- Open Access
Permanent draft genome sequence of Comamonas testosteroni KF-1
- Michael Weiss1, 2,
- Anna I. Kesberg1,
- Kurt M. LaButti3,
- Sam Pitluck3,
- David Bruce4,
- Loren Hauser5,
- Alex Copeland3,
- Tanja Woyke3,
- Stephen Lowry3,
- Susan Lucas3,
- Miriam Land5,
- Lynne Goodwin3, 4,
- Staffan Kjelleberg6,
- Alasdair M. Cook1, 2,
- Matthias Buhmann1,
- Torsten Thomas6 and
- David Schleheck1, 2Email author
© The Author(s) 2013
- Published: 15 June 2013
Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an average G+C content of 61.79% and is predicted to encode 5,492 protein-coding genes and 114 RNA genes.
- Comamonas testosteroni KF-1
- xenobiotic surfactant biodegradation
Comamonas testosteroni strain KF-1 (DSM14576) was isolated for its ability to degrade xenobiotic sulfophenylcarboxylates (SPC), which are degradation intermediates of the synthetic laundry surfactants linear alkylbenzenesulfonates (LAS) . LAS is in use worldwide (appr. 3 × 106 tons per year ) and consists of a complex mixture of linear alkanes (C10-C13) sub-terminally substituted by 4-sulfophenyl rings (i.e., 38 different compounds) . Commercial LAS is completely biodegradable, as known for more than 50 years , e.g., in sewage treatment plants, and its degradation is catalyzed by heterotrophic aerobic bacterial communities in two steps. First, an initial degradation step is catalyzed by bacteria such as Parvibaculum lavamentivorans DS-1T  through activation and shortening of the alkyl-chains of LAS, and many short-chain degradation intermediates are excreted by these organisms, i.e., approximately 50 different SPCs and related compounds [1,5–8]. Secondly, the ultimate degradation step, i.e., mineralization of all SPCs, is catalyzed by other bacteria in the community, and one representative of these is Comamonas testosteroni KF-1. In particular, strain KF-1 was isolated from a laboratory trickling filter that had been used to enrich a bacterial community from sewage sludge that completely degraded commercial LAS and SPCs [1,6]. Strain KF-1 is able to utilize four individual SPCs (both enantiomers), namely R/S-3-(4-sulfopenyl)butyrate (3-C4-SPC), enoyl-3-C4-SPC, R/S-3-(4-sulfopenyl)pentanoate (3-C5-SPC), and enoyl-3-C5-SPC (see therefore also below), as novel carbon an energy sources for its heterotrophic aerobic growth [1,9,10].
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 [12,13]. Since then, the physiology, biochemistry, genetics, and regulation of steroid degradation in this and in other C. testosteroni strains have been elucidated in great detail [e.g., 14–21]. Most recently, the genome of C. testosteroni ATCC 11996T has been sequenced in order to further improve the understanding of the molecular basis for the degradation of steroids .
In the environment, members of the genus Comamonas may also be important degraders of aromatic compounds other than steroids, especially of xenobiotic pollutants, since they have frequently been enriched and isolated for their ability to utilize (xenobiotic) aromatic compounds. For example, Comamonas sp. strain JS46 is able to grow with 3-nitrobenzoate , Comamonas sp. strain CNB-1 with 4-chloronitrobenzene , C. testosteroni T-2 with 4-toluenesulfonate and 4-sulfobenzoate , C. testosteroni WDL7 with chloroaniline , Comamonas sp. strain JS765 with nitrobenzene , Comamonas sp. strain B-9 with lignin-polymer fragments , C. testosteroni B-356 with biphenyl and 4-chlorobiphenyl , Comamonas sp. strain KD-7 with dibenzofuran , Comamonas sp. strain 4BC with naphthalene-2-sulfonate , or C. testosteroni SPB-2 (as well as strain KF-1) with 4-sulfophenylcarboxylates . In several C. testosteroni strains, the physiology, biochemistry, genetics, and/or regulation of the utilization of aromatic compounds have been elucidated [e.g., 10,23,25,27,29,32–48]. Furthermore, the genome sequence of (plasmid-cured) C. testosteroni CNB-2 has been published , and the sequence of its plasmid pCNB1 (of C. testosteroni CNB-1) , in order to further improve the understanding of the molecular basis for the ability of C. testosteroni to degrade such a large array of aromatic compounds.
Members of the genus Comamonas are able to cope with harsh environmental conditions such as high concentrations of arsenate [50,51], zinc , cobalt and nickel , or phenol , and can exhibit increased resistance to oxidative stress  or antibiotics . Another C. testosteroni genome sequence, of strain S44, has recently been established in order to improve the understanding of the molecular basis for its resistance to increased concentrations of zinc . Notably, an increased antibiotic resistance (and enhanced insecticide catabolism) as a consequence of induction of the steroid degradation pathway has been shown for C. testosteroni ATCC 11996T .
Here, we present a summary classification and a set of features for another C. testosteroni strain, strain KF-1, which has been genome-sequenced in order to improve the understanding of the molecular basis for its ability to degrade xenobiotic compounds, particularly xenobiotic, chiral 3-C4-SPC, and how this novel degradation pathway has been assembled in this organism, together with the description of its draft genome sequence and annotation. The genome sequence and its annotation have been established as part of the Microbial Genomics Program 2006 of the DOE Joint Genome Institute, and are accessible via the IMG platform .
Morphology and growth conditions
Classification and general features of Comamonas testosteroni KF-1 according to the MIGS recommendations .
Species Comamonas testosteroni
3-(4-sulfophenyl)butyrate (3-C4-SPC) and other SPCs [see text], 4-sulfoacetophenone, 4-sulfophenyl acetate, 4-sulfophenol, testosterone, progesterone, taurocholate, cholate, taurine, benzoate, 4-hydroxybenzoate, vanillate, isovanillate
Terminal electron receptor
nonpathogenic, Risk group 1 (classification according to German TRBA)
isolated from a LAS surfactant-degrading laboratory trickling filter (University of Konstanz, Germany) that had been inoculated with sludge from a communal sewage treatment plant (Herisau, Switzerland).
47° 41′ 27.24″
9° 11′ 16.25″
In respect to other aromatic compounds, strain KF-1 is known to utilize benzoate, 3- and 4-hydroxybenzoate, protocatechuate (3,4-dihydroxybenzoate), gentisate (2,5-dihydroxybenzoate), phthalate, terephthalate, vanillate, isovanillate, veratrate, 2- and 3-hydroxyphenylacetate (tested in this study, and ref. 1). Xenobiotic aromatic substrates for strain KF-1 known are the 4-sulfophenylcarboxylates R/S-3-(4-sulfophenyl)butyrate (R/S-3-C4-SPC), 3-(4-sulfophenyl)-Δ2-enoylbutyrate (enoyl-3-C4-SPC), R/S-3-(4-sulfophenyl)pentanoate (R/S-3-C5-SPC), 3-(4-sulfophenyl)-Δ2-enoylpentanoate (enoyl-3-C5-SPC), as well as the three xenobiotic metabolites in the 3-C4-SPC-pathway, 4-sulfoacetophenone (4-acetylbenzenesulfonate), 4-sulfophenol acetate, and 4-sulfophenol [1,9]. Finally, strain KF-1 did not utilize the following, other carbon sources tested (this study and refs. 1,9): n-alkanes (C6-C12), cycloalkanes (C8-C12), secondary-4-sulfophenylalkanes (LAS surfactants), secondary alkanesulfonates (SAS surfactants), dodecylsulfate (SDS surfactant), benzene sulfonate, 4-toluenesulfonate, 4-sulfobenzoate, phenylacetate, 3-phenylpropionate, 3- and 4-phenylbutyrate, 4-sulfostyrene, 4-sulfobenzoate, 4-sulfocatechol, cyclohexanone, 4-aminoacetophenone, gallic acid (3,4,5-trihydroxybenzoic acid) and gallotannic acid, pentanesulfonate, isethionate, sulfoacetate, D-tartaric acid, acetamide, gamma-aminobutyrate, oxalate, methanol, methylamine, methanesulfonate or formate, and not 2-C4-SPC (2-[4-sulfophenyl]butyrate), 4-C5-SPC, 4-C6-SPC, 5-C6-SPC, or any of the C7–C9 SPCs generated during commercial LAS surfactant degradation.
C. testosteroni KF-1 has been recognized for its poor ability to form structured biofilms on surfaces  [see also ref. 72], or micro- or macroscopic cellular aggregates in liquid cultures , in direct comparison to ‘good’ biofilm forming organisms such as Delftia acidovorans SPH-1 , Pseudomonas aeruginosa PAO1 , or C. testosteroni SPB-2 .
No significant production of siderophores could be observed for C. testosteroni KF-1 when grown in presence of non-inhibitory levels of iron chelator 2,2′-dipyridyl [see 74], in comparison to siderophore-producing Delftia acidovorans SPH-1, Pseudomonas aeruginosa PAO1, and Pseudoalteromonas tunicata D2  (reported in this study, data not shown).
Finally, strain KF-1 is able to grow in the presence of up to 500 µg/ml ampicillin or 600 µg/ml kanamycin in liquid cultures, as tested in this study.
Genome project history
3.5 kb, 9 kb and 37 kb DNA libraries
Gene calling method
Genbank Date of Release
January 14, 2009
Source material identifier
Growth conditions and DNA isolation
Comamonas testosteroni KF-1, obtained from the Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM14576), was grown on LB agar plates and transferred into selective medium (6 mM 4-sulfophenol/mineral-salts medium) in the 3-ml scale, and this culture was sub-cultivated in larger scale; cell pellets were stored frozen until DNA preparation. DNA was prepared following the JGI’s DNA Isolation Bacterial CTAB Protocol.
Genome sequencing and assembly
The genome of Comamonas testosteroni KF-1 was sequenced at the Joint Genome Institute (JGI) using a combination of 3.5 kb, 9 kb and 37 kb DNA libraries. All general aspects of library construction and sequencing performed at the JGI can be found at JGI website . In total, 66.91 Mbp of Sanger sequence data were generated for the assembly from all three libraries, which provided for a 12.8-fold coverage of the genome. The Phred/Phrap/Consed software package was used for sequence assembly and quality assessment [80–82]. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher , PCR amplification, or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI, USA). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification (Roche Applied Science, Indianapolis, IN, USA). The genome could not be closed due to clone viability issues, however, several clones circularized the contig, and a PCR product was obtained that spanned the ends, but all attempts at primer walking and transforming the amplicon were unsuccessful. At this time no additional work is planned for this project (labeled as Permanent Draft; one linear contig).
Genes were identified using Prodigal  as part of the genome annotation pipeline at Oak Ridge National Laboratory (ORNL), Oak Ridge, TN, USA, followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE , RNAMMer , Rfam , TMHMM , and signalP . Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform  developed by the Joint Genome Institute, Walnut Creek, CA, USA .
Nucleotide and gene count levels of the genome of C. testosteroni KF-1
% of totala
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Number of replicons
Genes total number
rRNA operon count
Genes with function prediction
Genes in paralog clusters
Genes assigned to COGs
Genes assigned to Pfam domains
Genes connected to KEGG pathways
Genes with transmembrane helices
Genes with signal peptides
Number of genes associated with the general COG functional categories in C. testosteroni KF-1
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
The chromosome of C. testosteroni KF-1 (6.03 Mb) is larger in comparison to these of the three other C. testosteroni strains whose sequences have been published, of strain S44  (5.53 Mb), strain CNB-2  (5.46 Mb), and strain ATCC 11996  (5.41 Mb), and in comparison to that of C. testosteroni NBRC 100989 (5.59 Mb) whose draft sequence has not yet been published (BioProject ID PRJNA70139). Upon genomic BLAST comparison however, the strain NBRC 100989 chromosome showed the highest similarity to the chromosome of C. testosteroni KF-1.
For the three C. testosteroni genomes accessible within the IMG platform for direct comparison , strains KF-1, S44 and CNB-2, the gene abundance profile indicated, most strikingly, a much higher abundance of transposases (COG2801, COG2826 and COG4644) in strain KF-1 (42 total) in comparison to strains S44 (4 total) and CNB-2 (9 total); retroviral integrases (pfam00665) are more abundant in strain KF-1 (36 total) in comparison to strains S44 (none) and CNB-2 (13 total), and hemagluttinin repeat proteins (pfam05594) implicated in cell aggregation are more abundant (10 total) in comparison to strains S44 (none) and CNB-2 (none).
In respect to candidate genes encoding the metabolic features of C. testosteroni KF-1 (see above), almost identical (syntenic) gene clusters were found for the main steroid degradation genes characterized in C. testosteroni TA441 [16,17,20], including the genes characterized in C. testosteroni ATCC 11996 [18,21,52,93–95]; the strain KF-1 genes are up to 98% identical in their amino-acid sequences. Candidate genes for the degradation of the acyl-sidechain of cholate in Pseudomonas sp. strain Chol1 [96,97] were also found (thiolase, locus tag CtesDRAFT_PD3654; acyl-CoA dehydrogenase, PD3666), and the genes for inversion of the cholate-stereochemistry in Comamonas testosteroni TA441  (PD3740-44). In respect to the complete degradation of taurocholate , several candidate genes for bile-salts hydrolase (taurocholate hydrolase) and candidate genes for the complete degradation of the taurine-moiety (2-aminoethanesulfonate) , e.g., for sulfoacetaldehyde acetyltransferase (Xsc, PD0776), were found.
Strain KF-1 has acquired the ability to utilize xenobiotic 3-C4-SPC, 3-C4-SPC-2H, 3-C5-SPC and 3-C5-SPC-2H, 4-sulfoacetophenone (SAP), and 4-sulfophenol (SP) (see above) [1,9]. The 3-C4-SPC is converted to SAP  and further to 4-sulfophenol acetate (SPAc) by a recently identified Baeyer-Villiger monooxygenase (‘SAPMO’, PD5437), and SPAc hydrolyzed by a recently identified carboxylester hydrolase encoded by the next gene in the genome (PD5438), to yield acetate and SP . The two identified genes, together with other (predicted) catabolic genes, are framed by IS1071 insertion sequence elements (Tn3-family transposase genes), which suggests that these genes have only recently been acquired, possibly in the form of a ‘catabolic composite transposon’ through horizontal gene transfer . Genes for other sections of the proposed 3-C4-SPC degradation pathway in strain KF-1, i.e., the ‘upper’ and ‘lower’ pathway, from 3-C4-SPC to SAP and from SP further to central metabolites, respectively , are examined in our present work (unpublished).
C. testosteroni KF-1 encodes a wealth of genes for aromatic ring-cleavage oxygenases and aromatic-ring hydroxylating oxygenase (systems), as commonly observed for members of the order Burkholderiales . Firstly, the complete protocatechuate 4,5-cleavage (meta) degradation operon (pmd-operon) characterized in C. testosteroni strain BR6020 [35,43], strain E6  and CNB-1  involved in the degradation pathways for vanillate, isovanillate and 3- and 4-hydroxybenzoate, was found in strain KF-1 (pmdB, PD1898) (and two pmdB paralogs, PD1614 and 1810). An ortholog of the 3-hydroxybenzoate monooxygenase characterized in C. testosteroni GZ39  was found in strain KF-1 (PD1242), as were the genes for conversion of vanillate and isovanillate (vanA/ivaA: PD0400/PD0403) .
Gene clusters of the meta-pathway enzymes for degradation of phenol as characterized in C. testosteroni TA441, i.e., aphCEFGHJI  and aphKLMNOPQB ), were not found in strain KF-1, but in strains S44 and CNB-2. However, homologs for all meta-pathway enzymes (corresponding to aphCEFGHJI) seem to be distributed at different locations in the strain KF-1 genome, but a valid candidate gene cluster of the phenol hydroxylase components (aph-  or phcKLMNOP  genes) and catechol 2,3-dioxygenase (aphB) could not be found in the strain KF-1 genome. Also the gene cluster for the 3-(3-hydroxyphenyl) propionic acid degradation pathway (mhp-operon) characterized in Comamonas testosteroni TA441  was not found in the genome of strain KF-1, nor in strain CNB-2, but was found in strain S44; homologs for all pathway enzymes (corresponding to mhpABDFE) seem to be distributed at different locations in the strain KF-1 genome.
An almost identical gene cluster for the terepthalate (benzene-1,4-dicarboxylic acid) pathway (tph-cluster) as characterized in C. testosteroni YZW-D  and strain E6 [44,46] was found in strain KF-1 (tphA, PD2130). The gene cluster for the isophthalate (benzene-1,3-dicarboxylic acid) pathway of C. testosteroni YZW-D  and strain E6  was also found in strain KF-1 (iphA, PD2139), encoded directly upstream of the tph-cluster. Notably, at least nine other Rieske-domain ring-hydroxylating oxygenase component genes (COG4638) similar to tpaA/iphA (PD2130/PD2139) and vanA/ivaA (see above, PD0400/PD0403), seem to be encoded in strain KF-1 (PD2042, 1888, 4205, 2022, 0968, 3693, 1612, 2032, 5293).
No ortholog of the catechol 2,3-ring cleavage dioxygenase (non-heme Fe2+) of the phenol-pathway gene cluster (aphB)  was found in strain KF-1, but two other class I/II extradiol ring-cleavage dioxygenase candidates (PD0021, 5290) in addition to a (decarboxylating) 4-hydroxyphenylpyruvate dioxygenase candidate (PD0347) (also in CNB-2 and S44), tesB of the steroid gene cluster (PD3739), and the class-III type extradiol ring-cleavage dioxygenases mentioned above (PmdAB) were found.
In respect to intradiol ring-cleavage dioxygenases, three candidates for (non-heme Fe3+) catechol 1,2-dioxygenase/protocatechuate 3,4-dioxygenase beta subunit/hydroxyquinol 1,2-dioxygenase were found in strain KF-1, i.e., PD0424, 5469, and 5471; notably, the latter two candidates are not represented in strains CNB-2 and S44.
Also not represented in the C. testosteroni KF-1 genome is the nitrobenzene (nbz) degradation gene cluster of Comamonas sp. JS765 , the 3-nitrobenzoate (mnb) degradation cluster of C. testosteroni BR6020 , the 4-chlorobenzoate uptake and degradation cluster of Comamonas sp. strain DJ-12 [51,105], and not the 4-chloronitrobenzene (cnb) cluster on plasmid pCNB1 in C. testosteroni CNB-1  and the upper-pathway chloroaniline (dca) cluster on plasmid pWDL7 in C. testosteroni WDL7 . Finally, an ortholog of the aliphatic nitrilase/cyanide hydratase (NitA) characterized in a C. testosteroni soil isolate  was also not found in the genome of strain KF-1, nor in those of CNB-2 or S44.
Strain KF-1 utilized none of the sugars tested (see above), and this observation is reflected by an absence of appropriate candidate genes in strain KF-1 for hexokinase and glucokinase in glycolysis, as well as of genes of the oxidative branch of the pentose phosphate pathway, as reported also for C. testosteroni CNB-2 .
Strain KF-1 is able to utilize nicotinate for growth and encodes an orthologous set of genes for the nicotinate dehydrogenase/hydroxylase complex (PD0815-13) characterized in C. testosteroni JA1 .
The poly(3-hydroxybutyrate) (PHB) biosynthesis and utilization operon of Comamonas sp. EB172  is also encoded in strain KF-1 (e.g., PD2272). Furthermore, strain KF-1 tested positive for growth with extracellular poly(3-hydroxybutyrate) (this study), and strain KF-1 encodes an ortholog (PD3795) of the characterized poly(3-hydroxybutyrate) depolymerase precursor (PhaZ) of Comamonas sp. strain 31A ; notably, the ortholog was also found in C. testosteroni ATCC 11996T, but not in strains S44 and CNB-2.
In respect to the ampicillin (beta-lactam) antibiotic resistance of strain KF-1, the genome encodes at least two beta-lactamase class A (PD2722, 4357) and one beta-lactamase class B (PD0340) candidates, and with respect to kanamycin (aminoglycoside) resistance, two aminoglycoside phosphotransferase candidates (PD3717, 1418); notably, the latter two are not represented in strains CNB-2 and S44.
All four heavy metal exporter ATPase genes (zntA) and five CzcA-family exporter gene clusters described for highly zinc-resistant C. testosteroni S44  were found in strain KF-1, and in total eight zntA and 11 cntA candidates. Two arsenical resistance gene clusters (PD1708-06 and 3544-42), each with candidates for arsenical pump (ArsB), arsenate reductase (ArsC), NADPH:FMN oxidoreductases (ArsH), and transcriptional regulator (ArsR), and a third arsC candidate (PD0567), were found in strain KF-1.
We thank Joachim Hentschel for SEM operation, and several students of our practical classes for testing growth substrates. The work was financially supported by the University of Konstanz and the Konstanz Research School Chemical Biology, the University of New South Wales and the Centre for Marine Bio-Innovation, and by the Deutsche Forschungsgemeinschaft (DFG grant SCHL 1936/1-1 to D.S.). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and by the University of California, Lawrence Berkeley National Laboratory under contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.
- Schleheck D, Knepper TP, Fischer K, Cook AM. Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria. Appl Environ Microbiol 2004; 70:4053–4063. PubMed http://dx.doi.org/10.1128/AEM.70.7.4053-4063.2004PubMed CentralPubMedView ArticleGoogle Scholar
- Knepper TP, Barceló D, deVoogt P. Analysis and fate of surfactants in the quatic environment. Amsterdam: Elsevier; 2003.Google Scholar
- Swisher RD. Surfactant biodegradation. New York: Marcel Dekker; 1970.Google Scholar
- Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, et al. Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T). Stand Genomic Sci 2011; 5:298–310. PubMed http://dx.doi.org/10.4056/sigs.2215005PubMed CentralPubMedView ArticleGoogle Scholar
- Schleheck D, Dong W, Denger K, Heinzle E, Cook AM. An alpha-proteobacterium converts linear alkylbenzenesulfonate surfactants into sulfophenylcarboxylates and linear alkyldiphenyletherdisulfonate surfactants into sulfodiphenylethercarboxylates. Appl Environ Microbiol 2000; 66:1911–1916. PubMed http://dx.doi.org/10.1128/AEM.66.5.1911-1916.2000PubMed CentralPubMedView ArticleGoogle Scholar
- Dong W, Eichhorn P, Radajewski S, Schleheck D, Denger K, Knepper TP, Murrell JC, Cook AM. Parvibaculum lavamentivorans converts linear alkylbenzenesulphonate surfactant to sulphophenylcarboxylates, alpha,beta-unsaturated sulphophenylcarboxylates and sulphophenyldicarboxylates, which are degraded in communities. J Appl Microbiol 2004; 96:630–640. PubMed http://dx.doi.org/10.1111/j.1365-2672.2004.02200.xPubMedView ArticleGoogle Scholar
- Schleheck D, Tindall BJ, Rossello-Mora R, Cook AM. Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. Int J Syst Evol Microbiol 2004; 54:1489–1497. PubMed http://dx.doi.org/10.1099/ijs.0.03020-0PubMedView ArticleGoogle Scholar
- Schleheck D, Knepper TP, Eichhorn P, Cook AM. Parvibaculum lavamentivorans DS-1T degrades centrally substituted congeners of commercial linear alkylbenzenesulfonate to sulfophenyl carboxylates and sulfophenyl dicarboxylates. Appl Environ Microbiol 2007; 73:4725–4732. PubMed http://dx.doi.org/10.1128/AEM.00632-07PubMed CentralPubMedView ArticleGoogle Scholar
- Schleheck D, von Netzer F, Fleischmann T, Rentsch D, Huhn T, Cook AM, Kohler HP. The missing link in linear alkylbenzenesulfonate surfactant degradation: 4-sulfoacetophenone as a transient intermediate in the degradation of 3-(4-sulfophenyl)butyrate by Comamonas testosteroni KF-1. Appl Environ Microbiol 2010; 76:196–202. PubMed http://dx.doi.org/10.1128/AEM.02181-09PubMed CentralPubMedView ArticleGoogle Scholar
- Weiss M, Denger K, Huhn T, Schleheck D. Two enzymes of a complete degradation pathway for linear alkylbenzenesulfonate (LAS) surfactants: 4-sulfoacetophenone Baeyer-Villiger monooxygenase and 4-sulfophenylacetate esterase in Comamonas testosteroni KF-1. Appl Environ Microbiol 2012; 78:8254–8263. PubMed http://dx.doi.org/10.1128/AEM.02412-12PubMed CentralPubMedView ArticleGoogle Scholar
- Tamaoka J, Ha DM, Komagata K. Reclassification of Pseudomonas acidovorans Den Dooren De Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an emended description of the genus Comamonas. Int J Syst Bacteriol 1987; 37:52–59. http://dx.doi.org/10.1099/00207713-37-1-52View ArticleGoogle Scholar
- Talalay P, Dobson MM, Tapley DF. Oxidative degradation of testosterone by adaptive enzymes. Nature 1952; 170:620–621. PubMed http://dx.doi.org/10.1038/170620a0PubMedView ArticleGoogle Scholar
- Talalay P. A fascination with enzymes: The journey not the arrival matters. J Biol Chem 2005; 280:28829–28847. PubMed http://dx.doi.org/10.1074/jbc.X500004200PubMedView ArticleGoogle Scholar
- Shaw DA, Borkenhagen LF, Talalay P. Enzymatic oxidation of steroids by cell-free extracts of Pseudomonas testosteroni: isolation of cleavage products of ring A. Proc Natl Acad Sci USA 1965; 54:837–844. PubMed http://dx.doi.org/10.1073/pnas.54.3.837PubMed CentralPubMedView ArticleGoogle Scholar
- Marcus PI, Talalay P. Induction and purification of alpha- and beta-hydroxysteroid dehydrogenases. J Biol Chem 1956; 218:661–674. PubMedPubMedGoogle Scholar
- Horinouchi M, Yamamoto T, Taguchi K, Arai H, Kudo T. Meta-cleavage enzyme gene tesB is necessary for testosterone degradation in Comamonas testosteroni TA441. Microbiology 2001; 147:3367–3375. PubMedPubMedView ArticleGoogle Scholar
- Horinouchi M, Hayashi T, Yamamoto T, Kudo T. A new bacterial steroid degradation gene cluster in Comamonas testosteroni TA441 which consists of aromatic-compound degradation genes for seco-steroids and 3-ketosteroid dehydrogenase genes. Appl Environ Microbiol 2003; 69:4421–4430. PubMed http://dx.doi.org/10.1128/AEM.69.8.4421-4430.2003PubMed CentralPubMedView ArticleGoogle Scholar
- Xiong G, Martin HJ, Maser E. Identification and characterization of a novel translational repressor of the steroid-inducible 3 alpha-hydroxysteroid dehydrogenase/carbonyl reductase gene in Comamonas testosteroni. J Biol Chem 2003; 278:47400–47407. PubMed http://dx.doi.org/10.1074/jbc.M309210200PubMedView ArticleGoogle Scholar
- Rösch V, Denger K, Schleheck D, Smits TH, Cook AM. Different bacterial strategies to degrade taurocholate. Arch Microbiol 2008; 190:11–18. PubMed http://dx.doi.org/10.1007/s00203-008-0357-7PubMedView ArticleGoogle Scholar
- Horinouchi M, Kurita T, Hayashi T, Kudo T. Steroid degradation genes in Comamonas testosteroni TA441: Isolation of genes encoding a delta 4(5)-isomerase and 3 alpha- and 3 beta-dehydrogenases and evidence for a 100 kb steroid degradation gene hot spot. J Steroid Biochem Mol Biol 2010; 122:253–263. PubMed http://dx.doi.org/10.1016/j.jsbmb.2010.06.002PubMedView ArticleGoogle Scholar
- Gong W, Xiong G, Maser E. Identification and characterization of the LysR-type transcriptional regulator HsdR for steroid-inducible expression of the 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase gene in Comamonas testosteroni. Appl Environ Microbiol 2012; 78:941–950. PubMed http://dx.doi.org/10.1128/AEM.06872-11PubMed CentralPubMedView ArticleGoogle Scholar
- Gong W, Kisiela M, Schilhabel MB, Xiong G, Maser E. Genome sequence of Comamonas testosteroni ATCC 11996, a representative strain involved in steroid degradation. J Bacteriol 2012; 194:1633–1634. PubMed http://dx.doi.org/10.1128/JB.06795-11PubMed CentralPubMedView ArticleGoogle Scholar
- Providenti MA, Shaye RE, Lynes KD, McKenna NT, O’Brien JM, Rosolen S, Wyndham RC, Lambert LB. The locus coding for the 3-nitrobenzoate dioxygenase of Comamonas sp. strain JS46 is flanked by IS1071 elements and is subject to deletion and inversion events. Appl Environ Microbiol 2006; 72:2651–2660. PubMed http://dx.doi.org/10.1128/AEM.72.4.2651-2660.2006PubMed CentralPubMedView ArticleGoogle Scholar
- Ma YF, Zhang Y, Zhang JY, Chen DW, Zhu YQ, Zheng HJ, Wang SY, Jiang CY, Zhao GP, Liu SJ. The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. Appl Environ Microbiol 2009; 75:6812–6819. PubMed http://dx.doi.org/10.1128/AEM.00933-09PubMed CentralPubMedView ArticleGoogle Scholar
- Locher HH, Leisinger TAMC. Degradation of p-toluenesulphonic acid via sidechain oxidation, desulphonation and meta ring cleavage in Pseudomonas (Comamonas) testosteroni T-2. J Gen Microbiol 1989; 135:1969–1978. PubMedPubMedGoogle Scholar
- Krol JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik AD, Dejonghe W, Brown CJ, Parales RE, Wuertz S, et al. Role of IncP-1beta plasmids pWDL7:rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses. Appl Environ Microbiol 2012; 78:828–838. PubMed http://dx.doi.org/10.1128/AEM.07480-11PubMed CentralPubMedView ArticleGoogle Scholar
- Nishino SF, Spain JC. Oxidative pathway for the biodegradation of nitrobenzene by Comamonas sp. strain JS765. Appl Environ Microbiol 1995; 61:2308–2313. PubMedPubMed CentralPubMedGoogle Scholar
- Chen YH, Chai LY, Zhu YH, Yang ZH, Zheng Y, Zhang H. Biodegradation of kraft lignin by a bacterial strain Comamonas sp. B-9 isolated from eroded bamboo slips. J Appl Microbiol 2012; 112:900–906. PubMed http://dx.doi.org/10.111365-2672.2012.05275.xPubMedView ArticleGoogle Scholar
- Ahmad D, Massé R, Sylvestre M. Cloning and expression of genes involved in 4-chlorobiphenyl transformation by Pseudomonas testosteroni: homology to polychlorobiphenyl-degrading genes in other bacteria. Gene 1990; 86:53–61. PubMed http://dx.doi.org/10.1016/0378-1119(90)90113-6PubMedView ArticleGoogle Scholar
- Wang Y, Yamazoe A, Suzuki S, Liu CT, Aono T, Oyaizu H. Isolation and characterization of dibenzofuran-degrading Comamonas sp. strains isolated from white clover roots. Curr Microbiol 2004; 49:288–294. PubMed http://dx.doi.org/10.1007/s00284-004-4348-xPubMedView ArticleGoogle Scholar
- Song Z, Edwards SR, Burns RG. Biodegradation of naphthalene-2-sulfonic acid present in tannery wastewater by bacterial isolates Arthrobacter sp. 2AC and Comamonas sp. 4BC. Biodegradation 2005; ⋯: 237–252. PubMed http://dx.doi.org/10.1007/s10532-004-0889-8
- Ornston MK, Ornston LN. Regulation of beta-ketoadipate pathway in Pseudomonas acidovorans and Pseudomonas testosteroni. J Gen Microbiol 1972; 73:455–464. PubMed http://dx.doi.org/10.1099/00221287-73-3-455PubMedView ArticleGoogle Scholar
- Schläfli HR, Weiss MA, Leisinger T, Cook AM. Terephthalate 1,2-dioxygenase system from Comamonas testosteroni T-2 — Purification and some properties of the oxygenase component. J Bacteriol 1994; 176:6644–6652. PubMedPubMed CentralPubMedGoogle Scholar
- Teramoto M, Futamata H, Harayama S, Watanabe K. Characterization of a high-affinity phenol hydroxylase from Comamonas testosteroni R5 by gene cloning, and expression in Pseudomonas aeruginosa PAO1c. Mol Gen Genet 1999; 262:552–558. PubMed http://dx.doi.org/10.1007/s004380051117PubMedView ArticleGoogle Scholar
- Providenti MA, Mampel J, MacSween S, Cook AM, Wyndham RC. Comamonas testosteroni BR6020 possesses a single genetic locus for extradiol cleavage of protocatechuate. Microbiology-Sgm 2001; 147:2157–2167. PubMedView ArticleGoogle Scholar
- Sylvestre M, Sirois M, Hurtubise Y, Bergeron J, Ahmad D, Shareck F, Barriault D, Guillemette I, Juteau JM. Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene 1996; 174:195–202. PubMed http://dx.doi.org/10.1016/0378-1119(96)00039-XPubMedView ArticleGoogle Scholar
- Tralau T, Cook AM, Ruff J. Map of the IncP1beta plasmid pTSA encoding the widespread genes (tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2. Appl Environ Microbiol 2001; 67:1508–1516. PubMed http://dx.doi.org/10.1128/AEM.67.4.1508-1516.2001PubMed CentralPubMedView ArticleGoogle Scholar
- Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT. Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl Environ Microbiol 2002; 68:634–641. PubMed http://dx.doi.org/10.1128/AEM.68.2.634-641.2002PubMed CentralPubMedView ArticleGoogle Scholar
- Tralau T, Cook AM, Ruff J. An additional regulator, TsaQ, is involved with TsaR in regulation of transport during the degradation of p-toluenesulfonate in Comamonas testosteroni T-2. Arch Microbiol 2003; 180:319–326. PubMed http://dx.doi.org/10.1007/s00203-003-0594-8PubMedView ArticleGoogle Scholar
- Tralau T, Mampel J, Cook AM, Ruff J. Characterization of TsaR, an oxygen-sensitive LysR-type regulator for the degradation of p-toluenesulfonate in Comamonas testosteroni T-2. Appl Environ Microbiol 2003; 69:2298–2305. PubMed http://dx.doi.org/10.1128/AEM.69.4.2298-2305.2003PubMed CentralPubMedView ArticleGoogle Scholar
- Mampel J, Maier E, Tralau T, Ruff J, Benz R, Cook AM. A novel outer-membrane anion channel (porin) as part of a putatively two-component transport system for 4-toluenesulphonate in Comamonas testosteroni T-2. Biochem J 2004; 383:91–99. PubMed http://dx.doi.org/10.1042/BJ20040652PubMed CentralPubMedView ArticleGoogle Scholar
- Mampel J, Providenti MA, Cook AM. Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases. Arch Microbiol 2005; 183:130–139. PubMed http://dx.doi.org/10.1007/s00203-004-0755-4PubMedView ArticleGoogle Scholar
- Providenti MA, O’Brien JM, Ruff J, Cook AM, Lambert IB. Metabolism of isovanillate, vanillate, and veratrate by Comamonas testosteroni strain BR6020. J Bacteriol 2006; 188:3862–3869. PubMed http://dx.doi.org/10.1128/JB.01675-05PubMed CentralPubMedView ArticleGoogle Scholar
- Sasoh M, Masai E, Ishibashi S, Hara H, Kamimura N, Miyauchi K, Fukuda M. Characterization of the terephthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol 2006; 72:1825–1832. PubMed http://dx.doi.org/10.1128/AEM.72.3.1825-1832.2006PubMed CentralPubMedView ArticleGoogle Scholar
- Fukuhara Y, Inakazu K, Kodama N, Kamimura N, Kasai D, Katayama Y, Fukuda M, Masai E. Characterization of the isophthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol 2010; 76:519–527. PubMed http://dx.doi.org/10.1128/AEM.01270-09PubMed CentralPubMedView ArticleGoogle Scholar
- Kasai D, Kitajima M, Fukuda M, Masai E. Transcriptional regulation of the terephthalate catabolism operon in Comamonas sp. strain E6. Appl Environ Microbiol 2010; 76:6047–6055. PubMed http://dx.doi.org/10.1128/AEM.00742-10PubMed CentralPubMedView ArticleGoogle Scholar
- Kamimura N, Aoyama T, Yoshida R, Takahashi K, Kasai D, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene. Appl Environ Microbiol 2010; 76:8093–8101. PubMed http://dx.doi.org/10.1128/AEM.01863-10PubMed CentralPubMedView ArticleGoogle Scholar
- Ni B, Zhang Y, Chen DW, Wang BJ, Liu SJ. Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria. Appl Microbiol Biotechnol 2012. PubMed http://dx.doi.org/10.1007/s00253-012-4402-8
- Ma YF, Wu JF, Wang SY, Jiang CY, Zhang Y, Qi SW, Liu L, Zhao GP, Liu SJ. Nucleotide sequence of plasmid pCNB1 from Comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. Appl Environ Microbiol 2007; 73:4477–4483. PubMed http://dx.doi.org/10.1128/AEM.00616-07PubMed CentralPubMedView ArticleGoogle Scholar
- Zhang Y, Ma YF, Qi SW, Meng B, Chaudhry MT, Liu SQ, Liu SJ. Responses to arsenate stress by Comamonas sp strain CNB-1 at genetic and proteomic levels. Microbiology-Sgm 2007; 153:3713–3721. PubMed http://dx.doi.org/10.1099/mic0.2007/011403-0View ArticleGoogle Scholar
- Cai L, Liu G, Rensing C, Wang G. Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol 2009; 9:4. PubMed http://dx.doi.org/10.1186/1471-2180-9-4PubMed CentralPubMedView ArticleGoogle Scholar
- Xiong J, Li D, Li H, He M, Miller SJ, Yu L, Rensing C, Wang G. Genome analysis and characterization of zinc efflux systems of a highly zincresistant bacterium, Comamonas testosteroni S44. Res Microbiol 2011; 162:671–679. PubMed http://dx.doi.org/10.1016/j.resmic.2011.06.002PubMedView ArticleGoogle Scholar
- Siunova TV, Siunov AV, Kochetkov VV, Boronin AM. The cnr-like operon in strain Comamonas sp. encoding resistance to cobalt and nickel. Genetika 2009; 45:336–341. PubMedPubMedGoogle Scholar
- Turek M, Vilimkova L, Kremlackova V, Paca JJ, Halecky M, Paca J, Stiborova M. Isolation and partial characterization of extracellular NADPH-dependent phenol hydroxylase oxidizing phenol to catechol in Comamonas testosteroni. Neuroendocrinol Lett 2011; 32:137–145. PubMedPubMedGoogle Scholar
- Godocíková J, Bohácová V, Zámocký M, Polek B. Production of catalases by Comamonas spp. and resistance to oxidative stress. Folia Microbiol (Praha) 2005; 50:113–118. PubMed http://dx.doi.org/10.1007/BF02931458View ArticleGoogle Scholar
- Oppermann UC, Belai I, Maser E. Antibiotic resistance and enhanced insecticide catabolism as consequences of steroid induction in the gramnegative bacterium Comamonas testosteroni. J Steroid Biochem Mol Biol 1996; 58:217–223. PubMed http://dx.doi.org/10.1016/0960-0760(96)00021-0PubMedView ArticleGoogle Scholar
- Markowitz VM, Chen IMA. Palaniappan, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P and others. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2012; 40:D115–D122. PubMed http://dx.doi.org/10.1093/nar/gkr1044PubMed CentralPubMedView ArticleGoogle Scholar
- Thurnheer T, Kohler T, Cook AM, Leisinger T. Orthanilic acid and analogs as carbon-sources for bacteria — Growth physiology and enzymatic desulfonation. J Gen Microbiol 1986; 132:1215–1220.Google Scholar
- Field D, Garrity GM, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralPubMedView ArticleGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576PubMed CentralPubMedView ArticleGoogle Scholar
- Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.View ArticleGoogle Scholar
- Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1–6. PubMed http://dx.doi.org/10.1099/ijs.0.64188-0
- Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.View ArticleGoogle Scholar
- Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.View ArticleGoogle Scholar
- Willems A, De Ley J, Gillis M, Kersters K. Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Bacteriol 1991; 41:445–450. http://dx.doi.org/10.1099/00207713-41-3-445View ArticleGoogle Scholar
- De Vos P, Kersters K, Gillis M, Segers P, de Ley J. Comamonas Davis and Park 1962 gen. nov., nom. rev. emend., and Comamonas terrigena Hugh 1962 sp. nov., nom. rev. Int J Syst Bacteriol 1985; 35:443–453. http://dx.doi.org/10.1099/00207713-35-4-443View ArticleGoogle Scholar
- Zhang J, Wang Y, Zhou S, Wu C, He J, Li F. Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus Comamonas. Int J Syst Evol Microbiol 2013; 63:809–814. PubMed http://dx.doi.org/10.1099/ijs.0.040188-0PubMedView ArticleGoogle Scholar
- Willems A, Pot B, Falsen E, Vandamme P, Gillis M, Kersters K, de Ley J. Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquaspirillum aquaticum, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol 1991; 41:427–444. http://dx.doi.org/10.1099/00207713-41-3-427View ArticleGoogle Scholar
- Davis GHG, Park RWA. A taxonomic study of certain bacteria currently classified as Vibrio species. J Gen Microbiol 1962; 27:101–119. PubMed http://dx.doi.org/10.1099/00221287-27-1-101PubMedView ArticleGoogle Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556PubMed CentralPubMedView ArticleGoogle Scholar
- Buhmann M. Charakterisierung der Biofilmbildung durch eine Tensid-abbauende Bakteriengemeinschaft [Master’s thesis]. Konstanz: University of Konstanz; 2008. 126 p.Google Scholar
- Li M, Peng L, Ji Z, Xu J, Li S. Establishment and characterization of dual-species biofilms formed from a 3,5-dinitrobenzoic-degrading strain and bacteria with high biofilm-forming capabilities. FEMS Microbiol Lett 2008; 278:15–21. PubMed http://dx.doi.org/10.1111/j.1574-6968.2007.00913.xPubMedView ArticleGoogle Scholar
- Schleheck D, Barraud N, Klebensberger J, Webb JS, McDougald D, Rice SA, Kjelleberg S. Pseudomonas aeruginosa PAO1 preferentially grows as aggregates in liquid batch cultures and disperses upon starvation. PLoS ONE 2009; 4:e5513. PubMed http://dx.doi.org/10.1371/journal.pone.0005513PubMed CentralPubMedView ArticleGoogle Scholar
- Stelzer S, Egan S, Larsen MR, Bartlett DH, Kjelleberg S. Unravelling the role of the ToxR-like transcriptional regulator WmpR in the marine antifouling bacterium Pseudoalteromonas tunicata. Microbiology 2006; 152:1385–1394. PubMed http://dx.doi.org/10.1099/mic.0.28740-0PubMedView ArticleGoogle Scholar
- Thomas T, Evans FF, Schleheck D, Mai-Prochnow A, Burke C, Penesyan A, Dalisay DS, Stelzer-Braid S, Saunders N, Johnson J, et al. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS ONE 2008; 3:e3252. PubMed http://dx.doi.org/10.1371/journal.pone.0003252PubMed CentralPubMedView ArticleGoogle Scholar
- Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37:D141–D145. PubMed http://dx.doi.org/10.1093/nar/gkn879PubMed CentralPubMedView ArticleGoogle Scholar
- Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596–1599. PubMed http://dx.doi.org/10.1093/molbev/msm092PubMedView ArticleGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralPubMedView ArticleGoogle Scholar
- DOE Joint Genome Institute. http://www.jgi.doe.gov
- Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186–194. PubMedPubMedView ArticleGoogle Scholar
- Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175–185. PubMedPubMedView ArticleGoogle Scholar
- Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195–202. PubMedPubMedView ArticleGoogle Scholar
- Han CS, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Arabnia HR, Valafar H, editors. Proceeding of the 2006 international conference on bioinformatics & computational biology: CSREA Press; 2006. p 141–146.Google Scholar
- Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119PubMed CentralPubMedView ArticleGoogle Scholar
- Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods 2010; 7:6. PubMed http://dx.doi.org/10.1038/nmeth.1457View ArticleGoogle Scholar
- Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMedPubMed CentralPubMedView ArticleGoogle Scholar
- Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100–3108. PubMed http://dx.doi.org/10.1093/nar/gkm160PubMed CentralPubMedView ArticleGoogle Scholar
- Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439–441. PubMed http://dx.doi.org/10.1093/nar/gkg006PubMed CentralPubMedView ArticleGoogle Scholar
- Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315PubMedView ArticleGoogle Scholar
- Dyrløv Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783–795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028View ArticleGoogle Scholar
- Integrated Microbial Genomes (IMG) platform. http://img.jgi.doe.gov
- Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IMA, Dubchak I, Anderson I, Lykidis A, Mavromatis K, et al. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 2008; 36:D528–D533. PubMed http://dx.doi.org/10.1093/nar/gkm846PubMed CentralPubMedView ArticleGoogle Scholar
- Möbus E, Maser E. Molecular cloning, overexpression, and characterization of steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni. A novel member of the short-chain dehydrogenase/reductase superfamily. J Biol Chem 1998; 273:30888–30896. PubMed http://dx.doi.org/10.1074/jbc.273.47.30888PubMedView ArticleGoogle Scholar
- Xiong G, Maser E. Regulation of the steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase gene in Comamonas testosteroni. J Biol Chem 2001; 276:9961–9970. PubMed http://dx.doi.org/10.1074/jbc.M010962200PubMedView ArticleGoogle Scholar
- Pruneda-Paz JL, Linares M, Cabrera JE, Genti-Raimondi S. TeiR, a LuxR-type transcription factor required for testosterone degradation in Comamonas testosteroni. J Bacteriol 2004; 186:1430–1437. PubMed http://dx.doi.org/10.1128/IB.186.5.1430-1437.2004PubMed CentralPubMedView ArticleGoogle Scholar
- Birkenmaier A, Holert J, Erdbrink H, Moeller HM, Friemel A, Schoenenberger R, Suter MJ, Klebensberger J, Philipp B. Biochemical and genetic investigation of initial reactions in aerobic degradation of the bile acid cholate in Pseudomonas sp. strain Chol1. J Bacteriol 2007; 189:7165–7173. PubMed http://dx.doi.org/10.1128/JB.00665-07PubMed CentralPubMedView ArticleGoogle Scholar
- Birkenmaier A, Möller HM, Philipp B. Identification of a thiolase gene essential for beta-oxidation of the acyl side chain of the steroid compound cholate in Pseudomonas sp. strain Chol1. FEMS Microbiol Lett 2011; 318:123–130. PubMed http://dx.doi.org/10.1111/j.1574-6968.2011.02250.xPubMedView ArticleGoogle Scholar
- Horinouchi M, Hayashi T, Koshino H, Malon M, Yamamoto T, Kudo T. Identification of genes involved in inversion of stereochemistry of a C-12 hydroxyl group in the catabolism of cholic acid by Comamonas testosteroni TA441. J Bacteriol 2008; 190:5545–5554. PubMed http://dx.doi.org/10.1128/JB.01080-07PubMed CentralPubMedView ArticleGoogle Scholar
- Pérez-Pantoja D, Donoso R, Agullo L, Cordova M, Seeger M, Pieper DH, Gonzalez B. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. Environ Microbiol 2012; 14:1091–1117. PubMed http://dx.doi.org/10.1111/j.1462-2920.2011.02613.xPubMedView ArticleGoogle Scholar
- Chang HK, Zylstra GJ. Examination and expansion of the substrate range of m-hydroxybenzoate hydroxylase. Biochem Biophys Res Commun 2008; 371:149–153. PubMed http://dx.doi.org/10.1016/j.bbrc.2008.04.032PubMedView ArticleGoogle Scholar
- Arai H, Ohishi T, Chang MY, Kudo T. Arrangement and regulation of the genes for meta-pathway enzymes required for degradation of phenol in Comamonas testosteroni TA441. Microbiology 2000; 146:1707–1715. PubMedPubMedView ArticleGoogle Scholar
- Arai H, Akahira S, Ohishi T, Maeda M, Kudo T. Adaptation of Comamonas testosteroni TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. Microbiology 1998; 144:2895–2903. PubMed http://dx.doi.org/10.1099/00221287-144-10-2895PubMedView ArticleGoogle Scholar
- Arai H, Yamamoto T, Ohishi T, Shimizu T, Nakata T, Kudo T. Genetic organization and characteristics of the 3-(3-hydroxyphenyl)propionic acid degradation pathway of Comamonas testosteroni TA441. Microbiology 1999; 145:2813–2820. PubMedPubMedView ArticleGoogle Scholar
- Wang YZ, Zhou Y, Zylstra GJ. Molecular analysis of isophthalate and terephthalate degradation by Comamonas testosteroni YZW-D. Environ Health Perspect 1995; 103:9–12. PubMedPubMed CentralPubMedView ArticleGoogle Scholar
- Chae JC, Zylstra GJ. 4-Chlorobenzoate uptake in Comamonas sp. strain DJ-12 is mediated by a tripartite ATP-independent periplasmic transporter. J Bacteriol 2006; 188:8407–8412. PubMed http://dx.doi.org/10.1128/JB.00880-06PubMed CentralPubMedView ArticleGoogle Scholar
- Lévy-Schil S, Soubrier F, Crutz-Le Coq AM, Faucher D, Crouzet J, Petre D. Aliphatic nitrilase from a soil-isolated Comamonas testosteroni sp.: gene cloning and overexpression, purification and primary structure. Gene 1995; 161:15–20. PubMed http://dx.doi.org/10.1016/0378-1119(95)00242-XPubMedView ArticleGoogle Scholar
- Yang Y, Chen T, Ma P, Shang G, Dai Y, Yuan S. Cloning, expression and functional analysis of nicotinate dehydrogenase gene cluster from Comamonas testosteroni JA1 that can hydroxylate 3-cyanopyridine. Biodegradation 2010; 21:593–602. PubMed http://dx.doi.org/10.1007/s10532-010-9327-2PubMedView ArticleGoogle Scholar
- Yee LN, Chuah JA, Chong ML, Phang LY, Raha AR, Sudesh K, Hassan MA. Molecular characterisation of phaCAB from Comamonas sp. EB172 for functional expression in Escherichia coli JM109. Microbiol Res 2012; 167:550–557. PubMed http://dx.doi.org/10.1016/j.micres.2011.12.006PubMedView ArticleGoogle Scholar
- Jendrossek D, Backhaus M, Andermann M. Characterization of the extracellular poly(3-hydroxybutyrate) depolymerase of Comamonas sp. and of its structural gene. Can J Microbiol 1995; 41(Suppl 1):160–169. PubMed http://dx.doi.org/10.1139/m95-183PubMedView ArticleGoogle Scholar