Genome Sequences of Three Novel Bacillus cereus Bacteriophages

Grose, Julianne H.; Jensen, Jordan D.; Merrill, Bryan D.; Fisher, Joshua N. B.; Burnett, Sandra H.; Breakwell, Donald P.

doi:10.1128/genomea.01118-13

Cited by 8 publications

(8 citation statements)

References 12 publications

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“…Two B. cereus isolates (BC6132 and BC7003) were collected from soil samples from Logan, UT, and were confirmed as B. cereus by 16S rRNA gene sequencing which revealed more than 99% identity to B. cereus strains. Phages were subsequently isolated from enrichment cultures containing BC7003 and soil from various apple orchards along the Wasatch Front of Utah County in Utah as previously reported (25). Each phage was plaque purified at least three times.…”

Section: Resultsmentioning

confidence: 99%

“…The genome sizes for Basilisk, JL, and Shanette were 81,790, 137,918, and 138,877 bp, respectively. Sequencing was accomplished with 454 pyrosequencing, and putative open reading frames (ORFs) of each genome were predicted using GeneMark and Glimmer within the DNA Master phage annotation software (http://cobamide2.bio.pitt .edu) as previously described (25). The data from coding potential (GeneMark [53]), BLASTX (54), and Shine-Dalgarno prediction (http://cobamide2.bio.pitt.edu) were used to determine the best call for annotation, with GeneMark and BLASTX given the most weight.…”

Section: Figmentioning

confidence: 99%

“…Functions were assigned on the basis of BLASTP hits with an E value of at least 10 Ϫ3 . The ends of the phages were recently determined by processing the raw sequencing data using the PAUSE method (https://cpt.tamu.edu/pause/) which resulted in a new bp 1 call than previously reported (25), and GenBank files were updated accordingly.…”

Section: Figmentioning

confidence: 99%

“…We are grateful for the BYU undergraduate student researchers Shanette M. Pettersson, Joshua Fisher, and Joshua Lloyd who aided in isolation, DNA purification, annotation of genomes (25), and collection of related genomes for analysis. We thank Michael Standing from the BYU Microscopy Lab, the Electron Microscopy Core Laboratory at the University of Utah, and Edward Wilcox from the BYU DNA Sequencing Center.…”

Section: Acknowledgmentsmentioning

confidence: 99%

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The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to wellcharacterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T‫9؍‬ icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. IMPORTANCEThe Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.

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Section: Resultsmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

Section: Acknowledgmentsmentioning

confidence: 99%

See 2 more Smart Citations

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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“…Phage DNA was sequenced using 454 sequencing technology and sequencing reads were assembled using Newbler 2.9 (454 Life Sciences, Roche), Consed [ 22 ], and Gepard [ 23 ]. Phage genomes were screened for direct terminal repeats using PAUSE ( https://cpt.tamu.edu/computer-resources/pause ) and were annotated using DNA Master [ 24 ] and other programs described previously [ 18 , 25 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages

et al. 2016

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Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.

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Characterization of LysPBC4, a novelBacillus cereus-specific endolysin of bacteriophage PBC4

Kong

Ryu

2016

FEMS Microbiology Letters

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Bacillus cereus is a spore-forming, Gram-positive bacterium and is a major food-borne pathogen. A B. cereus-specific bacteriophage PBC4 was isolated from the soil of a stock farm, and its genome was analyzed. PBC4 belongs to the Siphoviridae family and has a genome consisting of 80 647-bp-long double-stranded DNA, including 123 genes and two tRNAs. LysPBC4, the endolysin of PBC4, has an enzymatically active domain (EAD) on its N-terminal region and a putative cell wall-binding domain (CBD) on its C-terminal region, respectively. Although the phage PBC4 showed a very limited host range, LysPBC4 could lyse all of the B. cereus strains tested. However, LysPBC4 did not kill other bacteria such as B. subtilis or Listeria, indicating that the endolysin has specific lytic activity against the B. cereus group species. Furthermore, LysPBC4_CBD fused with enhanced green fluorescent protein (EGFP) could decorate limited strains of B. cereus group, suggesting that the LysPBC4_CBD may be a promising material for specific detection of B. cereus.

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Genome Sequences of Three Novel Bacillus cereus Bacteriophages

Cited by 8 publications

References 12 publications

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages

Characterization of LysPBC4, a novelBacillus cereus-specific endolysin of bacteriophage PBC4

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