Role of phages in the pathogenesis of Burkholderia, or ‘Where are the toxin genes in Burkholderia phages?’

Summer, Elizabeth J.; Gill, Jason J.; Upton, Chris; Gonzalez, Carlos F.; Young, Ry

doi:10.1016/j.mib.2007.05.016

Cited by 44 publications

(61 citation statements)

References 67 publications

(45 reference statements)

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“…B. thailandensis and B. pseudomallei are considered as two distinct species (Gevers et al 2005); however, their genomes are highly similar in sequence and content (Yu et al 2006). The abundant lateral gene transfer among these genomes is thought to be mediated mainly by transduction (Summer et al 2007). We find Figure 6.…”

Section: Types Of Genes and Types Of Genomesmentioning

confidence: 99%

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

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Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having #5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.

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Section: Types Of Genes and Types Of Genomesmentioning

confidence: 99%

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

View full text Add to dashboard Cite

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“…[2][3][4][5] For the Burkholderia cepacia complex (BCC)-a group of opportunistic pathogens infecting cystic fibrosis (CF) patients-characterization studies generally focus on the potential for medical application of a specific phage. Of particular importance are phages infecting B. cenocepacia due to the clinical predominance and virulence of this species.…”

Section: Introductionmentioning

confidence: 99%

“…[6][7][8] The use of such phages against Burkholderia is arguably safer than it is against many other pathogens because virulence factors in this genus have not been discovered to be encoded by temperate phages. 2 One of the challenges of prophage identification is the differentiation of inducible prophages from defective prophage remnants, a distinction with both evolutionary and practical implications. From an evolutionary standpoint, inducible prophages can transfer bacterial or phage genes through transduction, while prophage remnants do not actively facilitate horizontal exchange (with some exceptions, such as gene transfer agents).…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of ϕH111-1

et al. 2013

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“…Although examples have been documented in a wide variety of Gram-negative organisms (including Vibrio cholerae, Escherichia coli, Pseudomonas aeruginosa, Neisseria meningitidis, Salmonella enterica, and Shigella flexneri), there is limited evidence that prophage genes contribute to virulence in Burkholderia species (8,43). It has been suggested that because Burkholderia are not strictly pathogenic and can instead survive in a variety of both terrestrial and aquatic environments, classical toxin genes may not have provided a strong evolutionary advantage to these species (43). Instead, lysogenic conversion genes of Burkholderia prophages would be more likely to encode proteins that would increase the viability of the cell both in the environment and in vivo (43).…”

Section: Resultsmentioning

confidence: 99%

“…It has been suggested that because Burkholderia are not strictly pathogenic and can instead survive in a variety of both terrestrial and aquatic environments, classical toxin genes may not have provided a strong evolutionary advantage to these species (43). Instead, lysogenic conversion genes of Burkholderia prophages would be more likely to encode proteins that would increase the viability of the cell both in the environment and in vivo (43).…”

Section: Resultsmentioning

confidence: 99%

Inactivation of Burkholderia cepacia Complex Phage KS9 gp41 Identifies the Phage Repressor and Generates Lytic Virions

Lynch

Seed

Stothard

et al. 2010

J Virol

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The Burkholderia cepacia complex (BCC) is made up of at least 17 species of Gram-negative opportunistic bacterial pathogens that cause fatal infections in patients with cystic fibrosis and chronic granulomatous disease. KS9 (vB_BcenS_KS9), one of a number of temperate phages isolated from BCC species, is a prophage of Burkholderia pyrrocinia LMG 21824. Transmission electron micrographs indicate that KS9 belongs to the family Siphoviridae and exhibits the B1 morphotype. The 39,896-bp KS9 genome, comprised of 50 predicted genes, integrates into the 3 end of the LMG 21824 GTP cyclohydrolase II open reading frame. The KS9 genome is most similar to uncharacterized prophage elements in the genome of B. cenocepacia PC184 (vB_BcenZ_ PC184), as well as Burkholderia thailandensis phage E125 and Burkholderia pseudomallei phage 1026b. Using molecular techniques, we have disrupted KS9 gene 41, which exhibits similarity to genes encoding phage repressors, producing a lytic mutant named KS9c. This phage is incapable of stable lysogeny in either LMG 21824 or B. cenocepacia strain K56-2 and rescues a Galleria mellonella infection model from experimental B. cenocepacia K56-2 infections at relatively low multiplicities of infection. These results readily demonstrate that temperate phages can be genetically engineered to lytic form and that these modified phages can be used to treat bacterial infections in vivo.

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Role of phages in the pathogenesis of Burkholderia, or ‘Where are the toxin genes in Burkholderia phages?’

Cited by 44 publications

References 67 publications

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Identification and characterization of ϕH111-1

Inactivation of Burkholderia cepacia Complex Phage KS9 gp41 Identifies the Phage Repressor and Generates Lytic Virions

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