The Complete Genome of
            <i>Comamonas testosteroni</i>
            Reveals Its Genetic Adaptations to Changing Environments

Ma, Yingfei; Zhang, Yun; Zhang, Jia-Yue; Chen, Dongwei; Zhu, Yanbing; Zheng, Huajun; Wang, Shengyue; Jiang, Cheng‐Ying; Zhao, Guoping; Liu, Shuang‐Jiang

doi:10.1128/aem.00933-09

Cited by 91 publications

(83 citation statements)

References 56 publications

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“…The deduced amino acid sequence of the product of the DNA region correspond to repB showed high homology (around 96% identity) to C. testosteroni ATCC11996 RepB, but we were unable to find a stop codon, which resulted in a larger ORF (ORF64) containing the gene region correspond to repB. The entire deduced amino acid sequence of ORF64 showed the highest homology (92% identity) to the putative enzyme-regulator fusion protein of C. testosteroni CNB-2 [49], as well as several other putative enzyme-regulator fusion proteins belong to the GreA/GreB family of elongation factors. Other than C. testosteroni, Bordetella parapertussis showed the highest amino acid identity (73%) [50].…”

Section: Isolation Of a Putative 3ˇ17ˇ-dehydrogenase A 3˛-dehydrogementioning

confidence: 85%

“…The entire genome sequence of C. testosteroni CNB-2 was recently reported [49], and it has approximately 95% identity with the sequenced DNA region of C. testosteroni TA441. We compared the genes/ORFs of C. testosteroni TA441 that are involved in steroid degradation, the two main steroid degradation gene clusters (the region from steA to tesR and from tesG to ORF18) and the two DNA fragments isolated in this study, with the corresponding DNA region of C. testosteroni CNB-2.…”

Section: Discussionmentioning

confidence: 98%

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Steroid degradation genes in Comamonas testosteroni TA441: Isolation of genes encoding a Δ4(5)-isomerase and 3α- and 3β-dehydrogenases and evidence for a 100kb steroid degradation gene hot spot

Horinouchi

Kurita

Hayashi

et al. 2010

The Journal of Steroid Biochemistry and Molecular Biology

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Section: Isolation Of a Putative 3ˇ17ˇ-dehydrogenase A 3˛-dehydrogementioning

confidence: 85%

Section: Discussionmentioning

confidence: 98%

Steroid degradation genes in Comamonas testosteroni TA441: Isolation of genes encoding a Δ4(5)-isomerase and 3α- and 3β-dehydrogenases and evidence for a 100kb steroid degradation gene hot spot

Horinouchi

Kurita

Hayashi

et al. 2010

The Journal of Steroid Biochemistry and Molecular Biology

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“…In the Comamonas-type PCA45 pathway gene clusters reported to date, an ORF related to the transcriptional regulator has been found only upstream of the pmd gene cluster of a Gram-positive bacterium, A. keyseri 12B (pcmR). A database search of the genome sequences of C. testosteroni KF-1, C. testosteroni CNB-2 (20), and C. testosteroni S44 revealed the presence of LysR-type regulators that showed approximately 30% identity with pcmR, but they are not in the proximity of the PCA45 pathway genes. The isolation of the regulator gene(s) for the pmd operon will be essential in the future for clarification of the mechanism for the transcriptional regulation of the PCA45 pathway genes in E6.…”

Section: Resultsmentioning

confidence: 99%

Characterization of the Protocatechuate 4,5-Cleavage Pathway Operon in Comamonas sp. Strain E6 and Discovery of a Novel Pathway Gene

Kamimura

Aoyama

Yoshida

et al. 2010

Appl Environ Microbiol

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The protocatechuate (PCA) 4,5-cleavage (PCA45) pathway is the essential catabolic route for the degradation of various aromatic acids in the genus Comamonas. All of the PCA45 pathway genes, orf1-pmdKEFDABC, as well as another PCA 4,5-dioxygenase gene, pmdA II B II , were isolated from a phthalate-degrading bacterium, Comamonas sp. strain E6. Disruption of pmdB and pmdD in E6, which code for the ␤ subunit of PCA 4,5-dioxygenase and 2-pyrone-4,6-dicarboxylate (PDC) hydrolase, respectively, resulted in a growth defect on PCA, indicating that these genes are essential for the growth of E6 on PCA. On the other hand, inactivation of pmdB II did not affect the growth of E6 on PCA. Disruption of pmdK, which is related to a 4-hydroxybenzoate/ PCA transporter of Pseudomonas putida, resulted in growth retardation on PCA. The insertional inactivation of orf1 in E6, whose deduced amino acid sequence has no similarity with proteins of known function, led to the complete loss of growth on PCA and the accumulation of PDC and 4-oxalomesaconate (OMA) from PCA. These results indicated the involvement of orf1 in the PCA45 pathway, and this gene, designated pmdU, was suggested to code for OMA tautomerase. Reverse transcription-PCR analysis suggested that the pmdUKEFDABC genes constitute an operon. The transcription start site of the pmd operon was mapped at 167 nucleotides upstream of the initiation codon of pmdU. The pmd promoter activity was enhanced 20-fold when the cells were grown in the presence of PCA. Inducers of the pmd operon were found to be PCA and PDC, but PDC was the more effective inducer.Protocatechuate (PCA) is a key intermediate metabolite in the bacterial degradation pathways of various aromatic compounds, including phthalate isomers, vanillate, and hydroxybenzoates. It is known that PCA is degraded via three distinct catabolic pathways, including the PCA 2,3-cleavage (8, 18), PCA 3,4-cleavage (14), and PCA 4,5-cleavage (PCA45) (19,26,27) pathways. Our research group has discovered that 2-pyrone-4,6-dicarboxylic acid (PDC), an intermediate of the PCA45 pathway (Fig. 1A), is useful in the production of biodegradable and high-functional polymers, such as strong adhesives (15,16,30). The production of PDC via the PCA45 pathway from lignin-derived compounds and petrochemical aromatic compounds, including phthalates, would be worthwhile for reducing the environmental load. From this aspect, the catabolic functions of Comamonas sp. strain E6, which is able to utilize phthalate isomers as sole carbon and energy sources via the PCA45 pathway (11, 38), appears to be of importance.The PCA45 pathway was first enzymatically characterized by Kersten et al. (19) and . In this pathway (Fig. 1A), PCA is initially transformed to 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) by PCA 4,5-dioxygenase (4,5-PCD). CHMS is nonenzymatically converted to an intramolecular hemiacetal form and then oxidized by CHMS dehydrogenase. The resulting intermediate, PDC, is hydrolyzed by PDC hydrolase to yield the keto and enol tautomers of 4-oxa...

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“…The Blattabacterium genome sequenced, which is from a cockroach endosymbiotic strain, belongs to the class Flavobacteria in the phylum Bacteroidetes; the newly sequenced genome shows evolutionary convergence with gammaproteobacterium endosymbionts (Ló pezSánchez et al, 2009). Finally, Comamonas testosteroni strain CNB-2 was isolated from soil contaminated with 4-chloronitrobenzene and can grow on this pollutant using it as its sole carbon and nitrogen source (Ma et al, 2009). This betaproteobacterium is a member of the order Burkholderiales, and was given its name from its ability to metabolize testosterone.…”

Section: The 1000th Genome(s)mentioning

confidence: 99%

Genome update: the 1000th genome – a cautionary tale

2010

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There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families — more genes than are recognized in the human genome. Moreover, of the 1000 genomes available, not a single protein is conserved across all genomes. Excluding the members of the Archaea, only a total of four genes are conserved in all bacteria: two protein genes and two RNA genes.

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The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments

Cited by 91 publications

References 56 publications

Steroid degradation genes in Comamonas testosteroni TA441: Isolation of genes encoding a Δ4(5)-isomerase and 3α- and 3β-dehydrogenases and evidence for a 100kb steroid degradation gene hot spot

Steroid degradation genes in Comamonas testosteroni TA441: Isolation of genes encoding a Δ4(5)-isomerase and 3α- and 3β-dehydrogenases and evidence for a 100kb steroid degradation gene hot spot

Characterization of the Protocatechuate 4,5-Cleavage Pathway Operon in Comamonas sp. Strain E6 and Discovery of a Novel Pathway Gene

Genome update: the 1000th genome – a cautionary tale

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