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Lu JQ, Shou JW, Lo KC, Tang YS, Shi WW, Shaw PC. Pore-Forming Cardiotoxin VVA2 (Volvatoxin A2) Variant I82E/L86K Is an Atypical Duplex-Specific Nuclease. Toxins (Basel) 2022; 14:toxins14060392. [PMID: 35737053 PMCID: PMC9230820 DOI: 10.3390/toxins14060392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 12/04/2022] Open
Abstract
VVA2 (volvatoxin A chain 2) is a cardiotoxic protein purified from Volvariella volvacea. Its biological activities include hemolysis, writhing reaction, neurotoxicity, and ventricular systolic arresting activity. The cytotoxicity of VVA2 was mainly considered due to its pore-forming activity. Here we report a novel biological activity of its variants VVA2 I82E/K86K as a duplex-specific nuclease. Recombinant VVA2 variant I82E/L86K (Re-VVA2 I82E/L86K), deprived of the oligomerization property, shows increased nuclease activity compared to VVA2. Re-VVA2 I82E/L86K converts supercoiled DNA (Replicative form I, RF I) into nicked form (RF II) and linear form (RF III) in the presence of Mg2+ or Mn2+. Besides plasmid DNA, it also exhibits nuclease activity on E. coli genomic DNA rather than ssDNA or RNA. Re-VVA2 I82E/L86K preferentially cleaves dG-dC-rich dsDNA regions and shows the best performance at pH 6–9 and 55 °C. Our structure–function study has revealed amino acid E111 may take an active part in nuclease activity through interacting with metal ions. Based on the sequences of its cleavage sites, a “double-hit” mechanism was thereby proposed. Given that Re-VVA2 I82E/L86K did not exhibit the conserved nuclease structure and sequence, it is considered an atypical duplex-specific nuclease.
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Affiliation(s)
- Jia-Qi Lu
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (J.-Q.L.); (J.-W.S.); (K.-C.L.); (Y.-S.T.)
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jia-Wen Shou
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (J.-Q.L.); (J.-W.S.); (K.-C.L.); (Y.-S.T.)
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Ching Lo
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (J.-Q.L.); (J.-W.S.); (K.-C.L.); (Y.-S.T.)
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun-Sang Tang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (J.-Q.L.); (J.-W.S.); (K.-C.L.); (Y.-S.T.)
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei-Wei Shi
- BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen 518107, China;
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (J.-Q.L.); (J.-W.S.); (K.-C.L.); (Y.-S.T.)
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence:
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Gasmi L, Baek S, Kim JC, Kim S, Lee MR, Park SE, Shin TY, Lee SJ, Parker BL, Kim JS. Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana. Sci Rep 2021; 11:91. [PMID: 33420123 PMCID: PMC7794557 DOI: 10.1038/s41598-020-78910-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Beauveria bassiana is a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features of B. bassiana. In addition, other genes (i.e. DNA photolyase and cyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance of B. bassiana isolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.
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Affiliation(s)
- Laila Gasmi
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Sehyeon Baek
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Jong Cheol Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Sihyeon Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Mi Rong Lee
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - So Eun Park
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Tae Young Shin
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Se Jin Lee
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA
| | - Bruce L Parker
- Entomology Research Laboratory, University of Vermont, 661 Spear Street, Burlington, VT, 05405-0105, USA
| | - Jae Su Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea.
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54596, Korea.
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Xu C, Wang BC, Yu Z, Sun M. Structural insights into Bacillus thuringiensis Cry, Cyt and parasporin toxins. Toxins (Basel) 2014; 6:2732-70. [PMID: 25229189 PMCID: PMC4179158 DOI: 10.3390/toxins6092732] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/30/2022] Open
Abstract
Since the first X-ray structure of Cry3Aa was revealed in 1991, numerous structures of B. thuringiensis toxins have been determined and published. In recent years, functional studies on the mode of action and resistance mechanism have been proposed, which notably promoted the developments of biological insecticides and insect-resistant transgenic crops. With the exploration of known pore-forming toxins (PFTs) structures, similarities between PFTs and B. thuringiensis toxins have provided great insights into receptor binding interactions and conformational changes from water-soluble to membrane pore-forming state of B. thuringiensis toxins. This review mainly focuses on the latest discoveries of the toxin working mechanism, with the emphasis on structural related progress. Based on the structural features, B. thuringiensis Cry, Cyt and parasporin toxins could be divided into three categories: three-domain type α-PFTs, Cyt toxin type β-PFTs and aerolysin type β-PFTs. Structures from each group are elucidated and discussed in relation to the latest data, respectively.
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Affiliation(s)
- Chengchen Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Wibberg D, Jelonek L, Rupp O, Kröber M, Goesmann A, Grosch R, Pühler A, Schlüter A. Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal Biol 2014; 118:800-13. [PMID: 25209639 DOI: 10.1016/j.funbio.2014.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/27/2014] [Accepted: 06/27/2014] [Indexed: 10/25/2022]
Abstract
Rhizoctonia solani is a soil-borne plant pathogenic fungus of the phylum Basidiomycota. It affects a wide range of agriculturally important crops and hence is responsible for economically relevant crop losses. Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14) by applying high-throughput sequencing and bioinformatics methods addressing Expressed Sequence Tag (EST) data interpretation provided new insights in expressed genes of this fungus. Two normalized cDNA libraries representing different cultivation conditions of the fungus were sequenced on the 454 FLX (Roche) system. Subsequent to cDNA sequence assembly and quality control, ESTs were analysed applying advanced bioinformatics methods. More than 14 000 transcript isoforms originating from approximately 10 000 predictable R. solani AG1-IB 7/3/14 genes are represented in each dataset. Comparative analyses revealed several differentially expressed genes depending on the growth conditions applied. Determinants with predicted functions in recognition processes between the fungus and the host plant were identified. Moreover, many R. solani AG1-IB ESTs were predicted to encode putative cellulose, pectin, and lignin degrading enzymes. Furthermore, genes playing a possible role in mitogen-activated protein (MAP) kinase cascades, 4-aminobutyric acid (GABA) metabolism, melanin synthesis, plant defence antagonism, phytotoxin, and mycotoxin synthesis were detected.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Magdalena Kröber
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetables and Ornamental Crops (IGZ), D-14979 Großbeeren, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
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Isolation and characterization of a novel two-component hemolysin, erylysin A and B, from an edible mushroom, Pleurotus eryngii. Toxicon 2010; 56:1436-42. [DOI: 10.1016/j.toxicon.2010.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 11/21/2022]
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Lin SC, Lo YC, Lin JY, Liaw YC. Crystal structures and electron micrographs of fungal volvatoxin A2. J Mol Biol 2004; 343:477-91. [PMID: 15451675 DOI: 10.1016/j.jmb.2004.08.045] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 08/11/2004] [Accepted: 08/11/2004] [Indexed: 11/17/2022]
Abstract
Membrane adhesion and insertion of protein are essential to all organisms, but the underlying mechanisms remain largely unknown. Membrane pore-forming toxins (PFTs) are potential model systems for studying these mechanisms. We have determined the crystal structures of volvatoxin A2 (VVA2), a fungal PFT from Volvariella volvacea, using Br-multiple-wavelength anomalous diffraction (MAD). The VVA2 structures obtained at pH 4.6, pH 5.5 and pH 6.5 were refined to resolutions of 1.42 A, 2.6 A and 3.2 A, respectively. The structures reveal that the VVA2 monomer contains a single alpha/beta domain. Most of the VVA2 surface is occupied by its oligomerization motif and two putative heparin-binding motifs. Residues Ala91 to Ala101 display several conformations at different pH values, which might be under the control of His87. We also found that the shape of one putative heparin-binding motif in VVA2 appears similar to those found in fibroblast growth factors, and the other one displays a linear polypeptide. Our results suggest several possible intermediates of protein assembly in solution and protein adhering to cell membranes before conformational changes. The electron micrographs of VVA2 molecules in solution, at a protein concentration of 1 microg ml(-1), show that they can assemble into filament-like or braid-like oligomers in a pH-dependent way. In addition, the arc-shaped VVA2 structure obtained at pH 6.5 suggests that VVA2 could form a two-layered helical oligomer with 18 subunits per turn. The structures presented here could be used to elucidate the pore-formation mechanisms of VVA2 and its structural neighbors, Cyt toxins from Bacillus thuringiensis.
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Affiliation(s)
- Su-Chang Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan, ROC
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