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Doupnik CA, Luer CA, Walsh CJ, Restivo J, Brick JX. Bioactive Properties of Venoms Isolated from Whiptail Stingrays and the Search for Molecular Mechanisms and Targets. Pharmaceuticals (Basel) 2024; 17:488. [PMID: 38675448 PMCID: PMC11053709 DOI: 10.3390/ph17040488] [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: 02/27/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The venom-containing barb attached to their 'whip-like' tail provides stingrays a defensive mechanism for evading predators such as sharks. From human encounters, dermal stingray envenomation is characterized by intense pain often followed by tissue necrosis occurring over several days to weeks. The bioactive components in stingray venoms (SRVs) and their molecular targets and mechanisms that mediate these complex responses are not well understood. Given the utility of venom-derived proteins from other venomous species for biomedical and pharmaceutical applications, we set out to characterize the bioactivity of SRV extracts from three local species that belong to the Dasyatoidea 'whiptail' superfamily. Multiple cell-based assays were used to quantify and compare the in vitro effects of these SRVs on different cell lines. All three SRVs demonstrated concentration-dependent growth-inhibitory effects on three different human cell lines tested. In contrast, a mouse fibrosarcoma cell line was markedly resistant to all three SRVs, indicating the molecular target(s) for mediating the SRV effects are not expressed on these cells. The multifunctional SRV responses were characterized by an acute disruption of cell adhesion leading to apoptosis. These findings aim to guide future investigations of individual SRV proteins and their molecular targets for potential use in biomedical applications.
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Affiliation(s)
- Craig A. Doupnik
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Carl A. Luer
- Marine Biomedical Research Program, Mote Marine Laboratory, Sarasota, FL 34236, USA;
| | - Catherine J. Walsh
- Marine Immunology Program, Mote Marine Laboratory, Sarasota, FL 34236, USA; (C.J.W.); (J.R.)
| | - Jessica Restivo
- Marine Immunology Program, Mote Marine Laboratory, Sarasota, FL 34236, USA; (C.J.W.); (J.R.)
| | - Jacqueline Xinlan Brick
- Department of Biology, College of Arts & Sciences, Oberlin College and Conservatory, Oberlin, OH 44074, USA;
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Okumura T, Tanaka H, Nakao T, Anan T, Arita R, Shiraki M, Shiraki K, Miyabe T, Yamashita D, Matsuo K, Attri P, Kamataki K, Yamashita N, Itagaki N, Shiratani M, Hosoda S, Tanaka A, Ishibashi Y, Koga K. Health assessment of rice cultivated and harvested from plasma-irradiated seeds. Sci Rep 2023; 13:17450. [PMID: 37838753 PMCID: PMC10576742 DOI: 10.1038/s41598-023-43897-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: 05/08/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023] Open
Abstract
This study provides the health effects assessment of rice cultivated from plasma-irradiated seeds. The rice (Oryza sativa L.) cultivated from seeds with plasma irradiation showed a growth improvement (slope-ratios of with plasma to without plasma were 1.066, 1.042, and 1.255 for tiller, and earing, and ripening periods, respectively) and an 4% increase in yield. The cultivated rice was used for repeated oral administrations to mice for 4-week period. Distilled water and rice cultivated from seeds without plasma irradiation were also used as control. The weights of the lung, kidney, liver, and spleen, with corresponding average values of 0.22 g, 0.72 g, 2.1 g, and 0.17 g for w/ plasma group and 0.22 g, 0.68 g, 2.16 g, and 0.14 g for w/o plasma group, respectively, showing no effect due to the administration of rice cultivated from plasma-irradiated seeds. Nutritional status, liver function, kidney function, and lipid, neutral fat profiles, and glucose metabolism have no significant difference between with and without plasma groups. These results show no obvious subacute effects were observed on rice grains cultivated and harvested from the mother plant that experienced growth improvement by plasma irradiation. This study provides a new finding that there is no apparent adverse health effect on the grains harvested from the plasma-irradiated seeds.
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Affiliation(s)
- Takamasa Okumura
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Hayate Tanaka
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Takumi Nakao
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Teruki Anan
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Ryo Arita
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | | | - Kayo Shiraki
- Wano BARU Co. Ltd, Ogori, Fukuoka, 838-0106, Japan
| | | | - Daisuke Yamashita
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kayo Matsuo
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Pankaj Attri
- Center of Plasma Nano-interface Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kunihiro Kamataki
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Naoto Yamashita
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Naho Itagaki
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Masaharu Shiratani
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Satoshi Hosoda
- Japan Aerospace Exploration Agency, Sagamihara, Kanagawa, 252-5210, Japan
| | - Akiyo Tanaka
- Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yushi Ishibashi
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan.
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3
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Okumura T, Attri P, Kamataki K, Yamashita N, Tsukada Y, Itagaki N, Shiratani M, Ishibashi Y, Kuchitsu K, Koga K. Detection of NO 3- introduced in plasma-irradiated dry lettuce seeds using liquid chromatography-electrospray ionization quantum mass spectrometry (LC-ESI QMS). Sci Rep 2022; 12:12525. [PMID: 35869157 PMCID: PMC9307838 DOI: 10.1038/s41598-022-16641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/13/2022] [Indexed: 11/08/2022] Open
Abstract
Discharge plasma irradiates seeds with reactive oxygen and nitrogen species (RONS). However, RONS introduced in seeds by plasma irradiation have not been successfully detected thus far. This study provides experimental evidence that nitrate ion NO3- is introduced in lettuce seeds as RONS upon irradiation with atmospheric-pressure air dielectric barrier discharge plasma. Plasma irradiation for 5 min promotes seed germination. The components of the plasma-irradiated seeds were examined using electrospray ionization quantum mass spectrometry (ESI QMS), which revealed that the plasma irradiation introduced an ion with a mass of 62 m/z in detectable amounts. This ion was identified as NO3- by liquid chromatography (LC), multiple wavelength detector (MWD), and LC-ESI QMS. A one-dimensional simulation at electron temperature Te = 1 eV, electron density Ne = 1013/m3, and gas temperature Tg = 300 K indicated the introduction of NO3-, involving nitric oxide NO. NO3- is one of the most important ions that trigger signal transduction for germination when introduced in seeds. The scanning electron microscopy (SEM) images revealed that there was no change on the surface of the seeds after plasma irradiation. Plasma irradiation is an effective method of introducing NO3- in seeds in a dry process without causing damage.
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Affiliation(s)
- Takamasa Okumura
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan.
| | - Pankaj Attri
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kunihiro Kamataki
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Naoto Yamashita
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yuichi Tsukada
- Center of Plasma Nano-Interface Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Naho Itagaki
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Masaharu Shiratani
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yushi Ishibashi
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kazuyuki Kuchitsu
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Kazunori Koga
- Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Tokyo, 105-0001, Japan
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4
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Shelar A, Singh AV, Dietrich P, Maharjan RS, Thissen A, Didwal PN, Shinde M, Laux P, Luch A, Mathe V, Jahnke T, Chaskar M, Patil R. Emerging cold plasma treatment and machine learning prospects for seed priming: a step towards sustainable food production. RSC Adv 2022; 12:10467-10488. [PMID: 35425017 PMCID: PMC8982346 DOI: 10.1039/d2ra00809b] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/27/2022] [Indexed: 12/17/2022] Open
Abstract
Seeds are vulnerable to physical and biological stresses during the germination process. Seed priming strategies can alleviate such stresses. Seed priming is a technique of treating and drying seeds prior to germination in order to accelerate the metabolic process of germination. Multiple benefits are offered by seed priming techniques, such as reducing fertilizer use, accelerating seed germination, and inducing systemic resistance in plants, which are both cost-effective and eco-friendly. For seed priming, cold plasma (CP)-mediated priming could be an innovative alternative to synthetic chemical treatments. CP priming is an eco-friendly, safe and economical, yet relatively less explored technique towards the development of seed priming. In this review, we discussed in detail the application of CP technology for seed priming to enhance germination, the quality of seeds, and the production of crops in a sustainable manner. Additionally, the combination treatment of CP with nanoparticle (NP) priming is also discussed. The large numbers of parameters need to be monitored and optimized during CP treatment to achieve the desired priming results. Here, we discussed a new perspective of machine learning for modeling plasma treatment parameters in agriculture for the development of synergistic protocols for different types of seed priming.
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Affiliation(s)
- Amruta Shelar
- Department of Technology, Savitribai Phule Pune University Pune 411007 India
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR) Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Paul Dietrich
- SPECS Surface Nano Analysis GmbH Voltastrasse 5 13355 Berlin Germany
| | - Romi Singh Maharjan
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR) Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Andreas Thissen
- SPECS Surface Nano Analysis GmbH Voltastrasse 5 13355 Berlin Germany
| | - Pravin N Didwal
- Department of Materials, University of Oxford Parks Road Oxford OX1 3PH UK
| | - Manish Shinde
- Centre for Materials for Electronics Technology (C-MET) Panchawati Pune 411008 India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR) Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR) Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Vikas Mathe
- Department of Physics, Savitribai Phule Pune University Pune 411007 India
| | - Timotheus Jahnke
- Max Planck Institute for Medical Research 61920 Heidelberg Germany
| | - Manohar Chaskar
- Faculty of Science and Technology, Savitribai Phule Pune University Pune 411007 India
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University Pune 411007 India
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5
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Stingray Venom Proteins: Mechanisms of Action Revealed Using a Novel Network Pharmacology Approach. Mar Drugs 2021; 20:md20010027. [PMID: 35049882 PMCID: PMC8781517 DOI: 10.3390/md20010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/02/2023] Open
Abstract
Animal venoms offer a valuable source of potent new drug leads, but their mechanisms of action are largely unknown. We therefore developed a novel network pharmacology approach based on multi-omics functional data integration to predict how stingray venom disrupts the physiological systems of target animals. We integrated 10 million transcripts from five stingray venom transcriptomes and 848,640 records from three high-content venom bioactivity datasets into a large functional data network. The network featured 216 signaling pathways, 29 of which were shared and targeted by 70 transcripts and 70 bioactivity hits. The network revealed clusters for single envenomation outcomes, such as pain, cardiotoxicity and hemorrhage. We carried out a detailed analysis of the pain cluster representing a primary envenomation symptom, revealing bibrotoxin and cholecystotoxin-like transcripts encoding pain-inducing candidate proteins in stingray venom. The cluster also suggested that such pain-inducing toxins primarily activate the inositol-3-phosphate receptor cascade, inducing intracellular calcium release. We also found strong evidence for synergistic activity among these candidates, with nerve growth factors cooperating with the most abundant translationally-controlled tumor proteins to activate pain signaling pathways. Our network pharmacology approach, here applied to stingray venom, can be used as a template for drug discovery in neglected venomous species.
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6
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Coelho GR, Neto PP, Barbosa FC, Dos Santos RS, Brigatte P, Spencer PJ, Sampaio SC, D'Amélio F, Pimenta DC, Sciani JM. Biochemical and biological characterization of the Hypanus americanus mucus: A perspective on stingray immunity and toxins. FISH & SHELLFISH IMMUNOLOGY 2019; 93:832-840. [PMID: 31425832 DOI: 10.1016/j.fsi.2019.08.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Stingrays skin secretions are largely studied due to the human envenoming medical relevance of the sting puncture that evolves to inflammatory events, including necrosis. Such toxic effects can be correlated to the biochemical composition of the sting mucus, according to the literature. Fish skin plays important biological roles, such as the control of the osmotic pressure gradient, protection against mechanical forces and microorganism infections. The mucus, on the other hand, is a rich and complex fluid, acting on swimming, nutrition and the innate immune system. The elasmobranch's epidermis is a tissue composed mainly by mucus secretory cells, and marine stingrays have already been described to present secretory glands spread throughout the body. Little is known about the biochemical composition of the stingray mucus, but recent studies have corroborated the importance of mucus in the envenomation process. Aiming to assess the mucus composition, a new non-invasive mucus collection method was developed that focused on peptides and proteins, and biological assays were performed to analyze the toxic and immune activities of the Hypanus americanus mucus. Pathophysiological characterization showed the presence of peptidases on the mucus, as well as the induction of edema and leukocyte recruitment in mice. The fractionated mucus improved phagocytosis on macrophages and showed antimicrobial activity against T. rubrumç. neoformans and C. albicans in vitro. The proteomic analyses showed the presence of immune-related proteins like actin, histones, hemoglobin, and ribosomal proteins. This protein pattern is similar to those reported for other fish mucus and stingray venoms. This is the first report depicting the Hypanus stingray mucus composition, highlighting its biochemical composition and importance for the stingray immune system and the possible role on the envenomation process.
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Affiliation(s)
| | | | | | | | - Patrícia Brigatte
- Faculdade de Medicina, Universidade Cidade de São Paulo-UNICID, Brazil
| | | | | | | | | | - Juliana Mozer Sciani
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Brazil; Laboratório Multidisciplinar de Pesquisa, Universidade São Francisco, Brazil.
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7
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Silva F, Huang Y, Yang V, Mu X, Shi Q, Antunes A. Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. Toxins (Basel) 2018; 10:E544. [PMID: 30567320 PMCID: PMC6315956 DOI: 10.3390/toxins10120544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 01/16/2023] Open
Abstract
Venomous animals are found through a wide taxonomic range including cartilaginous fish such as the freshwater stingray Potamotrygon motoro occurring in South America, which can injure people and cause venom-related symptoms. Ensuring the efficacy of drug development to treat stingray injuries can be assisted by the knowledge of the venom composition. Here we performed a detailed transcriptomic characterization of the venom gland of the South American freshwater stingray Potamotrygon motoro. The transcripts retrieved showed 418 hits to venom components (comparably to 426 and 396 hits in other two Potamotrygon species), with high expression levels of hyaluronidase, cystatin and calglandulin along with hits uniquely found in P. motoro such as DELTA-alicitoxin-Pse1b, Augerpeptide hhe53 and PI-actitoxin-Aeq3a. We also identified undescribed molecules with extremely high expression values with sequence similarity to the SE-cephalotoxin and Rapunzel genes. Comparative analyses showed that despite being closely related, there may be significant variation among the venoms of freshwater stingrays, highlighting the importance of considering elicit care in handling different envenomation cases. Since hyaluronidase represents a major component of fish venom, we have performed phylogenetic and selective pressure analyses of this gene/protein across all fish with the available information. Results indicated an independent recruitment of the hyaluronidase into the stingray venom relative to that of venomous bony fish. The hyaluronidase residues were found to be mostly under negative selection, but 18 sites showed evidence of diversifying positive selection (P < 0.05). Our data provides new insight into stingray venom variation, composition, and selective pressure in hyaluronidase.
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Affiliation(s)
- Filipe Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Vítor Yang
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Xidong Mu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Recreational Fisheries, Ministry of Agriculture, Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Guangzhou 510380, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
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Redmond AK, Macqueen DJ, Dooley H. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evol Biol 2018; 18:169. [PMID: 30442091 PMCID: PMC6238376 DOI: 10.1186/s12862-018-1290-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elephant shark (Callorhinchus milii), a chimaera whose ancestors split from the elasmobranch lineage ~ 420 mya. Initial analysis of this resource led to proposals that key components of the cartilaginous fish adaptive immune system, most notably their array of T cell subsets, was primitive compared to mammals. This proposal is at odds with the robust, antigen-specific antibody responses reported in elasmobranchs following immunization. To explore this discrepancy, we generated a multi-tissue transcriptome for small-spotted catshark (Scyliorhinus canicula), a tractable elasmobranch model for functional studies. We searched this, and other newly available sequence datasets, for CD4+ T cell subset-defining genes, aiming to confirm the presence or absence of each subset in cartilaginous fishes. RESULTS We generated a new transcriptome based on a normalised, multi-tissue RNA pool, aiming to maximise representation of tissue-specific and lowly expressed genes. We utilized multiple transcriptomic datasets and assembly variants in phylogenetic reconstructions to unambiguously identify several T cell subset-specific molecules in cartilaginous fishes for the first time, including interleukins, interleukin receptors, and key transcription factors. Our results reveal the inability of standard phylogenetic reconstruction approaches to capture the site-specific evolutionary processes of fast-evolving immune genes but show that site-heterogeneous mixture models can adequately do so. CONCLUSIONS Our analyses reveal that cartilaginous fishes are capable of producing a range of CD4+ T cell subsets comparable to that of mammals. Further, that the key molecules required for the differentiation and functioning of these subsets existed in the jawed vertebrate ancestor. Additionally, we highlight the importance of considering phylogenetic diversity and, where possible, utilizing multiple datasets for individual species, to accurately infer gene presence or absence at higher taxonomic levels.
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Affiliation(s)
- Anthony K Redmond
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Centre for Genome-Enabled Biology & Medicine, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Present address: Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Institute of Marine & Environmental Technology, 701 E Pratt St, Baltimore, MD21202, USA.
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9
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Anderson KC, Knuckey R, Cánepa M, Elizur A. A transcriptomic investigation of appetite-regulation and digestive processes in giant grouper Epinephelus lanceolatus during early larval development. JOURNAL OF FISH BIOLOGY 2018; 93:694-710. [PMID: 30232812 DOI: 10.1111/jfb.13798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
The giant grouper Epinephelus lanceolatus is an ecologically vulnerable species with high market demand. However, efforts to improve larval husbandry are hindered by a lack of knowledge surrounding larval developmental physiology. To address this shortfall, a transcriptomic approach was applied to larvae between 1 and 14 days post hatch (dph) to characterise the molecular ontogenesis of genes that influence appetite and digestion. Appetite regulating factors were detected from 1 dph, including neuropeptide Y, nesfatin-1, cocaine and amphetamine regulated transcript, cholecystokinin and pituitary adenylate cyclase activating peptide and the expression level of several genes changed sharply with the onset of exogenous feeding. The level of expression for proteases, chitinases, lipases and amylases typically followed one of two expression patterns, a general increase as development progressed, or an inverted U-shape with maximal expression at c. 6 dph. Similarly, the tendency among both expression patterns was for the level of expression to increase around the time of mouth-opening. There was also evidence to suggest the presence of putative isoforms for several digestion-related genes. We have provided an insight into appetite-regulation and digestive processes in groupers during early larval development and have developed a transcriptomic database that will aid future efforts to rear this species in an aquaculture setting.
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Affiliation(s)
- Kelli C Anderson
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania Newnham Campus, Launceston, Australia
| | - Richard Knuckey
- The Company One, Grouper Breeding Facility, Cairns, Australia
| | | | - Abigail Elizur
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Australia
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10
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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: 16] [Impact Index Per Article: 2.3] [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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Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics. Toxins (Basel) 2018; 10:toxins10060249. [PMID: 29921759 PMCID: PMC6024825 DOI: 10.3390/toxins10060249] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/17/2022] Open
Abstract
Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions. Several methods have been employed to assemble venom-gland transcriptomes, with the Trinity assembler being the most commonly applied among them. Although previous evidence of variation in performance among assembly software exists, particularly regarding recovery of difficult-to-assemble multigene families such as snake venom metalloproteinases, much work to date still employs a single assembly method. We evaluated the performance of several commonly used de novo assembly methods for the recovery of both nontoxin transcripts and complete, high-quality venom-gene transcripts across eleven snake and four scorpion transcriptomes. We varied k-mer sizes used by some assemblers to evaluate the impact of k-mer length on transcript recovery. We showed that the recovery of nontoxin transcripts and toxin transcripts is best accomplished through different assembly software, with SDT at smaller k-mer lengths and Trinity being best for nontoxin recovery and a combination of SeqMan NGen and a seed-and-extend approach implemented in Extender as the best means of recovering a complete set of toxin transcripts. In particular, Extender was the only means tested capable of assembling multiple isoforms of the diverse snake venom metalloproteinase family, while traditional approaches such as Trinity recovered at most one metalloproteinase transcript. Our work demonstrated that traditional metrics of assembly performance are not predictive of performance in the recovery of complete and high quality toxin genes. Instead, effective venom-gland transcriptomic studies should combine and quality-filter the results of several assemblers with varying algorithmic strategies.
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New findings from the first transcriptome of the Bothrops moojeni snake venom gland. Toxicon 2017; 140:105-117. [DOI: 10.1016/j.toxicon.2017.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022]
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Li R, Yan Z, Wang J, Song Q, Wang Z. De novo characterization of venom apparatus transcriptome of Pardosa pseudoannulata and analysis of its gene expression in response to Bt protein. BMC Biotechnol 2017; 17:73. [PMID: 29115956 PMCID: PMC5678584 DOI: 10.1186/s12896-017-0392-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pardosa pseudoannulata is a prevailing spider species, and has been regarded as an important bio-control agent of insect pests in farmland of China. However, the available genomic and transcriptomic databases of P. pseudoannulata and their venom are limited, which severely hampers functional genomic analysis of P. pseudoannulata. Recently high-throughput sequencing technology has been proved to be an efficient tool for profiling the transcriptome of relevant non-target organisms exposed to Bacillus thuringiensis (Bt) protein through food webs. Results In this study, the transcriptome of the venom apparatus was analyzed. A total of 113,358 non-redundant unigenes were yielded, among which 34,041 unigenes with complete or various length encoding regions were assigned biological function annotations and annotated with gene ontology and karyotic orthologous group terms. In addition, 3726 unigenes involved in response to stimulus and 720 unigenes associated with immune-response pathways were identified. Furthermore, we investigated transcriptomic changes in the venom apparatus using tag-based DGE technique. A total of 1724 differentially expressed genes (DEGs) were detected, while 75 and 372 DEGs were functionally annotated with KEGG pathways and GO terms, respectively. qPCR analyses were performed to verify the DEGs directly or indirectly related to immune and stress responses, including genes encoding heat shock protein, toll-like receptor, GST and NADH dehydrogenase. Conclusion This is the first study conducted to specifically investigate the venom apparatus of P. pseudoannulata in response to Bt protein exposure through tritrophic chain. A substantial fraction of transcript sequences was generated by high-throughput sequencing of the venom apparatus of P. pseudoannulata. Then a comparative transcriptome analysis showing a large number of candidate genes involved in immune response were identified by the tag-based DGE technology. This transcriptome dataset will provide a comprehensive sequence resource for furture molecular genetic research of the venom apparatus of P. pseudoannulata. Electronic supplementary material The online version of this article (10.1186/s12896-017-0392-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Li
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.,Department of Biosciences, Hunan University of Arts and Science, Changde, 415000, China
| | - Zhenzhen Yan
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Juan Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Zhi Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.
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Dos Santos JC, Grund LZ, Seibert CS, Marques EE, Soares AB, Quesniaux VF, Ryffel B, Lopes-Ferreira M, Lima C. Stingray venom activates IL-33 producing cardiomyocytes, but not mast cell, to promote acute neutrophil-mediated injury. Sci Rep 2017; 7:7912. [PMID: 28801624 PMCID: PMC5554156 DOI: 10.1038/s41598-017-08395-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/12/2017] [Indexed: 12/30/2022] Open
Abstract
One of the hallmarks of acute inflammation is neutrophil infiltration of tissues. We investigated molecular mechanisms implicated in acute neutrophilic inflammation induced by the venom of a freshwater stingray (Potamotrygon cf. henlei) in mice. Ray venom induced early mobilization of neutrophil in the microvasculature of cremaster mice and infiltration of the peritoneal cavity 2 hours after injury, in a dose-response manner. IL-1β, IL-6, TNF-α, and KC were produced. The neutrophilic infiltration did not occur in mice with ST2 receptor and MyD88 adapters neutralized, or in those with PI3K and p38 MAPK signaling blocked. Drastic reduction of neutrophil infiltration to peritoneal cavities was observed in ST2−/−, TLR2/TLR4−/−, MyD88−/−, TRIF−/− and IL-17A−/− mice, and a partial reduction was observed in IL-18R−/− mice. Mast cell Kit W(sh)/W(sh)-, AHR-, NLRP3-, ICE-, IL-1β-, P2RX7-, CD39-, IL-17RA-, and TBX21 KO mice retain the ability to induce neutrophilia in peritoneal cavity after ray venom injection. IL-6 and TNF-α alone were insufficient for promote neutrophilia in the absence of ST2 signaling. Finally, abundant production of IL-33 by cardiomyocytes was observed. These results refine our understanding of the importance of the IL-33/ST2 axis and IL-33-producing cardiomyocytes in the early acute neutrophilia induced by freshwater stingray venoms.
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Affiliation(s)
| | - Lidiane Zito Grund
- Immunoregulation Unit of the Special Laboratory of Applied Toxinology(CEPID/FAPESP), Butantan Institute, São Paulo, Brazil
| | | | | | | | - Valerie F Quesniaux
- Allergy and Lung Inflammation Unit of the Molecular and Experimental Immunology and Neurogenetics (CNRS), Orléans, France
| | - Bernhard Ryffel
- Allergy and Lung Inflammation Unit of the Molecular and Experimental Immunology and Neurogenetics (CNRS), Orléans, France
| | - Monica Lopes-Ferreira
- Immunoregulation Unit of the Special Laboratory of Applied Toxinology(CEPID/FAPESP), Butantan Institute, São Paulo, Brazil
| | - Carla Lima
- Immunoregulation Unit of the Special Laboratory of Applied Toxinology(CEPID/FAPESP), Butantan Institute, São Paulo, Brazil.
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15
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Madio B, Undheim EAB, King GF. Revisiting venom of the sea anemone Stichodactyla haddoni: Omics techniques reveal the complete toxin arsenal of a well-studied sea anemone genus. J Proteomics 2017; 166:83-92. [PMID: 28739511 DOI: 10.1016/j.jprot.2017.07.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/04/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022]
Abstract
More than a century of research on sea anemone venoms has shown that they contain a diversity of biologically active proteins and peptides. However, recent omics studies have revealed that much of the venom proteome remains unexplored. We used, for the first time, a combination of proteomic and transcriptomic techniques to obtain a holistic overview of the venom arsenal of the well-studied sea anemone Stichodactyla haddoni. A purely search-based approach to identify putative toxins in a transcriptome from tentacles regenerating after venom extraction identified 508 unique toxin-like transcripts grouped into 63 families. However, proteomic analysis of venom revealed that 52 of these toxin families are likely false positives. In contrast, the combination of transcriptomic and proteomic data enabled positive identification of 23 families of putative toxins, 12 of which have no homology known proteins or peptides. Our data highlight the importance of using proteomics of milked venom to correctly identify venom proteins/peptides, both known and novel, while minimizing false positive identifications from non-toxin homologues identified in transcriptomes of venom-producing tissues. This work lays the foundation for uncovering the role of individual toxins in sea anemone venom and how they contribute to the envenomation of prey, predators, and competitors. BIOLOGICAL SIGNIFICANCE Proteomic analysis of milked venom combined with analysis of a tentacle transcriptome revealed the full extent of the venom arsenal of the sea anemone Stichodactyla haddoni. This combined approach led to the discovery of 12 entirely new families of disulfide-rich peptides and proteins in a genus of anemones that have been studied for over a century.
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Affiliation(s)
- Bruno Madio
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Glenn F King
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia.
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Perez-Riverol A, Dos Santos-Pinto JRA, Lasa AM, Palma MS, Brochetto-Braga MR. Wasp venomic: Unravelling the toxins arsenal of Polybia paulista venom and its potential pharmaceutical applications. J Proteomics 2017; 161:88-103. [PMID: 28435107 DOI: 10.1016/j.jprot.2017.04.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/06/2017] [Accepted: 04/17/2017] [Indexed: 02/08/2023]
Abstract
Polybia paulista (Hymenoptera: Vespidae) is a neotropical social wasp from southeast Brazil. As most social Hymenoptera, venom from P. paulista comprises a complex mixture of bioactive toxins ranging from low molecular weight compounds to peptides and proteins. Several efforts have been made to elucidate the molecular composition of the P. paulista venom. Data derived from proteomic, peptidomic and allergomic analyses has enhanced our understanding of the whole envenoming process caused by the insect sting. The combined use of bioinformatics, -omics- and molecular biology tools have allowed the identification, characterization, in vitro synthesis and recombinant expression of several wasp venom toxins. Some of these P. paulista - derived bioactive compounds have been evaluated for the rational design of antivenoms and the improvement of allergy specific diagnosis and immunotherapy. Molecular characterization of crude venom extract has enabled the description and isolation of novel toxins with potential biotechnological applications. Here, we review the different approaches that have been used to unravel the venom composition of P. paulista. We also describe the main groups of P. paulista - venom toxins currently identified and analyze their potential in the development of component-resolved diagnosis of allergy, and in the rational design of antivenoms and novel bioactive drugs.
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Affiliation(s)
- Amilcar Perez-Riverol
- Laboratório de Biologia Molecular de Artrópodes-LBMA-IBRC-UNESP (Univ Estadual Paulista), Av. 24-A, n° 1515, CEP 13506-900, Bela Vista, Rio Claro, SP, Brazil.
| | | | - Alexis Musacchio Lasa
- Center for Genetic Engineering and Biotechnology, Biomedical Research Division, System Biology Department, Ave. 31, e/158 and 190, P.O. Box 6162, Cubanacan, Playa, Havana 10600, Cuba.
| | - Mario Sergio Palma
- Centro de Estudos de Insetos Sociais-CEIS-IBRC-UNESP (Univ Estadual Paulista), Av. 24-A, n° 1515, CEP 13506-900, Bela Vista, Rio Claro, SP, Brazil.
| | - Márcia Regina Brochetto-Braga
- Laboratório de Biologia Molecular de Artrópodes-LBMA-IBRC-UNESP (Univ Estadual Paulista), Av. 24-A, n° 1515, CEP 13506-900, Bela Vista, Rio Claro, SP, Brazil; Centro de Estudos de Venenos e Animais Peçonhentos-CEVAP (Univ Estadual Paulista), Rua José Barbosa de Barros, 1780, Fazenda Experimental Lageado, Botucatu 18610-307, SP, Brazil.
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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: 1.4] [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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