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Li Y, Zhang H, Fu Y, Zhou Z, Yu W, Zhou J, Li J, Du G, Liu S. Enhancing Acid Resistance of Aspergillus niger Pectin Lyase through Surface Charge Design for Improved Application in Juice Clarification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11652-11662. [PMID: 38738910 DOI: 10.1021/acs.jafc.4c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Pectin lyases (PNLs) can enhance juice clarity and flavor by degrading pectin in highly esterified fruits, but their inadequate acid resistance leads to rapid activity loss in juice. This study aimed to improve the acid resistance of Aspergillus niger PNL pelA through surface charge design. A modification platform was established by fusing pelA with a protein tag and expressing the fusion enzyme in Escherichia coli. Four single-point mutants were identified to increase the surface charge using computational tools. Moreover, the combined mutant M6 (S514D/S538E) exhibited 99.8% residual activity at pH 3.0. The M6 gene was then integrated into the A. niger genome using a multigene integration system to obtain the recombinant PNL AM6. Notably, AM6 improved the light transmittance of orange juice to 45.3%, which was 8.39 times higher than that of pelA. In conclusion, AM6 demonstrated the best-reported acid resistance, making it a promising candidate for industrial juice clarification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Haiyun Zhang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yishan Fu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Zhitong Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Wenwen Yu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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You Y, Tang Y, Yin W, Liu X, Gao P, Zhang C, Tembrock LR, Zhao Y, Yang Z. From genome to proteome: Comprehensive identification of venom toxins from the Chinese funnel-web spider (Macrothelidae: Macrothele yani). Int J Biol Macromol 2024; 268:131780. [PMID: 38657926 DOI: 10.1016/j.ijbiomac.2024.131780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/26/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Macrothelidae is a family of mygalomorph spiders containing the extant genera Macrothele and Vacrothele. China is an important center of diversity for Macrothele with 65 % of the known species occurring there. Previous work on Macrothele was able to uncover several important toxin compounds including Raventoxin which may have applications in biomedicine and agricultural chemistry. Despite the importance of Macrothele spiders, high-quality reference genomes are still lacking, which hinders our understanding and application of the toxin compounds. In this study, we assembled the genome of the Macrothele yani to help fill gaps in our understanding of toxin biology in this lineage of spiders to encourage the future study and applications of these compounds. The final assembled genome was 6.79 Gb in total length, had a contig N50 of 21.44 Mb, and scaffold N50 of 156.16 Mb. Hi-C scaffolding assigned 98.19 % of the genome to 46 pseudo-chromosomes with a BUSCO score of 95.7 % for the core eukaryotic gene set. The assembled genome was found to contain 75.62 % repetitive DNA and a total of 39,687 protein-coding genes were annotated making it the spider genome with highest number of genes. Through integrated analysis of venom gland transcriptomics and venom proteomics, a total of 194 venom toxins were identified, including 38 disulfide-rich peptide neurotoxins, among which 12 were ICK knottin peptides. In summary, we present the first high-quality genome assembly at the chromosomal level for any Macrothelidae spider, filling an important gap in our knowledge of these spiders. Such high-quality genomic data will be invaluable as a reference in resolving Araneae spider phylogenies and in screening different spider species for novel compounds applicable to numerous medical and agricultural applications.
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Affiliation(s)
- Yongming You
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China
| | - Yani Tang
- Yunnan Key Laboratory for Palaeobiology, Institute of Palaeontology, Yunnan University, South Waihuan Road, Chenggong District, Kunming 650500, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650500, China
| | - Wenhao Yin
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China
| | - Xinxin Liu
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China
| | - Pengfei Gao
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China
| | - Chenggui Zhang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA..
| | - Yu Zhao
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China.
| | - Zizhong Yang
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R & D, Dali University, Dali 671000, China; National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali 671000, China; Innovative Team of Dali University for Medicinal Insects & Arachnids Resources Digital Development, Dali 671000, China.
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García-Villalvazo PE, Jiménez-Vargas JM, Lino-López GJ, Meneses EP, Bermúdez-Guzmán MDJ, Barajas-Saucedo CE, Delgado Enciso I, Possani LD, Valdez-Velazquez LL. Unveiling the Protein Components of the Secretory-Venom Gland and Venom of the Scorpion Centruroides possanii (Buthidae) through Omic Technologies. Toxins (Basel) 2023; 15:498. [PMID: 37624255 PMCID: PMC10467079 DOI: 10.3390/toxins15080498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Centruroides possanii is a recently discovered species of "striped scorpion" found in Mexico. Certain species of Centruroides are known to be toxic to mammals, leading to numerous cases of human intoxications in the country. Venom components are thought to possess therapeutic potential and/or biotechnological applications. Hence, obtaining and analyzing the secretory gland transcriptome and venom proteome of C. possanii is relevant, and that is what is described in this communication. Since this is a newly described species, first, its LD50 to mice was determined and estimated to be 659 ng/g mouse weight. Using RNA extracted from this species and preparing their corresponding cDNA fragments, a transcriptome analysis was obtained on a Genome Analyzer (Illumina) using the 76-base pair-end sequencing protocol. Via high-throughput sequencing, 19,158,736 reads were obtained and ensembled in 835,204 sequences. Of them, 28,399 transcripts were annotated with Pfam. A total of 244 complete transcripts were identified in the transcriptome of C. possanii. Of these, 109 sequences showed identity to toxins that act on ion channels, 47 enzymes, 17 protease inhibitors (PINs), 11 defense peptides (HDPs), and 60 in other components. In addition, a sample of the soluble venom obtained from this scorpion was analyzed using an Orbitrap Velos apparatus, which allowed for identification by liquid chromatography followed by mass spectrometry (LC-MS/MS) of 70 peptides and proteins: 23 toxins, 27 enzymes, 6 PINs, 3 HDPs, and 11 other components. Until now, this work has the highest number of scorpion venom components identified through omics technologies. The main novel findings described here were analyzed in comparison with the known data from the literature, and this process permitted some new insights in this field.
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Affiliation(s)
| | - Juana María Jiménez-Vargas
- Facultad de Ciencias Químicas, Universidad de Colima, Colima 28400, Mexico; (P.E.G.-V.); (J.M.J.-V.); (C.E.B.-S.)
- Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Mexico City 03940, Mexico
| | - Gisela Jareth Lino-López
- Centro Nacional de Referencia de Control Biológico, Dirección General de Sanidad Vegetal SENASICASADER, Colima 28110, Mexico;
| | - Erika Patricia Meneses
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | | | | | | | - Lourival Domingos Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
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Wang B, Xiao Q, Li X, Wang J, Zhu J. Proteinaceous Venom Expression of the Yellow Meadow Ant, Lasius flavus (Hymenoptera: Formicidae). Toxins (Basel) 2023; 15:toxins15020106. [PMID: 36828420 PMCID: PMC9961005 DOI: 10.3390/toxins15020106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
Ants are one of the important groups of venomous animals with about 14,000 described species. Studies so far focused on the discovery of venom proteins are only available for limited stinging ants, and the proteinaceous compositions of the stingless ants are completely unknown. Here, we used the transcriptomic approach to identify venom components from the yellow meadow ant, Lasius flavus, a stingless ant. The transcriptomic analysis yielded an extraordinary simplicity of the venom expression profile, with 17 venom proteins, such as phospholipase B, odorant binding protein, and apolipoprotein D. Ten of them were discovered as novel toxins for future functional investigations. Quantitative real time PCR analysis revealed that genes encoding the identified venom proteins display exclusively or highly expression profiles in venom glands, validating them as venom compositions. Our findings contribute to the understanding of the evolutional diversity of toxins between stinging and stingless ants.
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Affiliation(s)
- Binwei Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Qiaoli Xiao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Xun Li
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jun Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jiaying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
- Correspondence:
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A current perspective on snake venom composition and constituent protein families. Arch Toxicol 2023; 97:133-153. [PMID: 36437303 DOI: 10.1007/s00204-022-03420-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 11/28/2022]
Abstract
Snake venoms are heterogeneous mixtures of proteins and peptides used for prey subjugation. With modern proteomics there has been a rapid expansion in our knowledge of snake venom composition, resulting in the venom proteomes of 30% of vipers and 17% of elapids being characterised. From the reasonably complete proteomic coverage of front-fanged snake venom composition (179 species-68 species of elapids and 111 species of vipers), the venoms of vipers and elapids contained 42 different protein families, although 18 were only reported in < 5% of snake species. Based on the mean abundance and occurrence of the 42 protein families, they can be classified into 4 dominant, 6 secondary, 14 minor, and 18 rare protein families. The dominant, secondary and minor categories account for 96% on average of a snake's venom composition. The four dominant protein families are: phospholipase A2 (PLA2), snake venom metalloprotease (SVMP), three-finger toxins (3FTx), and snake venom serine protease (SVSP). The six secondary protein families are: L-amino acid oxidase (LAAO), cysteine-rich secretory protein (CRiSP), C-type lectins (CTL), disintegrins (DIS), kunitz peptides (KUN), and natriuretic peptides (NP). Venom variation occurs at all taxonomic levels, including within populations. The reasons for venom variation are complex, as variation is not always associated with geographical variation in diet. The four dominant protein families appear to be the most important toxin families in human envenomation, being responsible for coagulopathy, neurotoxicity, myotoxicity and cytotoxicity. Proteomic techniques can be used to investigate the toxicological profile of a snake venom and hence identify key protein families for antivenom immunorecognition.
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Anita S, Sadjuri AR, Rahmah L, Nugroho HA, Mulyadi, Trilaksono W, Ridhani W, Safira N, Bahtiar H, Maharani, Hamidy A, Azhari A. Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia. J Venom Anim Toxins Incl Trop Dis 2022; 28:e20210103. [PMID: 35875602 PMCID: PMC9261747 DOI: 10.1590/1678-9199-jvatitd-2021-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI- LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein familiesin T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusions: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom’s toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.
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Affiliation(s)
- Syahfitri Anita
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia.,Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | | | | | - Herjuno Ari Nugroho
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN) , Cibinong, Indonesia
| | - Mulyadi
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wahyu Trilaksono
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wiwit Ridhani
- PT Dermama Bioteknologi Laboratorium, Betshaida Hospital, Tangerang, Indonesia
| | | | | | - Maharani
- PT Bio Farma (Persero), Bandung, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
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Enhancing Soluble Expression of Phospholipase B for Efficient Catalytic Synthesis of L-Alpha-Glycerylphosphorylcholine. Catalysts 2022. [DOI: 10.3390/catal12060650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Phospholipase B (PLB) harbors three distinct activities with broad substrate specificities and application fields. Its hydrolyzing of sn-1 and sn-2 acyl ester bonds enables it to catalyze the production of L-alpha-glycerylphosphorylcholine (L-α-GPC) from phosphatidylcholine (PC) without speed-limiting acyl migration. This work was intended to obtain high-level active PLB and apply it to establish an efficient system for L-α-GPC synthesis. PLB from Pseudomonas fluorescens was co-expressed with five different molecular chaperones, including trigger factor (Tf), GroEL-GroES (GroELS), DnaK-DnaJ-GrpE (DnaKJE), GroELS and DnaKJE, or GroELS and Tf or fused with maltose binding protein (MBP) in Escherichia coli BL21(DE3) to improve PLB expression. PLB with DnaKJE-assisted expression exhibited the highest catalytic activity. Further optimization of the expression conditions identified an optimal induction OD600 of 0.8, IPTG concentration of 0.3 mmol/L, induction time of 9 h, and temperature of 25 °C. The PLB activity reached a maximum of 524.64 ± 3.28 U/mg under optimal conditions. Subsequently, to establish an efficient PLB-catalyzed system for L-α-GPC synthesis, a series of organic-aqueous mixed systems and surfactant-supplemented aqueous systems were designed and constructed. Furthermore, the factors of temperature, reaction pH, metal ions, and substrate concentration were further systematically identified. Finally, a high yield of 90.50 ± 2.21% was obtained in a Span 60-supplemented aqueous system at 40 °C and pH 6.0 with 0.1 mmol/L of Mg2+. The proposed cost-effective PLB production and an environmentally friendly PLB-catalyzed system offer a candidate strategy for the industrial production of L-α-GPC.
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Evaluation of the effects of Loxosceles intermedia’s venom in zebrafish. Toxicol Rep 2022; 9:1410-1418. [DOI: 10.1016/j.toxrep.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 11/21/2022] Open
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Damm M, Hempel BF, Süssmuth RD. Old World Vipers-A Review about Snake Venom Proteomics of Viperinae and Their Variations. Toxins (Basel) 2021; 13:toxins13060427. [PMID: 34204565 PMCID: PMC8235416 DOI: 10.3390/toxins13060427] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Fine-tuned by millions of years of evolution, snake venoms have frightened but also fascinated humanity and nowadays they constitute potential resources for drug development, therapeutics and antivenoms. The continuous progress of mass spectrometry techniques and latest advances in proteomics workflows enabled toxinologists to decipher venoms by modern omics technologies, so-called ‘venomics’. A tremendous upsurge reporting on snake venom proteomes could be observed. Within this review we focus on the highly venomous and widely distributed subfamily of Viperinae (Serpentes: Viperidae). A detailed public literature database search was performed (2003–2020) and we extensively reviewed all compositional venom studies of the so-called Old-World Vipers. In total, 54 studies resulted in 89 venom proteomes. The Viperinae venoms are dominated by four major, four secondary, six minor and several rare toxin families and peptides, respectively. The multitude of different venomics approaches complicates the comparison of venom composition datasets and therefore we differentiated between non-quantitative and three groups of quantitative workflows. The resulting direct comparisons within these groups show remarkable differences on the intra- and interspecies level across genera with a focus on regional differences. In summary, the present compilation is the first comprehensive up-to-date database on Viperinae venom proteomes and differentiating between analytical methods and workflows.
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Affiliation(s)
- Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, (BCRT), 10117 Berlin, Germany;
| | - Roderich D. Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
- Correspondence: ; Tel.: +49-(0)30-314-24205
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Cao Z, Wang JL, McNutt PM, Utkin YN, Shahbazzadeh D, Wulff H, Kovacic H, Sabatier JM. Editorial: Venoms, Animal and Microbial Toxins. Front Pharmacol 2021; 12:706573. [PMID: 34122121 PMCID: PMC8188234 DOI: 10.3389/fphar.2021.706573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhijian Cao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing-Lin Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | | | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Hervé Kovacic
- UMR7051 Institut de NeuroPhysiopathologie, Aix-Marseille Université, Marseille, France
| | - Jean-Marc Sabatier
- UMR7051 Institut de NeuroPhysiopathologie, Aix-Marseille Université, Marseille, France
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Ullah A, Ullah K. Inhibition of SARS-CoV-2 3CL M pro by Natural and Synthetic Inhibitors: Potential Implication for Vaccine Production Against COVID-19. Front Mol Biosci 2021; 8:640819. [PMID: 33912587 PMCID: PMC8072276 DOI: 10.3389/fmolb.2021.640819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19 has created a pandemic situation all over the world. It has spread in nearly every continent. Researchers all over the world are trying to produce an effective vaccine against this virus, however; no specific treatment for COVID-19 has been discovered -so far. The current work describes the inhibition study of the SARS-CoV-2 main proteinase or 3CL Mpro by natural and synthetic inhibitors, which include 2S albumin and flocculating protein from Moringa oleifera (M. oleifera) and Suramin. Molecular Docking study was carried out using the programs like AutoDock 4.0, HADDOCK2.4, patchdock, pardock, and firedock. The global binding energy of Suramin, 2S albumin, and flocculating proteins were −41.96, −9.12, and −14.78 kJ/mol, respectively. The docking analysis indicates that all three inhibitors bind at the junction of domains II and III. The catalytic function of 3CL Mpro is dependent on its dimeric form, and the flexibility of domain III is considered important for this dimerization. Our study showed that all three inhibitors reduce this flexibility and restrict their motion. The decrease in flexibility of domain III was further confirmed by analysis coming from Molecular dynamic simulation. The analysis results indicate that the temperature B-factor of the enzyme decreases tremendously when the inhibitors bind to it. This study will further explore the possibility of producing an effective treatment against COVID-19.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins (Basel) 2020; 12:toxins12110669. [PMID: 33105837 PMCID: PMC7690644 DOI: 10.3390/toxins12110669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/06/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022] Open
Abstract
Latest advancement of omics technologies allows in-depth characterization of venom compositions. In the present work we present a proteomic study of two snake venoms of the genus Naja i.e., Naja naja (black cobra) and Naja oxiana (brown cobra) of Pakistani origin. The present study has shown that these snake venoms consist of a highly diversified proteome. Furthermore, the data also revealed variation among closely related species. High throughput mass spectrometric analysis of the venom proteome allowed to identify for the N. naja venom 34 protein families and for the N. oxiana 24 protein families. The comparative evaluation of the two venoms showed that N. naja consists of a more complex venom proteome than N. oxiana venom. Analysis also showed N-terminal acetylation (N-ace) of a few proteins in both venoms. To the best of our knowledge, this is the first study revealing this posttranslational modification in snake venom. N-ace can shed light on the mechanism of regulation of venom proteins inside the venom gland. Furthermore, our data showed the presence of other body proteins, e.g., ankyrin repeats, leucine repeats, zinc finger, cobra serum albumin, transferrin, insulin, deoxyribonuclease-2-alpha, and other regulatory proteins in these venoms. Interestingly, our data identified Ras-GTpase type of proteins, which indicate the presence of extracellular vesicles in the venom. The data can support the production of distinct and specific anti-venoms and also allow a better understanding of the envenomation and mechanism of distribution of toxins. Data are available via ProteomeXchange with identifier PXD018726.
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