Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis

Yu, Yiting; Kim, Heenam Stanley; Chua, Hui Hoon; Lin, Chi Ho; Sim, Siew Hoon; Lin, Daoxun; Derr, Alan; Engels, Reinhard; DeShazer, David; Birren, Bruce W.; Nierman, William C.; Tan, Patrick

doi:10.1186/1471-2180-6-46

Cited by 146 publications

(117 citation statements)

References 54 publications

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“…The B. thailandensis genome contains multiple gene clusters that code for the production of four polysaccharides that contribute to the capsule (capsular polysaccharide [CPS]) or to EPS production: CPS I, CPS II, CPS III, and CPS IV (26,35). Our RNA-seq findings confirm a previous observation that B. thailandensis QS activates two clusters of genes (the bceI and bceII genes), which are similar to the Burkholderia cenocepacia cepacian biosynthetic genes (7,24).…”

Section: Ahl-regulated Genessupporting

confidence: 80%

“…The content and location of the GIs differ among strains of B. thailandensis and also among other Burkholderia species (26,28,29). Eighty-four QScontrolled genes mapped to 7 of the 15 genomic islands (see Table S6 in the supplemental material).…”

Section: Ahl-regulated Genesmentioning

confidence: 99%

“…2). Chromosome 1 is the larger of the two with 3,282 predicted ORFs, and chromosome 2 has 2,363 predicted ORFs (26). For many bacteria with two chromosomes, including members of the Bptm group, the larger chromosome is enriched in genes coding for essential functions, and the smaller chromosome is enriched in genes of unknown function and genes associated with adaptation (27).…”

Section: Ahl-regulated Genesmentioning

confidence: 99%

“…The B. thailandensis genome contains 15 genomic islands (GIs), which have atypical GC content or code for bacteriophagerelated genes or phage-like elements (26). The content and location of the GIs differ among strains of B. thailandensis and also among other Burkholderia species (26,28,29).…”

Section: Ahl-regulated Genesmentioning

confidence: 99%

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Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

et al. 2014

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c Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei.

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Section: Ahl-regulated Genessupporting

confidence: 80%

Section: Ahl-regulated Genesmentioning

confidence: 99%

Section: Ahl-regulated Genesmentioning

confidence: 99%

Section: Ahl-regulated Genesmentioning

confidence: 99%

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Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

et al. 2014

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“…E246 and pathogenic Burkholderia, including B. pseudomallei strains K96243, 1710b, and 1106a, and B. mallei strains ATCC 23344, NCTC 10229, SAVP1, and NCTC 10247. 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).…”

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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Burkholderia Pseudomallei

Stevens¹,

Stevens²

2009

Intracellular Niches of Microbes

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Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis

Cited by 146 publications

References 54 publications

Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

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

Burkholderia Pseudomallei

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