Genomic characterization of six novel Bacillus pumilus bacteriophages

Lorenz, Laura S.; Lins, Bridget; Barrett, Jonathan; Montgomery, Andrew; Trapani, Stephanie; Schindler, A. F.; Christie, Gail E.; Cresawn, Steven G.; Temple, Louise

doi:10.1016/j.virol.2013.07.004

Cited by 33 publications

(29 citation statements)

References 51 publications

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“…The contributions of the SEA-PHAGES students have been essential to our current understanding of the diversity of mycobacteriophages, demonstrating the substantial impact of the distributed approach compared to what would be accomplished by a single laboratory, and have resulted in several publications with student authors (29, 31–39). Since the start of the program in 2008, SEA-PHAGES students have isolated 3,000 new phages (with global positioning system [GPS] coordinates recorded) and characterized their phages by DNA restriction analysis and electron microscopy.…”

Section: Resultsmentioning

confidence: 99%

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Jordan

Burnett

Carson

et al. 2014

mBio

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Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

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Section: Resultsmentioning

confidence: 99%

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Jordan

Burnett

Carson

et al. 2014

mBio

Self Cite

461

440

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“…Each of the two phages had an isometric head with a diameter of 88 nm, a 189-nm-long contractile tail, a 60-nm-long tail needle, and a 20-nmlong and 46-nm-wide baseplate. To date, a few phages of B. pumilus have been isolated (17), while only one B. pumilus phage from the Myoviridae family has been morphologically characterized (16).…”

Section: Resultsmentioning

confidence: 99%

“…Before 1981, more than 33 different phages were reported to infect B. pumilus, and a few more have been characterized since (15). In addition, the genome of 10 B. pumilus phages have been characterized to date (16,17); however, the structural proteome of the phage virion has not yet been analyzed.…”

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confidence: 99%

Effects of Actin-Like Proteins Encoded by Two Bacillus pumilus Phages on Unstable Lysogeny, Revealed by Genomic Analysis

Yuan

Qin

et al. 2015

Appl Environ Microbiol

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We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease. Bacteriophages (phages) are viral predators of bacteria that propagate by infecting the host (1) and, based on the mode of replication of the phage genome, they are classified as lytic or lysogenic phages. To maintain the lysogenic state, phage gene expression is regulated by the phage lysogenic regulatory system. The lytic switch mechanism of the temperate phage has been well studied (2), which illustrates the classical lysogen conversion mechanism of and similar phages. Several other strategies for phage lysogenic conversion have also been observed. For example, a single nucleotide mutation in the LexA-binding site of phage SPC32H induces phage SPC32H to maintain the lysogenic state (1). According Yoshihiko et al., a temperate phage, c-st, with a linear genome can transform into a circular plasmid prophage in the host, Clostridium botulinum, which provides phage c-st the ability to exhibit unstable lysogeny (3). Meanwhile, the TubZ-like plasmid segregation system protein encoded by c-st is essential for partition of the prophage plasmid (4).Plasmid segregation systems are essential for accurate partition of large and essential plasmids to daughter cells during cell division (5). The plasmid segregation system typically consists of three components: a centromere-like DNA region, a small DNA-binding adaptor protein, and a nucleotide-driven motor protein with NTPase activity. Based on the nature of the motor proteins, three major classes of segregation systems have been identified to date and can be described as ParA-like system (type I, ParABS system), ParM-like system (type...

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“…Phamerator is popular among the large groups studying Mycobacteriophages [4] and Bacillus phages [5, 6] and is steadily gaining traction in other areas of phage research [7–11]. …”

Section: Introductionmentioning

confidence: 99%

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

et al. 2016

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BackgroundPhage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes.ResultsThe original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome.ConclusionsUsing available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.

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Genomic characterization of six novel Bacillus pumilus bacteriophages

Cited by 33 publications

References 51 publications

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

Effects of Actin-Like Proteins Encoded by Two Bacillus pumilus Phages on Unstable Lysogeny, Revealed by Genomic Analysis

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

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