Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3)

Kallimanis, A.; LaButti, Kurt; Lapidus, Alla; Clum, Alicia; Lykidis, Athanasios; Mavromatis, Konstantinos; Pagani, Ioanna; Liolios, Konstantinos; Ivanova, Natalia; Goodwin, Lynne; Pitluck, Sam; Chen, Amy; Palaniappan, Krishna; Markowitz, Victor; Bristow, James; Velentzas, Athanassios D.; Perisynakis, Angelos; Ouzounis, Christos A.; Kyrpides, Nikos C.; Koukkou, Anna‐Irini; Drainas, Constantin

doi:10.4056/sigs.1393494

Cited by 32 publications

(21 citation statements)

References 19 publications

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“…In addition, Sphe3 cells could grow on 1-H2NA, 2-carboxybenzaldehyde, protocatechuic acid, and phthalic acid as sole C sources, whereas no growth was observed on salicylic acid. Phenanthrene catabolism by strain Sphe3 via the phthalate pathway is also confirmed, since putative operons containing genes that encode enzymes involved in the degradation of phthalic acid and protocatechuic acid have been found in its total genome (21). It is likely that the enzymes involved in phenanthrene degradation are expressed only in the presence of phenanthrene, as no activity was detected in glucosegrown cells.…”

Section: Discussionmentioning

confidence: 67%

“…The amino acid sequences deduced from the 45-kDa band were further used in a BLAST search analysis of the strain Sphe3 genome (21). This analysis led to the identification of two putative ORFs in the Sphe3 genome coding for 1-H2NA dioxygenase, thereafter named diox1, located on an indigenous plasmid, pASPHE301, and diox2, located on the chromosome (Fig.…”

Section: Phenanthrene Metabolismmentioning

confidence: 99%

“…The complete genome sequence of A. phenanthrenivorans Sphe3 was analyzed by the Department of Energy (DOE)-Joint Genome Institute (JGI) and published recently (Genomes OnLine Database accession number Gi01675) (21,30). The identification of the Sphe3 1-H2NA dioxygenase genes was based on BLAST searches within the IMG-ER platform (31), using the sequences of the oligopeptide fragments deduced from the mass spectrometry analysis described above.…”

Section: Maldi-tof Ms] and Tandem Ms [Ms-ms])mentioning

confidence: 99%

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Heterologous Expression and Characterization of Two 1-Hydroxy-2-Naphthoic Acid Dioxygenases from Arthrobacter phenanthrenivorans

Vandera

Kavakiotis

Kallimanis

et al. 2012

Appl Environ Microbiol

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A protein fraction exhibiting 1-hydroxy-2-naphthoic acid (1-H2NA) dioxygenase activity was purified via ion exchange, hydrophobic interactions, and gel filtration chromatography from Arthrobacter phenanthrenivorans sp. nov. strain Sphe3 isolated from a Greek creosote-oil-polluted site. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and tandem MS (MS-MS) analysis revealed that the amino acid sequences of oligopeptides of the major 45-kDa protein species, as analyzed by SDS-PAGE and silver staining, comprising 29% of the whole sequence, exhibited strong homology with 1-H2NA dioxygenase of Nocardioides sp. strain KP7. A BLAST search of the recently sequenced Sphe3 genome revealed two putative open reading frames, named diox1 and diox2, showing 90% nucleotide identity to each other and 85% identity at the amino acid level with the Nocardia sp. homologue. diox1 was found on an indigenous Sphe3 plasmid, whereas diox2 was located on the chromosome. Both genes were induced by the presence of phenanthrene used as a sole carbon and energy source, and as expected, both were subject to carbon catabolite repression. The relative RNA transcription level of the chromosomal (diox2) gene was significantly higher than that of its plasmid (diox1) homologue. Both diox1 and diox2 putative genes were PCR amplified, cloned, and overexpressed in Escherichia coli. Recombinant E. coli cells expressed 1-H2NA dioxygenase activity. Recombinant enzymes exhibited Michaelis-Menten kinetics with an apparent K m of 35 M for Diox1 and 29 M for Diox2, whereas they showed similar kinetic turnover characteristics with K cat /K m values of 11 ؋ 10 6 M ؊1 s ؊1 and 12 ؋ 10 6 M ؊1 s ؊1 , respectively. Occurrence of two diox1 and diox2 homologues in the Sphe3 genome implies that a replicative transposition event has contributed to the evolution of 1-H2NA dioxygenase in A. phenanthrenivorans.

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Section: Discussionmentioning

confidence: 67%

Section: Phenanthrene Metabolismmentioning

confidence: 99%

Section: Maldi-tof Ms] and Tandem Ms [Ms-ms])mentioning

confidence: 99%

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Heterologous Expression and Characterization of Two 1-Hydroxy-2-Naphthoic Acid Dioxygenases from Arthrobacter phenanthrenivorans

Vandera

Kavakiotis

Kallimanis

et al. 2012

Appl Environ Microbiol

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“…chlorophenolicus A6 (NC_011886), A. phenanthrenivorans Sphe3 (CP002379 [10], Kocuria rhizophila DC2201, Microccus luteus Fleming NCTC 2665, Renibacterium salmoninarum ATCC 33209, Rothia dentocariosa ATCC 17931, and Rothia mucilaginous DY-18. The sequences were aligned in ClustalX and a consensus tree was generated using a 1,000× repeated bootstrapping process [11,12].…”

Section: Classification and Featuresmentioning

confidence: 99%

Complete genome sequence of Arthrobacter sp. strain FB24

Nakatsu¹,

Barabote²,

Thompson³

et al. 2013

Stand. Genomic Sci.

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Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

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“…The draft genome of AK-YN10 indicates the presence of genetic potential towards environmental stress tolerance capacity by the presence of a number of stress response genes (data not shown). Furthermore, it is resistant to many heavy metals (cobalt, copper, zinc, arsenic, and mercury) and antibiotics (Gentamycin (10 μg/disc), rifampicin (15 μg/disc), penicillin G (10 μnits/disc), ampicillin (25 μg/disc), polymyxin (50 μg/ disc) like Arthrobacter phenanthrenivorans type strain (Sphe3) (Kallimanis et al 2011) and Arthrobacter sp. Rue61a (Niewerth et al 2013).…”

Section: Discussionmentioning

confidence: 99%

s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil

Sagarkar

Bhardwaj

Storck

et al. 2015

Appl Microbiol Biotechnol

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The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides.

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Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3)

Cited by 32 publications

References 19 publications

Heterologous Expression and Characterization of Two 1-Hydroxy-2-Naphthoic Acid Dioxygenases from Arthrobacter phenanthrenivorans

Heterologous Expression and Characterization of Two 1-Hydroxy-2-Naphthoic Acid Dioxygenases from Arthrobacter phenanthrenivorans

Complete genome sequence of Arthrobacter sp. strain FB24

s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil

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