The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

Winsor, Geoffrey L.; Khaira, Bhavjinder K.; Rossum, Thea Van; Lo, Raymond; Whiteside, Matthew D.; Brinkman, Fiona S. L.

doi:10.1093/bioinformatics/btn524

Cited by 232 publications

(299 citation statements)

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“…After filtering to include genes present in one of three samples, followed by filtering on confidence (P Ͻ 0.05, t test with BenjaminiHochberg and false discovery rate postcorrection), the remaining genes were filtered using a 1.5-fold ratio change to identify genes showing increased or decreased expression in K56-2shvR::Tp compared to that in K56-2. Operon prediction was derived from analysis of B. cenocepacia genomes at http://www .burkholderia.com (60).…”

Section: Methodsmentioning

confidence: 99%

“…The locus carrying shvR lies adjacent to the predicted afcA and afcC operons that are divergently transcribed (60). Mutations affecting afcA, afcC, and afcD in Burkholderia pyrrocinia BC11 (formerly B. cepacia BC11 [56]) were previously shown to impair the production of an antifungal compound and inhibit antifungal activity against the soilborne phytopathogen Rhizoctonia solani (25).…”

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confidence: 99%

“…CciI primarily synthesizes HHL, with lesser amounts of OHL produced (36). All members of the Bcc have the CepIR system (19,32), whereas CciIR is found only in transmissible B. cenocepacia strains containing the cenocepacia island and is absent from genomes of other B. cenocepacia strains, including representatives of the transmissible PHDC lineage (AU1054, HI2424) (2,21,60). CepR2 is an orphan LuxR homolog found in all B. cenocepacia strains and can regulate gene expression in the absence of AHLs (37).…”

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confidence: 99%

“…In B. cenocepacia AU1054, a gspJ mutation resulted in reduced protease and polygalacturonase activities (52). Analysis of sequenced genomes at http://www.burkholderia.com (60) indicates that B. cenocepacia J2315 is the only Burkholderia strain which lacks gspL, which is part of the gspG operon (21). B. cenocepacia J2315 produces little or no protease activity on skim milk agar despite detection of high zmpA expression levels using qRT-PCR (17).…”

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confidence: 99%

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The Burkholderia cenocepacia LysR-Type Transcriptional Regulator ShvR Influences Expression of Quorum-Sensing, Protease, Type II Secretion, and afc Genes

et al. 2011

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Burkholderia cenocepacia is a significant opportunistic pathogen in individuals with cystic fibrosis. ShvR, a LysR-type transcriptional regulator, has previously been shown to influence colony morphology, biofilm formation, virulence in plant and animal infection models, and some quorum-sensing-dependent phenotypes. In the present study, it was shown that ShvR negatively regulates its own expression, as is typical for LysR-type regulators. The production of quorum-sensing signal molecules was detected earlier in growth in the shvR mutant than in the wild type, and ShvR repressed expression of the quorum-sensing regulatory genes cepIR and cciIR. Microarray analysis and transcriptional fusions revealed that ShvR regulated over 1,000 genes, including the zinc metalloproteases zmpA and zmpB. The shvR mutant displayed increased gene expression of the type II secretion system and significantly increased protease and lipase activities. Both ShvR and CepR influence expression of a 24-kb genomic region adjacent to shvR that includes the afcA and afcC operons, required for the production of an antifungal agent; however, the reduction in expression was substantially greater in the shvR mutant than in the cepR mutant. Only the shvR mutation resulted in reduced antifungal activity against Rhizoctonia solani. ShvR, but not CepR, was shown to directly regulate expression of the afcA and afcC promoters. In summary, ShvR was determined to have a significant influence on the expression of quorum-sensing, protease, lipase, type II secretion, and afc genes.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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The Burkholderia cenocepacia LysR-Type Transcriptional Regulator ShvR Influences Expression of Quorum-Sensing, Protease, Type II Secretion, and afc Genes

et al. 2011

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“…We then used biological databases such as KEGG (25), Metacyc (26), and the Burkholderia Genome Database (BGD) (27) to evaluate the draft reconstructions. Specifically, we used the gene and reaction annotations in KEGG and compared them with those of the draft reconstructions.…”

Section: Figmentioning

confidence: 99%

Comparative Metabolic Systems Analysis of Pathogenic Burkholderia

Bartell¹,

Yen²,

Varga³

et al. 2013

Journal of Bacteriology

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Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens. Multidrug-resistant pathogens are a severe health concern and can cause chronic infections in a variety of patient populations with limited recourse for treatment. Here, we investigate two multidrug-resistant species, Burkholderia cenocepacia and Burkholderia multivorans, of the Burkholderia cepacia complex (BCC) which are considered dangerous and difficult to treat in patients with cystic fibrosis (CF), chronic granulomatous disease, or compromised immune systems (1). With larger genomes (8.06 Mbp and 7.01 Mbp, respectively) than many other multidrug-resistant pathogens, they also contain an expanded reservoir of genes that may assist their ability to avoid clinical eradication (2-4). Because they are nosocomial, transmissible between patients, and also routinely acquired (and reacquired) from the environment, B. cenocepacia and B. multivorans are the two BCC species most commonly isolated from the sputum of CF patients (5-8). In patients with CF, pulmonary infection with BCC can contribute to the rapid deterioration of lung function known as cepacia syndrome, a necrotizing pneumonia that can lead to bacteremia, septicemia, and increased mortality (9, 10). A combination of high antibiotic resistance and decreased immune function in patients makes B. cen...

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