Journal:

Article Title: Novel 2,4-Dichlorophenoxyacetic Acid Degradation Genes from Oligotrophic Bradyrhizobium sp. Strain HW13 Isolated from a Pristine Environment

doi: 10.1128/JB.184.2.509-518.2002

Figure Lengend Snippet: Proteins homologous to ORFs found in pVBC (deduced amino acid sequence)

Article Snippet: ORF (protein encoded) Homolog (% identity) Origin (plasmid) Function or enzyme Accession no. ORF1 (CadR) NitR (21) Rhodococcus rhodochrous J1 Regulator for nitrilase D67026 FeaR (18) Escherichia coli K-12 Regulator for 2-phenylethylamine catabolism AE000235 ORF2 (CadA) TftA (46) Burkholderia cepacia AC1100 2,4,5-T oxygenase large subunit U11420 BenA (34) Acinetobacter sp. strain ADP1 Benzoate 1,2-dioxygenase terminal oxygenase large subunit AF009224 BenA (34) Rhodococcus sp. strain RHA1 Benzoate 1,2-dioxygenase terminal oxygenase large subunit AB055706 ORF3 (CadB) TftB (44) Burkholderia cepacia AC1100 2,4,5-T oxygenase small subunit U11420 BenB (32) Acinetobacter sp. strain ADP1 Benzoate 1,2-dioxygenase terminal oxygenase small subunit AF009224 BenB (31) Rhodococcus sp. strain RHA1 Benzoate 1,2-dioxygenase terminal oxygenase small subunit AB055706 ORF4 (CadK) TfdK (60) Ralstonia eutropha JMP134(pJP4) 2,4-D transporter U16782 Pcak (28) Acinetobacter sp. strain ADP1 4-Hydroxybenzoate transporter L05770 BenK (27) Acinetobacter sp. strain ADP1 Benzoate transporter AF009224 ORF5 (CadC) ThcC (37) Rhodococcus erythropolis NI86/21 Putative ferredoxin U17130 FdVI (37) Rhodobacter capsulatus B10 Putative ferredoxin Y11304 CamB (35) Pseudomonas putida ATCC 17453 Putidaredoxin for cytochrome P-450cam monooxygenase J05406 Open in a separate window Proteins homologous to ORFs found in pVBC (deduced amino acid sequence). .

Techniques: Sequencing, Plasmid Preparation

Journal: Applied and Environmental Microbiology

Article Title: Cloning, Baeyer-Villiger Biooxidations, and Structures of the Camphor Pathway 2-Oxo-? 3 -4,5,5-Trimethylcyclopentenylacetyl-Coenzyme A Monooxygenase of Pseudomonas putida ATCC 17453

doi: 10.1128/AEM.07694-11

Figure Lengend Snippet: Catabolic steps of conversion of camphor isomers to acetyl-CoA and isobutyryl-CoA in Pseudomonas putida ATCC 17453. A cytochrome P450-containing enzyme complex (CamCAB) hydroxylates (+)- and (−)-camphor at the 5-exo position to produce 5-exo-hydroxycamphor; upon dehydrogenation (5-exo-hydroxycamphor dehydrogenase [CamD]), the respective diketocamphane is formed. Ring oxygen insertion by the FMN- and NADH-dependent 2,5-diketocamphane monooxygenase for (+)-camphor or 3,6-diketocamphane monooxygenase for (−)-camphor (type 2 BVMOs) produces an unstable lactone that presumably undergoes spontaneous hydrolysis to form 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetic acid (compound 3). The activation of compound 3 by a putative CoA synthetase produces 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetyl-CoA, a substrate for OTEMO (type 1 BVMO), the subject of this study. Cumulative data are from references 30, 44, and 58. COSCoA, carbonyl-CoA; HSCoA, acetyl-CoA.

Article Snippet: DNA sequencing of the cloned inserts was performed by the conventional dideoxy method and analyzed as previously described ( 26 , 27 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 2 caption a7 Localizations of the OTEMO-encoding gene and BamHI fragment subclones in an 11-kb region of P. putida ATCC 17453.

Techniques: Activation Assay

Journal: Applied and Environmental Microbiology

Article Title: Cloning, Baeyer-Villiger Biooxidations, and Structures of the Camphor Pathway 2-Oxo-? 3 -4,5,5-Trimethylcyclopentenylacetyl-Coenzyme A Monooxygenase of Pseudomonas putida ATCC 17453

doi: 10.1128/AEM.07694-11

Figure Lengend Snippet: Localizations of the OTEMO-encoding gene and BamHI fragment subclones in an 11-kb region of P. putida ATCC 17453. The identified open reading frames are as follows, from left to right: putative DNA topoisomerase III (topo), OTEMO, 2,5-diketocamphane monooxygenase (DKCMO), a TetR-type regulator, lactone hydrolase, and a camR repressor that regulates the downstream camDCAB operon (camAB) (not shown) (5, 30).

Article Snippet: DNA sequencing of the cloned inserts was performed by the conventional dideoxy method and analyzed as previously described ( 26 , 27 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 2 caption a7 Localizations of the OTEMO-encoding gene and BamHI fragment subclones in an 11-kb region of P. putida ATCC 17453.

Techniques:

Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 1. a) Reported steps involved in the catabolic degradation of camphor by Pseudomonas putida (ATCC 17453). a Chemical structures of (+)-borneol, (L)-glutamic acid, (D)-glutamic acid, and 1-phenylimidazole. 1= (+)-camphor; 2 = 5-exo-hydroxycamphor; 3 = 5-ketocamphor; 4 = unstable lactone; 5 = 2-oxo-Δ3–4,5,5-trimethylcyclopentenylacetic acid; 6 = 2-oxo- Δ3–4,5,5-tri-methylcyclopentenylacetyl-CoA; 7 = 3,4,4-trimethyl-Δ3-pimelyl-CoA; 8 = (+)-borneol; 9 = (L)-glutamicacid; 10 = (D)-glutamic acid; 11 = 1-phe- nylimidazole; A = P450cam, PdR, & PdX; B = 5-exo-hydroxycamphor dehydrogenase; C = 2,5-diketocamphane monooxygenase; D = 2-oxo-Δ3–4,5,5-tri- methylcyclo-pentenylacetyl-CoA synthetase; E = 2-oxo-Δ3–4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques:

Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 2. Effects of1-phenylimidazole (a P450cam inhibitor) on growth P. putida ATCC 17453 (Strain 1). A)Survival dose response of Strain 1treated with 1-phenyli- midazole. B)Growthof Strain 1 on minimal medium with1-phenylimidazole as a sole carbon source. Each point represents the mean ± S. E. of 3 replicates.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques:

Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 4. Survival assay with (+)-camphor in the presence and absence of 1-phenylimidazole (a cytochrome P450cam inhibitor).A) Dose response for P. putida ATCC 17453 treated with (+)-camphor. B) Dose response for P. putida ATCC 17453, grown in the presence of 1-phenylimidazole (20 mM) and treated with (+)-camphor. Each point represents the mean ± S. E. of 3 replicates.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques: Clonogenic Cell Survival Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Sequence alignment of the cloned BDH gene from Pseudomonas sp. ATCC17453 with BDH from Pseudomonas sp. TCU-HL1 (Tsang et al. ) using ClustalW 1.7. Identical amino acids are marked with *. Active site amino acids are in bold

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques: Sequencing, Clone Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Characterization of BDH from Pseudomonas sp. ATCC17453. ( a + b ) Temperature and pH optimum for the oxidation of (±)-borneol. ( c + d ) Temperature and pH optimum for the reduction of camphor

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques:

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Model of the substrate binding pocket of BDH from Pseudomonas sp. ATCC17453. NADH is shown in red, camphor is shown in cyan, and amino acids chosen for mutagenesis are shown in green

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques: Binding Assay, Mutagenesis

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Kinetic resolution of racemic camphor catalyzed by improved mutants of borneol dehydrogenase from Pseudomonas sp. ATCC17453. The enantiomeric ratio E was calculated using Eq. ( 2 )

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques: Variant Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Kinetic resolution of camphor catalyzed by improved double mutants of borneol dehydrogenase from Pseudomonas sp. ATCC17453

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques: Variant Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Engineering of a borneol dehydrogenase from P. putida for the enzymatic resolution of camphor

doi: 10.1007/s00253-021-11239-5

Figure Lengend Snippet: Kinetic analysis of wild type as well as enantioselective borneol dehydrogenase variants from Pseudomonas sp. ATCC17453

Article Snippet: Pseudomonas sp. ATCC 17453 was used for cloning of the borneol dehydrogenase gene.

Techniques: Variant Assay

Journal: EMBO Molecular Medicine

Article Title: The clinical heterogeneity of coenzyme Q 10 deficiency results from genotypic differences in the Coq9 gene

doi: 10.15252/emmm.201404632

Figure Lengend Snippet: CoQ biosynthetic gene expression A–E mRNA expression levels of Coq9 (A), Coq7 (B), Adck3 (C), Coq5 (D) and Coq6 (E) on cerebrum of Coq9 +/+ , Coq9 Q95X and Coq9 Q95X mice at 3 months of age. ** P < 0.01; *** P < 0.001; Coq9 Q95X and Coq9 R239X mice versus Coq9 +/+ mice. ### P < 0.001; Coq9 Q95X versus Coq9 R239X mice. F–J mRNA expression levels of Coq9 (F), Coq7 (G), Adck3 (H), Coq5 (I) and Coq6 (J) on kidney of Coq9 +/+ , Coq9 Q95X and Coq9 Q95X mice at 3 months of age. *** P < 0.001; Coq9 Q95X and Coq9 R239X mice versus Coq9 +/+ mice. # P < 0.05; ### P < 0.001; Coq9 Q95X versus Coq9 R239X mice. K–O mRNA expression levels of Coq9 (K), Coq7 (L), Adck3 (M), Coq5 (N ) and Coq6 (O) on triceps surae of Coq9 +/+ , Coq9 Q95X and Coq9 Q95X mice at 3 months of age. * P < 0.05; *** P < 0.001; Coq9 Q95X and Coq9 R239X mice versus Coq9 +/+ mice. # P < 0.05; Coq9 Q95X versus Coq9 R239X mice. Data information: All values are presented as mean ± SD. One-way ANOVA with a Tukey's post hoc test. Numbers above columns indicate P -values of the one-way ANOVA test ( n = 5 for each group).

Article Snippet: The following primary antibodies were used: anti-COQ7 (generously provided by Dr Hekimi, McGill University, Canada), anti-COQ6 (Santa Cruz Biotechnology, sc-393932), anti-COQ5 (Proteintech™, 17453-1-AP), anti-ADCK3 (Abnova, M04A) anti-COQ9 (Santa Cruz, sc-271892), anti-COQ9 (Abcam, ab104189) and anti-VDAC1 (Abcam, ab14734).

Techniques: Expressing

Journal: EMBO Molecular Medicine

Article Title: The clinical heterogeneity of coenzyme Q 10 deficiency results from genotypic differences in the Coq9 gene

doi: 10.15252/emmm.201404632

Figure Lengend Snippet: Levels of COQ biosynthetic proteins A–D Representative Western blot and quantitation of Western blot bands of COQ7 (A), ADCK3 (B), COQ5 (C) and COQ6 (D), and VDAC1 as a loading control in the kidneys of 3-month-old mice. * P < 0.05; ** P < 0.01; *** P < 0.001; Coq9 Q95X and Coq9 R239X mice versus Coq9 +/+ mice. ## P < 0.01; ### P < 0.001; Coq9 Q95X versus Coq9 R239X mice. One-way ANOVA with a Tukey's post hoc test. E–H Representative Western blot and quantitation of Western blot bands of COQ7 (E), ADCK3 (F), COQ5 (G) and COQ6 (H), and VDAC1 as a loading control in skeletal muscle of 3-month-old mice. ** P < 0.01; *** P < 0.001; Coq9 Q95X and Coq9 R239X mice versus Coq9 +/+ mice. # P < 0.05; ## P < 0.01; Coq9 Q95X versus Coq9 R239X mice. Data information: All values are presented as mean ± SD. One-way ANOVA with a Tukey's post hoc test. Numbers above columns indicate P -values of the one-way ANOVA test. Coq9 +/+ mice n = 4; Coq9 Q95X and Coq9 R239X mice n = 5. Source data are available online for this figure.

Article Snippet: The following primary antibodies were used: anti-COQ7 (generously provided by Dr Hekimi, McGill University, Canada), anti-COQ6 (Santa Cruz Biotechnology, sc-393932), anti-COQ5 (Proteintech™, 17453-1-AP), anti-ADCK3 (Abnova, M04A) anti-COQ9 (Santa Cruz, sc-271892), anti-COQ9 (Abcam, ab104189) and anti-VDAC1 (Abcam, ab14734).

Techniques: Western Blot, Quantitation Assay