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Sauka DH, Peralta C, Pérez MP, Molla A, Fernandez-Göbel T, Ocampo F, Palma L. Bacillus thuringiensis Bt_UNVM-84, a Novel Strain Showing Insecticidal Activity against Anthonomus grandis Boheman (Coleoptera: Curculionidae). Toxins (Basel) 2023; 16:4. [PMID: 38276528 PMCID: PMC10819922 DOI: 10.3390/toxins16010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Bacillus thuringiensis is a Gram-positive bacterium known for its insecticidal proteins effective against various insect pests. However, limited strains and proteins target coleopteran pests like Anthonomous grandis Boheman, causing substantial economic losses in the cotton industry. This study focuses on characterizing a Bacillus sp. strain, isolated from Oncativo (Argentina), which exhibits ovoid to amorphous parasporal crystals and was designated Bt_UNVM-84. Its genome encodes genes for the production of two pairs of binary Vpb1/Vpa2 proteins and three Cry-like proteins showing similarity with different Cry8 proteins. Interestingly, this gene content was found to be conserved in a previously characterized Argentine isolate of B. thuringiensis designated INTA Fr7-4. SDS-PAGE analysis revealed a major band of 130 kDa that is proteolytically processed to an approximately 66-kDa protein fragment by trypsin. Bioassays performed with spore-crystal mixtures demonstrated an interesting insecticidal activity against the cotton boll weevil A. grandis neonate larvae, resulting in 91% mortality. Strain Bt_UNVM-84 is, therefore, an interesting candidate for the efficient biological control of this species, causing significant economic losses in the cotton industry in the Americas.
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Affiliation(s)
- Diego Herman Sauka
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina; (D.H.S.); (C.P.)
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMYZA), Hurlingham, Ciudad Autónoma de Buenos Aires 1686, Argentina;
| | - Cecilia Peralta
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina; (D.H.S.); (C.P.)
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María 1555, Argentina;
- Laboratorio de Control Biotecnológico de Plagas, Instituto BIOTECMED, Departamento de Genética, Universitat de València, 46100 València, Spain
| | - Melisa Paula Pérez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMYZA), Hurlingham, Ciudad Autónoma de Buenos Aires 1686, Argentina;
| | - Antonella Molla
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María 1555, Argentina;
| | - Tadeo Fernandez-Göbel
- Elytron Biotech S.A., 275 Ing. Enrique Butty Street, Ciudad Autónoma de Buenos Aires C1001, Argentina; (T.F.-G.); (F.O.)
| | - Federico Ocampo
- Elytron Biotech S.A., 275 Ing. Enrique Butty Street, Ciudad Autónoma de Buenos Aires C1001, Argentina; (T.F.-G.); (F.O.)
| | - Leopoldo Palma
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina; (D.H.S.); (C.P.)
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María 1555, Argentina;
- Laboratorio de Control Biotecnológico de Plagas, Instituto BIOTECMED, Departamento de Genética, Universitat de València, 46100 València, Spain
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Oliveira-Santos N, Pimentel Rodrigues Dos Santos LB, Fernandes JV, Cruz-Magalhães V, Loguercio LL. More than just an insect killer: The non-insecticidal activities of Bacillus thuringiensis with biotechnological potential. Toxicon 2023; 233:107261. [PMID: 37611671 DOI: 10.1016/j.toxicon.2023.107261] [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: 03/28/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Bacillus thuringiensis (Bt) is known for the biological control of important insect pests, but scientific advances have revealed several interesting characteristics, in addition to this classical function as a bioinsecticide. To investigate the current knowledge about these non-insecticidal activities, a systematic research on primary data in the scientific literature was conducted on alternative functions of Bt with biotechnological potential. Out of a total of 140 articles selected, 15 non-insecticidal Bt activities were found. Publications related to this topic are available since 1971, and different metadata were reported, such as biomolecules and genes involved in Bt performances in non-insecticidal bioactivities. A total of 11 Bt activities with different effect measures (response variables) were identified, with an average of 48 distinct Bt strains evaluated per activity. Approximately 81.2% of all identified experiments/tests deal with the direct effects of Bt on target cells/organisms, with 36.3% of the strains within these studies tested for antibacterial action; of all microbial targets tested, 92.8% are bacteria, which led to 75.2% of the experimental conditions for all direct activities being performed in vitro. Regarding indirect Bt activities, 67.6% of these studies reported tritrophic Bt-plant-pathogen interactions. Bioremediation also appears as a relevant Bt activity being investigated in-depth. Alternative Bt activities offer innovative ways of developing biotechnology for different areas of anthropic interest; hence, we also focus on the possibility of finding multifunctional strains of Bt, as this may be advantageous from a bioeconomic point of view. Our findings are discussed in terms of research trends, aspects, details and depth of the current knowledge on alternative non-insecticidal Bt traits. We also discuss the potential application of this science for useful technological developments, aiming at solving issues related to human health, sustainable agriculture and environmental preservation/restoration.
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Affiliation(s)
- Naiane Oliveira-Santos
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus, BA, 45662-900, Brazil.
| | | | - Jacquelline Viana Fernandes
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus, BA, 45662-900, Brazil.
| | - Valter Cruz-Magalhães
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus, BA, 45662-900, Brazil; Department of Phytophatology (DFP), Federal University of Lavras (UFLA), Lavras, MG, Brazil.
| | - Leandro Lopes Loguercio
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus, BA, 45662-900, Brazil.
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Buck M, Mehrshad M, Bertilsson S. mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation. NAR Genom Bioinform 2022; 4:lqac060. [PMID: 35979445 PMCID: PMC9376867 DOI: 10.1093/nargab/lqac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/25/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.
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Affiliation(s)
- Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
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Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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6
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Shikov AE, Malovichko YV, Lobov AA, Belousova ME, Nizhnikov AA, Antonets KS. The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis. Int J Mol Sci 2021; 22:2244. [PMID: 33668147 PMCID: PMC7956386 DOI: 10.3390/ijms22052244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Bacillus thuringiensis, commonly referred to as Bt, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make Bt a prominent source of biologicals. To categorize the exuberance of Bt strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of Bt 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 Bt 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 Bt culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the israelensis-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 israelensis strain were also compared to the spores of strains belonging to two other major Bt serovars, namely darmstadiensis and thuringiensis. The identified proteins were analyzed regarding the presence of the respective genes in the 104 Bt 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.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Arseniy A. Lobov
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
- Laboratory of Regenerative Biomedicine, Institute of Cytology of the Russian Academy of Science, 194064 St. Petersburg, Russia
| | - Maria E. Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (Y.V.M.); (M.E.B.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia;
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7
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Alves GB, Melo FL, Oliveira EE, Haddi K, Costa LTM, Dias ML, Campos FS, Pereira EJG, Corrêa RFT, Ascêncio SD, Santos GR, Smagghe G, Ribeiro BM, Aguiar RWS. Comparative genomic analysis and mosquito larvicidal activity of four Bacillus thuringiensis serovar israelensis strains. Sci Rep 2020; 10:5518. [PMID: 32218451 PMCID: PMC7099026 DOI: 10.1038/s41598-020-60670-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Bacillus thuringiensis serovar israelensis (Bti) is used to control insect vectors of human and animal diseases. In the present study, the toxicity of four strains of Bti, named T0124, T0131, T0137, and T0139, toward Aedes aegypti and Culex quinquefasciatus larvae was analyzed. The T0131 strain showed the highest larvicidal activity against A. aegypti (LC50 = 0.015 µg/ml) and C. quinquefasciatus larvae (LC50 = 0.035 µg/ml) when compared to the other strains. Furthermore, the genomic sequences of the four strains were obtained and compared. These Bti strains had chromosomes sizes of approximately 5.4 Mb with GC contents of ~35% and 5472–5477 putative coding regions. Three small plasmids (5.4, 6.8, and 7.6 kb) and three large plasmids (127, 235, and 359 kb) were found in the extrachromosomal content of all four strains. The SNP-based phylogeny revealed close relationship among isolates from this study and other Bti isolates, and SNPs analysis of the plasmids 127 kb did not reveal any mutations in δ-endotoxins genes. This newly acquired sequence data for these Bti strains may be useful in the search for novel insecticidal toxins to improve existing ones or develop new strategies for the biological control of important insect vectors of human and animal diseases.
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Affiliation(s)
- Giselly B Alves
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Fernando L Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Eugenio E Oliveira
- Departmento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Khalid Haddi
- Departamento de Entomologia, Universidade Federal de Lavras, Lavras, MG, 37200-900, Brazil
| | - Lara T M Costa
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Marcelo L Dias
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Fabrício S Campos
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Eliseu J G Pereira
- Departmento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Roberto F T Corrêa
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Sergio D Ascêncio
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal (Rede Bionorte), Universidade Federal do Tocantins, Palmas, TO, 77413-070, Brazil
| | - Gil R Santos
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Guy Smagghe
- Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Raimundo W S Aguiar
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil.
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Wirojsirasak W, Kalapanulak S, Saithong T. Pan- and core- gene association networks: Integrative approaches to understanding biological regulation. PLoS One 2019; 14:e0210481. [PMID: 30625202 PMCID: PMC6326509 DOI: 10.1371/journal.pone.0210481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023] Open
Abstract
The rapid increase in transcriptome data provides an opportunity to access the complex regulatory mechanisms in cellular systems through gene association network (GAN). Nonetheless, GANs derived from single datasets generally allow us to envisage only one side of the regulatory network, even under the particular condition of study. The circumstance is well demonstrated by inconsistent GANs of individual datasets proposed for similar experimental conditions, which always leads to ambiguous interpretation. Here, pan- and core-gene association networks (pan- and core-GANs), analogous to the pan- and core-genome concepts, are proposed to increase the power of inference through the integration of multiple, diverse datasets. The core-GAN represents the consensus associations of genes that were inferred from all individual networks. On the other hand, the pan-GAN represents the extensive gene-gene associations that occurred in each individual network. The pan- and core-GANs prospects were demonstrated based on three time series microarray datasets in leaves of Arabidopsis thaliana grown under diurnal conditions. We showed the overall performance of pan- and core-GANs was more robust to the number of data points in gene expression data compared to the GANs inferred from individual datasets. In addition, the incorporation of multiple data broadened our understanding of the biological regulatory system. While the pan-GAN enabled us to observe the landscape of gene association system, core-GAN highlighted the basic gene-associations in essence of the regulation regulating starch metabolism in leaves of Arabidopsis.
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Affiliation(s)
- Warodom Wirojsirasak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Saowalak Kalapanulak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Treenut Saithong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- * E-mail:
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9
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Lopes R, Cerdeira L, Tavares GS, Ruiz JC, Blom J, Horácio ECA, Mantovani HC, Queiroz MVD. Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens. World J Microbiol Biotechnol 2017; 33:185. [DOI: 10.1007/s11274-017-2347-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/19/2017] [Indexed: 02/02/2023]
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10
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Dai R, Su X, Jin X, Zhang J, Guan X, Chen C, Shu C, Huang T. Cloning, Expression, Purification, and Insecticidal Activity of a Novel Cry1Na3 Toxin From Bacillus thuringiensis BRC-ZYR2. JOURNAL OF ECONOMIC ENTOMOLOGY 2016; 109:1064-1070. [PMID: 27170729 DOI: 10.1093/jee/tow031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Bacillus thuringiensis produces a variety of insecticidal crystal proteins (ICPs). Genome sequencing is a promising strategy for detecting and identifying B. thuringiensis ICPs, which are of great interest to the biocontrol field. In this study, a novel ICP gene was cloned from B. thuringiensis BRC-ZYR2 based on genomic data from 454 GS-FLX Titanium sequencing and an analysis of the results using the B. thuringiensis Toxin_Scanner ( http://bcam.hzaubmb.net/BtToxin_scanner/index.php ). cry1Na3 designated by the B. thuringiensis Toxin Nomenclature Committee, encoded a 601-amino acid, 68.0-kDa protein that exhibited 95% identity with Cry1Na1 and 99% identity with Cry1Na2. Cry1Na3 contained three conserved domains commonly found in three-domain ICPs. Cry1Na3 was toxic to Plutella xylostella (L.) and Ostrinia furnacalis (Guenée), with LC 50 values of 3.69 μg/ml and 31.30 μg/ml, respectively. However, Laodelphax striatellus (Fallén) nymphs were unaffected when fed purified Cry1Na3 (250 μg/ml) in their diet. Spodoptera exigua (Hübner) and Colaphellus bowringi (Baly) larvae survived even when the concentration of Cry1Na3 protein reached 500 μg/ml. Cry1Na3 is a promising agent for the control of lepidopteran insect pests.
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11
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Ruan L, Crickmore N, Peng D, Sun M. Are nematodes a missing link in the confounded ecology of the entomopathogen Bacillus thuringiensis? Trends Microbiol 2015; 23:341-6. [DOI: 10.1016/j.tim.2015.02.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 01/29/2015] [Accepted: 02/25/2015] [Indexed: 01/23/2023]
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A brief review of software tools for pangenomics. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:73-6. [PMID: 25721608 PMCID: PMC4411478 DOI: 10.1016/j.gpb.2015.01.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 01/22/2015] [Accepted: 01/25/2015] [Indexed: 02/06/2023]
Abstract
Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
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De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PRJ, Coutinho TA. Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genomics 2014; 15:404. [PMID: 24884520 PMCID: PMC4070556 DOI: 10.1186/1471-2164-15-404] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms. Results The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors. Conclusions P. ananatis has an ‘open’ pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-404) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South Africa.
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Argôlo-Filho RC, Loguercio LL. Bacillus thuringiensis Is an Environmental Pathogen and Host-Specificity Has Developed as an Adaptation to Human-Generated Ecological Niches. INSECTS 2013; 5:62-91. [PMID: 26462580 PMCID: PMC4592628 DOI: 10.3390/insects5010062] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 11/16/2022]
Abstract
Bacillus thuringiensis (Bt) has been used successfully as a biopesticide for more than 60 years. More recently, genes encoding their toxins have been used to transform plants and other organisms. Despite the large amount of research on this bacterium, its true ecology is still a matter of debate, with two major viewpoints dominating: while some understand Bt as an insect pathogen, others see it as a saprophytic bacteria from soil. In this context, Bt's pathogenicity to other taxa and the possibility that insects may not be the primary targets of Bt are also ideas that further complicate this scenario. The existence of conflicting research results, the difficulty in developing broader ecological and genetics studies, and the great genetic plasticity of this species has cluttered a definitive concept. In this review, we gathered information on the aspects of Bt ecology that are often ignored, in the attempt to clarify the lifestyle, mechanisms of transmission and target host range of this bacterial species. As a result, we propose an integrated view to account for Bt ecology. Although Bt is indeed a pathogenic bacterium that possesses a broad arsenal for virulence and defense mechanisms, as well as a wide range of target hosts, this seems to be an adaptation to specific ecological changes acting on a versatile and cosmopolitan environmental bacterium. Bt pathogenicity and host-specificity was favored evolutionarily by increased populations of certain insect species (or other host animals), whose availability for colonization were mostly caused by anthropogenic activities. These have generated the conditions for ecological imbalances that favored dominance of specific populations of insects, arachnids, nematodes, etc., in certain areas, with narrower genetic backgrounds. These conditions provided the selective pressure for development of new hosts for pathogenic interactions, and so, host specificity of certain strains.
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Affiliation(s)
- Ronaldo Costa Argôlo-Filho
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus-BA 45662-900, Brazil.
| | - Leandro Lopes Loguercio
- Department of Biological Sciences, State University of Santa Cruz (UESC), Rod, Ilhéus-Itabuna, Km-16, Ilhéus-BA 45662-900, Brazil.
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Jia S, Zhang X, Zhang G, Yin A, Zhang S, Li F, Wang L, Zhao D, Yun Q, Tala, Wang J, Sun G, Baabdullah M, Yu X, Hu S, Al-Mssallem IS, Yu J. Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus). Environ Microbiol 2013; 15:3020-9. [PMID: 24102776 PMCID: PMC4253082 DOI: 10.1111/1462-2920.12262] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 06/26/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
The intestinal microbes residing in the red palm weevil (RPW, Rhynchophorus ferrugineus) larva consume tender interior fibrous tissues of date palm trunks. The understanding of such microbiota at molecular level provides vital clues for the biological control of this devastating pest. Using pyrosequencing and shotgun strategy, we first study taxonomic profiles of the microbiota sampled at different months (March, July and November), and then confirm the impact of high-temperature stress on the microbial populations based on data from 16S rRNA amplicons using both field and laboratory samples. We further identify Klebsiella pneumoniae in November and Lactococcus lactis in July as the dominant species of the microbiota. We find that the RPW gut microbiota degrades polysaccharides and sucrose with hydrolases and that different active bacterial species in November and July are responsible for the symbiotic relationship between the microbiota and the host. Our results provide vital information for pest control and cellulolytic bacterial species characterization.
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Affiliation(s)
- Shangang Jia
- Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guangyu Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - An Yin
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Sun Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fusen Li
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Duojun Zhao
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Quanzheng Yun
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Tala
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jixiang Wang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Gaoyuan Sun
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mohammed Baabdullah
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
| | - Xiaoguang Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ibrahim S Al-Mssallem
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Hofuf, Kingdom of Saudi Arabia
| | - Jun Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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