Divergence and Mosaicism among Virulent Soil Phages of the
            <i>Burkholderia cepacia</i>
            Complex

Summer, Elizabeth J.; Gonzalez, Carlos F.; Bomer, Morgan; Carlile, Thomas M.; Embry, Addie; Kucherka, Amalie M.; Lee, Jonte; Mebane, Leslie M.; Morrison, William C.; Mark, Louise; King, Maria D.; LiPuma, John J.; Vidaver, Anne K.; Young, Ry

doi:10.1128/jb.188.1.255-268.2006

Cited by 63 publications

(52 citation statements)

References 61 publications

(57 reference statements)

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“…As in Xop2, the lysis cassette of the Xfp1-like prophage elements has an atypical gene arrangement, with the endolysin gene preceding the holin gene. The endolysin (XF0707 in Xfp1) is a glycoside hydrolase and is followed by XF0708, a homologue of the class I (3-TMD) holin from Burkholderia phage Bcep781 (56). The holin gene is followed by the Rz equivalent (XF0709 in Xfp1).…”

Section: Resultsmentioning

confidence: 99%

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Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

et al. 2010

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We report the plaque propagation and genomic analysis of Xfas53, a temperate phage of Xylella fastidiosa. Xfas53 was isolated from supernatants of X. fastidiosa strain 53 and forms plaques on the sequenced strain Temecula. Xfas53 forms short-tailed virions, morphologically similar to podophage P22. The 36.7-kb genome is predicted to encode 45 proteins. The Xfas53 terminase and structural genes are related at a protein and gene order level to P22. The left arm of the Xfas53 genome has over 90% nucleotide identity to multiple prophage elements of the sequenced X. fastidiosa strains. This arm encodes proteins involved in DNA metabolism, integration, and lysogenic control. In contrast to Xfas53, each of these prophages encodes head and DNA packaging proteins related to the siphophage lambda and tail morphogenesis proteins related to those of myophage P2. Therefore, it appears that Xfas53 was formed by recombination between a widespread family of X. fastidiosa P2-related prophage elements and a podophage distantly related to phage P22. The lysis cassette of Xfas53 is predicted to encode a pinholin, a signal anchor and release (SAR) endolysin, and Rz and Rz1 equivalents. The holin gene encodes a pinholin and appears to be subject to an unprecedented degree of negative regulation at both the level of expression, with rho-independent transcriptional termination and RNA structure-dependent translational repression, and the level of holin function, with two upstream translational starts predicted to encode antiholin products. A notable feature of Xfas53 and related prophages is the presence of 220-to 390-nucleotide degenerate tandem direct repeats encoding putative DNA binding proteins. Additionally, each phage encodes at least two BroN domain-containing proteins possibly involved in lysogenic control. Xfas53 exhibits unusually slow adsorption kinetics, possibly an adaptation to the confined niche of its slow-growing host.

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Section: Resultsmentioning

confidence: 99%

“…Genomic DNA was sized by pulsed-field gel electrophoresis. Library preparation, sequencing, sequence assembly, and analyses were performed essentially as described previously (54,56,57). The genomic DNA library was prepared in the pSmart-LCKan vector (Lucigen).…”

Section: Methodsmentioning

confidence: 99%

Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

et al. 2010

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“…Further investigation uncovered that all nine separate viromes generated numerous hits to phages infectious to Burkholderia: 50% of the 72 annotated protein-coding genes within the 47 399 bp genome of the Burkholderia phage BcepB1A (NC_005886) (Summer et al 2006) were found within the Lake Michigan virome. Most of the hits were from three of our original samples (Fig.…”

Section: Viral-associated Proteinsmentioning

confidence: 99%

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

Watkins

Kuehnle

Ruggeri

et al. 2016

Mar. Freshwater Res.

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Abstract. Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generally.

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“…The two other genes contained in this IS element, 33 and 34, are conserved hypothetical genes. gp34 is closely related to gp55 of Bcep781 and gp54 of Bcep43, both of which are virulent phages that infect the related bacterium Burkholderia cepacia (76).…”

Section: Vol 193 2011mentioning

confidence: 99%

Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia

et al. 2011

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Within the Burkholderia cepacia complex, B. cenocepacia is the most common species associated with aggressive infections in the lungs of cystic fibrosis patients, causing disease that is often refractive to treatment by antibiotics. Phage therapy may be a potential alternative form of treatment for these infections. Here we describe the genome of the previously described therapeutic B. cenocepacia podophage BcepIL02 and its close relative, Bcep22. Phage Bcep22 was found to contain a circularly permuted genome of 63,882 bp containing 77 genes; BcepIL02 was found to be 62,714 bp and contains 76 predicted genes. Major virion-associated proteins were identified by proteomic analysis. We propose that these phages comprise the founding members of a novel podophage lineage, the Bcep22-like phages. Among the interesting features of these phages are a series of tandemly repeated putative tail fiber genes that are similar to each other and also to one or more such genes in the other phages. Both phages also contain an extremely large (ca. 4,600-amino-acid), virion-associated, multidomain protein that accounts for over 20% of the phages' coding capacity, is widely distributed among other bacterial and phage genomes, and may be involved in facilitating DNA entry in both phage and other mobile DNA elements. The phages, which were previously presumed to be virulent, show evidence of a temperate lifestyle but are apparently unable to form stable lysogens in their hosts. This ambiguity complicates determination of a phage lifestyle, a key consideration in the selection of therapeutic phages.

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Divergence and Mosaicism among Virulent Soil Phages of the Burkholderia cepacia Complex

Cited by 63 publications

References 61 publications

Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia

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