comamonas  (ATCC)


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    Structured Review

    ATCC comamonas
    (A) Physical map of the cpn gene cluster in <t>Comamonas</t> sp. strain NCIMB 9872 and subclones in the 16,058-bp region. The orientation of the arrows indicates the direction of gene transcription. The black arrows are genes involved in cyclopentanol degradation. cpnR is a putative regulatory gene. Other ORFs are marked by open arrows. An arrowhead in the cpnB gene indicates the point of insertion of a lacZ -Km r cassette at the Nsi I site resulting in a mutant strain designated 9872MB. Probes 1 and 2 are PCR or restriction fragments used in hybridization experiments. (B) Gene organization of the cyclohexanol degradation ( chn ) pathway in Acinetobacter ). The chnABCDE genes (black arrows) encode cyclohexanol dehydrogenase, CHMO, caprolactone hydrolase, 6-hydroxyhexanoate dehydrogenase, and 6-oxohexanoate dehydrogenase, respectively; chnR ); orf5 is an equivalent of orf6 in the cpn pathway; orf3 encodes a potential pilin gene inverting protein; orf8 and - 9 ). The chn gene cluster as shown is different from that present in strain SE19 (19) with the absence of “chnZ” in between chnR and orf3 ( chnY designation in 19), and there are no equivalents of orf8 and - 9 in the latter strain.
    Comamonas, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase †"

    Article Title: Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase †

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.68.11.5671-5684.2002

    (A) Physical map of the cpn gene cluster in Comamonas sp. strain NCIMB 9872 and subclones in the 16,058-bp region. The orientation of the arrows indicates the direction of gene transcription. The black arrows are genes involved in cyclopentanol degradation. cpnR is a putative regulatory gene. Other ORFs are marked by open arrows. An arrowhead in the cpnB gene indicates the point of insertion of a lacZ -Km r cassette at the Nsi I site resulting in a mutant strain designated 9872MB. Probes 1 and 2 are PCR or restriction fragments used in hybridization experiments. (B) Gene organization of the cyclohexanol degradation ( chn ) pathway in Acinetobacter ). The chnABCDE genes (black arrows) encode cyclohexanol dehydrogenase, CHMO, caprolactone hydrolase, 6-hydroxyhexanoate dehydrogenase, and 6-oxohexanoate dehydrogenase, respectively; chnR ); orf5 is an equivalent of orf6 in the cpn pathway; orf3 encodes a potential pilin gene inverting protein; orf8 and - 9 ). The chn gene cluster as shown is different from that present in strain SE19 (19) with the absence of “chnZ” in between chnR and orf3 ( chnY designation in 19), and there are no equivalents of orf8 and - 9 in the latter strain.
    Figure Legend Snippet: (A) Physical map of the cpn gene cluster in Comamonas sp. strain NCIMB 9872 and subclones in the 16,058-bp region. The orientation of the arrows indicates the direction of gene transcription. The black arrows are genes involved in cyclopentanol degradation. cpnR is a putative regulatory gene. Other ORFs are marked by open arrows. An arrowhead in the cpnB gene indicates the point of insertion of a lacZ -Km r cassette at the Nsi I site resulting in a mutant strain designated 9872MB. Probes 1 and 2 are PCR or restriction fragments used in hybridization experiments. (B) Gene organization of the cyclohexanol degradation ( chn ) pathway in Acinetobacter ). The chnABCDE genes (black arrows) encode cyclohexanol dehydrogenase, CHMO, caprolactone hydrolase, 6-hydroxyhexanoate dehydrogenase, and 6-oxohexanoate dehydrogenase, respectively; chnR ); orf5 is an equivalent of orf6 in the cpn pathway; orf3 encodes a potential pilin gene inverting protein; orf8 and - 9 ). The chn gene cluster as shown is different from that present in strain SE19 (19) with the absence of “chnZ” in between chnR and orf3 ( chnY designation in 19), and there are no equivalents of orf8 and - 9 in the latter strain.

    Techniques Used: Mutagenesis, Polymerase Chain Reaction, Hybridization

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    ATCC comamonas testosteroni
    Illustration of the phylogenetic position of <t>Comamonas</t> <t>testosteroni</t> KF-1 within the order Burkholderiales of Betaproteobacteria . The 16S rRNA gene alignment included the three other C. testosteroni strains whose genome sequences have been published, strain S44 [ 52 ], strain CNB-2 [ 24 ], and type-strain ATCC 11996 [ 22 ], and some of other genome-sequenced representatives of the family Comamonadaceae or of other families within the order Burkholderiales . The corresponding genome-project accession numbers, or 16S rRNA gene accession numbers, are indicated. “T” indicates a type strain. The sequences were aligned using the RDP tree builder [ 76 ] and displayed using MEGA4 [ 77 ]. Bootstrap values are indicated; bar, 0.02 substitutions per nucleotide position.
    Comamonas Testosteroni, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illustration of the phylogenetic position of Comamonas testosteroni KF-1 within the order Burkholderiales of Betaproteobacteria . The 16S rRNA gene alignment included the three other C. testosteroni strains whose genome sequences have been published, strain S44 [ 52 ], strain CNB-2 [ 24 ], and type-strain ATCC 11996 [ 22 ], and some of other genome-sequenced representatives of the family Comamonadaceae or of other families within the order Burkholderiales . The corresponding genome-project accession numbers, or 16S rRNA gene accession numbers, are indicated. “T” indicates a type strain. The sequences were aligned using the RDP tree builder [ 76 ] and displayed using MEGA4 [ 77 ]. Bootstrap values are indicated; bar, 0.02 substitutions per nucleotide position.

    Journal: Standards in Genomic Sciences

    Article Title: Permanent draft genome sequence of Comamonas testosteroni KF-1

    doi: 10.4056/sigs.3847890

    Figure Lengend Snippet: Illustration of the phylogenetic position of Comamonas testosteroni KF-1 within the order Burkholderiales of Betaproteobacteria . The 16S rRNA gene alignment included the three other C. testosteroni strains whose genome sequences have been published, strain S44 [ 52 ], strain CNB-2 [ 24 ], and type-strain ATCC 11996 [ 22 ], and some of other genome-sequenced representatives of the family Comamonadaceae or of other families within the order Burkholderiales . The corresponding genome-project accession numbers, or 16S rRNA gene accession numbers, are indicated. “T” indicates a type strain. The sequences were aligned using the RDP tree builder [ 76 ] and displayed using MEGA4 [ 77 ]. Bootstrap values are indicated; bar, 0.02 substitutions per nucleotide position.

    Article Snippet: The first Comamonas testosteroni (formerly Pseudomonas testosteroni [ ]) strain, type-strain ATCC 11996, was enriched from soil and isolated in 1952 for its ability to degrade testosterone [ , ].

    Techniques:

    Scanning electron micrograph of Comamonas testosteroni KF-1 . Cells derived from a liquid culture that grew in LB medium.

    Journal: Standards in Genomic Sciences

    Article Title: Permanent draft genome sequence of Comamonas testosteroni KF-1

    doi: 10.4056/sigs.3847890

    Figure Lengend Snippet: Scanning electron micrograph of Comamonas testosteroni KF-1 . Cells derived from a liquid culture that grew in LB medium.

    Article Snippet: The first Comamonas testosteroni (formerly Pseudomonas testosteroni [ ]) strain, type-strain ATCC 11996, was enriched from soil and isolated in 1952 for its ability to degrade testosterone [ , ].

    Techniques: Derivative Assay

    (A) Physical map of the cpn gene cluster in Comamonas sp. strain NCIMB 9872 and subclones in the 16,058-bp region. The orientation of the arrows indicates the direction of gene transcription. The black arrows are genes involved in cyclopentanol degradation. cpnR is a putative regulatory gene. Other ORFs are marked by open arrows. An arrowhead in the cpnB gene indicates the point of insertion of a lacZ -Km r cassette at the Nsi I site resulting in a mutant strain designated 9872MB. Probes 1 and 2 are PCR or restriction fragments used in hybridization experiments. (B) Gene organization of the cyclohexanol degradation ( chn ) pathway in Acinetobacter ). The chnABCDE genes (black arrows) encode cyclohexanol dehydrogenase, CHMO, caprolactone hydrolase, 6-hydroxyhexanoate dehydrogenase, and 6-oxohexanoate dehydrogenase, respectively; chnR ); orf5 is an equivalent of orf6 in the cpn pathway; orf3 encodes a potential pilin gene inverting protein; orf8 and - 9 ). The chn gene cluster as shown is different from that present in strain SE19 (19) with the absence of “chnZ” in between chnR and orf3 ( chnY designation in 19), and there are no equivalents of orf8 and - 9 in the latter strain.

    Journal: Applied and Environmental Microbiology

    Article Title: Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase †

    doi: 10.1128/AEM.68.11.5671-5684.2002

    Figure Lengend Snippet: (A) Physical map of the cpn gene cluster in Comamonas sp. strain NCIMB 9872 and subclones in the 16,058-bp region. The orientation of the arrows indicates the direction of gene transcription. The black arrows are genes involved in cyclopentanol degradation. cpnR is a putative regulatory gene. Other ORFs are marked by open arrows. An arrowhead in the cpnB gene indicates the point of insertion of a lacZ -Km r cassette at the Nsi I site resulting in a mutant strain designated 9872MB. Probes 1 and 2 are PCR or restriction fragments used in hybridization experiments. (B) Gene organization of the cyclohexanol degradation ( chn ) pathway in Acinetobacter ). The chnABCDE genes (black arrows) encode cyclohexanol dehydrogenase, CHMO, caprolactone hydrolase, 6-hydroxyhexanoate dehydrogenase, and 6-oxohexanoate dehydrogenase, respectively; chnR ); orf5 is an equivalent of orf6 in the cpn pathway; orf3 encodes a potential pilin gene inverting protein; orf8 and - 9 ). The chn gene cluster as shown is different from that present in strain SE19 (19) with the absence of “chnZ” in between chnR and orf3 ( chnY designation in 19), and there are no equivalents of orf8 and - 9 in the latter strain.

    Article Snippet: As a result, the near-complete 1,449-base-long 16S sequence of strain 9872 was found to be 100% identical to that of Comamonas (previously Pseudomonas ) testosteroni (ATCC 11996), a prototype strain in testosterone metabolism ( , , ).

    Techniques: Mutagenesis, Polymerase Chain Reaction, Hybridization

    Proposed degradation pathway of steroidal B, C, and D rings in Comamonas testosteroni TA441. The compounds are 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (compound V), 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (compound

    Journal: Journal of Bacteriology

    Article Title: Identification of 9α-Hydroxy-17-Oxo-1,2,3,4,10,19-Hexanorandrostan-5-Oic Acid in Steroid Degradation by Comamonas testosteroni TA441 and Its Conversion to the Corresponding 6-En-5-Oyl Coenzyme A (CoA) Involving Open Reading Frame 28 (ORF28)- and ORF30-Encoded Acyl-CoA Dehydrogenases

    doi: 10.1128/JB.01878-14

    Figure Lengend Snippet: Proposed degradation pathway of steroidal B, C, and D rings in Comamonas testosteroni TA441. The compounds are 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (compound V), 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (compound

    Article Snippet: The identity of the deduced amino acid sequence of ORF28 to the corresponding protein of C. testosteroni (strains CNB-2, S44, ATCC 11996, and KF-1) is more than 90%.

    Techniques:

    Proposed steroid degradation pathway in Comamonas testosteroni TA441 and degradation genes. The compounds are androsta-1,4-diene-3,17-dione (ADD; compound I), 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione (3-HSA; compound II), 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic

    Journal: Journal of Bacteriology

    Article Title: Identification of 9α-Hydroxy-17-Oxo-1,2,3,4,10,19-Hexanorandrostan-5-Oic Acid in Steroid Degradation by Comamonas testosteroni TA441 and Its Conversion to the Corresponding 6-En-5-Oyl Coenzyme A (CoA) Involving Open Reading Frame 28 (ORF28)- and ORF30-Encoded Acyl-CoA Dehydrogenases

    doi: 10.1128/JB.01878-14

    Figure Lengend Snippet: Proposed steroid degradation pathway in Comamonas testosteroni TA441 and degradation genes. The compounds are androsta-1,4-diene-3,17-dione (ADD; compound I), 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione (3-HSA; compound II), 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic

    Article Snippet: The identity of the deduced amino acid sequence of ORF28 to the corresponding protein of C. testosteroni (strains CNB-2, S44, ATCC 11996, and KF-1) is more than 90%.

    Techniques:

    Genetic contexts of the IMP-1 encoding plasmid (pNR4028_IMP1) isolated from Comamonas thiooxydans NR4028. (A) Structural comparison of similar plasmid replicase in Gram-negative bacterial isolates. Regions with a homology are indicated by gray color. Genetic structure inside the red square frame is indicated in (B) , (B) Genetic environment of bla IMP−1 previously reported and NR4028. Genes were grouped and colored according to their predicted functions as indicated by the key. Arrows designate directions of transcription of genes and ORFs.

    Journal: Frontiers in Microbiology

    Article Title: Comamonas thiooxydans Expressing a Plasmid-Encoded IMP-1 Carbapenemase Isolated From Continuous Ambulatory Peritoneal Dialysis of an Inpatient in Japan

    doi: 10.3389/fmicb.2022.808993

    Figure Lengend Snippet: Genetic contexts of the IMP-1 encoding plasmid (pNR4028_IMP1) isolated from Comamonas thiooxydans NR4028. (A) Structural comparison of similar plasmid replicase in Gram-negative bacterial isolates. Regions with a homology are indicated by gray color. Genetic structure inside the red square frame is indicated in (B) , (B) Genetic environment of bla IMP−1 previously reported and NR4028. Genes were grouped and colored according to their predicted functions as indicated by the key. Arrows designate directions of transcription of genes and ORFs.

    Article Snippet: For species identification, average nucleotide identity (ANI) analysis was performed using C. testosteroni ATCC 11996 (GenBank accession no. AHIL01000000), C. testosteroni TK102 (GenBank accession no. CP006704), C. thiooxydans ZDHYF418 (GenBank accession no. CP063057), C. thiooxydans PHE2-6 (GenBank accession no. LKFB01000000), and C. thiooxydans DSM 17888 (GenBank accession no. LIOM01000000) as the reference genome ( https://www.ezbiocloud.net/tools/ani ).

    Techniques: Plasmid Preparation, Isolation