Biological and genomic analysis of a PBSX-like defective phage induced from Bacillus pumilus AB94180

Jin, Tingting; Zhang, Xiaoming; Zhang, Yang; Hu, Zhongsheng; Fu, Zhengwei; Fan, Junpeng; Wu, Ming-Jiuan; Wang, Yi; Shen, Ping; Chen, Xiangdong

doi:10.1007/s00705-013-1898-x

Cited by 9 publications

(19 citation statements)

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“…Induction of PBSX. Induction of the defective bacteriophage (PBSX) was performed as described previously (56). Cell-to-cell gene transfer assay on a filter membrane.…”

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confidence: 99%

Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis

et al. 2018

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Horizontal gene transfer (HGT) is a driving force for bacterial evolution that occurs via conjugation, transduction, and transformation. Whereas conjugation and transduction depend on nonbacterial vehicles, transformation is considered a naturally occurring process in which naked DNA molecules are taken up by a competent recipient cell. Here, we report that HGT occurred between two strains cocultured on a minimum medium agar plate for 10 h. This process was almost completely resistant to DNase treatment and appeared to require close proximity between cells. The deletion of in the recipient completely abolished gene transfer, indicating that the process involved transformation. This process was also highly efficient, reaching 1.75 × 10 transformants/μg DNA compared to 5.3 × 10 and 1.86 × 10 transformants/μg DNA for DNA-to-cell transformation by the same agar method and the standard two-step procedure, respectively. Interestingly, when three distantly localized chromosomal markers were selected simultaneously, the efficiency of cell-to-cell transformation still reached 6.26 × 10 transformants/μg DNA, whereas no transformants were obtained when free DNA was used as the donor. Stresses, such as starvation and exposure to antibiotics, further enhanced transformation efficiency by affecting the donor cells, suggesting that stress served as an important signal for promoting this type of HGT. Taken together, our results defined a bona fide process of cell-to-cell natural transformation (CTCNT) in and related species. This finding reveals the previously unrecognized role of donor cells in bacterial natural transformation and improves our understanding of how HGT drives bacterial evolution at a mechanistic level. Because DNA is easily prepared, studies of bacterial natural genetic transformation traditionally focus on recipient cells. However, such laboratory artifacts cannot explain how this process occurs in nature. In most cases, competence is only transient and involves approximately 20 to 50 genes, and it is unreasonable for bacteria to spend so many genetic resources on unpredictable and uncertain environmental DNA. Here, we characterized a donor cell-dependent CTCNT process in and related species that was almost completely resistant to DNase treatment and was more efficient than classical natural transformation using naked DNA as a donor, i.e., DNA-to-cell transformation, suggesting that DNA donor cells were also important in the transformation process in natural environments.

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“…Induction of PBSX. Induction of the defective bacteriophage (PBSX) was performed as described previously (56). Cell-to-cell gene transfer assay on a filter membrane.…”

mentioning

confidence: 99%

Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis

et al. 2018

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“…4A ). The intact prophage region was located between sites 12,281 to 39,856 nt with a G+C content of 41.47%, which was similar to the G+C content of the GR8 genome, and it exhibited 87% genomic similarity to the genome of the defective phage, PBP180, from B. pumilus strain CCTCC AB94180 43 . The GR8 strain was inducible by mitomycin C, but the induced phage could not infect the GR8 strain ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 96%

Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy

Yuan

Gao

2015

Sci Rep

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Bacillus pumilus has been widely identified as a pathogen of plant and human, while the genetic information is rarely available for pathogenic B. pumilus strains. B. pumilus GR8 is a pathogen that causes ginger rhizome rot disease by invading ginger rhizome parenchymatous tissues, growing in the extracellular space, and producing plant cell wall-degrading enzymes to destroy ginger cells. In this study, the genome of GR8 was sequenced and characterized. This genome was the third completely sequenced genome of the B. pumilus species, and it exhibited high similarity to the genome of the B. pumilus strain B6033. The genome of GR8 was 3.67 Mb in length and encoded 3,713 putative ORFs. Among these predicted proteins, numerous plant cell wall-degrading enzymes and several proteins associated with invading and adapting to the environment in the extracellular space of the ginger rhizome parenchymatous tissue were found. The GR8 genome contained only one restriction-modification system and no CRISPR/Cas system. The lack of phage-resistant system suggested that phages might be potential agents for the control of GR8. The genomic analysis of GR8 provided the understanding to the pathogenesis and the phage-control strategy of pathogenic B. pumilus strains.

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“…The general distribution of reads over the whole genome indicates random packing of chromosomal DNA and supports the assumption of a PBSX ortholog prophage in B . licheniformis DSM13, since PBSX-like prophages are described to randomly pack 13 kb fragments of the host chromosome instead of their own genome with a size of about 30 kb [ 24 , 35 , 47 , 48 ]. The comparison of the results from strains B .…”

Section: Resultsmentioning

confidence: 99%

Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

et al. 2015

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Prophages are viruses, which have integrated their genomes into the genome of a bacterial host. The status of the prophage genome can vary from fully intact with the potential to form infective particles to a remnant state where only a few phage genes persist. Prophages have impact on the properties of their host and are therefore of great interest for genomic research and strain design. Here we present a genome- and next generation sequencing (NGS)-based approach for identification and activity evaluation of prophage regions. Seven prophage or prophage-like regions were identified in the genome of Bacillus licheniformis DSM13. Six of these regions show similarity to members of the Siphoviridae phage family. The remaining region encodes the B. licheniformis orthologue of the PBSX prophage from Bacillus subtilis. Analysis of isolated phage particles (induced by mitomycin C) from the wild-type strain and prophage deletion mutant strains revealed activity of the prophage regions BLi_Pp2 (PBSX-like), BLi_Pp3 and BLi_Pp6. In contrast to BLi_Pp2 and BLi_Pp3, neither phage DNA nor phage particles of BLi_Pp6 could be visualized. However, the ability of prophage BLi_Pp6 to generate particles could be confirmed by sequencing of particle-protected DNA mapping to prophage locus BLi_Pp6. The introduced NGS-based approach allows the investigation of prophage regions and their ability to form particles. Our results show that this approach increases the sensitivity of prophage activity analysis and can complement more conventional approaches such as transmission electron microscopy (TEM).

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Biological and genomic analysis of a PBSX-like defective phage induced from Bacillus pumilus AB94180

Cited by 9 publications

References 50 publications

Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis

Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis

Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy

Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

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