1
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Gopalan SS, Perry BW, Francioli YZ, Schield DR, Guss HD, Bernstein JM, Ballard K, Smith CF, Saviola AJ, Adams RH, Mackessy SP, Castoe TA. Diverse Gene Regulatory Mechanisms Alter Rattlesnake Venom Gene Expression at Fine Evolutionary Scales. Genome Biol Evol 2024; 16:evae110. [PMID: 38753011 PMCID: PMC11243404 DOI: 10.1093/gbe/evae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.
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Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yannick Z Francioli
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Hannah D Guss
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Justin M Bernstein
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kaas Ballard
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas Agricultural Experimental Station, University of Arkansas, Fayetteville, AR 72701, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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2
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Schendel V, Müller CHG, Kenning M, Maxwell M, Jenner RA, Undheim EAB, Sombke A. The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues. BMC Biol 2024; 22:135. [PMID: 38867210 PMCID: PMC11170834 DOI: 10.1186/s12915-024-01925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Evolution of novelty is a central theme in evolutionary biology, yet studying the origins of traits with an apparently discontinuous origin remains a major challenge. Venom systems are a well-suited model for the study of this phenomenon because they capture several aspects of novelty across multiple levels of biological complexity. However, while there is some knowledge on the evolution of individual toxins, not much is known about the evolution of venom systems as a whole. One way of shedding light on the evolution of new traits is to investigate less specialised serial homologues, i.e. repeated traits in an organism that share a developmental origin. This approach can be particularly informative in animals with repetitive body segments, such as centipedes. RESULTS Here, we investigate morphological and biochemical aspects of the defensive telopodal glandular organs borne on the posterior legs of venomous stone centipedes (Lithobiomorpha), using a multimethod approach, including behavioural observations, comparative morphology, proteomics, comparative transcriptomics and molecular phylogenetics. We show that the anterior venom system and posterior telopodal defence system are functionally convergent serial homologues, where one (telopodal defence) represents a model for the putative early evolutionary state of the other (venom). Venom glands and telopodal glandular organs appear to have evolved from the same type of epidermal gland (four-cell recto-canal type) and while the telopodal defensive secretion shares a great degree of compositional overlap with centipede venoms in general, these similarities arose predominantly through convergent recruitment of distantly related toxin-like components. Both systems are composed of elements predisposed to functional innovation across levels of biological complexity that range from proteins to glands, demonstrating clear parallels between molecular and morphological traits in the properties that facilitate the evolution of novelty. CONCLUSIONS The evolution of the lithobiomorph telopodal defence system provides indirect empirical support for the plausibility of the hypothesised evolutionary origin of the centipede venom system, which occurred through functional innovation and gradual specialisation of existing epidermal glands. Our results thus exemplify how continuous transformation and functional innovation can drive the apparent discontinuous emergence of novelties on higher levels of biological complexity.
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Affiliation(s)
- Vanessa Schendel
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Carsten H G Müller
- Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, Greifswald, 17489, Germany
| | - Matthes Kenning
- Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, Greifswald, 17489, Germany
| | - Michael Maxwell
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | | | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, 0316, Norway.
| | - Andy Sombke
- Centre for Anatomy and Cell Biology, Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, 1090, Austria.
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Austria.
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3
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Smith CF, Modahl CM, Ceja Galindo D, Larson KY, Maroney SP, Bahrabadi L, Brandehoff NP, Perry BW, McCabe MC, Petras D, Lomonte B, Calvete JJ, Castoe TA, Mackessy SP, Hansen KC, Saviola AJ. Assessing Target Specificity of the Small Molecule Inhibitor MARIMASTAT to Snake Venom Toxins: A Novel Application of Thermal Proteome Profiling. Mol Cell Proteomics 2024; 23:100779. [PMID: 38679388 PMCID: PMC11154231 DOI: 10.1016/j.mcpro.2024.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024] Open
Abstract
New treatments that circumvent the pitfalls of traditional antivenom therapies are critical to address the problem of snakebite globally. Numerous snake venom toxin inhibitors have shown promising cross-species neutralization of medically significant venom toxins in vivo and in vitro. The development of high-throughput approaches for the screening of such inhibitors could accelerate their identification, testing, and implementation and thus holds exciting potential for improving the treatments and outcomes of snakebite envenomation worldwide. Energetics-based proteomic approaches, including thermal proteome profiling and proteome integral solubility alteration (PISA) assays, represent "deep proteomics" methods for high throughput, proteome-wide identification of drug targets and ligands. In the following study, we apply thermal proteome profiling and PISA methods to characterize the interactions between venom toxin proteoforms in Crotalus atrox (Western Diamondback Rattlesnake) and the snake venom metalloprotease (SVMP) inhibitor marimastat. We investigate its venom proteome-wide effects and characterize its interactions with specific SVMP proteoforms, as well as its potential targeting of non-SVMP venom toxin families. We also compare the performance of PISA thermal window and soluble supernatant with insoluble precipitate using two inhibitor concentrations, providing the first demonstration of the utility of a sensitive high-throughput PISA-based approach to assess the direct targets of small molecule inhibitors for snake venom.
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Affiliation(s)
- Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Cassandra M Modahl
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David Ceja Galindo
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Sean P Maroney
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Lilyrose Bahrabadi
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Nicklaus P Brandehoff
- Rocky Mountain Poison and Drug Center, Denver Health and Hospital Authority, Denver, Colorado, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Daniel Petras
- CMFI Cluster of Excellence, University of Tuebingen, Tuebingen, Germany; Department of Biochemistry, University of California Riverside, Riverside, California, USA
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Texas, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA.
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4
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Surm JM, Landau M, Columbus-Shenkar YY, Moran Y. Sea Anemone Membrane Attack Complex/Perforin Superfamily Demonstrates an Evolutionary Transitional State between Venomous and Developmental Functions. Mol Biol Evol 2024; 41:msae082. [PMID: 38676945 PMCID: PMC11090067 DOI: 10.1093/molbev/msae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Gene duplication is a major force driving evolutionary innovation. A classic example is generating new animal toxins via duplication of physiological protein-encoding genes and recruitment into venom. While this process drives the innovation of many animal venoms, reverse recruitment of toxins into nonvenomous cells remains unresolved. Using comparative genomics, we find members of the Membrane Attack Complex and Perforin Family (MAC) have been recruited into venom-injecting cells (cnidocytes), in soft and stony corals and sea anemones, suggesting that the ancestral MAC was a cnidocyte expressed toxin. Further investigation into the model sea anemone Nematostella vectensis reveals that three members have undergone Nematostella-specific duplications leading to their reverse recruitment into endomesodermal cells. Furthermore, simultaneous knockdown of all three endomesodermally expressed MACs leads to mis-development, supporting that these paralogs have nonvenomous function. By resolving the evolutionary history and function of MACs in Nematostella, we provide the first proof for reverse recruitment from venom to organismal development.
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Affiliation(s)
- Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Morani Landau
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yaara Y Columbus-Shenkar
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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5
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Clare RH, Dawson CA, Westhorpe A, Albulescu LO, Woodley CM, Mosallam N, Chong DJW, Kool J, Berry NG, O’Neill PM, Casewell NR. Snakebite drug discovery: high-throughput screening to identify novel snake venom metalloproteinase toxin inhibitors. Front Pharmacol 2024; 14:1328950. [PMID: 38273820 PMCID: PMC10808794 DOI: 10.3389/fphar.2023.1328950] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Snakebite envenoming results in ∼100,000 deaths per year, with close to four times as many victims left with life-long sequelae. Current antivenom therapies have several limitations including high cost, variable cross-snake species efficacy and a requirement for intravenous administration in a clinical setting. Next-generation snakebite therapies are being widely investigated with the aim to improve cost, efficacy, and safety. In recent years several small molecule drugs have shown considerable promise for snakebite indication, with oral bioavailability particularly promising for community delivery rapidly after a snakebite. However, only two such drugs have entered clinical development for snakebite. To offset the risk of attrition during clinical trials and to better explore the chemical space for small molecule venom toxin inhibitors, here we describe the first high throughput drug screen against snake venom metalloproteinases (SVMPs)-a pathogenic toxin family responsible for causing haemorrhage and coagulopathy. Following validation of a 384-well fluorescent enzymatic assay, we screened a repurposed drug library of 3,547 compounds against five geographically distinct and toxin variable snake venoms. Our drug screen resulted in the identification of 14 compounds with pan-species inhibitory activity. Following secondary potency testing, four SVMP inhibitors were identified with nanomolar EC50s comparable to the previously identified matrix metalloproteinase inhibitor marimastat and superior to the metal chelator dimercaprol, doubling the current global portfolio of SVMP inhibitors. Following analysis of their chemical structure and ADME properties, two hit-to-lead compounds were identified. These clear starting points for the initiation of medicinal chemistry campaigns provide the basis for the first ever designer snakebite specific small molecules.
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Affiliation(s)
- Rachel H. Clare
- Department of Tropical Disease Biology, Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Charlotte A. Dawson
- Department of Tropical Disease Biology, Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Adam Westhorpe
- Department of Tropical Disease Biology, Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Laura-Oana Albulescu
- Department of Tropical Disease Biology, Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Nada Mosallam
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - Daniel J. W. Chong
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas R. Casewell
- Department of Tropical Disease Biology, Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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6
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Davalos-Dehullu E, Baty SM, Fisher RN, Scott PA, Dolby GA, Munguia-Vega A, Cortez D. Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard. Genome Biol Evol 2023; 15:evad210. [PMID: 38056449 PMCID: PMC10699878 DOI: 10.1093/gbe/evad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127 Mb) representing macrochromosomes and 8 small scaffolds (63-22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.
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Affiliation(s)
- Elizabeth Davalos-Dehullu
- Centro de Ciencias Genómicas, Programa de Biología de Sistemas, UNAM, Cuernavaca, Morelos, Mexico
- Baja GeoGenomics Consortium
| | - Sarah M Baty
- Baja GeoGenomics Consortium
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, California, USA
| | - Peter A Scott
- Natural Sciences Collegium, Eckerd College, St Petersburg, Florida, USA
| | - Greer A Dolby
- Baja GeoGenomics Consortium
- Department of Biology, University of Alabama at Birmingham, Alabama USA
| | - Adrian Munguia-Vega
- Baja GeoGenomics Consortium
- Conservation Genetics Laboratory, The University of Arizona, Tucson, Arizona, USA
- Applied Genomics Lab, La Paz, Baja California Sur, Mexico
| | - Diego Cortez
- Centro de Ciencias Genómicas, Programa de Biología de Sistemas, UNAM, Cuernavaca, Morelos, Mexico
- Baja GeoGenomics Consortium
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7
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Koludarov I, Senoner T, Jackson TNW, Dashevsky D, Heinzinger M, Aird SD, Rost B. Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily. Nat Commun 2023; 14:4861. [PMID: 37567881 PMCID: PMC10421932 DOI: 10.1038/s41467-023-40550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.
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Affiliation(s)
- Ivan Koludarov
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany.
| | - Tobias Senoner
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel Dashevsky
- Australian National Insect Collection, Commonwealth Scientific & Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Heinzinger
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Steven D Aird
- 7744-23 Hotaka Ariake, 399-8301, Azumino-shi, Nagano-ken, Japan
| | - Burkhard Rost
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
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8
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Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, de la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Castañeda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium. J Mol Evol 2023; 91:514-535. [PMID: 37269364 PMCID: PMC10995822 DOI: 10.1007/s00239-023-10115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.
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Affiliation(s)
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Science Department, Cape Fear Community College, Wilmington, NC, 28401, USA
| | | | - Hector Franz-Chavez
- Herp.mx A.C., Colima, Mexico
- Biodiversa A. C., Chapala, Jalisco, 45900, Mexico
| | | | | | | | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Gamaliel Castañeda-Gaytan
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mahmood Sasa
- Centro Investigaciones en Biodiversidad y Ecología Tropical and Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA.
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9
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Westfall AK, Gopalan SS, Perry BW, Adams RH, Saviola AJ, Mackessy SP, Castoe TA. Single-Cell Heterogeneity in Snake Venom Expression Is Hardwired by Co-Option of Regulators from Progressively Activated Pathways. Genome Biol Evol 2023; 15:evad109. [PMID: 37311204 PMCID: PMC10289209 DOI: 10.1093/gbe/evad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
The ubiquitous cellular heterogeneity underlying many organism-level phenotypes raises questions about what factors drive this heterogeneity and how these complex heterogeneous systems evolve. Here, we use single-cell expression data from a Prairie rattlesnake (Crotalus viridis) venom gland to evaluate hypotheses for signaling networks underlying snake venom regulation and the degree to which different venom gene families have evolutionarily recruited distinct regulatory architectures. Our findings suggest that snake venom regulatory systems have evolutionarily co-opted trans-regulatory factors from extracellular signal-regulated kinase and unfolded protein response pathways that specifically coordinate expression of distinct venom toxins in a phased sequence across a single population of secretory cells. This pattern of co-option results in extensive cell-to-cell variation in venom gene expression, even between tandemly duplicated paralogs, suggesting this regulatory architecture has evolved to circumvent cellular constraints. While the exact nature of such constraints remains an open question, we propose that such regulatory heterogeneity may circumvent steric constraints on chromatin, cellular physiological constraints (e.g., endoplasmic reticulum stress or negative protein-protein interactions), or a combination of these. Regardless of the precise nature of these constraints, this example suggests that, in some cases, dynamic cellular constraints may impose previously unappreciated secondary constraints on the evolution of gene regulatory networks that favors heterogeneous expression.
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Affiliation(s)
| | | | - Blair W Perry
- Department of Biology, The University of Texas Arlington, Texas, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Texas, USA
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10
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Yee KT, Macrander J, Vasieva O, Rojnuckarin P. Exploring Toxin Genes of Myanmar Russell's Viper, Daboia siamensis, through De Novo Venom Gland Transcriptomics. Toxins (Basel) 2023; 15:toxins15050309. [PMID: 37235344 DOI: 10.3390/toxins15050309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The Russell's viper (Daboia siamensis) is a medically important venomous snake in Myanmar. Next-generation sequencing (NGS) shows potential to investigate the venom complexity, giving deeper insights into snakebite pathogenesis and possible drug discoveries. mRNA from venom gland tissue was extracted and sequenced on the Illumina HiSeq platform and de novo assembled by Trinity. The candidate toxin genes were identified via the Venomix pipeline. Protein sequences of identified toxin candidates were compared with the previously described venom proteins using Clustal Omega to assess the positional homology among candidates. Candidate venom transcripts were classified into 23 toxin gene families including 53 unique full-length transcripts. C-type lectins (CTLs) were the most highly expressed, followed by Kunitz-type serine protease inhibitors, disintegrins and Bradykinin potentiating peptide/C-type natriuretic peptide (BPP-CNP) precursors. Phospholipase A2, snake venom serine proteases, metalloproteinases, vascular endothelial growth factors, L-amino acid oxidases and cysteine-rich secretory proteins were under-represented within the transcriptomes. Several isoforms of transcripts which had not been previously reported in this species were discovered and described. Myanmar Russell's viper venom glands displayed unique sex-specific transcriptome profiles which were correlated with clinical manifestation of envenoming. Our results show that NGS is a useful tool to comprehensively examine understudied venomous snakes.
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Affiliation(s)
- Khin Than Yee
- Department of Medical Research, Ministry of Health, Yangon 11191, Myanmar
| | - Jason Macrander
- Department of Biology, Florida Southern College, Lakeland, FL 33801, USA
| | - Olga Vasieva
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- BioSynthetic Machines, Inc., Chicago, IL 60062, USA
| | - Ponlapat Rojnuckarin
- Excellence Center in Translational Hematology, Division of Hematology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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11
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Genomic, transcriptomic, and epigenomic analysis of a medicinal snake, Bungarus multicinctus, to provides insights into the origin of Elapidae neurotoxins. Acta Pharm Sin B 2022; 13:2234-2249. [DOI: 10.1016/j.apsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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12
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Schield DR, Perry BW, Adams RH, Holding ML, Nikolakis ZL, Gopalan SS, Smith CF, Parker JM, Meik JM, DeGiorgio M, Mackessy SP, Castoe TA. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nat Ecol Evol 2022; 6:1367-1380. [PMID: 35851850 PMCID: PMC9888523 DOI: 10.1038/s41559-022-01829-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/15/2022] [Indexed: 02/02/2023]
Abstract
The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | | | | | | | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Joshua M Parker
- Life Science Department, Fresno City College, Fresno, CA, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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13
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Perry BW, Gopalan SS, Pasquesi GIM, Schield DR, Westfall AK, Smith CF, Koludarov I, Chippindale PT, Pellegrino MW, Chuong EB, Mackessy SP, Castoe TA. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Res 2022; 32:1058-1073. [PMID: 35649579 PMCID: PMC9248877 DOI: 10.1101/gr.276251.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Understanding how regulatory mechanisms evolve is critical for understanding the processes that give rise to novel phenotypes. Snake venom systems represent a valuable and tractable model for testing hypotheses related to the evolution of novel regulatory networks, yet the regulatory mechanisms underlying venom production remain poorly understood. Here, we use functional genomics approaches to investigate venom regulatory architecture in the prairie rattlesnake and identify cis-regulatory sequences (enhancers and promoters), trans-regulatory transcription factors, and integrated signaling cascades involved in the regulation of snake venom genes. We find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity of transposable elements. Patterns of snake venom gene enhancer conservation, in some cases spanning 50 million yr of lineage divergence, highlight early origins and subsequent lineage-specific adaptations that have accompanied the evolution of venom regulatory architecture. We also identify features of chromatin structure involved in venom regulation, including topologically associated domains and CTCF loops that underscore the potential importance of novel chromatin structure to coevolve when duplicated genes evolve new regulatory control. Our findings provide a model for understanding how novel regulatory systems may evolve through a combination of genomic processes, including tandem duplication of genes and regulatory sequences, cis-regulatory sequence seeding by transposable elements, and diverse transcriptional regulatory proteins controlled by a co-opted regulatory cascade.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Ivan Koludarov
- Animal Venomics Group, Justus Liebig University, Giessen, 35390, Germany
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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14
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Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
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Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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15
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Rao WQ, Kalogeropoulos K, Allentoft ME, Gopalakrishnan S, Zhao WN, Workman CT, Knudsen C, Jiménez-Mena B, Seneci L, Mousavi-Derazmahalleh M, Jenkins TP, Rivera-de-Torre E, Liu SQ, Laustsen AH. The rise of genomics in snake venom research: recent advances and future perspectives. Gigascience 2022; 11:giac024. [PMID: 35365832 PMCID: PMC8975721 DOI: 10.1093/gigascience/giac024] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 12/12/2022] Open
Abstract
Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has matured rapidly over the past 2 decades, owing to the development of next-generation sequencing technologies, snake genomics remains in its infancy. Here, we provide an overview of the state of the art in snake genomics and discuss its potential implications for studying venom evolution and toxinology. On the basis of current knowledge, gene duplication and positive selection are key mechanisms in the neofunctionalization of snake venom proteins. This makes snake venoms important evolutionary drivers that explain the remarkable venom diversification and adaptive variation observed in these reptiles. Gene duplication and neofunctionalization have also generated a large number of repeat sequences in snake genomes that pose a significant challenge to DNA sequencing, resulting in the need for substantial computational resources and longer sequencing read length for high-quality genome assembly. Fortunately, owing to constantly improving sequencing technologies and computational tools, we are now able to explore the molecular mechanisms of snake venom evolution in unprecedented detail. Such novel insights have the potential to affect the design and development of antivenoms and possibly other drugs, as well as provide new fundamental knowledge on snake biology and evolution.
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Affiliation(s)
- Wei-qiao Rao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Konstantinos Kalogeropoulos
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Wei-ning Zhao
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Cecilie Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Belén Jiménez-Mena
- DTU Aqua, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Lorenzo Seneci
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Si-qi Liu
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
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16
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Almeida DD, Viala VL, Nachtigall PG, Broe M, Gibbs HL, Serrano SMDT, Moura-da-Silva AM, Ho PL, Nishiyama-Jr MY, Junqueira-de-Azevedo ILM. Tracking the recruitment and evolution of snake toxins using the evolutionary context provided by the Bothrops jararaca genome. Proc Natl Acad Sci U S A 2021; 118:e2015159118. [PMID: 33972420 PMCID: PMC8157943 DOI: 10.1073/pnas.2015159118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Venom is a key adaptive innovation in snakes, and how nonvenom genes were co-opted to become part of the toxin arsenal is a significant evolutionary question. While this process has been investigated through the phylogenetic reconstruction of toxin sequences, evidence provided by the genomic context of toxin genes remains less explored. To investigate the process of toxin recruitment, we sequenced the genome of Bothrops jararaca, a clinically relevant pitviper. In addition to producing a road map with canonical structures of genes encoding 12 toxin families, we inferred most of the ancestral genes for their loci. We found evidence that 1) snake venom metalloproteinases (SVMPs) and phospholipases A2 (PLA2) have expanded in genomic proximity to their nonvenomous ancestors; 2) serine proteinases arose by co-opting a local gene that also gave rise to lizard gilatoxins and then expanded; 3) the bradykinin-potentiating peptides originated from a C-type natriuretic peptide gene backbone; and 4) VEGF-F was co-opted from a PGF-like gene and not from VEGF-A. We evaluated two scenarios for the original recruitment of nontoxin genes for snake venom: 1) in locus ancestral gene duplication and 2) in locus ancestral gene direct co-option. The first explains the origins of two important toxins (SVMP and PLA2), while the second explains the emergence of a greater number of venom components. Overall, our results support the idea of a locally assembled venom arsenal in which the most clinically relevant toxin families expanded through posterior gene duplications, regardless of whether they originated by duplication or gene co-option.
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Affiliation(s)
- Diego Dantas Almeida
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Vincent Louis Viala
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Michael Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Solange Maria de Toledo Serrano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus 69040-000, Brazil
| | - Paulo Lee Ho
- Serviço de Bacteriologia, Divisão BioIndustrial, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Milton Yutaka Nishiyama-Jr
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil;
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17
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Holding ML, Strickland JL, Rautsaw RM, Hofmann EP, Mason AJ, Hogan MP, Nystrom GS, Ellsworth SA, Colston TJ, Borja M, Castañeda-Gaytán G, Grünwald CI, Jones JM, Freitas-de-Sousa LA, Viala VL, Margres MJ, Hingst-Zaher E, Junqueira-de-Azevedo ILM, Moura-da-Silva AM, Grazziotin FG, Gibbs HL, Rokyta DR, Parkinson CL. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proc Natl Acad Sci U S A 2021; 118:e2015579118. [PMID: 33875585 PMCID: PMC8092465 DOI: 10.1073/pnas.2015579118] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.
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Affiliation(s)
- Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | | | - Jason M Jones
- HERP.MX A.C., Villa del Álvarez, Colima 28973, Mexico
| | | | - Vincent Louis Viala
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Ana M Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040, Brazil
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, Brazil
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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18
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Surm JM, Moran Y. Insights into how development and life-history dynamics shape the evolution of venom. EvoDevo 2021; 12:1. [PMID: 33413660 PMCID: PMC7791878 DOI: 10.1186/s13227-020-00171-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Venomous animals are a striking example of the convergent evolution of a complex trait. These animals have independently evolved an apparatus that synthesizes, stores, and secretes a mixture of toxic compounds to the target animal through the infliction of a wound. Among these distantly related animals, some can modulate and compartmentalize functionally distinct venoms related to predation and defense. A process to separate distinct venoms can occur within and across complex life cycles as well as more streamlined ontogenies, depending on their life-history requirements. Moreover, the morphological and cellular complexity of the venom apparatus likely facilitates the functional diversity of venom deployed within a given life stage. Intersexual variation of venoms has also evolved further contributing to the massive diversity of toxic compounds characterized in these animals. These changes in the biochemical phenotype of venom can directly affect the fitness of these animals, having important implications in their diet, behavior, and mating biology. In this review, we explore the current literature that is unraveling the temporal dynamics of the venom system that are required by these animals to meet their ecological functions. These recent findings have important consequences in understanding the evolution and development of a convergent complex trait and its organismal and ecological implications.
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Affiliation(s)
- Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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19
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Jackson TNW, Koludarov I. How the Toxin got its Toxicity. Front Pharmacol 2020; 11:574925. [PMID: 33381030 PMCID: PMC7767849 DOI: 10.3389/fphar.2020.574925] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Venom systems are functional and ecological traits, typically used by one organism to subdue or deter another. A predominant subset of their constituent molecules—“toxins”—share this ecological function and are therefore molecules that mediate interactions between organisms. Such molecules have been referred to as “exochemicals.” There has been debate within the field of toxinology concerning the evolutionary pathways leading to the “recruitment” of a gene product for a toxic role within venom. We review these discussions and the evidence interpreted in support of alternate pathways, along with many of the most popular models describing the origin of novel molecular functions in general. We note that such functions may arise with or without gene duplication occurring and are often the consequence of a gene product encountering a novel “environment,” i.e., a range of novel partners for molecular interaction. After stressing the distinction between “activity” and “function,” we describe in detail the results of a recent study which reconstructed the evolutionary history of a multigene family that has been recruited as a toxin and argue that these results indicate that a pluralistic approach to understanding the origin of novel functions is advantageous. This leads us to recommend that an expansive approach be taken to the definition of “neofunctionalization”—simply the origins of a novel molecular function by any process—and “recruitment”—the “weaponization” of a molecule via the acquisition of a toxic function in venom, by any process. Recruitment does not occur at the molecular level or even at the level of gene expression, but only when a confluence of factors results in the ecological deployment of a physiologically active molecule as a toxin. Subsequent to recruitment, the evolutionary regime of a gene family may shift into a more dynamic form of “birth-and-death.” Thus, recruitment leads to a form of “downwards causation,” in which a change at the ecological level at which whole organisms interact leads to a change in patterns of evolution at the genomic level.
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Affiliation(s)
- Timothy N W Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
| | - Ivan Koludarov
- Animal Venomics Group, Justus Leibig University, Giessen, Germany
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20
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Colella F, Scillitani G, Pierri CL. Sweet as honey, bitter as bile: Mitochondriotoxic peptides and other therapeutic proteins isolated from animal tissues, for dealing with mitochondrial apoptosis. Toxicology 2020; 447:152612. [PMID: 33171268 DOI: 10.1016/j.tox.2020.152612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria are subcellular organelles involved in cell metabolism and cell life-cycle. Their role in apoptosis regulation makes them an interesting target of new drugs for dealing with cancer or rare diseases. Several peptides and proteins isolated from animal and plant sources are known for their therapeutic properties and have been tested on cancer cell-lines and xenograft murine models, highlighting their ability in inducing cell-death by triggering mitochondrial apoptosis. Some of those molecules have been even approved as drugs. Conversely, many other bioactive compounds are still under investigation for their proapoptotic properties. In this review we report about a group of peptides, isolated from animal venoms, with potential therapeutic properties related to their ability in triggering mitochondrial apoptosis. This class of compounds is known with different names, such as mitochondriotoxins or mitocans.
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Affiliation(s)
- Francesco Colella
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | | | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy.
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21
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Perry BW, Schield DR, Westfall AK, Mackessy SP, Castoe TA. Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Sci Rep 2020; 10:18083. [PMID: 33093509 PMCID: PMC7582160 DOI: 10.1038/s41598-020-75048-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/09/2020] [Indexed: 01/30/2023] Open
Abstract
Despite the extensive body of research on snake venom, many facets of snake venom systems, such as the physiology and regulation of the venom gland itself, remain virtually unstudied. Here, we use time series gene expression analyses of the rattlesnake venom gland in comparison with several non-venom tissues to characterize physiological and cellular processes associated with venom production and to highlight key distinctions of venom gland cellular and physiological function. We find consistent evidence for activation of stress response pathways in the venom gland, suggesting that mitigation of cellular stress is a crucial component of venom production. Additionally, we demonstrate evidence for an unappreciated degree of cellular and secretory activity in the steady state venom gland relative to other secretory tissues and identify vacuolar ATPases as the likely mechanisms driving acidification of the venom gland lumen during venom production and storage.
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Affiliation(s)
- Blair W Perry
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Aundrea K Westfall
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.
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22
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Toxin-like neuropeptides in the sea anemone Nematostella unravel recruitment from the nervous system to venom. Proc Natl Acad Sci U S A 2020; 117:27481-27492. [PMID: 33060291 DOI: 10.1073/pnas.2011120117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The sea anemone Nematostella vectensis (Anthozoa, Cnidaria) is a powerful model for characterizing the evolution of genes functioning in venom and nervous systems. Although venom has evolved independently numerous times in animals, the evolutionary origin of many toxins remains unknown. In this work, we pinpoint an ancestral gene giving rise to a new toxin and functionally characterize both genes in the same species. Thus, we report a case of protein recruitment from the cnidarian nervous to venom system. The ShK-like1 peptide has a ShKT cysteine motif, is lethal for fish larvae and packaged into nematocysts, the cnidarian venom-producing stinging capsules. Thus, ShK-like1 is a toxic venom component. Its paralog, ShK-like2, is a neuropeptide localized to neurons and is involved in development. Both peptides exhibit similarities in their functional activities: They provoke contraction in Nematostella polyps and are toxic to fish. Because ShK-like2 but not ShK-like1 is conserved throughout sea anemone phylogeny, we conclude that the two paralogs originated due to a Nematostella-specific duplication of a ShK-like2 ancestor, a neuropeptide-encoding gene, followed by diversification and partial functional specialization. ShK-like2 is represented by two gene isoforms controlled by alternative promoters conferring regulatory flexibility throughout development. Additionally, we characterized the expression patterns of four other peptides with structural similarities to studied venom components and revealed their unexpected neuronal localization. Thus, we employed genomics, transcriptomics, and functional approaches to reveal one venom component, five neuropeptides with two different cysteine motifs, and an evolutionary pathway from nervous to venom system in Cnidaria.
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23
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Zhu W, Gao H, Luo X, Ye X, Ding L, Hao J, Shu Z, Li S, Li J, Chen Z. Cloning and identification of a new multifunctional Ascaris-type peptide from the hemolymph of Buthus martensii Karsch. Toxicon 2020; 184:167-174. [PMID: 32565098 DOI: 10.1016/j.toxicon.2020.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Only a few work have been done for peptides from non-venom gland tissues of venomous animals. Here, with the help of the whole body transcriptomic and the hemolymph proteomic data of the Chinese scorpion Buthus martensii Karsch, we identified the first Ascaris-type peptide BmHDP from scorpion hemolymph. The precursor of BmHDP has 80 residues, including a 16 residue signal peptide and a 64 residue mature peptide. The mature peptide has 10 conserved cysteines and adopts a conserved Ascaris-type fold. Using combined inclusion body refolding and biochemical identification strategies, recombinant BmHDP was obtained successfully. Protease inhibitory assays showed that BmHDP inhibited chymotrypsin apparently at a concentration of 8 nM. Patch-clamp experiments showed that BmHDP inhibited the Kv1.3 potassium channel apparently at a concentration of 1000 nM. Coagulation experiment assays showed that BmHDP inhibited intrinsic coagulation pathway apparently at a concentration of 500 nM. To the best of our knowledge, BmHDP is the first Ascaris-type peptide from scorpion hemolymph. Our work highlighted a functional link between scorpion non-venom gland peptides and venom gland toxin peptides, and suggested that scorpion hemolymph might be a new source of bioactive peptides.
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Affiliation(s)
- Wen Zhu
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China
| | - Huanhuan Gao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China
| | - Xudong Luo
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China; Institute of Biomedicine and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Hubei, China
| | - Xiangdong Ye
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China; Institute of Biomedicine and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Hubei, China
| | - Li Ding
- Department of Clinical Laboratory, Dongfeng Hospital, Hubei University of Medicine, Hubei, China; Institute of Biomedicine and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Hubei, China
| | - Jinbo Hao
- Department of Clinical Laboratory, Shiyan Occupational Disease Hospital, Hubei, China
| | - Zhan Shu
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China
| | - Shan Li
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China
| | - Jian Li
- Department of Human Parasitology, College of Basic Medical Sciences, Hubei University of Medicine, Hubei, China
| | - Zongyun Chen
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Hubei, China; Institute of Biomedicine and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Hubei, China.
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24
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Kini RM. Toxinology provides multidirectional and multidimensional opportunities: A personal perspective. Toxicon X 2020; 6:100039. [PMID: 32550594 PMCID: PMC7285919 DOI: 10.1016/j.toxcx.2020.100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 01/16/2023] Open
Abstract
In nature, toxins have evolved as weapons to capture and subdue the prey or to counter predators or competitors. When they are inadvertently injected into humans, they cause symptoms ranging from mild discomfort to debilitation and death. Toxinology is the science of studying venoms and toxins that are produced by a wide variety of organisms. In the past, the structure, function and mechanisms of most abundant and/or most toxic components were characterized to understand and to develop strategies to neutralize their toxicity. With recent technical advances, we are able to evaluate and determine the toxin profiles using transcriptomes of venom glands and proteomes of tiny amounts of venom. Enormous amounts of data from these studies have opened tremendous opportunities in many directions of basic and applied research. The lower costs for profiling venoms will further fuel the expansion of toxin database, which in turn will provide greater exciting and bright opportunities in toxin research.
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Affiliation(s)
- R. Manjunatha Kini
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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25
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Jenner RA, von Reumont BM, Campbell LI, Undheim EAB. Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses. Mol Biol Evol 2019; 36:2748-2763. [PMID: 31396628 PMCID: PMC6878950 DOI: 10.1093/molbev/msz181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Centipedes are among the most ancient groups of venomous predatory arthropods. Extant species belong to five orders, but our understanding of the composition and evolution of centipede venoms is based almost exclusively on one order, Scolopendromorpha. To gain a broader and less biased understanding we performed a comparative proteotranscriptomic analysis of centipede venoms from all five orders, including the first venom profiles for the orders Lithobiomorpha, Craterostigmomorpha, and Geophilomorpha. Our results reveal an astonishing structural diversity of venom components, with 93 phylogenetically distinct protein and peptide families. Proteomically-annotated gene trees of these putative toxin families show that centipede venom composition is highly dynamic across macroevolutionary timescales, with numerous gene duplications as well as functional recruitments and losses of toxin gene families. Strikingly, not a single family is found in the venoms of representatives of all five orders, with 67 families being unique for single orders. Ancestral state reconstructions reveal that centipede venom originated as a simple cocktail comprising just four toxin families, with very little compositional evolution happening during the approximately 50 My before the living orders had diverged. Venom complexity then increased in parallel within the orders, with scolopendromorphs evolving particularly complex venoms. Our results show that even venoms composed of toxins evolving under the strong constraint of negative selection can have striking evolutionary plasticity on the compositional level. We show that the functional recruitments and losses of toxin families that shape centipede venom arsenals are not concentrated early in their evolutionary history, but happen frequently throughout.
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Affiliation(s)
- Ronald A Jenner
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bjoern M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig University Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Animal Venomics, Giessen, Germany
| | - Lahcen I Campbell
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, United Kingdom
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Ecology and Evolutionary Synthesis, Department of Bioscience, University of Oslo, Oslo, Norway
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26
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27
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Margres MJ, Patton A, Wray KP, Hassinger ATB, Ward MJ, Lemmon EM, Lemmon AR, Rokyta DR. Tipping the Scales: The Migration-Selection Balance Leans toward Selection in Snake Venoms. Mol Biol Evol 2019; 36:271-282. [PMID: 30395254 DOI: 10.1093/molbev/msy207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The migration-selection interaction is the strongest determinant of whether a beneficial allele increases in frequency within a population. Results of empirical studies examining the role of gene flow in an adaptive context, however, have largely been equivocal, with examples of opposing outcomes being repeatedly documented (e.g., local adaptation with high levels of gene flow vs. gene swamping). We compared neutral genomic and venom expression divergence for three sympatric pit vipers with differing ecologies to determine if and how migration-selection disequilibria result in local adaptation. We specifically tested whether neutral differentiation predicted phenotypic differentiation within an isolation-by-distance framework. The decoupling of neutral and phenotypic differentiation would indicate selection led to adaptive divergence irrespective of migration, whereas a significant relationship between neutral and venom expression differentiation would provide evidence in favor of the constraining force of gene flow. Neutral differentiation and geographic distance predicted phenotypic differentiation only in the generalist species, indicating that selection was the predominant mechanism in the migration-selection balance underlying adaptive venom evolution in both specialists. Dispersal is thought to be a stronger influence on genetic differentiation than specialization, but our results suggest the opposite. Greater specialization may lead to greater diversification rates, and extreme spatial and temporal variation in selective pressures can favor generalist phenotypes evolving under strong stabilizing selection. Our results are consistent with these expectations, suggesting that the equivocal findings of studies examining the role of gene flow in an adaptive context may be explained by ecological specialization theory.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL.,School of Biological Sciences, Washington State University, Pullman, WA.,Department of Biological Sciences, Clemson University, Clemson, SC
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Alyssa T B Hassinger
- Department of Biological Science, Florida State University, Tallahassee, FL.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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28
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Leth JM, Leth-Espensen KZ, Kristensen KK, Kumari A, Lund Winther AM, Young SG, Ploug M. Evolution and Medical Significance of LU Domain-Containing Proteins. Int J Mol Sci 2019; 20:ijms20112760. [PMID: 31195646 PMCID: PMC6600238 DOI: 10.3390/ijms20112760] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Proteins containing Ly6/uPAR (LU) domains exhibit very diverse biological functions and have broad taxonomic distributions in eukaryotes. In general, they adopt a characteristic three-fingered folding topology with three long loops projecting from a disulfide-rich globular core. The majority of the members of this protein domain family contain only a single LU domain, which can be secreted, glycolipid anchored, or constitute the extracellular ligand binding domain of type-I membrane proteins. Nonetheless, a few proteins contain multiple LU domains, for example, the urokinase receptor uPAR, C4.4A, and Haldisin. In the current review, we will discuss evolutionary aspects of this protein domain family with special emphasis on variations in their consensus disulfide bond patterns. Furthermore, we will present selected cases where missense mutations in LU domain-containing proteins leads to dysfunctional proteins that are causally linked to genesis of human disease.
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Affiliation(s)
- Julie Maja Leth
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Katrine Zinck Leth-Espensen
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Kristian Kølby Kristensen
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Anni Kumari
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Anne-Marie Lund Winther
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Michael Ploug
- Finsen Laboratory, Ole Maaloes Vej 5, Righospitalet, DK-2200 Copenhagen, Denmark.
- Biotechnology Research Innovation Centre (BRIC), Ole Maaloes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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29
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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30
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Surm JM, Smith HL, Madio B, Undheim EA, King GF, Hamilton BR, Burg CA, Pavasovic A, Prentis PJ. A process of convergent amplification and tissue‐specific expression dominates the evolution of toxin and toxin‐like genes in sea anemones. Mol Ecol 2019; 28:2272-2289. [DOI: 10.1111/mec.15084] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/09/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim M. Surm
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Hayden L. Smith
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
| | - Bruno Madio
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Eivind A.B. Undheim
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
| | - Glenn F. King
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Brett R. Hamilton
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
- Centre for Microscopy and Microanalysis University of Queensland Saint Lucia Queensland Australia
| | - Chloé A. Burg
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Ana Pavasovic
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
| | - Peter J. Prentis
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
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31
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Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, Castoe TA. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Res 2019; 29:590-601. [PMID: 30898880 PMCID: PMC6442385 DOI: 10.1101/gr.240952.118] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/15/2019] [Indexed: 01/28/2023]
Abstract
Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Giulia M Pasquesi
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas 76402, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
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32
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Harrison JA, Kelso C, Pukala TL, Beck JL. Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:256-267. [PMID: 30324262 DOI: 10.1007/s13361-018-2074-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/14/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A2 (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database. Graphical Abstract ᅟ.
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Affiliation(s)
- Julian A Harrison
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Celine Kelso
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Tara L Pukala
- Discipline of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer L Beck
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia.
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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Hofmann EP, Rautsaw RM, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation. Sci Rep 2018; 8:15534. [PMID: 30341342 PMCID: PMC6195556 DOI: 10.1038/s41598-018-33943-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
Changes in gene expression can rapidly influence adaptive traits in the early stages of lineage diversification. Venom is an adaptive trait comprised of numerous toxins used for prey capture and defense. Snake venoms can vary widely between conspecific populations, but the influence of lineage diversification on such compositional differences are unknown. To explore venom differentiation in the early stages of lineage diversification, we used RNA-seq and mass spectrometry to characterize Sidewinder Rattlesnake (Crotalus cerastes) venom. We generated the first venom-gland transcriptomes and complementary venom proteomes for eight individuals collected across the United States and tested for expression differences across life history traits and between subspecific, mitochondrial, and phylotranscriptomic hypotheses. Sidewinder venom was comprised primarily of hemorrhagic toxins, with few cases of differential expression attributable to life history or lineage hypotheses. However, phylotranscriptomic lineage comparisons more than doubled instances of significant expression differences compared to all other factors. Nevertheless, only 6.4% of toxins were differentially expressed overall, suggesting that shallow divergence has not led to major changes in Sidewinder venom composition. Our results demonstrate the need for consensus venom-gland transcriptomes based on multiple individuals and highlight the potential for discrepancies in differential expression between different phylogenetic hypotheses.
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Affiliation(s)
- Erich P Hofmann
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Rhett M Rautsaw
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Jason L Strickland
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- University of Central Florida, Department of Biology, Orlando, FL, 32816, USA
| | - Matthew L Holding
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Michael P Hogan
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Andrew J Mason
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA.
- Clemson University, Department of Forestry and Environmental Conservation, Clemson, SC, 29634, USA.
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35
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Engineering varied serine protease inhibitors by converting P1 site of BF9, a weakly active Kunitz-type animal toxin. Int J Biol Macromol 2018; 120:1190-1197. [PMID: 30172807 DOI: 10.1016/j.ijbiomac.2018.08.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022]
Abstract
Although there were a lot of weakly active animal toxins in the venoms, their values and applications are still mysterious, such as BF9, which is a Kunitz-type toxin isolated from the venom of the elapid snake Bungarus fasciatus. Here, we used BF9 to be a molecular scaffold, and engineered eight BF9-derived peptides by changing P1 site Asn17 of BF9, such as BF9-N17Y and BF9-N17T designed from the polar subfamily, BF9-N17L and BF9-N17G designed from the Non-polar subfamily, BF9-N17D designed from acidic subfamily, and BF9-N17H, BF9-N17K and BF9-N17R designed from basic subfamily. Through enzyme inhibitor experiment assays, we found a potent and selective chymotrypsin inhibitor BF9-N17Y, a potent and selective coagulation factor XIa inhibitor BF9-N17H, and two highly potent coagulation factor XIa inhibitors BF9-N17K and BF9-N17. APTT and PT assays further showed that BF9-N17H, BF9-N17K and BF9-N17R were three novel anticoagulants with selectively intrinsic coagulation pathway inhibitory activity. Considering that natural weakly active animal toxins are also a huge peptide resource, our present work might open a new window about pharmacological applications of weakly active animal toxins, which might be good templates for potent and selective molecular probe and lead drug designs.
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Macrander J, Panda J, Janies D, Daly M, Reitzel AM. Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data. PeerJ 2018; 6:e5361. [PMID: 30083468 PMCID: PMC6074769 DOI: 10.7717/peerj.5361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of “venomics”: a rapidly growing field using combined transcriptomic and proteomic datasets to characterize toxin diversity in a variety of venomous taxa. Ultimately, the transcriptomic portion of these analyses follows very similar pathways after transcriptome assembly often including candidate toxin identification using BLAST, expression level screening, protein sequence alignment, gene tree reconstruction, and characterization of potential toxin function. Here we describe the Python package Venomix, which streamlines these processes using common bioinformatic tools along with ToxProt, a publicly available annotated database comprised of characterized venom proteins. In this study, we use the Venomix pipeline to characterize candidate venom diversity in four phylogenetically distinct organisms, a cone snail (Conidae; Conus sponsalis), a snake (Viperidae; Echis coloratus), an ant (Formicidae; Tetramorium bicarinatum), and a scorpion (Scorpionidae; Urodacus yaschenkoi). Data on these organisms were sampled from public databases, with each original analysis using different approaches for transcriptome assembly, toxin identification, or gene expression quantification. Venomix recovered numerically more candidate toxin transcripts for three of the four transcriptomes than the original analyses and identified new toxin candidates. In summary, we show that the Venomix package is a useful tool to identify and characterize the diversity of toxin-like transcripts derived from transcriptomic datasets. Venomix is available at: https://bitbucket.org/JasonMacrander/Venomix/.
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Affiliation(s)
- Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, United States of America
| | - Jyothirmayi Panda
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Daniel Janies
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America.,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, United States of America
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
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Baumann K, Dashevsky D, Sunagar K, Fry B. Scratching the Surface of an Itch: Molecular Evolution of Aculeata Venom Allergens. J Mol Evol 2018; 86:484-500. [DOI: 10.1007/s00239-018-9860-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
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38
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Margres MJ, Wray KP, Hassinger ATB, Ward MJ, McGivern JJ, Moriarty Lemmon E, Lemmon AR, Rokyta DR. Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation. Mol Biol Evol 2018; 34:3099-3110. [PMID: 28962003 DOI: 10.1093/molbev/msx231] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A trait's genomic architecture can affect the rate and mechanism of adaptation, and although many ecologically-important traits are polygenic, most studies connecting genotype, phenotype, and fitness in natural populations have focused on traits with relatively simple genetic bases. To understand the genetic basis of polygenic adaptation, we must integrate genomics, phenotypic data, ecology, and fitness effects for a genetically tractable, polygenic trait; snake venoms provide such a system for studying polygenic adaptation because of their genetic tractability and vital ecological role in feeding and defense. We used a venom transcriptome-proteome map, quantitative proteomics, genomics, and fitness assays in sympatric prey to construct a genotype-phenotype-fitness map for the venoms of an island-mainland pair of rattlesnake populations. Reciprocal fitness experiments demonstrated that each population was locally adapted to sympatric prey. We identified significant expression differentiation with little to no coding-sequence variation across populations, demonstrating that expression differentiation was exclusively the genetic basis of polygenic adaptation. Previous research on the genetics of adaptation, however, has largely been biased toward investigating protein-coding regions because of the complexity of gene regulation. Our results showed that biases at the molecular level can be in the opposite direction, highlighting the need for more systematic comparisons of different molecular mechanisms underlying rapid, adaptive evolution in polygenic traits.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - James J McGivern
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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Andrade-Silva D, Ashline D, Tran T, Lopes AS, Travaglia Cardoso SR, Reis MDS, Zelanis A, Serrano SMT, Reinhold V. Structures of N-Glycans of Bothrops Venoms Revealed as Molecular Signatures that Contribute to Venom Phenotype in Viperid Snakes. Mol Cell Proteomics 2018; 17:1261-1284. [PMID: 29716988 DOI: 10.1074/mcp.ra118.000748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/26/2018] [Indexed: 11/06/2022] Open
Abstract
The complexity of snake venoms has long been investigated to explore a myriad of biologically active proteins and peptides that are used for immobilizing or killing prey, and are responsible for the pathological effects observed on envenomation. Glycosylation is the main post-translational modification (PTM) of viperid venoms but currently there is little understanding of how protein glycosylation impacts the variation of venom proteomes. We have previously reported that Bothrops venom glycoproteomes contain a core of components that markedly define their composition and parallel their phylogenetic classification. Here we extend those observations to eight Bothrops species evaluating the N-glycomes by LC-MS as assigned cartoon structures and detailing those structures separately as methylated analogs using ion-trap mass spectrometry (MSn). Following ion disassembly through multiple steps provided sequence and linkage isomeric details that characterized 52 unique compositions in Bothrops venoms. These occurred as 60 structures, of which 26 were identified in the venoms of the Jararaca Complex (B. alcatraz, B. insularis, and B. jararaca), 20 in B. erythromelas, B. jararacussu, B. moojeni and B. neuwiedi venoms, and 22 in B. cotiara venom. Further, quantitative analysis of these N-glycans showed variable relative abundances in the venoms. For the first time a comprehensive set of N-glycan structures present in snake venoms are defined. Despite the fact that glycosylation is not template-defined, the N-glycomes of these venoms mirror the phylogeny cladograms of South American bothropoid snakes reported in studies on morphological, molecular data and feeding habits, exhibiting distinct molecular signatures for each venom. Considering the complexity of N-glycan moieties generally found in glycoproteins, characterized by different degrees of branching, isomer structures, and variable abundances, our findings point to these factors as another level of complexity in Bothrops venoms, features that could dramatically contribute to their distinct biological activities.
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Affiliation(s)
| | - David Ashline
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Thuy Tran
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Aline Soriano Lopes
- ‖Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, 09913-030 Brazil
| | | | - Marcelo da Silva Reis
- ¶Laboratório Especial de Ciclo Celular, Center of Toxins, Immune-Response, and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | - André Zelanis
- ‡‡Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (ICT-UNIFESP), São José dos Campos, 12231-280, Brazil
| | | | - Vernon Reinhold
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824;
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40
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Zhao F, Lan X, Li T, Xiang Y, Zhao F, Zhang Y, Lee WH. Proteotranscriptomic Analysis and Discovery of the Profile and Diversity of Toxin-like Proteins in Centipede. Mol Cell Proteomics 2018; 17:709-720. [PMID: 29339413 DOI: 10.1074/mcp.ra117.000431] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/15/2017] [Indexed: 12/17/2022] Open
Abstract
Centipedes are one of the oldest venomous animals and use their venoms as weapons to attack prey or protect themselves. Their venoms contain various components with different biomedical and pharmacological properties. However, little attention has been paid to the profiles and diversity of their toxin-like proteins/peptides. In this study, we used a proteotranscriptomic approach to uncover the diversity of centipede toxin-like proteins in Scolopendra subspinipes mutilans Nine hundred twenty-three and 6,736 peptides, which were separately isolated from venom and torso tissues, respectively, were identified by ESI-MS/MS and deduced from their transcriptomes. Finally, 1369 unique proteins were identified in the proteome, including 100 proteins that exhibited overlapping expression in venom and torso tissues. Of these proteins, at least 40 proteins were identified as venom toxin-like proteins. Meanwhile, transcriptome mining identified ∼10-fold more toxin-like proteins and enabled the characterization of the precursor architecture of mature toxin-like peptides. Importantly, combined with proteomic and transcriptomic analyses, 25 toxin-like proteins/peptides (neurotoxins accounted for 50%) were expressed outside the venom gland and involved in gene recruitment processes. These findings highlight the extensive diversity of centipede toxin-like proteins and provide a new foundation for the medical-pharmaceutical use of centipede toxin-like proteins. Moreover, we are the first group to report the gene recruitment activity of venom toxin-like proteins in centipede, similar to snakes.
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Affiliation(s)
- Feng Zhao
- From the ‡Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, China; .,§Key Laboratory of Subtropical Medicinal Edible Resources Development and Utilization in Yunnan Province, Department of Biology and Chemistry, Puer University, 6 Xueyuan Road, Puer, Yunnan 665000, China.,¶Institute of Comparative Study of Traditional Materia Medica, Institute of Integrative Medicine of Fudan University, Shanghai China
| | - Xinqiang Lan
- From the ‡Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, China.,‖Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Tao Li
- §Key Laboratory of Subtropical Medicinal Edible Resources Development and Utilization in Yunnan Province, Department of Biology and Chemistry, Puer University, 6 Xueyuan Road, Puer, Yunnan 665000, China.,¶Institute of Comparative Study of Traditional Materia Medica, Institute of Integrative Medicine of Fudan University, Shanghai China
| | - Yang Xiang
- From the ‡Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, China
| | - Fang Zhao
- §Key Laboratory of Subtropical Medicinal Edible Resources Development and Utilization in Yunnan Province, Department of Biology and Chemistry, Puer University, 6 Xueyuan Road, Puer, Yunnan 665000, China.,¶Institute of Comparative Study of Traditional Materia Medica, Institute of Integrative Medicine of Fudan University, Shanghai China
| | - Yun Zhang
- From the ‡Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, China; .,**Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Hui Lee
- From the ‡Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiao-Chang Road, Kunming, Yunnan 650223, China;
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41
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Snake Genome Sequencing: Results and Future Prospects. Toxins (Basel) 2016; 8:toxins8120360. [PMID: 27916957 PMCID: PMC5198554 DOI: 10.3390/toxins8120360] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 12/16/2022] Open
Abstract
Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.
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42
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Yang DC, Deuis JR, Dashevsky D, Dobson J, Jackson TNW, Brust A, Xie B, Koludarov I, Debono J, Hendrikx I, Hodgson WC, Josh P, Nouwens A, Baillie GJ, Bruxner TJC, Alewood PF, Lim KKP, Frank N, Vetter I, Fry BG. The Snake with the Scorpion's Sting: Novel Three-Finger Toxin Sodium Channel Activators from the Venom of the Long-Glanded Blue Coral Snake (Calliophis bivirgatus). Toxins (Basel) 2016; 8:E303. [PMID: 27763551 PMCID: PMC5086663 DOI: 10.3390/toxins8100303] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 02/06/2023] Open
Abstract
Millions of years of evolution have fine-tuned the ability of venom peptides to rapidly incapacitate both prey and potential predators. Toxicofera reptiles are characterized by serous-secreting mandibular or maxillary glands with heightened levels of protein expression. These glands are the core anatomical components of the toxicoferan venom system, which exists in myriad points along an evolutionary continuum. Neofunctionalisation of toxins is facilitated by positive selection at functional hotspots on the ancestral protein and venom proteins have undergone dynamic diversification in helodermatid and varanid lizards as well as advanced snakes. A spectacular point on the venom system continuum is the long-glanded blue coral snake (Calliophis bivirgatus), a specialist feeder that preys on fast moving, venomous snakes which have both a high likelihood of prey escape but also represent significant danger to the predator itself. The maxillary venom glands of C. bivirgatus extend one quarter of the snake's body length and nestle within the rib cavity. Despite the snake's notoriety its venom has remained largely unstudied. Here we show that the venom uniquely produces spastic paralysis, in contrast to the flaccid paralysis typically produced by neurotoxic snake venoms. The toxin responsible, which we have called calliotoxin (δ-elapitoxin-Cb1a), is a three-finger toxin (3FTx). Calliotoxin shifts the voltage-dependence of NaV1.4 activation to more hyperpolarised potentials, inhibits inactivation, and produces large ramp currents, consistent with its profound effects on contractile force in an isolated skeletal muscle preparation. Voltage-gated sodium channels (NaV) are a particularly attractive pharmacological target as they are involved in almost all physiological processes including action potential generation and conduction. Accordingly, venom peptides that interfere with NaV function provide a key defensive and predatory advantage to a range of invertebrate venomous species including cone snails, scorpions, spiders, and anemones. Enhanced activation or delayed inactivation of sodium channels by toxins is associated with the extremely rapid onset of tetanic/excitatory paralysis in envenomed prey animals. A strong selection pressure exists for the evolution of such toxins where there is a high chance of prey escape. However, despite their prevalence in other venomous species, toxins causing delay of sodium channel inhibition have never previously been described in vertebrate venoms. Here we show that NaV modulators, convergent with those of invertebrates, have evolved in the venom of the long-glanded coral snake. Calliotoxin represents a functionally novel class of 3FTx and a structurally novel class of NaV toxins that will provide significant insights into the pharmacology and physiology of NaV. The toxin represents a remarkable case of functional convergence between invertebrate and vertebrate venom systems in response to similar selection pressures. These results underscore the dynamic evolution of the Toxicofera reptile system and reinforces the value of using evolution as a roadmap for biodiscovery.
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Affiliation(s)
- Daryl C Yang
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton 3168, Australia.
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
| | - Daniel Dashevsky
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - James Dobson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Timothy N W Jackson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Andreas Brust
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
| | - Bing Xie
- Bejing Genomics Institute-Shenzhen, Shenzhen 518083, China.
| | - Ivan Koludarov
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Iwan Hendrikx
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Wayne C Hodgson
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton 3168, Australia.
| | - Peter Josh
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia 4072, Australia.
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia 4072, Australia.
| | - Gregory J Baillie
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
| | - Paul F Alewood
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
| | - Kelvin Kok Peng Lim
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore.
| | | | - Irina Vetter
- Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, Australia.
- School of Pharmacy, University of Queensland, Woolloongabba 4102, Australia.
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
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43
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Rodríguez de la Vega RC, Giraud T. Intragenome Diversity of Gene Families Encoding Toxin-like Proteins in Venomous Animals. Integr Comp Biol 2016; 56:938-949. [PMID: 27543626 DOI: 10.1093/icb/icw097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolution of venoms is the story of how toxins arise and of the processes that generate and maintain their diversity. For animal venoms these processes include recruitment for expression in the venom gland, neofunctionalization, paralogous expansions, and functional divergence. The systematic study of these processes requires the reliable identification of the venom components involved in antagonistic interactions. High-throughput sequencing has the potential of uncovering the entire set of toxins in a given organism, yet the existence of non-venom toxin paralogs and the misleading effects of partial census of the molecular diversity of toxins make necessary to collect complementary evidence to distinguish true toxins from their non-venom paralogs. Here, we analyzed the whole genomes of two scorpions, one spider and one snake, aiming at the identification of the full repertoires of genes encoding toxin-like proteins. We classified the entire set of protein-coding genes into paralogous groups and monotypic genes, identified genes encoding toxin-like proteins based on known toxin families, and quantified their expression in both venom-glands and pooled tissues. Our results confirm that genes encoding toxin-like proteins are part of multigene families, and that these families arise by recruitment events from non-toxin genes followed by limited expansions of the toxin-like protein coding genes. We also show that failing to account for sequence similarity with non-toxin proteins has a considerable misleading effect that can be greatly reduced by comparative transcriptomics. Our study overall contributes to the understanding of the evolutionary dynamics of proteins involved in antagonistic interactions.
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Affiliation(s)
- Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, UMR8079, CNRS, Univ. of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, UMR8079, CNRS, Univ. of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
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44
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Holding ML, Drabeck DH, Jansa SA, Gibbs HL. Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations. Integr Comp Biol 2016; 56:1032-1043. [PMID: 27444525 DOI: 10.1093/icb/icw082] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
SynopsisVenom and venom resistance are molecular phenotypes widely considered to have diversified through coevolution between predators and prey. However, while evolutionary and functional studies on venom have been extensive, little is known about the molecular basis, variation, and complexity of venom resistance. We review known mechanisms of venom resistance and relate these mechanisms to their predicted impact on coevolutionary dynamics with venomous enemies. We then describe two conceptual approaches which can be used to examine venom/resistance systems. At the intraspecific level, tests of local adaptation in venom and resistance phenotypes can identify the functional mechanisms governing the outcomes of coevolution. At deeper evolutionary timescales, the combination of phylogenetically informed analyses of protein evolution coupled with studies of protein function promise to elucidate the mode and tempo of evolutionary change on potentially coevolving genes. We highlight case studies that use each approach to extend our knowledge of these systems as well as address larger questions about coevolutionary dynamics. We argue that resistance and venom are phenotypic traits which hold exceptional promise for investigating the mechanisms, dynamics, and outcomes of coevolution at the molecular level. Furthermore, extending the understanding of single gene-for-gene interactions to the whole resistance and venom phenotypes may provide a model system for examining the molecular and evolutionary dynamics of complex multi-gene interactions.
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Affiliation(s)
- Matthew L Holding
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,*Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Danielle H Drabeck
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.,J. F. Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.,J. F. Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
| | - H Lisle Gibbs
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,Ohio Biodiversity Conservation Partnership, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
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45
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Zelanis A, Menezes MC, Kitano ES, Liberato T, Tashima AK, Pinto AF, Sherman NE, Ho PL, Fox JW, Serrano SM. Proteomic identification of gender molecular markers in Bothrops jararaca venom. J Proteomics 2016; 139:26-37. [DOI: 10.1016/j.jprot.2016.02.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/10/2016] [Accepted: 02/24/2016] [Indexed: 01/13/2023]
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46
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Haney RA, Clarke TH, Gadgil R, Fitzpatrick R, Hayashi CY, Ayoub NA, Garb JE. Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders. Genome Biol Evol 2016; 8:228-42. [PMID: 26733576 PMCID: PMC4758249 DOI: 10.1093/gbe/evv253] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland–specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species.
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Affiliation(s)
- Robert A Haney
- Department of Biological Sciences, University of Massachusetts, Lowell
| | - Thomas H Clarke
- Department of Biology, Washington and Lee University Department of Biology, University of California, Riverside
| | - Rujuta Gadgil
- Department of Biological Sciences, University of Massachusetts, Lowell
| | - Ryan Fitzpatrick
- Department of Biological Sciences, University of Massachusetts, Lowell
| | | | - Nadia A Ayoub
- Department of Biology, Washington and Lee University
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts, Lowell
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47
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Gacesa R, Chung R, Dunn SR, Weston AJ, Jaimes-Becerra A, Marques AC, Morandini AC, Hranueli D, Starcevic A, Ward M, Long PF. Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia). BMC Genomics 2015; 16:774. [PMID: 26464356 PMCID: PMC4604070 DOI: 10.1186/s12864-015-1976-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background Gene duplication followed by adaptive selection is a well-accepted process leading to toxin diversification in venoms. However, emergent genomic, transcriptomic and proteomic evidence now challenges this role to be at best equivocal to other processess . Cnidaria are arguably the most ancient phylum of the extant metazoa that are venomous and such provide a definitive ancestral anchor to examine the evolution of this trait. Methods Here we compare predicted toxins from the translated genome of the coral Acropora digitifera to putative toxins revealed by proteomic analysis of soluble proteins discharged from nematocysts, to determine the extent to which gene duplications contribute to venom innovation in this reef-building coral species. A new bioinformatics tool called HHCompare was developed to detect potential gene duplications in the genomic data, which is made freely available (https://github.com/rgacesa/HHCompare). Results A total of 55 potential toxin encoding genes could be predicted from the A. digitifera genome, of which 36 (65 %) had likely arisen by gene duplication as evinced using the HHCompare tool and verified using two standard phylogeny methods. Surprisingly, only 22 % (12/55) of the potential toxin repertoire could be detected following rigorous proteomic analysis, for which only half (6/12) of the toxin proteome could be accounted for as peptides encoded by the gene duplicates. Biological activities of these toxins are dominatedby putative phospholipases and toxic peptidases. Conclusions Gene expansions in A. digitifera venom are the most extensive yet described in any venomous animal, and gene duplication plays a significant role leading to toxin diversification in this coral species. Since such low numbers of toxins were detected in the proteome, it is unlikely that the venom is evolving rapidly by prey-driven positive natural selection. Rather we contend that the venom has a defensive role deterring predation or harm from interspecific competition and overgrowth by fouling organisms. Factors influencing translation of toxin encoding genes perhaps warrants more profound experimental consideration. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1976-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ranko Gacesa
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, UK
| | - Ray Chung
- Proteomics Facility, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AF, UK
| | - Simon R Dunn
- Coral Reefs Ecosystems Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Andrew J Weston
- Mass Spectrometry Laboratory, UCL School of Pharmacy, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Adrian Jaimes-Becerra
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil
| | - Antonio C Marques
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil.,Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, km. 131,5, 11600-000, São Sebastião, Brazil
| | - André C Morandini
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Malcolm Ward
- Proteomics Facility, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AF, UK
| | - Paul F Long
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, UK. .,Department of Chemistry, King's College London, Strand, London, WC2R 2LS, UK. .,Brazil Institute, King's College London, Strand, London, WC2R 2LS, UK. .,Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000, São Paulo, SP, Brazil.
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48
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Petras D, Heiss P, Süssmuth RD, Calvete JJ. Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches. J Proteome Res 2015; 14:2539-56. [DOI: 10.1021/acs.jproteome.5b00305] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daniel Petras
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Paul Heiss
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Juan J. Calvete
- Laboratorio
de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, 46010 Valencia, Spain
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49
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Jouiaei M, Sunagar K, Federman Gross A, Scheib H, Alewood PF, Moran Y, Fry BG. Evolution of an ancient venom: recognition of a novel family of cnidarian toxins and the common evolutionary origin of sodium and potassium neurotoxins in sea anemone. Mol Biol Evol 2015; 32:1598-610. [PMID: 25757852 DOI: 10.1093/molbev/msv050] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite Cnidaria (sea anemones, corals, jellyfish, and hydroids) being the oldest venomous animal lineage, structure-function relationships, phyletic distributions, and the molecular evolutionary regimes of toxins encoded by these intriguing animals are poorly understood. Hence, we have comprehensively elucidated the phylogenetic and molecular evolutionary histories of pharmacologically characterized cnidarian toxin families, including peptide neurotoxins (voltage-gated Na(+) and K(+) channel-targeting toxins: NaTxs and KTxs, respectively), pore-forming toxins (actinoporins, aerolysin-related toxins, and jellyfish toxins), and the newly discovered small cysteine-rich peptides (SCRiPs). We show that despite long evolutionary histories, most cnidarian toxins remain conserved under the strong influence of negative selection-a finding that is in striking contrast to the rapid evolution of toxin families in evolutionarily younger lineages, such as cone snails and advanced snakes. In contrast to the previous suggestions that implicated SCRiPs in the biomineralization process in corals, we demonstrate that they are potent neurotoxins that are likely involved in the envenoming function, and thus represent the first family of neurotoxins from corals. We also demonstrate the common evolutionary origin of type III KTxs and NaTxs in sea anemones. We show that type III KTxs have evolved from NaTxs under the regime of positive selection, and likely represent a unique evolutionary innovation of the Actinioidea lineage. We report a correlation between the accumulation of episodically adaptive sites and the emergence of novel pharmacological activities in this rapidly evolving neurotoxic clade.
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Affiliation(s)
- Mahdokht Jouiaei
- Venom Evolution Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Kartik Sunagar
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute for Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aya Federman Gross
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Holger Scheib
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute for Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bryan G Fry
- Venom Evolution Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
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50
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Combinations of long peptide sequence blocks can be used to describe toxin diversification in venomous animals. Toxicon 2015; 95:84-92. [DOI: 10.1016/j.toxicon.2015.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/07/2015] [Accepted: 01/13/2015] [Indexed: 11/19/2022]
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