially novel functions.
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Affiliation(s)
- Nicolas Puillandre
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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45
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Zhang L, Shao X, Chi C, Wang C. Two short D-Phe-containing cysteine-free conopeptides from Conus marmoreus. Peptides 2010; 31:177-9. [PMID: 19879909 DOI: 10.1016/j.peptides.2009.10.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 10/18/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
The cysteine-free conopeptides are naturally occurring components of the venom of cone snails and have been relatively less investigated than the cysteine-containing conopeptides. In this work, we used thiol-exchange chromatography to isolate cysteine-free conopeptides from the venom of Conus marmoreus. The full-length previously reported conomarphin and two novel shortened forms of it were found in the cysteine-free conopeptide fraction. The two shortened conomarphins also contain a D-Phe and a hydroxylated proline residue, suggesting complex post-translational modifications of these conopeptides. In particular, the shorter conomarphin fragment shares significant sequence similarity with conophans. This work demonstrated that thiol-exchange chromatography is a useful approach to isolate cysteine-free conopeptides from venom cocktail. The newly identified conopeptides further revealed the complexity of post-translational processing and the high diversity of conotoxins.
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Affiliation(s)
- Ling Zhang
- Institute of Protein Research, Tongji University, Shanghai, China
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46
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Peng C, Chen W, Han Y, Sanders T, Chew G, Liu J, Hawrot E, Chi C, Wang C. Characterization of a novel alpha4/4-conotoxin, Qc1.2, from vermivorous Conus quercinus. Acta Biochim Biophys Sin (Shanghai) 2009; 41:858-64. [PMID: 19779652 DOI: 10.1093/abbs/gmp077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As part of continuing studies of the identification of gene organization and cloning of novel alpha-conotoxins, the first alpha4/4-conotoxin identified in a vermivorous Conus species, designated Qc1.2, was originally obtained by cDNA and genomic DNA cloning from Conus quercinus collected in the South China Sea. The predicted mature toxin of Qc1.2 contains 14 amino acid residues with two disulfide bonds (I-III, II-IV connectivity) in a native globular configuration. The mature peptide of Qc1.2 is supposed to contain an N-terminal post-translationally processed pyroglutamate residue and a free carboxyl C-terminus. This peptide was chemically synthesized and refolded for further characterization of its functional properties. The synthetic Qc1.2 has two interconvertible conformations in aqueous solution, which may be due to the cis-trans isomerization of the two successive Pro residues in its first Cys loop. Using the Xenopus oocyte heterologous expression system, Qc1.2 was shown to selectively inhibit both rat neuronal alpha3beta2 and alpha3beta4 subtypes of nicotinic acetylcholine receptors with low potency. A block of about 63% and 37% of the ACh-evoked currents was observed, respectively, and the toxin dissociated rapidly from the receptors. Compared with other characterized alpha-conotoxin members, the unusual structural features in Qc1.2 that confer to its receptor recognition profile are addressed.
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Affiliation(s)
- Can Peng
- Institute of Protein Research, Tongji University, Shanghai, China
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47
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Liu Z, Xu N, Hu J, Zhao C, Yu Z, Dai Q. Identification of novel I-superfamily conopeptides from several clades of Conus species found in the South China Sea. Peptides 2009; 30:1782-7. [PMID: 19595726 DOI: 10.1016/j.peptides.2009.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 06/26/2009] [Accepted: 06/26/2009] [Indexed: 11/20/2022]
Abstract
The I-superfamily of Conus peptides represents a new class of peptides with four disulfide bridges (-C-C-CC-CC-C-C-) that falls into three (I1, I2 and I3) categories according to the different signal peptide sequences. The I-superfamily has received increasing attention because it targets K+ ion channels, a function that is relatively rare in conotoxins. Herein we report 11 novel I-superfamily conotoxins from the venom ducts of five Cone snails (Conus eburneus, Conus imperialis, Conus vitulinus, Conus emaciatus and Conus litteratus) native to the South China Sea using a primer designed according to the N-terminus of the signal sequence of I2-superfamily conotoxins. The alignment of sequences revealed that signal regions exhibited moderate conservation with the exception of Eb11.3 from C. eburneus with homologies of 21.1%, 38.5% and 30.0% to the signal peptides of I1, I2 and I3 superfamily conotoxins, respectively. The mature peptides ranged from almost identical to highly divergent between species. Analyses of the evolutionary trees of these peptides with those of reported I-superfamily conotoxins showed that nine of them fall in I2 superfamily clades, but two of them were neither I1- and I2- nor I3-superfamily clades. Notably, some peptides exhibited significantly different amino acid residues in the intercysteine loops compared with group A, B and C of I-superfamily conopeptides, suggesting that they may have different bioactivities and functions.
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Affiliation(s)
- Zhuguo Liu
- Beijing Institute of Biotechnology, Beijing 100071, People's Republic of China
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48
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Zamora-Bustillos R, Aguilar MB, Falcón A, Heimer de la Cotera EP. Identification, by RT-PCR, of four novel T-1-superfamily conotoxins from the vermivorous snail Conus spurius from the Gulf of Mexico. Peptides 2009; 30:1396-404. [PMID: 19447151 DOI: 10.1016/j.peptides.2009.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 05/05/2009] [Accepted: 05/05/2009] [Indexed: 11/27/2022]
Abstract
cDNA was prepared from the venom duct of a single Conus spurius specimen collected near the coast of Campeche, Mexico. From it, PCR products were generated, sequenced, and predicted to encode eight distinct precursors of T-1-conotoxins. These precursors contain five different mature toxins, of which four are novel and one (sr5a) has been previously purified and characterized from the venom of this species. Three of the novel toxins are very similar to sr5a: two have one amino acid substitution at position 8, whereas the other is predicted to have one additional residue at the C-terminus; the fourth toxin has five amino acid substitutions and is predicted to have two additional residues at the C-terminus. In general, the precursors include a 22-residue signal peptide, a 24-residue "pro" region, and a 13- to 16-residue mature toxin region; however, the C-termini of two mature toxin regions are predicted to be altered by post-translational processing. Three precursors lack, in the same positions, 15 amino acid residues included in the "pre" (one residue) and "pro" (14 residues) regions, which suggests the existence of an exon encoding the last signal peptide residue and the first 14 residues of the "pro" region. Phylogenetic analysis indicates that the T-1-conotoxin precursors and mature toxins of C. spurius are more similar to certain precursors and toxins from molluscivorous Conus species than to any precursors and toxins from vermivorous cones. The results reported here will be useful for synthesizing the novel toxins in order to identify their molecular targets.
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Affiliation(s)
- Roberto Zamora-Bustillos
- Laboratorio de Neurofarmacología Marina, Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro 76230, Mexico
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Abstract
We purified two novel conotoxins, designated as ca11a and ca11b, from the venom of Conus caracteristicus. Based on the amino acid sequence of mature ca11a, we cloned its full-length cDNA. Based on the signal peptide of ca11a, several ca11a-like conotoxins were cloned from C. caracteristicus and C. pulicarius. These novel conotoxins have an I-superfamily cysteine pattern but with a novel signal peptide sequence, suggesting they belong to a new branch of I-superfamily, designated as I(3)-superfamily. Additionally, two O-superfamily conotoxins were also cloned based on the signal peptide of ca11a, suggesting a possible evolutionary relationship between O- and I-superfamilies.
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Affiliation(s)
- Duo-Duo Yuan
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai, PR China
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Armishaw C, Jensen AA, Balle T, Clark RJ, Harpsøe K, Skonberg C, Liljefors T, Strømgaard K. Rational design of alpha-conotoxin analogues targeting alpha7 nicotinic acetylcholine receptors: improved antagonistic activity by incorporation of proline derivatives. J Biol Chem 2009; 284:9498-512. [PMID: 19131337 PMCID: PMC2666602 DOI: 10.1074/jbc.m806136200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 01/07/2009] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that belong to the superfamily of Cys loop receptors. Valuable insight into the orthosteric ligand binding to nAChRs in recent years has been obtained from the crystal structures of acetylcholine-binding proteins (AChBPs) that share significant sequence homology with the amino-terminal domains of the nAChRs. alpha-Conotoxins, which are isolated from the venom of carnivorous marine snails, selectively inhibit the signaling of neuronal nAChR subtypes. Co-crystal structures of alpha-conotoxins in complex with AChBP show that the side chain of a highly conserved proline residue in these toxins is oriented toward the hydrophobic binding pocket in the AChBP but does not have direct interactions with this pocket. In this study, we have designed and synthesized analogues of alpha-conotoxins ImI and PnIA[A10L], by introducing a range of substituents on the Pro(6) residue in these toxins to probe the importance of this residue for their binding to the nAChRs. Pharmacological characterization of the toxin analogues at the alpha(7) nAChR shows that although polar and charged groups on Pro(6) result in analogues with significantly reduced antagonistic activities, analogues with aromatic and hydrophobic substituents in the Pro(6) position exhibit moderate activity at the receptor. Interestingly, introduction of a 5-(R)-phenyl substituent at Pro(6) in alpha-conotoxin ImI gives rise to a conotoxin analogue with a significantly higher binding affinity and antagonistic activity at the alpha(7) nAChR than those exhibited by the native conotoxin.
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Affiliation(s)
- Christopher Armishaw
- Department of Medicinal Chemistry and Pharmaceutics and Analytical Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen Ø DK-2100, Denmark
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