Archive BacDiveID:10.13145/bacdive1965.20250331.9.3

Strain identifier

BacDive ID: 1965

Type strain:

Species: Paraburkholderia xenovorans

Strain Designation: LB400

Strain history: CIP <- 2004, CCUG <- 2002, LMG: strain LB400

NCBI tax ID(s): 36873 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 6837

BacDive-ID: 1965

DSM-Number: 17367

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Paraburkholderia xenovorans LB400 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from PCB-contaminated soil.

NCBI tax id

NCBI tax id: 36873
Matching level: species

strain history

@ref	history
6837	<- CCUG <- G. Goris, LMG Gent <- J. Tiedje, Michigan State Univ. <-NRRL <- L. Bopp, General Electric Research Labs NY
123975	CIP <- 2004, CCUG <- 2002, LMG: strain LB400

doi: 10.13145/bacdive1965.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Paraburkholderia
species: Paraburkholderia xenovorans
full scientific name: Paraburkholderia xenovorans (Goris et al. 2004) Sawana et al. 2015
synonyms
- @ref: 20215
- synonym: Burkholderia xenovorans

@ref: 6837

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia xenovorans

full scientific name: Paraburkholderia xenovorans (Goris et al. 2004) Sawana et al. 2015

strain designation: LB400

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31232	negative	1.5 µm	0.5 µm	rod-shaped	yes
123975	negative			rod-shaped	no
125438	negative					98.469

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
6837	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	yes	https://mediadive.dsmz.de/medium/545	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
6837	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6837	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	yes	https://mediadive.dsmz.de/medium/220	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
6837	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)	yes	https://mediadive.dsmz.de/medium/457	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
41992	MEDIUM 72- for trypto casein soja agar	yes		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123975	CIP Medium 72	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@ref	growth	type	temperature
6837	positive	growth	28
6837	positive	growth	30
41992	positive	growth	30
57422	positive	growth	28
123975	positive	growth	10-37
123975	no	growth	5
123975	no	growth	41

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
57422	aerobe
123975	obligate aerobe
125439	aerobe	96.3

spore formation

@ref	spore formation	confidence
31232	no
125439	no	90.9

compound production

@ref: 6837
compound: biphenyl dioxygenase

halophily

@ref	salt	growth	tested relation	concentration
123975	NaCl	positive	growth	0 %
123975	NaCl	no	growth	2 %
123975	NaCl	no	growth	4 %
123975	NaCl	no	growth	6 %
123975	NaCl	no	growth	8 %
123975	NaCl	no	growth	10 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31232	17128	adipate	+	carbon source
31232	29016	arginine	+	carbon source
31232	27689	decanoate	+	carbon source
31232	16947	citrate	+	carbon source
31232	28757	fructose	+	carbon source
31232	24265	gluconate	+	carbon source
31232	17234	glucose	+	carbon source
31232	24996	lactate	+	carbon source
31232	25115	malate	+	carbon source
31232	29864	mannitol	+	carbon source
31232	37684	mannose	+	carbon source
31232	506227	N-acetylglucosamine	+	carbon source
31232	18401	phenylacetate	+	carbon source
31232	18222	xylose	+	carbon source
123975	4853	esculin	-	hydrolysis
123975	17632	nitrate	+	reduction
123975	16301	nitrite	-	reduction
123975	17632	nitrate	-	respiration
68369	25115	malate	+	assimilation
68369	17128	adipate	+	assimilation
68369	27689	decanoate	+	assimilation
68369	24265	gluconate	+	assimilation
68369	17306	maltose	-	assimilation
68369	59640	N-acetylglucosamine	+	assimilation
68369	16899	D-mannitol	+	assimilation
68369	16024	D-mannose	+	assimilation
68369	30849	L-arabinose	-	assimilation
68369	17634	D-glucose	+	assimilation
68369	5291	gelatin	-	hydrolysis
68369	4853	esculin	-	hydrolysis
68369	16199	urea	+	hydrolysis
68369	29016	arginine	-	hydrolysis
68369	17634	D-glucose	-	fermentation
68369	27897	tryptophan	-	energy source
68369	17632	nitrate	-	reduction

antibiotic resistance

@ref: 123975
metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
is antibiotic: yes
is sensitive: no
is resistant: yes

metabolite production

@ref	Chebi-ID	metabolite	production
68369	35581	indole	no
123975	35581	indole	no

metabolite tests

@ref: 68369
Chebi-ID: 35581
metabolite: indole
indole test: -

enzymes

@ref	value	activity	ec
31232	acid phosphatase	+	3.1.3.2
31232	alkaline phosphatase	+	3.1.3.1
31232	catalase	+	1.11.1.6
31232	cytochrome oxidase	+	1.9.3.1
68382	alpha-fucosidase	-	3.2.1.51
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68382	alpha-mannosidase	-	3.2.1.24
68382	alpha-glucosidase	-	3.2.1.20
68382	beta-glucosidase	-	3.2.1.21
68382	beta-glucuronidase	-	3.2.1.31
68382	beta-galactosidase	-	3.2.1.23
68382	alpha-galactosidase	-	3.2.1.22
68382	naphthol-AS-BI-phosphohydrolase	+
68382	acid phosphatase	-	3.1.3.2
68382	alpha-chymotrypsin	-	3.4.21.1
68382	trypsin	-	3.4.21.4
68382	valine arylamidase	-
68382	cystine arylamidase	-	3.4.11.3
68382	leucine arylamidase	+	3.4.11.1
68382	lipase (C 14)	-
68382	esterase (C 4)	-
68382	esterase lipase (C 8)	+
68382	alkaline phosphatase	+	3.1.3.1
123975	oxidase	-
123975	beta-galactosidase	+	3.2.1.23
123975	alcohol dehydrogenase	+	1.1.1.1
123975	gelatinase	-
123975	amylase	-
123975	DNase	-
123975	caseinase	-	3.4.21.50
123975	catalase	+	1.11.1.6
123975	tween esterase	-
123975	lecithinase	-
123975	lipase	-
123975	lysine decarboxylase	-	4.1.1.18
123975	ornithine decarboxylase	-	4.1.1.17
123975	protease	-
123975	tryptophan deaminase	-
123975	urease	+	3.5.1.5
68369	cytochrome oxidase	-	1.9.3.1
68369	gelatinase	-
68369	beta-glucosidase	-	3.2.1.21
68369	urease	+	3.5.1.5
68369	arginine dihydrolase	-	3.5.3.6

API zym

@ref	Control	Alkaline phosphatase	Esterase	Esterase Lipase	Lipase	Leucine arylamidase	Valine arylamidase	Cystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123975	-	+	-	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

API 20NE

@ref	NO3	TRP	GLU_ Ferm	ADH Arg	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6837	-	-	-	-	+	-	-	-	+	-	+	+	+	-	+	+	+	+	+	+	-

API biotype100

@ref	GLU	FRU	GAL	TRE	MNE	SBE	MEL	SAC	RAF	MTE	MAL	LAC	LTE	MbGa	MaGa	CEL	GEN	MbGu	ESC	RIB	ARA	XYL	PLE	RHA	FUC	MLZ	DARL	LARL	XLT	DUL	TAG	GLY	INO	MAN	MTL	TUR	SOR	ADO	HBG	LYX	ERY	MDG	3MDG	SAT	MUC	LTAT	DTAT	MTAT	DMLT	LMLT	CATE	TATE	TTE	CIT	GRT	GAT	2KG	5KG	TRY	NAG	GNT	PAC	PAT	pOBE	QAT	GTE	mOBE	BAT	PPAT	CMT	TGE	BET	PCE	ABT	HIN	LAT	CAP	CYT	HIS	SUC	FUM	GRE	GYT	AVT	ETN	TTN	GLN	ITA	3OBU	APT	GTT	PRO	DALA	LALA	SER	MNT	PROP	TYR	2KT
123975	+	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	+	+	-	+	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	+	+	+	-	-	-	+	+	-	-	+	+	+	+	-	-	+	+	-	+	+	+	-	-	-	-	+	-	+	-	+	-	+	+	+	-	+	+	+	+	+	+	-	+	+	+	+	+	+	-	+	+	-	-	+	-

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
6837	PCB-contaminated soil	Moreau, New York	USA	USA	North America
57422	Soil,PCB-contaminated	New York,Moreau	USA	USA	North America
123975	Environment, Soil	New York	United States of America	USA	North America

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination
#Environmental	#Terrestrial	#Soil

taxonmaps

@ref: 69479
File name: preview.99_2904.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_187;98_2245;99_2904&stattab=map
Last taxonomy: Paraburkholderia xenovorans
16S sequence: U86373
Sequence Identity:
Total samples: 156
soil counts: 107
aquatic counts: 30
animal counts: 10
plant counts: 9

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
6837	1	Risk group (German classification)
123975	1	Risk group (French classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Burkholderia sp. DNA for 16S rRNA, partial sequence	D87109	884	nuccore	36873
20218	Burkholderia xenovorans strain LMG 21463 16S ribosomal RNA gene, partial sequence	HQ849108	1124	nuccore	36873
31232	Burkholderia xenovorans strain LB400 16S ribosomal RNA gene, partial sequence	U86373	1466	nuccore	266265

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Paraburkholderia xenovorans LB400	GCA_000013645	complete	ncbi	266265
66792	Paraburkholderia xenovorans LB400	GCA_000756045	complete	ncbi	266265
66792	Paraburkholderia xenovorans LB400	2775506700	complete	img	266265
66792	Paraburkholderia xenovorans LB400	637000053	complete	img	266265
66792	Paraburkholderia xenovorans LB400	2597490151	complete	img	266265

GC content

@ref: 31232
GC-content: 62.6

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	98.469	yes
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	95.978	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	86.478	yes
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	84.28	yes
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	98	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	yes	84.03	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	no	90.9
125439	BacteriaNet	motility	Ability to perform movement	yes	66.8
125439	BacteriaNet	gram_stain	Reaction to gram-staining	negative	88.1
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	aerobe	96.3

External links

@ref: 6837

culture collection no.: DSM 17367, CCUG 46959, CIP 108558, LMG 21463, NRRL B-18064

straininfo link

@ref: 71610
straininfo: 89198

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	15294836	Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.	Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM	Appl Environ Microbiol	10.1128/AEM.70.8.4961-4970.2004	2004	Bacterial Proteins/genetics/metabolism, Benzoates/metabolism, Burkholderia/genetics/growth & development/metabolism, Culture Media, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, Oligonucleotide Array Sequence Analysis/methods, Polychlorinated Biphenyls/*metabolism, Reverse Transcriptase Polymerase Chain Reaction	Cultivation
Metabolism	15342624	Evolution of the biphenyl dioxygenase BphA from Burkholderia xenovorans LB400 by random mutagenesis of multiple sites in region III.	Barriault D, Sylvestre M	J Biol Chem	10.1074/jbc.M406805200	2004	Bacterial Proteins/chemistry/genetics/metabolism, Base Sequence, Burkholderia/enzymology/genetics, Color, Evolution, Molecular, Iron-Sulfur Proteins/chemistry/genetics/metabolism, Molecular Conformation, Molecular Sequence Data, Molecular Structure, Mutagenesis, Oxygen/metabolism, Oxygenases/chemistry/genetics/metabolism, Polychlorinated Biphenyls/chemistry/metabolism, Protein Structure, Tertiary, Substrate Specificity	Genetics
Metabolism	15342625	Revisiting the regiospecificity of Burkholderia xenovorans LB400 biphenyl dioxygenase toward 2,2'-dichlorobiphenyl and 2,3,2',3'-tetrachlorobiphenyl.	Barriault D, Lepine F, Mohammadi M, Milot S, Leberre N, Sylvestre M	J Biol Chem	10.1074/jbc.M406808200	2004	Bacterial Proteins/metabolism, Burkholderia/enzymology, Iron-Sulfur Proteins/metabolism, Magnetic Resonance Spectroscopy, Molecular Conformation, Molecular Structure, Oxygen/metabolism, Oxygenases/metabolism, Polychlorinated Biphenyls/chemistry/*metabolism, Substrate Specificity	Enzymology
Phylogeny	15388727	Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.	Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.63101-0	2004	Arabinose/metabolism, Base Composition, Biodegradation, Environmental, Biphenyl Compounds/metabolism, Blood/microbiology, Burkholderia/classification/genetics/isolation & purification/metabolism, Burkholderia Infections/microbiology, DNA, Bacterial/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Humans, Nucleic Acid Hybridization, Phylogeny, Polychlorinated Biphenyls/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology	Metabolism
Metabolism	15614396	Stereochemistry of the reaction catalysed by 2-hydroxy-6-keto-6-phenyl-hexa-2,4-dienoic acid 5,6-hydrolase (BphD).	Li JJ, Bugg TD	Chem Commun (Camb)	10.1039/b415491f	2004	Alkadienes/chemistry/metabolism, Benzoates/chemistry, Catalysis, Hydrogen/chemistry, Hydrolases/chemistry/metabolism, Magnetic Resonance Spectroscopy, Models, Chemical, Stereoisomerism
Enzymology	15649544	Insight into pollutant bioavailability and toxicity using Raman confocal microscopy.	Singer AC, Huang WE, Helm J, Thompson IP	J Microbiol Methods	10.1016/j.mimet.2004.10.016	2005	Alkanes/pharmacokinetics/toxicity, Biological Availability, Biphenyl Compounds/pharmacokinetics/toxicity, Burkholderia/drug effects/metabolism, Environmental Pollutants/pharmacokinetics/toxicity, Microscopy, Confocal, Organic Chemicals/pharmacokinetics/toxicity, Pentachlorophenol/pharmacokinetics/toxicity, Phenanthrenes/pharmacokinetics/toxicity, Principal Component Analysis, Spectrum Analysis, Raman	Pathogenicity
Metabolism	15700128	Metabolism of dibenzofuran and dibenzo-p-dioxin by the biphenyl dioxygenase of Burkholderia xenovorans LB400 and Comamonas testosteroni B-356.	L'Abbee JB, Barriault D, Sylvestre M	Appl Microbiol Biotechnol	10.1007/s00253-004-1791-3	2005	Benzofurans/metabolism, Biodegradation, Environmental, Biphenyl Compounds/metabolism, Burkholderia/enzymology/genetics, Comamonas testosteroni/enzymology/genetics, Dioxins/metabolism, Dioxygenases/genetics/*metabolism, Escherichia coli/enzymology/genetics, Polychlorinated Biphenyls	Enzymology
Metabolism	16039530	Resolving the profile of metabolites generated during oxidation of dibenzofuran and chlorodibenzofurans by the biphenyl catabolic pathway enzymes.	Mohammadi M, Sylvestre M	Chem Biol	10.1016/j.chembiol.2005.05.017	2005	Amino Acids/genetics/metabolism, Benzofurans/chemistry/metabolism, Biotransformation, Biphenyl Compounds/metabolism, Burkholderia/enzymology/genetics/metabolism, Catalysis, Cells, Cultured, Dibenzofurans, Polychlorinated, Dioxygenases/metabolism, Escherichia coli/enzymology/genetics, Mass Spectrometry, Mutagenesis, Oxidation-Reduction, Substrate Specificity	Enzymology
Metabolism	16217654	Active-site engineering of biphenyl dioxygenase: effect of substituted amino acids on substrate specificity and regiospecificity.	Suenaga H, Goto M, Furukawa K	Appl Microbiol Biotechnol	10.1007/s00253-005-0135-2	2005	Amino Acid Substitution, Amino Acids/genetics/metabolism, Binding Sites, Biodegradation, Environmental, DNA, Bacterial/genetics, Escherichia coli/genetics, Iron-Sulfur Proteins/genetics/metabolism, Models, Molecular, Mutagenesis, Site-Directed, Oxygenases/genetics/metabolism, Polychlorinated Biphenyls/metabolism, Protein Conformation, Protein Engineering/methods, Pseudomonas pseudoalcaligenes/enzymology/genetics/metabolism, Recombinant Proteins/genetics/metabolism, Structure-Activity Relationship, Substrate Specificity	Biotechnology
Metabolism	16291673	Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.	Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD	J Bacteriol	10.1128/JB.187.23.7996-8005.2005	2005	Aerobiosis, Bacterial Proteins/analysis/biosynthesis, Benzoates/chemistry/metabolism, Biphenyl Compounds/chemistry/metabolism, Burkholderia/growth & development/metabolism, Carbon/metabolism, Culture Media, Cytosol/metabolism, Electrophoresis, Gel, Two-Dimensional, Substrate Specificity	Cultivation
Enzymology	16310831	Biphenyl degradation kinetics by Burkholderia xenovorans LB400 in two-phase partitioning bioreactors.	Rehmann L, Daugulis AJ	Chemosphere	10.1016/j.chemosphere.2005.08.076	2005	Biodegradation, Environmental, Bioreactors/microbiology, Biphenyl Compounds/analysis, Burkholderia/growth & development, Molecular Structure, Water Pollutants, Chemical/analysis, Water Purification/*methods	Metabolism
Genetics	16391095	Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.	Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JL, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM	Appl Environ Microbiol	10.1128/AEM.72.1.585-595.2006	2006	Bacterial Proteins/genetics/metabolism, Benzoates/metabolism, Biodegradation, Environmental, Burkholderia/genetics/growth & development/metabolism/physiology, Gene Deletion, Gene Expression Regulation, Bacterial, Genome, Bacterial, Heat-Shock Response, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Oxidative Stress, *Proteome, Transcription, Genetic	Metabolism
Metabolism	16484212	The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties.	Gaillard M, Vallaeys T, Vorholter FJ, Minoia M, Werlen C, Sentchilo V, Puhler A, van der Meer JR	J Bacteriol	10.1128/JB.188.5.1999-2013.2006	2006	Aminophenols/metabolism, Bacterial Proteins/genetics/metabolism, Catechols/metabolism, Dioxygenases/genetics, Genomic Islands/physiology, Molecular Sequence Data, Pseudomonas/*genetics/physiology	Genetics
Enzymology	16517671	Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity.	Zielinski M, Kahl S, Standfuss-Gabisch C, Camara B, Seeger M, Hofer B	Appl Environ Microbiol	10.1128/AEM.72.3.2191-2199.2006	2006	Amino Acid Sequence, Amino Acid Substitution, Biphenyl Compounds/metabolism, Burkholderia/enzymology/genetics/growth & development, Dioxygenases/chemistry/genetics/metabolism, Directed Molecular Evolution, Molecular Sequence Data, Mutagenesis, Substrate Specificity	Metabolism
Metabolism	16542399	Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria.	King GM	FEMS Microbiol Ecol	10.1111/j.1574-6941.2006.00065.x	2006	Aerobiosis/physiology, Alphaproteobacteria/metabolism, Anaerobiosis/physiology, Bradyrhizobium/metabolism, Burkholderia/metabolism, Carbon Monoxide/metabolism, Gram-Negative Aerobic Rods and Cocci/metabolism, Nitrates/metabolism, Oxidation-Reduction, *Soil Microbiology, Trees, Xanthobacter/metabolism
Phylogeny	16597927	Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site.	Leigh MB, Prouzova P, Mackova M, Macek T, Nagle DP, Fletcher JS	Appl Environ Microbiol	10.1128/AEM.72.4.2331-2342.2006	2006	Actinomycetales/classification/genetics/isolation & purification/metabolism, Bacteria/classification/genetics/isolation & purification/metabolism, Biodegradation, Environmental, Molecular Sequence Data, Pinus/microbiology, Plant Roots/microbiology, Polychlorinated Biphenyls/metabolism, Rhodococcus/classification/genetics/isolation & purification/metabolism, Salix/microbiology, Soil Microbiology, Soil Pollutants/metabolism, Trees/*microbiology, Xanthomonadaceae/classification/genetics/isolation & purification/metabolism	Metabolism
Metabolism	16597946	Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb).	Rodrigues JL, Kachel CA, Aiello MR, Quensen JF, Maltseva OV, Tsoi TV, Tiedje JM	Appl Environ Microbiol	10.1128/AEM.72.4.2476-2482.2006	2006	Aroclors/metabolism, Biodegradation, Environmental, Burkholderia/genetics/growth & development/metabolism, Chlorine/metabolism, Chlorobenzoates/metabolism, Environmental Pollutants/metabolism, Genetic Engineering/methods, Geologic Sediments/microbiology, Operon, Polychlorinated Biphenyls/metabolism, Recombination, Genetic, Rhodococcus/genetics/growth & development/*metabolism, Soil Pollutants/metabolism
Metabolism	16597983	Chlorophenol hydroxylases encoded by plasmid pJP4 differentially contribute to chlorophenoxyacetic acid degradation.	Ledger T, Pieper DH, Gonzalez B	Appl Environ Microbiol	10.1128/AEM.72.4.2783-2792.2006	2006	2,4-Dichlorophenoxyacetic Acid/metabolism/pharmacology, 2-Methyl-4-chlorophenoxyacetic Acid/metabolism/pharmacology, Bacterial Proteins/genetics/metabolism, Biodegradation, Environmental, Burkholderiaceae/enzymology/genetics/growth & development, Chlorophenols/metabolism, Herbicides/metabolism/pharmacology, Mixed Function Oxygenases/genetics/metabolism, Plasmids/genetics, Substrate Specificity	Enzymology
Metabolism	16740949	A glutathione S-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls.	Fortin PD, Horsman GP, Yang HM, Eltis LD	J Bacteriol	10.1128/JB.01849-05	2006	Burkholderia/enzymology, Diltiazem/analogs & derivatives, Fatty Acids, Unsaturated/metabolism, Glutathione Transferase/metabolism/pharmacokinetics, Polychlorinated Biphenyls/*metabolism	Enzymology
Enzymology	16920719	Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites.	Tocheva EI, Fortin PD, Eltis LD, Murphy ME	J Biol Chem	10.1074/jbc.M603125200	2006	Binding Sites, Burkholderia/enzymology, Crystallography, X-Ray, Disulfides/chemistry, Escherichia coli/metabolism, Fatty Acids, Unsaturated/chemistry, Glutathione/chemistry, Glutathione Transferase/chemistry, Polychlorinated Biphenyls/chemistry, Protein Binding, Protein Conformation, Protein Structure, Tertiary	Metabolism
Metabolism	16964968	Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway.	Horsman GP, Ke J, Dai S, Seah SY, Bolin JT, Eltis LD	Biochemistry	10.1021/bi0611098	2006	Binding Sites, Burkholderia/enzymology, Fatty Acids, Unsaturated/metabolism, Hydrolases/chemistry/metabolism, Kinetics, Models, Molecular, Phenols/metabolism, Protein Conformation	Enzymology
Metabolism	17006888	Expression of bacterial biphenyl-chlorobiphenyl dioxygenase genes in tobacco plants.	Mohammadi M, Chalavi V, Novakova-Sura M, Laliberte JF, Sylvestre M	Biotechnol Bioeng	10.1002/bit.21188	2007	Biodegradation, Environmental, Burkholderia/enzymology/metabolism, Cloning, Molecular, Gene Expression, Genes, Bacterial, Iron-Sulfur Proteins/genetics/metabolism, Oxygenases/genetics/metabolism, Plants, Genetically Modified/genetics/metabolism, Polychlorinated Biphenyls/chemistry/metabolism, Tobacco/genetics/metabolism	Enzymology
Pathogenicity	17021212	Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.	Parnell JJ, Park J, Denef V, Tsoi T, Hashsham S, Quensen J 3rd, Tiedje JM	Appl Environ Microbiol	10.1128/AEM.01129-06	2006	Aroclors/pharmacology, Biodegradation, Environmental, Burkholderia/cytology/drug effects/physiology, Environmental Pollutants/metabolism/pharmacology, Gene Expression/drug effects, Genome, Bacterial/physiology, Polychlorinated Biphenyls/metabolism/pharmacology	Metabolism
Enzymology	17029401	Evidence for a gem-diol reaction intermediate in bacterial C-C hydrolase enzymes BphD and MhpC from 13C NMR spectroscopy.	Li JJ, Li C, Blindauer CA, Bugg TD	Biochemistry	10.1021/bi0612519	2006	Amino Acid Substitution, Base Sequence, Burkholderia/enzymology/genetics, DNA, Bacterial/genetics, Escherichia coli/enzymology/genetics, Escherichia coli Proteins/chemistry/genetics/metabolism, Genes, Bacterial, Hydrolases/chemistry/genetics/metabolism, Kinetics, Magnetic Resonance Spectroscopy, Mutagenesis, Site-Directed, Recombinant Proteins/chemistry/genetics/metabolism, Substrate Specificity	Metabolism
Enzymology	17029402	Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD.	Li C, Li JJ, Montgomery MG, Wood SP, Bugg TD	Biochemistry	10.1021/bi061253t	2006	Amino Acid Sequence, Amino Acid Substitution, Arginine/chemistry, Base Sequence, Burkholderia/enzymology/genetics, Catalytic Domain/genetics, Crystallography, X-Ray, DNA, Bacterial/genetics, Escherichia coli/enzymology/genetics, Escherichia coli Proteins/chemistry/genetics/metabolism, Hydrolases/chemistry/genetics/metabolism, Kinetics, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Conformation, Recombinant Proteins/chemistry/genetics/metabolism, Sequence Homology, Amino Acid	Metabolism
Genetics	17030794	The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.	McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD	Proc Natl Acad Sci U S A	10.1073/pnas.0607048103	2006	Bacterial Proteins/classification/genetics, Biological Evolution, Chromosome Mapping, Genome, Bacterial, Metabolism, Molecular Sequence Data, Phylogeny, Rhodococcus/genetics/metabolism	Phylogeny
Genetics	17030797	Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.	Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM	Proc Natl Acad Sci U S A	10.1073/pnas.0606924103	2006	Burkholderia/chemistry/genetics/metabolism/pathogenicity, Chromosomes, Bacterial, Evolution, Molecular, Gene Expression Profiling, Genome, Bacterial, Molecular Structure, Oligonucleotide Array Sequence Analysis, *Replicon	Metabolism
Phylogeny	17082385	Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64387-0	2006	Bacterial Typing Techniques, Burkholderia/classification/cytology/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flagella, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil Microbiology, beta-Glucosidase/*biosynthesis	Genetics
Metabolism	17142386	Family shuffling of soil DNA to change the regiospecificity of Burkholderia xenovorans LB400 biphenyl dioxygenase.	Vezina J, Barriault D, Sylvestre M	J Bacteriol	10.1128/JB.01267-06	2006	Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Benzene/metabolism, Biphenyl Compounds/metabolism, Burkholderia/enzymology/genetics, DNA, Bacterial/chemistry/genetics/isolation & purification, Dioxygenases/chemistry/genetics/metabolism, Gas Chromatography-Mass Spectrometry, Models, Genetic, Molecular Sequence Data, Molecular Structure, Mutagenesis, Site-Directed, Polychlorinated Biphenyls/metabolism, Protein Structure, Secondary, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Soil, Soil Microbiology, Structure-Activity Relationship, Substrate Specificity, Toluene/metabolism	Enzymology
Metabolism	17166226	Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress.	Agullo L, Camara B, Martinez P, Latorre V, Seeger M	FEMS Microbiol Lett	10.1111/j.1574-6968.2006.00554.x	2006	Bacterial Proteins/metabolism, Biphenyl Compounds/pharmacology, Burkholderia/drug effects/metabolism/physiology, Electrophoresis, Gel, Two-Dimensional, Heat-Shock Response, *Oxidative Stress	Enzymology
Metabolism	17322323	Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls.	Camara B, Seeger M, Gonzalez M, Standfuss-Gabisch C, Kahl S, Hofer B	Appl Environ Microbiol	10.1128/AEM.02523-06	2007	Biotransformation, Burkholderia/enzymology/genetics, Dioxygenases/genetics/metabolism, Metabolic Networks and Pathways/genetics/physiology, Oxidation-Reduction, Polychlorinated Biphenyls/metabolism, Protein Engineering, Pseudomonas/enzymology/genetics, Recombinant Fusion Proteins/metabolism, Substrate Specificity	Enzymology
Pathogenicity	17374130	Motility and chemotaxis of Pseudomonas sp. B4 towards polychlorobiphenyls and chlorobenzoates.	Gordillo F, Chavez FP, Jerez CA	FEMS Microbiol Ecol	10.1111/j.1574-6941.2007.00293.x	2007	Bacterial Physiological Phenomena/drug effects, Chemotaxis/drug effects, Chlorobenzoates/pharmacology, Polychlorinated Biphenyls/pharmacology, Pseudomonas/*drug effects/physiology
Enzymology	17401562	Synthesis of highly hydroxylated aromatics by evolved biphenyl dioxygenase and subsequent dihydrodiol dehydrogenase.	Shindo K, Shindo Y, Hasegawa T, Osawa A, Kagami O, Furukawa K, Misawa N	Appl Microbiol Biotechnol	10.1007/s00253-007-0928-6	2007	Amino Acid Sequence, Animals, Dioxygenases/physiology, Directed Molecular Evolution, Escherichia coli/enzymology/genetics, Hydrocarbons, Aromatic/metabolism, Hydroxylation, Molecular Sequence Data, Oxidoreductases/physiology, Rats	Genetics
Metabolism	17416660	Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites.	Seah SY, Ke J, Denis G, Horsman GP, Fortin PD, Whiting CJ, Eltis LD	J Bacteriol	10.1128/JB.01950-06	2007	Amino Acid Sequence, Bacterial Proteins/genetics/metabolism, Benzofurans/chemistry/metabolism, Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Dibenzofurans, Polychlorinated, Dioxins/chemistry/metabolism, Fatty Acids, Unsaturated/chemistry/metabolism, Hydrolases/genetics/metabolism, Kinetics, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sphingomonas/enzymology/genetics/metabolism, Substrate Specificity	Enzymology
Metabolism	17442675	The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad.	Horsman GP, Bhowmik S, Seah SY, Kumar P, Bolin JT, Eltis LD	J Biol Chem	10.1074/jbc.M702237200	2007	Bacterial Proteins/chemistry/metabolism, Burkholderia/enzymology, Catalysis, Catalytic Domain, Crystallography, X-Ray, Fatty Acids, Unsaturated/chemistry/metabolism, Histidine, Hydrolases/chemistry/metabolism, Hydrolysis, Kinetics, *Models, Molecular, Protein Structure, Quaternary	Enzymology
Metabolism	17522847	Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400.	Martinez P, Agullo L, Hernandez M, Seeger M	Arch Microbiol	10.1007/s00203-007-0247-4	2007	Biodegradation, Environmental, Burkholderia/drug effects/enzymology/growth & development/metabolism, Chlorobenzoates/pharmacology, Electrophoresis, Gel, Two-Dimensional/methods, Heat-Shock Proteins/antagonists & inhibitors/biosynthesis/metabolism, Microscopy, Electron/methods, Peptide Elongation Factor G/genetics/metabolism, Polychlorinated Biphenyls/metabolism/pharmacokinetics, Proteome/*metabolism, Sequence Analysis, Protein	Enzymology
Enzymology	17526697	Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme.	Gomez-Gil L, Kumar P, Barriault D, Bolin JT, Sylvestre M, Eltis LD	J Bacteriol	10.1128/JB.01476-06	2007	Amino Acid Substitution, Biotransformation, Burkholderiaceae/chemistry/enzymology, Crystallography, X-Ray, Gas Chromatography-Mass Spectrometry, Iron-Sulfur Proteins/chemistry/isolation & purification/metabolism, Kinetics, Magnetic Resonance Spectroscopy, Models, Molecular, Oxygenases/chemistry/isolation & purification/metabolism, Polychlorinated Biphenyls/*metabolism, Protein Structure, Tertiary, Substrate Specificity	Metabolism
Metabolism	17559230	Polymer selection for biphenyl degradation in a solid-liquid two-phase partitioning bioreactor.	Rehmann L, Sun B, Daugulis AJ	Biotechnol Prog	10.1021/bp0700962	2007	Biodegradation, Environmental, Bioreactors, Biotechnology/methods, Burkholderia/metabolism, Catalysis, Cell Culture Techniques, Fermentation, Methanol/chemistry, Phenol, Phenols/chemistry, Polymers/*chemistry, Time Factors, Water/chemistry	Biotechnology
Metabolism	17586638	A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism.	Smith DJ, Park J, Tiedje JM, Mohn WW	J Bacteriol	10.1128/JB.00179-07	2007	Abietanes/metabolism, Burkholderia/genetics/growth & development/metabolism, Cytochrome P-450 Enzyme System/genetics, Dioxygenases/genetics, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genome, Bacterial, Membrane Transport Proteins/genetics, Metabolism/genetics, *Multigene Family, Mutagenesis, Insertional, Oligonucleotide Array Sequence Analysis, Oxidoreductases/genetics, Phenanthrenes/metabolism, Plasmids/genetics, Pseudomonas/genetics, Sequence Homology, Up-Regulation	Genetics
Metabolism	17705226	Enhancement of PCB degradation by Burkholderia xenovorans LB400 in biphasic systems by manipulating culture conditions.	Rehmann L, Daugulis AJ	Biotechnol Bioeng	10.1002/bit.21610	2008	Biodegradation, Environmental, Bioreactors/microbiology, Burkholderia/growth & development/metabolism, Cell Culture Techniques/methods, Cell Proliferation, Cell Survival, Phase Transition, Polychlorinated Biphenyls/*metabolism
Metabolism	17884091	Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway.	Bains J, Boulanger MJ	J Mol Biol	10.1016/j.jmb.2007.08.008	2007	Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Benzoates/metabolism, Binding Sites, Burkholderia/enzymology/genetics, Catalysis, Coenzyme A Ligases/chemistry/genetics/metabolism, Crystallography, X-Ray/methods, Models, Molecular, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Protein Structure, Secondary, Protein Structure, Tertiary	Genetics
Metabolism	17929320	Biodegradation of PCBs in two-phase partitioning bioreactors following solid extraction from soil.	Rehmann L, Daugulis AJ	Biotechnol Bioeng	10.1002/bit.21674	2008	Aroclors/chemistry/metabolism, Biodegradation, Environmental, Bioreactors, Burkholderia/metabolism, Polyesters/chemistry, Soil Pollutants/chemistry/metabolism
Metabolism	18156276	Distinct roles for two CYP226 family cytochromes P450 in abietane diterpenoid catabolism by Burkholderia xenovorans LB400.	Smith DJ, Patrauchan MA, Florizone C, Eltis LD, Mohn WW	J Bacteriol	10.1128/JB.01530-07	2007	Abietanes/metabolism, Bacterial Proteins/genetics/metabolism, Burkholderia/genetics/growth & development/metabolism, Cytochrome P-450 Enzyme System/genetics/metabolism, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Multigene Family/genetics, Mutagenesis, Insertional, Phenanthrenes/metabolism, Protein Binding, Substrate Specificity, Succinic Acid/metabolism
Enzymology	18424535	Biphenyl dioxygenase from an arctic isolate is not cold adapted.	Master ER, Agar NY, Gomez-Gil L, Powlowski JB, Mohn WW, Eltis LD	Appl Environ Microbiol	10.1128/AEM.02928-07	2008	Biphenyl Compounds/metabolism, Burkholderia/enzymology, Cold Temperature, Dioxygenases/chemistry/isolation & purification/metabolism, Environmental Microbiology, Enzyme Stability, Hot Temperature, Kinetics, Pseudomonas/enzymology/isolation & purification	Metabolism
Enzymology	18453716	Purification, crystallization and X-ray diffraction analysis of a novel ring-cleaving enzyme (BoxC(C)) from Burkholderia xenovorans LB400.	Bains J, Boulanger MJ	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309108010919	2008	Bacterial Proteins/chemistry/isolation & purification/metabolism, Burkholderia/enzymology, Cloning, Molecular, Crystallization/methods, Enoyl-CoA Hydratase/*chemistry/isolation & purification/metabolism, X-Ray Diffraction	Phylogeny
Metabolism	18462753	Structural and biochemical characterization of a novel aldehyde dehydrogenase encoded by the benzoate oxidation pathway in Burkholderia xenovorans LB400.	Bains J, Boulanger MJ	J Mol Biol	10.1016/j.jmb.2008.04.031	2008	Aldehyde Dehydrogenase/chemistry/genetics/metabolism, Aldehydes/chemistry/metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Benzoates/chemistry/metabolism, Binding Sites, Burkholderia/chemistry/enzymology, Coenzymes/chemistry/metabolism, Crystallography, X-Ray, Dimerization, Models, Molecular, Molecular Sequence Data, Molecular Structure, NAD/chemistry/metabolism, NADP/chemistry/metabolism, Oxidation-Reduction, *Protein Structure, Quaternary, Protein Structure, Tertiary, Sequence Alignment	Enzymology
Metabolism	18685266	Bacterial metabolism of polychlorinated biphenyls.	Pieper DH, Seeger M	J Mol Microbiol Biotechnol	10.1159/000121325	2008	Bacteria/genetics/metabolism, Environmental Pollutants/metabolism, Metabolic Networks and Pathways/genetics, Polychlorinated Biphenyls/metabolism, Rhodococcus/enzymology/genetics/metabolism	Enzymology
Metabolism	18685267	Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit.	Vezina J, Barriault D, Sylvestre M	J Mol Microbiol Biotechnol	10.1159/000121326	2008	Bacterial Proteins/chemistry/genetics/metabolism, Biodegradation, Environmental, Burkholderia/enzymology/genetics, Genes, Bacterial, Oxygenases/chemistry/genetics/metabolism, Polychlorinated Biphenyls/chemistry/metabolism, Substrate Specificity	Enzymology
Enzymology	19369256	Structural and biophysical characterization of BoxC from Burkholderia xenovorans LB400: a novel ring-cleaving enzyme in the crotonase superfamily.	Bains J, Leon R, Boulanger MJ	J Biol Chem	10.1074/jbc.M900226200	2009	Binding Sites, Burkholderia/enzymology, Catalysis, Catalytic Domain, Crystallography, Dimerization, Enoyl-CoA Hydratase/chemistry/metabolism, Evolution, Molecular, Hydrocarbons, Aromatic/metabolism, Protein Structure, Secondary, Protein Structure, Tertiary	Metabolism
Pathogenicity	19390985	New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria.	Van Houdt R, Monchy S, Leys N, Mergeay M	Antonie Van Leeuwenhoek	10.1007/s10482-009-9345-4	2009	Betaproteobacteria/drug effects/genetics, Bordetella/genetics, Burkholderia/genetics, Chemoautotrophic Growth, Cupriavidus/drug effects/genetics/metabolism, DNA Transposable Elements, Delftia/genetics, Drug Resistance, Bacterial, Gene Expression Regulation, Bacterial, Genomic Islands, Genomics, Integrases, Metals, Heavy/pharmacology, Recombinases, Synteny, Tyrosine	Genetics
Enzymology	19476337	Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway.	Baker P, Pan D, Carere J, Rossi A, Wang W, Seah SY	Biochemistry	10.1021/bi9006644	2009	Allosteric Regulation, Base Sequence, Burkholderia/enzymology, Catalysis, DNA Primers, Electrophoresis, Polyacrylamide Gel, Fructose-Bisphosphate Aldolase/metabolism, Hydrolysis, Kinetics, Oxidoreductases/metabolism, Polychlorinated Biphenyls/*metabolism, Substrate Specificity	Metabolism
Enzymology	19539670	Investigative mining of sequence data for novel enzymes: a case study with nitrilases.	Seffernick JL, Samanta SK, Louie TM, Wackett LP, Subramanian M	J Biotechnol	10.1016/j.jbiotec.2009.06.004	2009	Acetonitriles/metabolism, Amino Acid Sequence, Aminohydrolases/chemistry, Biotechnology/methods, Bradyrhizobium/enzymology, Burkholderia/enzymology, Catalysis, Chromatography, High Pressure Liquid, Escherichia coli/enzymology, Genome, Bacterial, Hydrolases/chemistry, Kinetics, Molecular Sequence Data, Sequence Homology, Amino Acid, Substrate Specificity	Genetics
Metabolism	19672561	Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.	Parnell JJ, Denef VJ, Park J, Tsoi T, Tiedje JM	Biodegradation	10.1007/s10532-009-9289-4	2009	Bacterial Proteins/genetics/metabolism, Biodegradation, Environmental, Burkholderia/genetics/growth & development/metabolism, Carbon/metabolism, Gene Expression Regulation, Bacterial, Polychlorinated Biphenyls/metabolism
Metabolism	19731666	Aerobic biotransformation of polybrominated diphenyl ethers (PBDEs) by bacterial isolates.	Robrock KR, Coelhan M, Sedlak DL, Alvarez-Cohent L	Environ Sci Technol	10.1021/es900411k	2009	Biodegradation, Environmental, Biotransformation, Bromides/chemistry, Burkholderia/metabolism, Chlorine/chemistry, Environment, Environmental Pollutants, Ethers/chemistry, Gas Chromatography-Mass Spectrometry/methods, Halogenated Diphenyl Ethers/chemistry/metabolism, Models, Statistical, Rhodococcus/metabolism, Time Factors
Metabolism	19835952	Terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil.	Capodicasa S, Fedi S, Carnevali M, Caporali L, Viti C, Fava F, Zannoni D	Res Microbiol	10.1016/j.resmic.2009.10.001	2009	Bacteria/enzymology/genetics, Burkholderia/genetics/metabolism, DNA Fingerprinting, Dioxygenases/genetics/metabolism, Environmental Monitoring, Genes, Bacterial, Phylogeny, Polychlorinated Biphenyls/analysis, Polymorphism, Restriction Fragment Length, Pseudomonas pseudoalcaligenes/genetics/metabolism, RNA, Messenger/analysis, Sequence Analysis, DNA, Soil Pollutants/analysis	Phylogeny
Enzymology	19851006	Purification and crystallization of a putative transcriptional regulator of the benzoate oxidation pathway in Burkholderia xenovorans LB400.	Law AM, Bains J, Boulanger MJ	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309109032321	2009	Bacterial Proteins/chemistry/isolation & purification, Benzoates/metabolism, Burkholderia/metabolism, Cloning, Molecular, Crystallization, Oxidation-Reduction, Transcription Factors/chemistry/isolation & purification	Phylogeny
Metabolism	20414654	Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil.	Saavedra JM, Acevedo F, Gonzalez M, Seeger M	Appl Microbiol Biotechnol	10.1007/s00253-010-2575-6	2010	Biodegradation, Environmental, Cupriavidus necator/genetics/metabolism, Genetic Engineering, Mutagenesis, Insertional, Polychlorinated Biphenyls/metabolism, Soil Pollutants/metabolism
Metabolism	20809076	Hybrid pseudomonads engineered by two-step homologous recombination acquire novel degradation abilities toward aromatics and polychlorinated biphenyls.	Suenaga H, Nonaka K, Fujihara H, Goto M, Furukawa K	Appl Microbiol Biotechnol	10.1007/s00253-010-2840-8	2010	Biodegradation, Environmental, Genetic Engineering, Multigene Family, Oxygenases/metabolism, Polychlorinated Biphenyls/metabolism, Pseudomonas pseudoalcaligenes/genetics/metabolism, Recombination, Genetic, Substrate Specificity
Metabolism	20830605	Biodegradation of polyfluorinated biphenyl in bacteria.	Hughes D, Clark BR, Murphy CD	Biodegradation	10.1007/s10532-010-9411-7	2010	Benzoates/metabolism, Biodegradation, Environmental, Biphenyl Compounds/metabolism, Burkholderia/metabolism, Environmental Pollution/prevention & control, Fluorine/chemistry/metabolism, Fluorine Compounds/chemistry/metabolism, Fungicides, Industrial/chemistry/metabolism, Gas Chromatography-Mass Spectrometry, Magnetic Resonance Spectroscopy, Pseudomonas pseudoalcaligenes/*metabolism	Biotechnology
Metabolism	21041079	Triclosan susceptibility and co-metabolism--a comparison for three aerobic pollutant-degrading bacteria.	Kim YM, Murugesan K, Schmidt S, Bokare V, Jeon JR, Kim EJ, Chang YS	Bioresour Technol	10.1016/j.biortech.2010.10.009	2010	Anti-Infective Agents, Local/pharmacology, Bacteria, Aerobic/classification/drug effects/metabolism, Biodegradation, Environmental, Cell Survival/drug effects, Humans, Metabolism, Species Specificity, Triclosan/metabolism/*pharmacology	Pathogenicity
Enzymology	21073881	Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution.	Kumar P, Mohammadi M, Viger JF, Barriault D, Gomez-Gil L, Eltis LD, Bolin JT, Sylvestre M	J Mol Biol	10.1016/j.jmb.2010.11.009	2010	Amino Acid Substitution, Biological Evolution, Burkholderiaceae/enzymology, Crystallography, X-Ray, Gas Chromatography-Mass Spectrometry, Iron-Sulfur Proteins/chemistry/genetics/metabolism, Kinetics, Models, Molecular, Mutagenesis, Site-Directed, Mutation/genetics, Oxygenases/chemistry/genetics/metabolism, Polychlorinated Biphenyls/metabolism, Protein Structure, Tertiary, Substrate Specificity	Metabolism
Genetics	21206025	Anaerobic crystallization and initial X-ray diffraction data of biphenyl 2,3-dioxygenase from Burkholderia xenovorans LB400: addition of agarose improved the quality of the crystals.	Kumar P, Gomez-Gil L, Mohammadi M, Sylvestre M, Eltis LD, Bolin JT	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309110043393	2010	Anaerobiosis, Bacterial Proteins/chemistry, Burkholderia/enzymology, Crystallization/methods, Crystallography, X-Ray, Iron-Sulfur Proteins/chemistry, Molecular Sequence Data, Oxygenases/chemistry, Sepharose/chemistry	Enzymology
Enzymology	21219561	Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins.	Zafra O, Fraile S, Gutierrez C, Haro A, Paez-Espino AD, Jimenez JI, de Lorenzo V	Environ Microbiol	10.1111/j.1462-2920.2010.02401.x	2011	Animals, Arsenate Reductases/immunology/metabolism, Bacterial Proteins/immunology/metabolism, Biodegradation, Environmental, Burkholderia/enzymology, Camelus/immunology, Dioxygenases/immunology/metabolism, Gene Library, Immunoglobulin Heavy Chains/biosynthesis, Male, Models, Molecular, Peptide Library, Sequence Analysis, Protein, Staphylococcus aureus/*enzymology	Metabolism
Metabolism	21237173	A product analog bound form of 3-oxoadipate-enol-lactonase (PcaD) reveals a multifunctional role for the divergent cap domain.	Bains J, Kaufman L, Farnell B, Boulanger MJ	J Mol Biol	10.1016/j.jmb.2011.01.007	2011	Burkholderia/enzymology, Carboxylic Ester Hydrolases/chemistry/metabolism, Catalytic Domain, Crystallography, X-Ray, Levulinic Acids/chemistry/metabolism, Models, Molecular, Protein Conformation, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary	Enzymology
Metabolism	21423751	The homogentisate and homoprotocatechuate central pathways are involved in 3- and 4-hydroxyphenylacetate degradation by Burkholderia xenovorans LB400.	Mendez V, Agullo L, Gonzalez M, Seeger M	PLoS One	10.1371/journal.pone.0017583	2011	3,4-Dihydroxyphenylacetic Acid/metabolism/pharmacology, Biodegradation, Environmental/drug effects, Burkholderia/enzymology/genetics/growth & development/metabolism, Gene Expression Regulation, Bacterial/drug effects, Genes, Bacterial/genetics, Homogentisic Acid/metabolism, Metabolic Networks and Pathways/drug effects, Models, Biological, Multigene Family/genetics, Phenylacetates/*metabolism, Phylogeny, Proteomics, Reverse Transcriptase Polymerase Chain Reaction	Pathogenicity
Enzymology	21495107	Elucidating the reaction mechanism of the benzoate oxidation pathway encoded aldehyde dehydrogenase from Burkholderia xenovorans LB400.	Bains J, Leon R, Temke KG, Boulanger MJ	Protein Sci	10.1002/pro.639	2011	Acylation, Aldehyde Dehydrogenase/chemistry/metabolism, Benzoates/metabolism, Burkholderia/chemistry/*enzymology, Catalytic Domain, Crystallography, X-Ray, Models, Molecular	Metabolism
Metabolism	21519854	Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400.	Patrauchan MA, Parnell JJ, McLeod MP, Florizone C, Tiedje JM, Eltis LD	Arch Microbiol	10.1007/s00203-011-0705-x	2011	Acetyl Coenzyme A/metabolism, Burkholderia/genetics/growth & development/metabolism, Gene Expression, Genes, Bacterial, Genome, Bacterial, Oxidative Stress/genetics, Polychlorinated Biphenyls/metabolism, Proteomics, Transcriptome	Genetics
Enzymology	21653696	Retuning Rieske-type oxygenases to expand substrate range.	Mohammadi M, Viger JF, Kumar P, Barriault D, Bolin JT, Sylvestre M	J Biol Chem	10.1074/jbc.M111.255174	2011	Burkholderia/enzymology, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Gas Chromatography-Mass Spectrometry, Kinetics, Models, Molecular, Oxygenases/chemistry/genetics/*metabolism, Substrate Specificity	Metabolism
Enzymology	21898128	Isolation, characterization and docking studies of 2,3-dihydroxybiphenyl 1,2-dioxygenase from an activated sludge metagenome.	Gou M, Qu Y, Xu B, Zhou J, Li X, Zhou H	Biotechnol Lett	10.1007/s10529-011-0738-x	2011	Biphenyl Compounds/metabolism, Burkholderia/enzymology/genetics, Catechols/metabolism, Dioxygenases/genetics/isolation & purification/metabolism, Enzyme Stability, Escherichia coli/genetics, Hydrogen-Ion Concentration, Kinetics, Metagenome, Molecular Dynamics Simulation, Molecular Sequence Data, Molecular Weight, Polymerase Chain Reaction, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sewage/microbiology, Substrate Specificity, Temperature	Metabolism
Metabolism	22001737	Insight into the metabolism of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by biphenyl dioxygenases.	L'Abbee JB, Tu Y, Barriault D, Sylvestre M	Arch Biochem Biophys	10.1016/j.abb.2011.09.016	2011	Amino Acid Sequence, Biphenyl Compounds/metabolism, Burkholderia/chemistry/enzymology, Burkholderiaceae/chemistry/enzymology, Catalytic Domain, DDT/chemistry/metabolism, Dioxygenases/chemistry/metabolism, Insecticides/chemistry/*metabolism, Models, Molecular, Molecular Sequence Data, Protein Binding, Sequence Alignment	Enzymology
Metabolism	22142725	Antioxidant compounds improved PCB-degradation by Burkholderia xenovorans strain LB400.	Ponce BL, Latorre VK, Gonzalez M, Seeger M	Enzyme Microb Technol	10.1016/j.enzmictec.2011.04.021	2011	Aerobiosis, Antioxidants/pharmacology, Biodegradation, Environmental/drug effects, Burkholderia/drug effects/growth & development/metabolism/ultrastructure, Kinetics, Microscopy, Electron, Transmission, Polychlorinated Biphenyls/metabolism, Soil Microbiology, Soil Pollutants/*metabolism, alpha-Tocopherol/pharmacology	Pathogenicity
Metabolism	22159613	Adaptation mechanisms of bacteria during the degradation of polychlorinated biphenyls in the presence of natural and synthetic terpenes as potential degradation inducers.	Zoradova-Murinova S, Dudasova H, Lukacova L, Certik M, Silharova K, Vrana B, Dercova K	Appl Microbiol Biotechnol	10.1007/s00253-011-3763-8	2011	Biomass, Biotransformation, Burkholderia/drug effects/growth & development/metabolism/physiology, Cell Membrane/drug effects/physiology, Gene Expression Regulation, Bacterial/drug effects, Lipid Metabolism/drug effects, Polychlorinated Biphenyls/metabolism, Pseudomonas stutzeri/drug effects/growth & development/metabolism/physiology, Stress, Physiological/drug effects, Terpenes/*metabolism	Pathogenicity
Enzymology	22316175	Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes.	Baker P, Hillis C, Carere J, Seah SY	Biochemistry	10.1021/bi201832a	2012	Bacterial Proteins/chemistry/metabolism, Binding Sites, Burkholderia/enzymology/metabolism, Catalysis, Escherichia coli/genetics/metabolism, Fructose-Bisphosphate Aldolase/chemistry/metabolism, Kinetics, Models, Molecular, Oxidoreductases/*chemistry/metabolism, Protein Conformation, Substrate Specificity, Thermus thermophilus/enzymology/metabolism	Metabolism
Metabolism	22342725	Metabolism of chlorobiphenyls by a variant biphenyl dioxygenase exhibiting enhanced activity toward dibenzofuran.	Viger JF, Mohammadi M, Barriault D, Sylvestre M	Biochem Biophys Res Commun	10.1016/j.bbrc.2012.02.029	2012	Benzofurans/chemistry/metabolism, Biphenyl Compounds/chemistry/metabolism, Burkholderia/enzymology/genetics, Catalysis, Dioxygenases/chemistry/genetics/metabolism, Escherichia coli/enzymology/genetics, Mutagenesis, Site-Directed, Oxidation-Reduction, Polychlorinated Biphenyls/*metabolism, Recombinant Proteins/chemistry/genetics/metabolism	Enzymology
Metabolism	22427498	Remarkable ability of Pandoraea pnomenusa B356 biphenyl dioxygenase to metabolize simple flavonoids.	Pham TT, Tu Y, Sylvestre M	Appl Environ Microbiol	10.1128/AEM.00225-12	2012	Amino Acid Substitution, Biphenyl Compounds/metabolism, Burkholderiaceae/enzymology/metabolism, Dioxygenases/chemistry/metabolism, Flavonoids/metabolism, Gene Expression Regulation, Bacterial, Kinetics, Metabolic Networks and Pathways, Protein Conformation	Enzymology
Metabolism	22504819	Dioxygenation of the biphenyl dioxygenation product.	Overwin H, Gonzalez M, Mendez V, Seeger M, Wray V, Hofer B	Appl Environ Microbiol	10.1128/AEM.00492-12	2012	Biphenyl Compounds/metabolism, Burkholderia/enzymology/growth & development/metabolism, Carbon/metabolism, Dioxygenases/metabolism, Energy Metabolism, Oxidation-Reduction	Enzymology
Metabolism	22546558	Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase.	Kumar P, Mohammadi M, Dhindwal S, Pham TT, Bolin JT, Sylvestre M	Biochem Biophys Res Commun	10.1016/j.bbrc.2012.04.078	2012	Benzofurans/metabolism, Burkholderia/enzymology, Catalysis, Crystallization, Dioxygenases/*chemistry/genetics, Glycine/chemistry/genetics, Mutation, Protein Conformation, Serine/chemistry/genetics	Enzymology
Metabolism	22923594	Burkholderia xenovorans RcoM(Bx)-1, a transcriptional regulator system for sensing low and persistent levels of carbon monoxide.	Kerby RL, Roberts GP	J Bacteriol	10.1128/JB.01024-12	2012	Bacterial Proteins/genetics/isolation & purification/metabolism, Burkholderia/genetics/metabolism, Carbon Monoxide/metabolism, Cloning, Molecular, DNA Footprinting, DNA, Bacterial/metabolism, Gene Expression, Gene Expression Regulation, Bacterial, Protein Binding, Recombinant Proteins/genetics/isolation & purification/metabolism, Transcription Factors/genetics/isolation & purification/metabolism	Enzymology
Phylogeny	23384335	Quantification of the 16S-23S rRNA internal transcribed spacers of Burkholderia xenovorans strain LB400 using real-time PCR in soil samples.	Norini MP, Secher C, Lollier M, Jezequel K, Cornu JY, Lebeau T	Lett Appl Microbiol	10.1111/lam.12057	2013	Burkholderia/genetics/physiology, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal Spacer, Geologic Sediments/microbiology, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Sequence Analysis, DNA, *Soil Microbiology	Transcriptome
Metabolism	23418504	Genomic and functional analyses of the gentisate and protocatechuate ring-cleavage pathways and related 3-hydroxybenzoate and 4-hydroxybenzoate peripheral pathways in Burkholderia xenovorans LB400.	Romero-Silva MJ, Mendez V, Agullo L, Seeger M	PLoS One	10.1371/journal.pone.0056038	2013	Burkholderia/genetics/metabolism, Gene Expression Regulation, Bacterial, Genomics, Gentisates/metabolism, Hydroxybenzoates/metabolism, Parabens/metabolism	Genetics
Metabolism	23440572	Decontamination of a polychlorinated biphenyls-contaminated soil by phytoremediation-assisted bioaugmentation.	Secher C, Lollier M, Jezequel K, Cornu JY, Amalric L, Lebeau T	Biodegradation	10.1007/s10532-013-9625-6	2013	Biodegradation, Environmental, Burkholderia/genetics/isolation & purification/metabolism, Environmental Restoration and Remediation/methods, Festuca/metabolism, Polychlorinated Biphenyls/metabolism, Soil Microbiology, Soil Pollutants/*metabolism	Enzymology
Metabolism	23463900	Remediation of polychlorinated biphenyl impacted sediment by concurrent bioaugmentation with anaerobic halorespiring and aerobic degrading bacteria.	Payne RB, Fagervold SK, May HD, Sowers KR	Environ Sci Technol	10.1021/es304372t	2013	Aerobiosis, Anaerobiosis, Baltimore, Biodegradation, Environmental, Burkholderia/metabolism, Chloroflexi/metabolism, Chromatography, High Pressure Liquid, Geologic Sediments/microbiology, Halogenation, Oxidation-Reduction, Polychlorinated Biphenyls/*metabolism, Polymerase Chain Reaction
Metabolism	23568428	Enhanced degradation of haloacid by heterologous expression in related Burkholderia species.	Su X, Deng L, Kong KF, Tsang JS	Biotechnol Bioeng	10.1002/bit.24917	2013	Acetates/metabolism, Bacterial Proteins/genetics/metabolism, Biodegradation, Environmental, Burkholderia/enzymology/genetics/metabolism, Hydrolases/genetics/metabolism, Metabolic Engineering/methods, RNA, Messenger/analysis/genetics/metabolism, Substrate Specificity	Enzymology
Metabolism	23589238	Transformation of hydroxylated derivatives of 2,5-dichlorobiphenyl and 2,4,6-trichlorobiphenyl by Burkholderia xenovorans LB400.	Tehrani R, Lyv MM, Van Aken B	Environ Sci Pollut Res Int	10.1007/s11356-013-1629-6	2013	Biotransformation, Burkholderia/metabolism, Chlorobenzoates/metabolism, Environmental Pollutants/metabolism, Hydroxylation, Polychlorinated Biphenyls/*metabolism
	23658554	The Three-Species Consortium of Genetically Improved Strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120 Grows with Technical Polychlorobiphenyl, Aroclor 1242.	Hernandez-Sanchez V, Lang E, Wittich RM	Front Microbiol	10.3389/fmicb.2013.00090	2013
Genetics	23686262	Regulon studies and in planta role of the BraI/R quorum-sensing system in the plant-beneficial Burkholderia cluster.	Coutinho BG, Mitter B, Talbi C, Sessitsch A, Bedmar EJ, Halliday N, James EK, Camara M, Venturi V	Appl Environ Microbiol	10.1128/AEM.00635-13	2013	Acyl-Butyrolactones/metabolism, Burkholderia/genetics/physiology, Chromatography, Liquid, Genome, Bacterial, Oligonucleotide Array Sequence Analysis, Quorum Sensing, *Regulon, Reverse Transcriptase Polymerase Chain Reaction, Species Specificity, Spectrometry, Mass, Electrospray Ionization, Tandem Mass Spectrometry	Phylogeny
Metabolism	23749969	Has the bacterial biphenyl catabolic pathway evolved primarily to degrade biphenyl? The diphenylmethane case.	Pham TT, Sylvestre M	J Bacteriol	10.1128/JB.00161-13	2013	Bacteriological Techniques, Benzhydryl Compounds/metabolism/pharmacology, Benzophenones/metabolism/pharmacology, Biphenyl Compounds/chemistry/metabolism, Burkholderiaceae/genetics/metabolism, Gene Expression Regulation, Bacterial/physiology, Models, Molecular, Molecular Structure
Metabolism	23879719	The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites.	Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD	Biochemistry	10.1021/bi400774m	2013	Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Binding Sites/genetics, Burkholderia/enzymology/genetics, Crystallography, X-Ray, Fatty Acids, Unsaturated/chemistry/metabolism, Hydrolases/chemistry/genetics/metabolism, Hydrolysis, Hydrophobic and Hydrophilic Interactions, Models, Chemical, Models, Molecular, Molecular Sequence Data, Molecular Structure, Mutation, Polychlorinated Biphenyls/chemistry/metabolism, Protein Multimerization, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Spectrophotometry, Sphingomonas/enzymology/genetics	Enzymology
Metabolism	23890965	Effects of growth substrate on triclosan biodegradation potential of oxygenase-expressing bacteria.	Lee DG, Chu KH	Chemosphere	10.1016/j.chemosphere.2013.06.069	2013	Biodegradation, Environmental, Burkholderia/genetics/growth & development/metabolism, Endocrine Disruptors/metabolism/toxicity, Oxygenases/genetics/metabolism, Rhodococcus/genetics/growth & development/metabolism, Triclosan/*metabolism/toxicity
Metabolism	24124510	Genomic and functional analyses of the 2-aminophenol catabolic pathway and partial conversion of its substrate into picolinic acid in Burkholderia xenovorans LB400.	Chirino B, Strahsburger E, Agullo L, Gonzalez M, Seeger M	PLoS One	10.1371/journal.pone.0075746	2013	Aminophenols/metabolism, Burkholderia/genetics/metabolism, Models, Biological, Picolinic Acids/*metabolism, Reverse Transcriptase Polymerase Chain Reaction
Metabolism	24257816	Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400.	Acosta-Navarrete YM, Leon-Marquez YL, Salinas-Herrera K, Jacome-Galarza IE, Meza-Carmen V, Ramirez-Diaz MI, Cervantes C	Microbiology (Reading)	10.1099/mic.0.073783-0	2013	Burkholderia/enzymology/genetics/metabolism, Chromates/metabolism, Escherichia coli/enzymology/genetics/metabolism, Gene Expression, Gene Expression Profiling, Ions/metabolism, Membrane Transport Proteins/genetics/metabolism, Real-Time Polymerase Chain Reaction, Recombinant Proteins/genetics/metabolism, Sulfates/metabolism	Enzymology
Enzymology	24317404	Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily.	Schurmann M, Demming RM, Krewing M, Rose J, Wubbeler JH, Steinbuchel A	J Bacteriol	10.1128/JB.01265-13	2013	Acyl Coenzyme A/metabolism, Acyl-CoA Dehydrogenases/genetics/isolation & purification/metabolism, Bacteria/*enzymology/genetics, Chromatography, Gel, Cloning, Molecular, Gene Expression, Kinetics, Oxidation-Reduction, Protein Multimerization, Recombinant Proteins/genetics/isolation & purification/metabolism, Spectrophotometry, Substrate Specificity	Metabolism
Biotechnology	24974981	Bacterial production of the biodegradable plastics polyhydroxyalkanoates.	Urtuvia V, Villegas P, Gonzalez M, Seeger M	Int J Biol Macromol	10.1016/j.ijbiomac.2014.06.001	2014	Bacteria/metabolism, Biodegradable Plastics, Biodegradation, Environmental, Biopolymers, Biotransformation, Environmental Pollution, Petroleum, Polyhydroxyalkanoates	Metabolism
	25246731	Enhanced Polychlorinated Biphenyl Removal in a Switchgrass Rhizosphere by Bioaugmentation with Burkholderia xenovorans LB400.	Liang Y, Meggo R, Hu D, Schnoor JL, Mattes TE	Ecol Eng	10.1016/j.ecoleng.2014.07.046	2014
Metabolism	25679799	Nano/bio treatment of polychlorinated biphenyls with evaluation of comparative toxicity.	Le TT, Nguyen KH, Jeon JR, Francis AJ, Chang YS	J Hazard Mater	10.1016/j.jhazmat.2015.02.001	2015	Aroclors/chemistry/metabolism/toxicity, Benzoic Acid/metabolism, Burkholderia/metabolism, Environmental Restoration and Remediation/methods, Escherichia coli/drug effects, Iron/chemistry, Metal Nanoparticles/chemistry, Palladium/chemistry, Soil Pollutants/chemistry/metabolism/toxicity	Pathogenicity
Metabolism	25693402	[Enhanced aerobic degradation of low chlorinated biphenyls by constructing surfactants Burkholderia xenovorans LB400 based system].	Chen SY, Zhang J, Wang H, Ren Y	Huan Jing Ke Xue		2014	Biodegradation, Environmental, Burkholderia/metabolism, Micelles, Polychlorinated Biphenyls/chemistry, Polyethylene Glycols/chemistry, Polysorbates/chemistry, Solubility, Surface-Active Agents/*chemistry
Metabolism	25956777	Metabolism of Doubly para-Substituted Hydroxychlorobiphenyls by Bacterial Biphenyl Dioxygenases.	Pham TT, Sondossi M, Sylvestre M	Appl Environ Microbiol	10.1128/AEM.00786-15	2015	Bacterial Proteins/chemistry/metabolism, Biocatalysis, Biodegradation, Environmental, Burkholderia/chemistry/enzymology, Burkholderiaceae/chemistry/enzymology, Dioxygenases/chemistry/metabolism, Molecular Structure, Oxidation-Reduction, Polychlorinated Biphenyls/chemistry/*metabolism, Substrate Specificity	Enzymology
Metabolism	26297047	Permissivity of the biphenyl-specific aerobic bacterial metabolic pathway towards analogues with various steric requirements.	Overwin H, Standfuss-Gabisch C, Gonzalez M, Mendez V, Seeger M, Reichelt J, Wray V, Hofer B	Microbiology (Reading)	10.1099/mic.0.000138	2015	Bacteria, Aerobic/genetics/growth & development/metabolism, Biphenyl Compounds/metabolism, Dioxygenases/metabolism, Gas Chromatography-Mass Spectrometry, Hydrocarbons, Aromatic/metabolism, Hydrolysis, *Metabolic Networks and Pathways, Nuclear Magnetic Resonance, Biomolecular, Oxidation-Reduction
Metabolism	26873556	chr genes from adaptive replicons are responsible for chromate resistance by Burkholderia xenovorans LB400.	Reyes-Gallegos RI, Ramirez-Diaz MI, Cervantes C	World J Microbiol Biotechnol	10.1007/s11274-015-1996-x	2016	Burkholderia/drug effects/genetics, Chromates/toxicity, Cloning, Molecular, Membrane Transport Proteins/genetics/metabolism, Metabolism, Inborn Errors, Mutagenesis, Insertional, Plasmids, Transformation, Bacterial	Enzymology
Metabolism	26963250	Genetic and Functional Analysis of the Biosynthesis of a Non-Ribosomal Peptide Siderophore in Burkholderia xenovorans LB400.	Vargas-Straube MJ, Camara B, Tello M, Montero-Silva F, Cardenas F, Seeger M	PLoS One	10.1371/journal.pone.0151273	2016	Bacterial Proteins/genetics/metabolism, Burkholderia/genetics/metabolism, Ion Transport/physiology, Iron/metabolism, Multigene Family, *Siderophores/biosynthesis/genetics
Metabolism	27147529	An aryl dioxygenase shows remarkable double dioxygenation capacity for diverse bis-aryl compounds, provided they are carbocyclic.	Overwin H, Gonzalez M, Mendez V, Seeger M, Wray V, Hofer B	Appl Microbiol Biotechnol	10.1007/s00253-016-7570-0	2016	Carboxylic Acids/metabolism, Dioxygenases/metabolism, Hydrocarbons, Cyclic/*metabolism, Oxidation-Reduction, Recombinant Fusion Proteins/metabolism, Substrate Specificity
Metabolism	27977154	In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products.	Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP	Environ Sci Technol	10.1021/acs.est.6b04345	2016	Biodegradation, Environmental, Carbamazepine/metabolism, Waste Water/chemistry, Water Purification, Water Supply	Enzymology
Genetics	28072820	p-Cymene Promotes Its Catabolism through the p-Cymene and the p-Cumate Pathways, Activates a Stress Response and Reduces the Biofilm Formation in Burkholderia xenovorans LB400.	Agullo L, Romero-Silva MJ, Domenech M, Seeger M	PLoS One	10.1371/journal.pone.0169544	2017	Biofilms/growth & development, Burkholderia/physiology, Cymenes, Gene Order, Genome, Bacterial, Genomics/methods, Metabolic Networks and Pathways, Monoterpenes/metabolism, *Stress, Physiological, Transcription, Genetic	Metabolism
Metabolism	28783597	A water-assisted nucleophilic mechanism utilized by BphD, the meta-cleavage product hydrolase in biphenyl degradation.	Dong L, Zhang S, Liu Y	J Mol Graph Model	10.1016/j.jmgm.2017.07.016	2017	Acylation, Biotransformation, Biphenyl Compounds/chemistry/metabolism, Catalysis, Hydrolases/chemistry/metabolism, Hydrolysis, Metabolic Networks and Pathways, Models, Molecular, Molecular Conformation, Molecular Dynamics Simulation, Water/chemistry
Metabolism	28823514	Bacterial polyhydroxybutyrate for electrospun fiber production.	Acevedo F, Villegas P, Urtuvia V, Hermosilla J, Navia R, Seeger M	Int J Biol Macromol	10.1016/j.ijbiomac.2017.08.066	2017	Ammonium Chloride/metabolism/pharmacology, Burkholderia/drug effects/metabolism, Culture Media/chemistry/pharmacology, Electrochemical Techniques, Fermentation, Glucose/metabolism, Hydroxybutyrates/metabolism, Mannitol/metabolism/pharmacology, Mineral Fibers/analysis, Polyesters/*metabolism, Xylose/metabolism/pharmacology	Biotechnology
Metabolism	29781800	Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source.	Jones LB, Ghosh P, Lee JH, Chou CN, Kunz DA	Microbiology (Reading)	10.1099/mic.0.000668	2018	Aminohydrolases/genetics/metabolism, Bacteria/genetics/growth & development/metabolism, Bacterial Proteins/genetics/metabolism, Conserved Sequence, Cyanides/metabolism, Evolution, Molecular, Gene Deletion, Genetic Linkage, Multigene Family/genetics, Transcription, Genetic
Phylogeny	29869675	Paraburkholderia panacihumi sp. nov., an isolate from ginseng-cultivated soil, is antagonistic against root rot fungal pathogen.	Huo Y, Kang JP, Kim YJ, Yang DC	Arch Microbiol	10.1007/s00203-018-1530-2	2018	Antibiosis/physiology, Bacterial Typing Techniques, Base Composition/genetics, Burkholderiaceae/classification/genetics/isolation & purification, Catalase/metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Fungi/growth & development, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Panax/microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Ubiquinone/analysis	Enzymology
	30050515	The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2.	Obi CC, Vayla S, de Gannes V, Berres ME, Walker J, Pavelec D, Hyman J, Hickey WJ	Front Microbiol	10.3389/fmicb.2018.01532	2018
Metabolism	30203106	Analysis of the ars gene cluster from highly arsenic-resistant Burkholderia xenovorans LB400.	Serrato-Gamino N, Salgado-Lora MG, Chavez-Moctezuma MP, Campos-Garcia J, Cervantes C	World J Microbiol Biotechnol	10.1007/s11274-018-2526-4	2018	Arsenate Reductases/genetics, Arsenates/metabolism/toxicity, Arsenic/metabolism/toxicity, Arsenites/metabolism/toxicity, Bacterial Proteins/genetics/metabolism, Base Sequence, Burkholderia/drug effects/genetics/growth & development, Cloning, Molecular, DNA, Bacterial/analysis, Drug Resistance, Bacterial/genetics, Escherichia coli/genetics, Gene Expression Regulation, Bacterial, Microbial Sensitivity Tests, Multigene Family/*genetics, Operon, Phenotype, Phylogeny, Pseudomonas aeruginosa/genetics, Sequence Alignment, Sequence Analysis, Protein, Trans-Activators/genetics	Enzymology
Metabolism	30810921	Burkholderia xenovorans LB400 possesses a functional polyhydroxyalkanoate anabolic pathway encoded by the pha genes and synthesizes poly(3-hydroxybutyrate) under nitrogen-limiting conditions.	Urtuvia V, Villegas P, Fuentes S, Gonzalez M, Seeger M	Int Microbiol	10.1007/s10123-018-0004-3	2018	Bacterial Proteins/genetics/metabolism, Biosynthetic Pathways, Burkholderia/genetics/growth & development/metabolism, Glucose/metabolism, Hydroxybutyrates/metabolism, Nitrogen/metabolism, Polyesters/metabolism, Polyhydroxyalkanoates/*metabolism
Enzymology	30885321	Manipulating intradiol dioxygenases by C-terminus truncation.	Nazmi AR, Muthu M, Lloyd-Jones G	Enzyme Microb Technol	10.1016/j.enzmictec.2019.02.007	2019	Amino Acid Sequence, Bacteria/classification/enzymology/genetics, Bacterial Proteins/chemistry/genetics/metabolism, Catechols/metabolism, Dioxygenases/chemistry/genetics/metabolism, Enzyme Stability, Kinetics, Protein Conformation, Protein Engineering, Sequence Alignment, Sequence Deletion, Structure-Activity Relationship, Substrate Specificity, Thermodynamics	Metabolism
Pathogenicity	31469877	Long-chain flavodoxin FldX1 improves Paraburkholderia xenovorans LB400 tolerance to oxidative stress caused by paraquat and H2O2.	Rodriguez-Castro L, Mendez V, Duran RE, Seeger M	PLoS One	10.1371/journal.pone.0221881	2019	Adaptation, Biological/drug effects, Amino Acid Sequence, Betaproteobacteria/drug effects/physiology, Computational Biology/methods, Flavodoxin/chemistry/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics/methods, Hydrogen Peroxide/pharmacology, Oxidative Stress/drug effects, Paraquat/*pharmacology, Phylogeny	Genetics
Metabolism	32057856	Influence of the carbon source on the properties of poly-(3)-hydroxybutyrate produced by Paraburkholderia xenovorans LB400 and its electrospun fibers.	Sanhueza C, Diaz-Rodriguez P, Villegas P, Gonzalez A, Seeger M, Suarez-Gonzalez J, Concheiro A, Alvarez-Lorenzo C, Acevedo F	Int J Biol Macromol	10.1016/j.ijbiomac.2020.02.080	2020	Animals, Biotechnology, Burkholderiaceae/metabolism, Carbon/metabolism, Cell Adhesion/drug effects, Cell Proliferation/drug effects, Cell Survival/drug effects, Electricity, Fibroblasts/cytology/drug effects, Hydroxybutyrates/chemistry/metabolism/pharmacology, Mechanical Phenomena, Mice, Polyesters/chemistry/*metabolism/pharmacology, Prohibitins, Temperature	Pathogenicity
Metabolism	32709719	Engineering Burkholderia xenovorans LB400 BphA through Site-Directed Mutagenesis at Position 283.	Li J, Min J, Wang Y, Chen W, Kong Y, Guo T, Mahto JK, Sylvestre M, Hu X	Appl Environ Microbiol	10.1128/AEM.01040-20	2020	Bacterial Proteins/genetics/metabolism, Burkholderiaceae/genetics/metabolism, Dioxygenases/genetics/metabolism, Genetic Engineering, Mutagenesis, Site-Directed, Polychlorinated Biphenyls/metabolism	Biotechnology
Metabolism	33412450	Biodegradation of PCB congeners by Paraburkholderia xenovorans LB400 in presence and absence of sediment during lab bioreactor experiments.	Bako CM, Mattes TE, Marek RF, Hornbuckle KC, Schnoor JL	Environ Pollut	10.1016/j.envpol.2020.116364	2020	Biodegradation, Environmental, Bioreactors, Burkholderiaceae, Environmental Pollutants, Gas Chromatography-Mass Spectrometry, Laboratories, Polychlorinated Biphenyls, Virginia
Metabolism	33604434	Dataset describing biodegradation of individual polychlorinated biphenyl congeners (PCBs) by Paraburkholderia xenovorans LB400 in presence and absence of sediment slurry.	Bako CM, Mattes TE, Marek RF, Hornbuckle KC, Schnoor JL	Data Brief	10.1016/j.dib.2021.106821	2021
Phylogeny	34542391	Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor.	Herpell JB, Vanwijnsberghe S, Peeters C, Schindler F, Fragner L, Bejtovic M, Weckwerth W, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijsem.0.004969	2021	Bacterial Typing Techniques, Base Composition, Burkholderiaceae, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Ubiquinone	Transcriptome
Metabolism	34937186	Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution.	Hara T, Takatsuka Y, Nakata E, Morii T	Microbiol Spectr	10.1128/spectrum.01926-21	2021	Biodegradation, Environmental, Escherichia coli/genetics/metabolism, Metabolic Engineering, Polychlorinated Biphenyls/metabolism, Water Pollutants, Chemical/metabolism, Water Pollution/analysis	Biotechnology
Metabolism	35184754	The OxyR and SoxR transcriptional regulators are involved in a broad oxidative stress response in Paraburkholderia xenovorans LB400.	Mendez V, Rodriguez-Castro L, Duran RE, Padron G, Seeger M	Biol Res	10.1186/s40659-022-00373-7	2022	Bacterial Proteins/genetics/metabolism, Burkholderiaceae, Chromatography, Liquid, Escherichia coli/genetics, Escherichia coli Proteins/genetics/metabolism, Gene Expression Regulation, Bacterial, Hydrogen Peroxide/pharmacology, Oxidation-Reduction, Oxidative Stress, Repressor Proteins/genetics/metabolism, Tandem Mass Spectrometry	Proteome
Metabolism	35560986	Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway.	Ullah R, Zhu B, Kakar KU, Nawaz Z, Mushtaq M, Durrani TS, Islam ZU, Nawaz F	Environ Microbiol Rep	10.1111/1758-2229.13081	2022
Metabolism	36178372	Aerobic Bioaugmentation to Decrease Polychlorinated Biphenyl (PCB) Emissions from Contaminated Sediments to Air.	Bako CM, Martinez A, Ewald JM, Hua JBX, Ramotowski DJ, Dong Q, Schnoor JL, Mattes TE	Environ Sci Technol	10.1021/acs.est.2c01043	2022	Biodegradation, Environmental, Dioxygenases, Hydroxylamines, Polychlorinated Biphenyls/metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
6837	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17367)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17367
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
31232	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information		28776041	27557
41992	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/6193
57422	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 46959)	https://www.ccug.se/strain?id=46959
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369				Automatically annotated from API 20NE
68382				Automatically annotated from API zym
69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
71610	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID89198.1	StrainInfo: A central database for resolving microbial strain identifiers
123975	Curators of the CIP	Collection of Institut Pasteur (CIP 108558)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108558
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

spore formation

compound production

halophily

metabolite utilization

antibiotic resistance

metabolite production

metabolite tests

enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference