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Piligrimova EG, Kazantseva OA, Kazantsev AN, Nikulin NA, Skorynina AV, Koposova ON, Shadrin AM. Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity. Sci Rep 2021; 11:7611. [PMID: 33828147 PMCID: PMC8026635 DOI: 10.1038/s41598-021-87111-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022] Open
Abstract
Bacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.
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Affiliation(s)
- Emma G Piligrimova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
| | - Olesya A Kazantseva
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey N Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, Pushchino, 142290, Russia
| | - Nikita A Nikulin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Anna V Skorynina
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Olga N Koposova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey M Shadrin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
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Zuo W, Li J, Zheng J, Zhang L, Yang Q, Yu Y, Zhang Z, Ding Q. Whole genome sequencing of a multidrug-resistant Bacillus thuringiensis HM-311 obtained from the Radiation and Heavy metal-polluted soil. J Glob Antimicrob Resist 2020; 21:275-277. [PMID: 32353525 DOI: 10.1016/j.jgar.2020.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Bacillus thuringiensis (BT) is distributed widely in the environment and utilised frequently for its highly specific toxins to target insect. However, BT is potentially pathogenic due to the high similarity between BT and Bacillus anthracis (BA). Meanwhile, there are reports that heavy metal pressure can promote the proliferation of antibiotic resistance in microorganisms through the co-selection of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). The aim of this work was revealed the MRGs and ARGs in a novel heavy metal tolerant and drug-resistant strain - B. thuringiensis HM-311, which was isolated from radiation and heavy metal-contaminated soil in Xinjiang (China). METHODS The genome of B. thuringiensis HM-311 was sequenced using a PacBio RS II platform and Illumina HiSeq 4000 platform at the Beijing Genomics Institute (BGI, Shenzhen, China). RESULTS The total size of B. thuringiensis HM-311 genome was 6,019,481bp with a GC content of 35.85%. 134 genes related to antibiotics resistance and 75 genes related to heavy metal resistance were predicted in the B. thuringiensis HM-311 genome, the main ARGs and MRGs were discussed. Moreover, 30 verified virulence factor genes and 297 predicted virulence factor genes were annotated in the B. thuringiensis HM-311 genome. CONCLUSIONS This genome can be used as a reference sequence for comparative genomic studies, elucidating antibiotic resistance development and the relationship between antibiotic resistance genes and heavy metal resistance genes in B. thuringiensis.
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Affiliation(s)
- Wenlu Zuo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China
| | - Jingchen Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China
| | - Jie Zheng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China
| | - Lei Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China
| | - Qi Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China
| | - Yadong Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, People's Republic of China; School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang Uigur Autonomous Region, People's Republic of China
| | - Qingqing Ding
- Department of Geriatric Oncology, Jiangsu Province Hospital (The First Affiliated Hospital with Nanjing Medical University), Nanjing 210029, People's Republic of China.
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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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Jin Y, Wang J, Liu Q, Qiu H, Wang Y, Zhou J, Sun J, Li P, Wang R, Zhang W. Genome of Bacillus sp. strain QHF158 provides insights into its parasporal inclusions encoded by the S-layer gene. Braz J Microbiol 2019; 51:1145-1150. [PMID: 31836963 DOI: 10.1007/s42770-019-00205-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022] Open
Abstract
Bacillus sp. strain QHF158, a Gram-positive, spore-forming and parasporal crystal-secreting bacterium, was isolated from soil of Limushan National Forest Park in China. Here we present the significant feature of parasporal inclusions of this organism, together with the draft genome sequence and annotation. Phylogenetic analysis suggested that strain QHF158 is possibly a novel species, most closely related to Bacillus mycoides. Genome annotation results revealed that strain QHF158 did not contain any typical Cry or Cyt toxin coding gene. Furthermore, the mass spectrometry analyses demonstrated that the parasporal crystalline inclusions were encoded by the orf_05273 gene, with 95% similarity to the S-layer protein (SLP) EA1 of B. mycoides, which indicated that the parasporal crystal from Bacillus sp. strain QHF158 was mainly formed by SLP, instead of the typical Cry or Cyt toxin proteins.
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Affiliation(s)
- Yinghong Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Junhui Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Qian Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Haifang Qiu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Yangyang Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Jiayi Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Jie Sun
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Peng Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Ruiping Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
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Domínguez-Arrizabalaga M, Villanueva M, Fernandez AB, Caballero P. A Strain of Bacillus thuringiensis Containing a Novel cry7Aa2 Gene that Is Toxic to Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae). INSECTS 2019; 10:E259. [PMID: 31438609 PMCID: PMC6780604 DOI: 10.3390/insects10090259] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/26/2019] [Accepted: 08/16/2019] [Indexed: 12/03/2022]
Abstract
The genome of the Bacillus thuringiensis BM311.1 strain was sequenced and assembled in 359 contigs containing a total of 6,390,221 bp. The plasmidic ORF of a putative cry gene from this strain was identified as a potential novel Cry protein of 1138 amino acid residues with a 98% identity compared to Cry7Aa1 and a predicted molecular mass of 129.4 kDa. The primary structure of Cry7Aa2, which had eight conserved blocks and the classical structure of three domains, differed in 28 amino acid residues from that of Cry7Aa1. The cry7Aa2 gene was amplified by PCR and then expressed in the acrystalliferous strain BMB171. SDS-PAGE analysis confirmed the predicted molecular mass for the Cry7Aa2 protein and revealed that after in vitro trypsin incubation, the protein was degraded to a toxin of 62 kDa. However, when treated with digestive fluids from Leptinotarsa decemlineata larvae, one major proteinase-resistant fragment of slightly smaller size was produced. The spore and crystal mixture produced by the wild-type BM311.1 strain against L. decemlineata neonate larvae resulted in a LC50 value of 18.8 μg/mL, which was statistically similar to the estimated LC50 of 20.8 μg/mL for the recombinant BMB17-Cry7Aa2 strain. In addition, when this novel toxin was activated in vitro with commercial trypsin, the LC50 value was reduced 3.8-fold to LC50 = 4.9 μg/mL. The potential advantages of Cry7Aa2 protoxin compared to Cry7Aa1 protoxin when used in the control of insect pests are discussed.
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Affiliation(s)
- Mikel Domínguez-Arrizabalaga
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, 31192 Mutilva, Navarra, Spain
| | - Maite Villanueva
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, 31192 Mutilva, Navarra, Spain
- Bioinsectis SL, Avda Pamplona 123, Mutilva, Navarra, Spain
| | - Ana Beatriz Fernandez
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, 31192 Mutilva, Navarra, Spain
| | - Primitivo Caballero
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, 31192 Mutilva, Navarra, Spain.
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Nair K, Al-Thani R, Al-Thani D, Al-Yafei F, Ahmed T, Jaoua S. Diversity of Bacillus thuringiensis Strains From Qatar as Shown by Crystal Morphology, δ-Endotoxins and Cry Gene Content. Front Microbiol 2018; 9:708. [PMID: 29696009 PMCID: PMC5904277 DOI: 10.3389/fmicb.2018.00708] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/27/2018] [Indexed: 11/29/2022] Open
Abstract
Bacillus thuringiensis (Bt) based insecticidal formulations have been recognized as one of the most successful, environmentally safe and sustainable method of controlling insect pests. Research teams worldwide are in search of Bt diversity giving more choices of bio-insecticides and alternatives to address insect resistance. In fact, there are many unexplored ecologies that could harbor novel Bt strains. This study is the first initiative to explore Bt strain diversity in Qatar. A collection of 700 Bt isolates was constructed. Scanning electron microscopy of Bt crystals showed different crystal forms, with a high abundance of spherical crystals compared to the bipyramidal ones. Among the spherical crystals, four different morphologies were observed. The δ-endotoxin content of parasporal crystals from each Bt isolate revealed that there are 16 different protein profiles among the isolates of the collection. On the other hand, plasmid pattern analysis showed seven different plasmid profiles. Their insecticidal activity was predicted by exploring the δ-endotoxin coding genes and conducting qualitative insecticidal bioassays. 19 smooth spherical crystal producing isolates have been identified that could be possible candidates for endotoxin production targeting Dipteran insects. Another group of 259 isolates producing bipyramidal and cuboidal crystals could target Lepidopteran and Coleopteran insects. The remaining 422 isolates have novel profiles. In conclusion, Qatari soil ecology provides a good collection and diversity of Bt isolates. In addition to strains harboring genes encoding common endotoxins, the majority are different and very promising for the search of novel insecticidal endotoxins.
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Affiliation(s)
- Kavita Nair
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Roda Al-Thani
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Dhabia Al-Thani
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Fatima Al-Yafei
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Samir Jaoua
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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Bacillus thuringiensis: a successful insecticide with new environmental features and tidings. Appl Microbiol Biotechnol 2017; 101:2691-2711. [PMID: 28235989 DOI: 10.1007/s00253-017-8175-y] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 12/15/2022]
Abstract
Bacillus thuringiensis (Bt) is known as the most successful microbial insecticide against different orders of insect pests in agriculture and medicine. Moreover, Bt toxin genes also have been efficiently used to enhance resistance to insect pests in genetically modified crops. In light of the scientific advantages of new molecular biology technologies, recently, some other new potentials of Bt have been explored. These new environmental features include the toxicity against nematodes, mites, and ticks, antagonistic effects against plant and animal pathogenic bacteria and fungi, plant growth-promoting activities (PGPR), bioremediation of different heavy metals and other pollutants, biosynthesis of metal nanoparticles, production of polyhydroxyalkanoate biopolymer, and anticancer activities (due to parasporins). This review comprehensively describes recent advances in the Bt whole-genome studies, the last updated known Bt toxins and their functions, and application of cry genes in plant genetic engineering. Moreover, the review thoroughly describes the new features of Bt which make it a suitable cell factory that might be used for production of different novel valuable bioproducts.
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