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Rodríguez de la Vega RC. Coming of age in venom research. Proc Natl Acad Sci U S A 2024; 121:e2405708121. [PMID: 38687800 PMCID: PMC11087774 DOI: 10.1073/pnas.2405708121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
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Modahl CM, Han SX, van Thiel J, Vaz C, Dunstan NL, Frietze S, Jackson TNW, Mackessy SP, Kini RM. Distinct regulatory networks control toxin gene expression in elapid and viperid snakes. BMC Genomics 2024; 25:186. [PMID: 38365592 PMCID: PMC10874052 DOI: 10.1186/s12864-024-10090-y] [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: 07/28/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris). RESULTS Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis. CONCLUSIONS Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype.
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Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K..
| | - Summer Xia Han
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Fulcrum Therapeutics, Cambridge, MA, U.S.A
| | - Jory van Thiel
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Candida Vaz
- Human Development, Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, U.S.A
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, U.S.A
| | - R Manjunatha Kini
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, U.S.A..
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Transcriptional Silencers: Driving Gene Expression with the Brakes On. Trends Genet 2021; 37:514-527. [PMID: 33712326 DOI: 10.1016/j.tig.2021.02.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
Abstract
Silencers are regulatory DNA elements that reduce transcription from their target promoters; they are the repressive counterparts of enhancers. Although discovered decades ago, and despite evidence of their importance in development and disease, silencers have been much less studied than enhancers. Recently, however, a series of papers have reported systematic studies of silencers in various model systems. Silencers are often bifunctional regulatory elements that can also act as enhancers, depending on cellular context, and are enriched for expression quantitative trait loci (eQTLs) and disease-associated variants. There is not yet evidence of a 'silencer chromatin signature', in the distribution of histone modifications or associated proteins, that is common to all silencers; instead, silencers may fall into various subclasses, acting by distinct (and possibly overlapping) mechanisms.
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Walker AA, Robinson SD, Hamilton BF, Undheim EAB, King GF. Deadly Proteomes: A Practical Guide to Proteotranscriptomics of Animal Venoms. Proteomics 2020; 20:e1900324. [PMID: 32820606 DOI: 10.1002/pmic.201900324] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/07/2020] [Indexed: 11/11/2022]
Abstract
Animal venoms are renowned for their toxicity, biochemical complexity, and as a source of compounds with potential applications in medicine, agriculture, and industry. Polypeptides underlie much of the pharmacology of animal venoms, and elucidating these arsenals of polypeptide toxins-known as the venom proteome or venome-is an important step in venom research. Proteomics is used for the identification of venom toxins, determination of their primary structure including post-translational modifications, as well as investigations into the physiology underlying their production and delivery. Advances in proteomics and adjacent technologies has led to a recent upsurge in publications reporting venom proteomes. Improved mass spectrometers, better proteomic workflows, and the integration of next-generation sequencing of venom-gland transcriptomes and venomous animal genomes allow quicker and more accurate profiling of venom proteomes with greatly reduced starting material. Technologies such as imaging mass spectrometry are revealing additional insights into the mechanism, location, and kinetics of venom toxin production. However, these numerous new developments may be overwhelming for researchers designing venom proteome studies. Here, the field of venom proteomics is reviewed and some practical solutions for simplifying mass spectrometry workflows to study animal venoms are offered.
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Affiliation(s)
- Andrew A Walker
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Brett F Hamilton
- Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, Queensland, 4072, Australia.,Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland, 4072, Australia.,Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, 7491, Norway.,Department of Bioscience, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindern, Oslo, 0316, Norway
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
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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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Zancolli G, Casewell NR. Venom Systems as Models for Studying the Origin and Regulation of Evolutionary Novelties. Mol Biol Evol 2020; 37:2777-2790. [DOI: 10.1093/molbev/msaa133] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties.
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Affiliation(s)
- Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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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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