The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i>
<i>Bacillus thuringiensis</i>, commonly referred to as <i>Bt</i>, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make <i>Bt</i> a prominent source of biologicals. To categorize the exuberance of &...
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2021-02-01
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| author | Anton E. Shikov Yury V. Malovichko Arseniy A. Lobov Maria E. Belousova Anton A. Nizhnikov Kirill S. Antonets |
| author_facet | Anton E. Shikov Yury V. Malovichko Arseniy A. Lobov Maria E. Belousova Anton A. Nizhnikov Kirill S. Antonets |
| author_sort | Anton E. Shikov |
| collection | DOAJ |
| description | <i>Bacillus thuringiensis</i>, commonly referred to as <i>Bt</i>, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make <i>Bt</i> a prominent source of biologicals. To categorize the exuberance of <i>Bt</i> strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of <i>Bt</i> strains’ phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in <i>Bt</i> strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of <i>Bt</i> culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the <i>israelensis</i>-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the <i>israelensis</i> strain were also compared to the spores of strains belonging to two other major <i>Bt</i> serovars, namely <i>darmstadiensis</i> and <i>thuringiensis</i>. The identified proteins were analyzed regarding the presence of the respective genes in the 104 <i>Bt</i> genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains’ phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains. |
| first_indexed | 2024-03-09T00:35:35Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T00:35:35Z |
| publishDate | 2021-02-01 |
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| spelling | doaj.art-89aaefc913774e2dbee63270190643692023-12-11T18:13:39ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-02-01225224410.3390/ijms22052244The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i>Anton E. Shikov0Yury V. Malovichko1Arseniy A. Lobov2Maria E. Belousova3Anton A. Nizhnikov4Kirill S. Antonets5Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaLaboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaFaculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, RussiaLaboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaLaboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, RussiaLaboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia<i>Bacillus thuringiensis</i>, commonly referred to as <i>Bt</i>, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make <i>Bt</i> a prominent source of biologicals. To categorize the exuberance of <i>Bt</i> strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of <i>Bt</i> strains’ phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in <i>Bt</i> strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of <i>Bt</i> culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the <i>israelensis</i>-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the <i>israelensis</i> strain were also compared to the spores of strains belonging to two other major <i>Bt</i> serovars, namely <i>darmstadiensis</i> and <i>thuringiensis</i>. The identified proteins were analyzed regarding the presence of the respective genes in the 104 <i>Bt</i> genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains’ phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains.https://www.mdpi.com/1422-0067/22/5/2244<i>Bacillus thuringiensis</i><i>Bt</i>virulence factorsproteomics2D-DIGEmass spectrometry |
| spellingShingle | Anton E. Shikov Yury V. Malovichko Arseniy A. Lobov Maria E. Belousova Anton A. Nizhnikov Kirill S. Antonets The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> International Journal of Molecular Sciences <i>Bacillus thuringiensis</i> <i>Bt</i> virulence factors proteomics 2D-DIGE mass spectrometry |
| title | The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> |
| title_full | The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> |
| title_fullStr | The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> |
| title_full_unstemmed | The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> |
| title_short | The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of <i>Bacillus thuringiensis</i> |
| title_sort | distribution of several genomic virulence determinants does not corroborate the established serotyping classification of i bacillus thuringiensis i |
| topic | <i>Bacillus thuringiensis</i> <i>Bt</i> virulence factors proteomics 2D-DIGE mass spectrometry |
| url | https://www.mdpi.com/1422-0067/22/5/2244 |
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