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Figueroa A, Low MEY, Lim KKP. Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution. Zootaxa 2023; 5287:1-378. [PMID: 37518684 DOI: 10.11646/zootaxa.5287.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 08/01/2023]
Abstract
Given Singapore's location at the confluence of important maritime trading routes, and that it was established as a British East India Company trading post in 1819, it is unsurprising that Singapore has become one of the centres of natural history collecting and research in Southeast Asia. Despite its small size, Singapore is home to a diverse herpetofauna assemblage and boasts a rich herpetological history. The first systematic studies of Singapore's herpetofauna (within the Linnaean binomial framework) date back to Stamford Raffles and the naturalists hired by him who first came to the island in 1819. Specimens that were collected during and after this time were deposited in museums worldwide. Over time, 39 species from Singapore were described as new to science. Due to the entrepôt nature of Singapore with its associated purchasing and trading of specimens (both alive and dead), poor record-keeping, and human introductions, numerous extraneous species from outside of Singapore were reported to occur on the island. Such issues have left a complicated legacy of ambiguous records and taxonomic complications concerning the identity of Singapore's species-rich herpetofauna, many of which were only resolved in the past 30-40 years. By compiling a comprehensive collection of records and publications relating to the herpetofauna of Singapore, we construct an updated and more accurate listing of the herpetofauna of Singapore. Our investigation culminated in the evaluation of 309 species, in which we compiled a final species checklist recognising 166 species (149 native and 17 non-native established species). Among the 149 native species are two caecilians, 24 frogs, one crocodilian, 13 turtles (three visitors), 34 lizards, and 75 snakes. Of the 17 non-native species are five frogs, four turtles, six lizards, and two snakes. The remaining 143 species represent species to be excluded from Singapore's herpetofauna species checklist. For each of the 309 species examined, we provide species accounts and explanatory annotations. Furthermore, we discuss Singapore's herpetofauna from a historical and conservation perspective. Immediate deforestation and nationwide urbanisation following colonisation completely eliminated many species from throughout much of the country and restricted them to small, degraded forest patches. We hope this publication highlights the importance of publishing observations and serves as a valuable resource to future researchers, naturalists, biological consultants, and policy makers in initiating studies on species ecology, distribution, status, and promoting conservation efforts to safeguard Singapore's herpetofauna.
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Affiliation(s)
| | - Martyn E Y Low
- Lee Kong Chian Natural History Museum; 2 Conservatory Drive; Singapore 117377.
| | - Kelvin K P Lim
- Lee Kong Chian Natural History Museum; 2 Conservatory Drive; Singapore 117377.
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2
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Wan H, Liu Q, Ju Y. Utilize a few features to classify presynaptic and postsynaptic neurotoxins. Comput Biol Med 2023; 152:106380. [PMID: 36473343 DOI: 10.1016/j.compbiomed.2022.106380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/21/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Neurotoxins are a class of proteins that have a significant damaging effect on nerve tissue. Neurotoxins are classified into presynaptic neurotoxins and postsynaptic neurotoxins, and accurate identification of neurotoxins plays a key role in drug development. In this study, 90 presynaptic neurotoxins and 165 postsynaptic neurotoxins were classified. The features of the presynaptic and postsynaptic neurotoxin sequences were extracted using the AutoProp feature extraction method and feature selection was performed using the maximum relevance maximum distance (MRMD) program, Finally, only two features were retained to achieve 84.7% classification accuracy. Moreover, it was found that the two retained features were present in the conserved sites and motifs of presynaptic neurotoxins and could represent the critical structures of presynaptic neurotoxins. This method demonstrates that using a few key features to classify proteins can effectively identify critical protein structures.
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Affiliation(s)
- Hao Wan
- Institute of Advanced Cross-field Science, College of Life Science, Qingdao University, Qingdao, China
| | - Qing Liu
- Department of Anesthesiology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China.
| | - Ying Ju
- School of Informatics, Xiamen University, Xiamen, China.
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3
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Zhu W, Guo Y, Zou Q. Prediction of presynaptic and postsynaptic neurotoxins based on feature extraction. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:5943-5958. [PMID: 34517517 DOI: 10.3934/mbe.2021297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A neurotoxin is essentially a protein that mainly acts on the nervous system; it has a selective toxic effect on the central nervous system and neuromuscular nodes, can cause muscle paralysis and respiratory paralysis, and has strong lethality. According to their principle of action, neurotoxins are divided into presynaptic neurotoxins and postsynaptic neurotoxins. Correctly identifying presynaptic and postsynaptic nerve toxins provides important clues for future drug development and the discovery of drug targets. Therefore, a predictive model, Neu_LR, was constructed in this paper. The monoMonokGap method was used to extract the frequency characteristics of presynaptic and postsynaptic neurotoxin sequences and carry out feature selection, then, based on the important features obtained after dimensionality reduction, the prediction model Neu_LR was constructed using a logistic regression algorithm, and ten-fold cross-validation and independent test set validation were used. The final accuracy rates were 99.6078 and 94.1176%, respectively, which proved that the Neu_LR model had good predictive performance and robustness, and could meet the prediction requirements of presynaptic and postsynaptic neurotoxins. The data and source code of the model can be freely download from https://github.com/gyx123681/.
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Affiliation(s)
- Wen Zhu
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou, China
- Key Laboratory of Data Science and Intelligence Education, Hainan Normal University, Ministry of Education, Haikou, China
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
| | - Yuxin Guo
- Key Laboratory of Computational Science and Application of Hainan Province, Haikou, China
- Key Laboratory of Data Science and Intelligence Education, Hainan Normal University, Ministry of Education, Haikou, China
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
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4
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Cao Y, Yu C, Huang S, Wang S, Zuo Y, Yang L. Characterization and Prediction of Presynaptic and Postsynaptic Neurotoxins Based on Reduced Amino Acids and Biological Properties. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200707150512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Presynaptic and postsynaptic neurotoxins are two important neurotoxins. Due to the important
role of presynaptic and postsynaptic neurotoxins in pharmacology and neuroscience, identification of them becomes very
important in biology.
Method:
In this study, the statistical test and F-score were used to calculate the difference between amino acids and
biological properties. The support vector machine was used to predict the presynaptic and postsynaptic neurotoxins by
using the reduced amino acid alphabet types.
Results:
By using the reduced amino acid alphabet as the input parameters of support vector machine, the overall accuracy
of our classifier had increased to 91.07%, which was the highest overall accuracy in this study. When compared with the
other published methods, better predictive results were obtained by our classifier.
Conclusion:
In summary, we analyzed the differences between two neurotoxins in amino acids and biological properties,
and constructed a classifier that could predict these two neurotoxins by using the reduced amino acid alphabet.
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Affiliation(s)
- Yiyin Cao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chunlu Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shenghui Huang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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5
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Li P, Zhang H, Zhao X, Jia C, Li F, Song J. Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins. J Bioinform Comput Biol 2020; 18:2050008. [PMID: 32372714 DOI: 10.1142/s0219720020500080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Presynaptic and postsynaptic neurotoxins are two types of neurotoxins from venomous animals and functionally important molecules in the neurosciences; however, their experimental characterization is difficult, time-consuming, and costly. Therefore, bioinformatics tools that can identify presynaptic and postsynaptic neurotoxins would be very useful for understanding their functions and mechanisms. In this study, we propose Pippin, a novel machine learning-based method that allows users to rapidly and accurately identify these two types of neurotoxins. Pippin was developed using the random forest (RF) algorithm and evaluated based on an up-to-date dataset. A variety of sequence and motif features were combined, and a two-step feature-selection algorithm was employed to characterize the optimal feature subset for presynaptic and postsynaptic neurotoxin prediction. Extensive benchmark tests illustrate that Pippin significantly improved predictive performance as compared with six other commonly used machine-learning algorithms, including the naïve Bayes classifier, Multinomial Naïve Bayes classifier (MNBC), AdaBoost, Bagging, K-nearest neighbors, and XGBoost. Additionally, we developed an online webserver for Pippin to facilitate public use. To the best of our knowledge, this is the first webserver for presynaptic and postsynaptic neurotoxin prediction.
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Affiliation(s)
- Pengyu Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - He Zhang
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Xuyang Zhao
- College of Information Engineering, Northwest A&F University, Yangling, 712100, P. R. China
| | - Cangzhi Jia
- School of Science, Dalian Maritime University, Dalian 116026, P. R. China
| | - Fuyi Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
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6
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Mei J, Zhao J. Analysis and prediction of presynaptic and postsynaptic neurotoxins by Chou's general pseudo amino acid composition and motif features. J Theor Biol 2018; 447:147-153. [DOI: 10.1016/j.jtbi.2018.03.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 11/26/2022]
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7
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Huo H, Li T, Wang S, Lv Y, Zuo Y, Yang L. Prediction of presynaptic and postsynaptic neurotoxins by combining various Chou's pseudo components. Sci Rep 2017; 7:5827. [PMID: 28724993 PMCID: PMC5517432 DOI: 10.1038/s41598-017-06195-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/08/2017] [Indexed: 11/09/2022] Open
Abstract
Presynaptic and postsynaptic neurotoxins are two groups of neurotoxins. Identification of presynaptic and postsynaptic neurotoxins is an important work for numerous newly found toxins. It is both costly and time consuming to determine these two neurotoxins by experimental methods. As a complement, using computational methods for predicting presynaptic and postsynaptic neurotoxins could provide some useful information in a timely manner. In this study, we described four algorithms for predicting presynaptic and postsynaptic neurotoxins from sequence driven features by using Increment of Diversity (ID), Multinomial Naive Bayes Classifier (MNBC), Random Forest (RF), and K-nearest Neighbours Classifier (IBK). Each protein sequence was encoded by pseudo amino acid (PseAA) compositions and three biological motif features, including MEME, Prosite and InterPro motif features. The Maximum Relevance Minimum Redundancy (MRMR) feature selection method was used to rank the PseAA compositions and the 50 top ranked features were selected to improve the prediction accuracy. The PseAA compositions and three kinds of biological motif features were combined and 12 different parameters that defined as P1-P12 were selected as the input parameters of ID, MNBC, RF, and IBK. The prediction results obtained in this study were significantly better than those of previously developed methods.
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Affiliation(s)
- Haiyan Huo
- Department of Environmental Engineering, Hohhot University for Nationalities, Hohhot, 010051, China
| | - Tao Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongchun Zuo
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, 010021, China.
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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8
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Predicting Presynaptic and Postsynaptic Neurotoxins by Developing Feature Selection Technique. BIOMED RESEARCH INTERNATIONAL 2017; 2017:3267325. [PMID: 28303250 PMCID: PMC5337787 DOI: 10.1155/2017/3267325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 12/18/2016] [Indexed: 02/06/2023]
Abstract
Presynaptic and postsynaptic neurotoxins are proteins which act at the presynaptic and postsynaptic membrane. Correctly predicting presynaptic and postsynaptic neurotoxins will provide important clues for drug-target discovery and drug design. In this study, we developed a theoretical method to discriminate presynaptic neurotoxins from postsynaptic neurotoxins. A strict and objective benchmark dataset was constructed to train and test our proposed model. The dipeptide composition was used to formulate neurotoxin samples. The analysis of variance (ANOVA) was proposed to find out the optimal feature set which can produce the maximum accuracy. In the jackknife cross-validation test, the overall accuracy of 94.9% was achieved. We believe that the proposed model will provide important information to study neurotoxins.
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9
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Tan T, Xiang X, Qu H, Zhu S, Bi Q. The study on venom proteins of Lapemis hardwickii by cDNA phage display. Toxicol Lett 2011; 206:252-7. [DOI: 10.1016/j.toxlet.2011.05.1028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/06/2011] [Accepted: 05/06/2011] [Indexed: 11/29/2022]
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10
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Chu ER, Weinstein SA, White J, Warrell DA. Venom ophthalmia caused by venoms of spitting elapid and other snakes: Report of ten cases with review of epidemiology, clinical features, pathophysiology and management. Toxicon 2010; 56:259-72. [DOI: 10.1016/j.toxicon.2010.02.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 02/10/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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11
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Yang L, Li Q. Prediction of presynaptic and postsynaptic neurotoxins by the increment of diversity. Toxicol In Vitro 2009; 23:346-8. [DOI: 10.1016/j.tiv.2008.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 11/29/2008] [Accepted: 12/09/2008] [Indexed: 11/26/2022]
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12
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Pawlak J, Mackessy SP, Sixberry NM, Stura EA, Le Du MH, Ménez R, Foo CS, Ménez A, Nirthanan S, Kini RM. Irditoxin, a novel covalently linked heterodimeric three-finger toxin with high taxon-specific neurotoxicity. FASEB J 2008; 23:534-45. [PMID: 18952712 DOI: 10.1096/fj.08-113555] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel heterodimeric three-finger neurotoxin, irditoxin, was isolated from venom of the brown treesnake Boiga irregularis (Colubridae). Irditoxin subunit amino acid sequences were determined by Edman degradation and cDNA sequencing. The crystal structure revealed two subunits with a three-finger protein fold, typical for "nonconventional" toxins such as denmotoxin, bucandin, and candoxin. This is the first colubrid three-finger toxin dimer, covalently connected via an interchain disulfide bond. Irditoxin showed taxon-specific lethality toward birds and lizards and was nontoxic toward mice. It produced a potent neuromuscular blockade at the avian neuromuscular junction (IC(50)=10 nM), comparable to alpha-bungarotoxin, but was three orders of magnitude less effective at the mammalian neuromuscular junction. Covalently linked heterodimeric three-finger toxins found in colubrid venoms constitute a new class of venom peptides, which may be a useful source of new neurobiology probes and therapeutic leads.
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Affiliation(s)
- Joanna Pawlak
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Science Dr. 4, Singapore 117543
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13
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Unique gene organization of colubrid three-finger toxins: Complete cDNA and gene sequences of denmotoxin, a bird-specific toxin from colubrid snake Boiga dendrophila (Mangrove Catsnake). Biochimie 2008; 90:868-77. [DOI: 10.1016/j.biochi.2008.02.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
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14
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He YY, Lee WH, Zhang Y. Cloning and purification of α-neurotoxins from king cobra (Ophiophagus hannah). Toxicon 2004; 44:295-303. [PMID: 15302536 DOI: 10.1016/j.toxicon.2004.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2004] [Revised: 06/02/2004] [Accepted: 06/04/2004] [Indexed: 10/26/2022]
Abstract
Thirteen complete and three partial cDNA sequences were cloned from the constructed king cobra (Ophiophagus hannah) venom gland cDNA library. Phylogenetic analysis of nucleotide sequences of king cobra with those from other snake venoms revealed that obtained cDNAs are highly homologous to snake venom alpha-neurotoxins. Alignment of deduced mature peptide sequences of the obtained clones with those of other reported alpha-neurotoxins from the king cobra venom indicates that our obtained 16 clones belong to long-chain neurotoxins (seven), short-chain neurotoxins (seven), weak toxin (one) and variant (one), respectively. Up to now, two out of 16 newly cloned king cobra alpha-neurotoxins have identical amino acid sequences with CM-11 and Oh-6A/6B, which have been characterized from the same venom. Furthermore, five long-chain alpha-neurotoxins and two short-chain alpha-neurotoxins were purified from crude venom and their N-terminal amino acid sequences were determined. The cDNAs encoding the putative precursors of the purified native peptide were also determined based on the N-terminal amino acid sequencing. The purified alpha-neurotoxins showed different lethal activities on mice.
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Affiliation(s)
- Ying-Ying He
- Department of Animal Toxinology, Kunming Institute of Zoology, The Chinese Academy of Sciences, 32 East Jiao Chang Road, Kunming 650223, Yunnan, China
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15
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Peng LS, Zhong XF, Huang YS, Zhang Y, Zheng SL, Wei JW, Wu WY, Xu AL. Molecular cloning, expression and characterization of three short chain alpha-neurotoxins from the venom of sea snake--Hydrophiinae Hydrophis cyanocinctus Daudin. Toxicon 2004; 42:753-61. [PMID: 14757206 DOI: 10.1016/j.toxicon.2003.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three different genes named sn311, sn316 and sn285 were discovered by large-scale randomly sequencing the high quality cDNA library of the venom glands from Hydrophiinae Hydrophis cyanocinctus Daudin. Sequence analysis showed that these three genes encoded three different short chain alpha-neurotoxins of 81 amino acids, which contained a signal peptide of 21 amino acids and followed by a mature peptide of 60 amino acids. Amino acid comparison reveals that mature peptides of sn311 and sn316 are highly homologous, with the only variance at position 46, which is Lys46 and Ser46, respectively. Whereas the mature peptide of sn285 lacks the most conserved amino acids in short chain alpha-neurotoxins, Asp31 and Arg33. The coding sequences of three neurotoxins were cloned into a thioredoxin (TRX) fusion expression vector (pTRX) and expressed as soluble recombinant fusion proteins in E. coli. After purification, approximately 10 mg/l recombinant proteins with the purity up to 95% were obtained. These three recombinant proteins are designated as rSN311, rSN316 and rSN285, they have a molecular weight of 6.963, 6.920 and 6.756 kDa, respectively, which are similar to those predicted from amino acid sequences. LD50 values of rSN311, rSN316 and rSN285 are 0.0827, 0.095, and 0.0647 mg/kg to mice, respectively. Studies on effects of these recombinant proteins on neuromuscular transmission were carried out, and results indicate that they all can produce prompt blockade of neuromuscular transmission, but display distinct biological activity characteristic individually. The results from UV-circular dichroism (CD) spectra indicate that they share similar secondary structure compared to other identified alpha-neurotoxins, and no significant structural differences in these recombinant proteins are observed.
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Affiliation(s)
- Li-Sheng Peng
- The Open Laboratory for Marine Functional Genomics of State High-Tech Development, Department of Biochemistry, College of Life Science, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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16
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Phui Yee JS, Nanling G, Afifiyan F, Donghui M, Siew Lay P, Armugam A, Jeyaseelan K. Snake postsynaptic neurotoxins: gene structure, phylogeny and applications in research and therapy. Biochimie 2004; 86:137-49. [PMID: 15016453 DOI: 10.1016/j.biochi.2003.11.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2003] [Accepted: 11/28/2003] [Indexed: 11/15/2022]
Abstract
Snake venoms are complex mixtures of biologically active polypeptides that target a variety of vital physiological functions in mammals. alpha-Neurotoxins, toxins that cause paralysis by binding to the nicotinic receptors at the postsynaptic region of the neuromuscular junction have been widely studied in terms of their structure-function relationships as well as gene structure, organization and expression. In this review, we describe the structure of alpha-neurotoxin genes and discuss their evolutionary relationships. Almost all members of neurotoxins have been found to exhibit a common evolutionary origin. The importance of alpha-neurotoxins in therapy and research has also been discussed to highlight their potential applications especially in the area of drug discovery.
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Affiliation(s)
- Joyce Siew Phui Yee
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
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17
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Jeyaseelan K, Poh SL, Nair R, Armugam A. Structurally conserved α-neurotoxin genes encode functionally diverse proteins in the venom of Naja sputatrix
1. FEBS Lett 2003; 553:333-41. [PMID: 14572646 DOI: 10.1016/s0014-5793(03)01039-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The structure and organization of the genes encoding the long-chain neurotoxins and four other isoforms of weak neurotoxins in the venom of Naja sputatrix are reported. The genes contained three exons interrupted by two introns, a structure similar to other members of the three-finger toxin family. The proteins encoded by these genes, however, show varied affinity towards nicotinic acetylcholine receptors. Phylogenetic analysis of these genes showed that the weak neurotoxin gene is confined to a distinct group. We also observe that specific mutations of the gene provide the diversity in function in these toxins while maintaining a common structural scaffold. This forms the first report where the molecular basis of evolution of postsynaptic neurotoxins from an ancestral gene can be demonstrated using the same species of snake.
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Affiliation(s)
- Kandiah Jeyaseelan
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore.
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18
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Ma D, Armugam A, Jeyaseelan K. Cytotoxic potency of cardiotoxin from Naja sputatrix: development of a new cytolytic assay. Biochem J 2002; 366:35-43. [PMID: 12027804 PMCID: PMC1222773 DOI: 10.1042/bj20020437] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2002] [Revised: 05/21/2002] [Accepted: 05/24/2002] [Indexed: 11/17/2022]
Abstract
The possible involvement of specific regions/loops of cardiotoxin from Naja sputatrix venom in mediating its cytolytic activity is evaluated using a new cytolytic assay. In this assay, the amount of chloramphenicol acetyltransferase (CAT) that is released upon lysis of the cellular membranes by the cytotoxin has been measured as an index of cytolysis. This newly developed CAT system is more sensitive than the traditional haemolysis method utilizing red blood cells or the lactate dehydrogenase assay for cytolysis. Series of chimaeric toxin molecules have been constructed by swapping the loops between highly hydrophilic neurotoxin and highly hydrophobic cardiotoxin molecules from Naja sputatrix, which are known to exhibit structural similarity (three-finger conformation) but to have different functional properties. Comparison of the cytolytic activities of the recombinant chimaeric toxins demonstrated the possible involvement of all three loops of cardiotoxin in its cytolytic potency. However, the first two loops of the protein appear to make the major contribution to its lytic activity. cDNAs encoding cardiotoxin and the chimaeric toxins, when expressed in transfected cultured Chinese hamster ovary cells, resulted in cell lysis, indicating that these cDNAs can be developed as useful cytolytic agents.
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Affiliation(s)
- Donghui Ma
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 10 Medical Drive, Singapore 119260
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19
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Ma D, Armugam A, Jeyaseelan K. Alpha-neurotoxin gene expression in Naja sputatrix: identification of a silencer element in the promoter region. Arch Biochem Biophys 2002; 404:98-105. [PMID: 12127074 DOI: 10.1016/s0003-9861(02)00245-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Alpha-neurotoxin (alpha-NTX) from the venom of cobra, Naja sputatrix, is a highly lethal post-synaptic toxin that is responsible for the lethality caused by the venom. However, this toxin is found at low levels (3%) in the crude venom. The expression of its gene is determined by a promoter which is 90% similar to the promoter of another three-fingered toxin, cardiotoxin (CTX), which is produced in large amounts (60%) in the same venom. Functional analysis of the NTX-2 gene promoter demonstrated the presence of a silencer element of 24 nucleotides (nt -678 to -655) at its 5(') flanking region. This element has been found to play a major role in the down-regulation of NTX-2 gene expression. A point mutation on this silencer appears to attenuate its repressive property in CTX-2 gene.
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Affiliation(s)
- Donghui Ma
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, Singapore
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Gong N, Armugam A, Mirtschin P, Jeyaseelan K. Cloning and characterization of the pseudonajatoxin b precursor. Biochem J 2001; 358:647-56. [PMID: 11535126 PMCID: PMC1222099 DOI: 10.1042/0264-6021:3580647] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An Australian common brown snake, Pseudonaja textilis, is known to contain highly lethal neurotoxins. Among them, a long-chain alpha-neurotoxin, pseudonajatoxin b, has been identified. In this report, while presenting evidence for the presence of at least four such long-chain alpha-neurotoxins in the venom of P. textilis, we describe the characteristics of both the mRNA and the gene responsible for the synthesis of these neurotoxins. A precursor toxin synthesized from the gene has been identified as being capable of producing the isoforms possibly by post-translational modifications at its C-terminal end. Recombinant toxins corresponding to the precursor and its product have been found to possess similar binding affinities for muscular acetylcholine receptors (IC(50)=3x10(-8) M) and a lethality, LD(50), of 0.15 microg/g in mice.
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Affiliation(s)
- N Gong
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 10 Medical Drive, Singapore 119260
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Gong N, Armugam A, Jeyaseelan K. Molecular cloning, characterization and evolution of the gene encoding a new group of short-chain alpha-neurotoxins in an Australian elapid, Pseudonaja textilis. FEBS Lett 2000; 473:303-10. [PMID: 10818230 DOI: 10.1016/s0014-5793(00)01549-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The structure and organization of five genes responsible for the synthesis of six isoforms of short-chain alpha-neurotoxins in Pseudonaja textilis venom are reported in this paper. This also forms the first report which describes the synthesis of two neurotoxin mRNA variants from one of these genes (Pt-sntx1) as a result of alternative splicing. Each gene consists of three exons which are separated by two introns and each has a functional promoter. The promoter activity was confirmed by both CAT assay and Real-Time PCR. A transcription initiation site, two putative TATA boxes, one CCAAT box and the transcription factor binding consensus sites for AP-1, GATA-2, c/EBPb were identified in the 5' non-coding region of each gene. Phylogenetic analysis showed that these five genes from P. textilis constituted a distinct group which has evolved by gene duplication followed by accelerated evolution from an ancestral gene.
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Affiliation(s)
- N Gong
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 10 Medical Drive, 119260, Singapore, Singapore
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Gong N, Armugam A, Jeyaseelan K. Postsynaptic short-chain neurotoxins from Pseudonaja textilis. cDNA cloning, expression and protein characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:982-9. [PMID: 10518793 DOI: 10.1046/j.1432-1327.1999.00800.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two lethal proteins, which specifically bind to the nAChR from Torpedo californica, were isolated from the venom of Pseudonaja textilis, the common brown snake from Australia. The isolated proteins have masses of 6236 and 6345 Da and are structurally related to short-chain neurotoxins from other elapids. Six cDNAs encoding isoforms of related neurotoxins were cloned using the RT-PCR of the venom gland mRNAs. The sequences of the corresponding proteins consist of 57-58 amino acid residues and display several unique features when compared with all known short-chain neurotoxins. Accordingly, they grouped separately in phylogenetic analysis. The six cDNAs were expressed in Escherichia coli and the recombinant proteins were characterized. They have similar masses and display similar toxicities and binding constants to the nAChR as the native toxins isolated from the venom. Thus, a new group of short-chain postsynaptic neurotoxins from the venom of an Australian elapid has been characterized.
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Affiliation(s)
- N Gong
- Department of Biochemistry, National University of Singapore, Singapore
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Afifiyan F, Armugam A, Tan CH, Gopalakrishnakone P, Jeyaseelan K. Postsynaptic α-Neurotoxin Gene of the Spitting Cobra, Naja naja sputatrix: Structure, Organization, and Phylogenetic Analysis. Genome Res 1999. [DOI: 10.1101/gr.9.3.259] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The venom of the spitting cobra, Naja naja sputatrixcontains highly potent α-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of α-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5′ and 3′ UTRs. Each NTX isoform is ∼4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and −45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the α-NTX and κ-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene.[The genomic DNA sequences reported in this paper have been submitted to GenBank databases under accession nos. AF096999 to AF097001.]
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