Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m -xylene degradation by Sphingomonas yanoikuyae B1

Kim, E; Zylstra, Gerben J.

doi:10.1038/sj.jim.2900724

Cited by 92 publications

(66 citation statements)

References 43 publications

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“…A straightforward explanation would be the existence of more than one ARHDO in these strains. This has previously been observed in bacteria (Kim & Zylstra, 1999;Kitagawa et al, 2001).…”

Section: Experimental Evaluation Of the Systemmentioning

confidence: 59%

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Kahl

Höfer

2003

Microbiology

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Aromatic-ring-hydroxylating dioxygenases (ARHDOs) are key enzymes in the aerobic bacterial metabolism of aromatic compounds. They are of biotechnological importance as they function as biocatalysts in the stereospecific synthesis of chiral synthons and the degradation of aromatic pollutants. This report describes the development and validation of a system for the rapid isolation and characterization of specific ARHDO activities. The system is based on the identification of ARHDO gene segments that encode the enzymes' major functional determinants, on consensus primers for the direct amplification of such partial genes and on a 'recipient' ARHDO gene cluster for the insertion of the amplified segments. Previously, it has been shown that neither the N-nor the C-terminal portions but only the core region of the large or a-subunit of a class II ARHDO significantly influence substrate and product spectra. On the basis of these observations, consensus primers were designed for the amplification of the gene segment encoding the catalytic core of the large subunit. These primers were tested on 11 bacterial isolates known to metabolize aromatic compounds. In 10 cases, a gene fragment of expected length was amplified. DNA sequencing confirmed similarity to ARHDO a-subunit gene cores. The heterologously well-expressible bphA gene cluster of Burkholderia sp. strain LB400 was modified to facilitate the in-frame insertion of amplified segments. It was used successfully to express the resulting hybrid gene clusters and to form catalytically active chimaeric ARHDOs. The metabolic properties of these enzymes differed significantly from each other and from the parental ARHDO of strain LB400. These results indicate that the system described here can be used to rapidly isolate and functionally characterize ARHDO activities, starting from isolated strains, mixtures of organisms or samples of nucleic acids. Applications of the system range from the recruitment of novel ARHDO activities to an improved characterization of natural ARHDO diversity.

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“…A straightforward explanation would be the existence of more than one ARHDO in these strains. This has previously been observed in bacteria (Kim & Zylstra, 1999;Kitagawa et al, 2001).…”

Section: Experimental Evaluation Of the Systemmentioning

confidence: 59%

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Kahl

Höfer

2003

Microbiology

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“…With those characteristics examined in this study, it is now clear that strain ATCC 27551 is not a member of the genus Flavobacterium, and should be identifi ed as Sphingobium fuliginis. The members of the genus Sphingobium contain many species that degrade pesticides or environmental pollutants (Kim and Zylstra, 1999;Nohynek et al, 1995;Pal et al, 2005;Ushiba et al, 2003). This general character of the genus Sphingobium is also shared by strain ATCC 27551.…”

Section: Discussionmentioning

confidence: 95%

Reclassification of a parathione-degrading Flavobacterium sp. ATCC 27551 as Sphingobium fuliginis

Kawahara

Tanaka

Yoon

et al. 2010

J. Gen. Appl. Microbiol.

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IntroductionFlavobacterium sp. ATCC 27551 was isolated from paddy fi eld water of the Philippines as a degrader of organophosphorus pesticides such as diazinon and parathion (Sethunathan and Yoshida, 1973a). The pesticides were found to be degraded by organophosphorus hydrolase (Mulbry and Karns, 1989) which was encoded on a 43-kb plasmid (Mulbry et al., 1986). The organophosphorus hydrolase has a broad range of substrates and functions at broad pH and temperature (Mulbry et al., 1986), and therefore considered to be useful for the detoxifi cation of the pesticide-polluted environment. Moreover, it has been recently applied to the degradation of nerve agents such as sarin and soman (Dumas et al., 1990) for decontamination in the case of chemical terrorism.In spite of the intensive study of the degrading enzyme, classifi cation of the producer of the enzyme has not attracted attention, and strain ATCC 27551 has been kept as Flavobacterium sp. since the early studies of this bacterium in 1970s (Sethunathan and Yoshida, 1973b). However, bacterial taxonomy has developed in these several decades and the members of the genus Flavobacterium have been reclassifi ed to other taxa.Sphingomonas was fi rst proposed by Yabuuchi et al. (1990) with fi ve species, but later developed to large group of species, and the new family Sphin- J. Gen. Appl. Microbiol., 56, 249 255 (2010) A parathione-degrading bacterium isolated from rice fi eld in the Philippines, Flavobacterium sp. ATCC 27551 (Sethunathan and Yoshida, 1973, Can. J. Microbiol., 19, 873 875), was re-examined chemotaxonomically and phylogenetically. The strain contained 2-hydroxymyristic acid (2-OH 14 0), cis-vaccenic acid (18 1 ω7c), and palmitic acid (16 0) as major cellular fatty acids, two kinds of glycosphingolipids, and ubiquinone-10 as a sole quinone component. The G+C content of genomic DNA of the strain was 65.9 mol%. The phylogenetic analyses of the 16S rRNA gene indicated that the strain was included in the family Sphingomonadaceae, and most closely related to Sphingobium fuliginis (98.0% similarity) and Sphingobium herbicidovorans (97.3%). The strain showed similar physiological characteristics and a moderate value of DNA DNA relatedness to S. fuliginis. These data suggested it reasonable to conclude that strain ATCC 27551 was identifi ed as S. fuliginis.

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“…The tree was constructed by the NJ method with CarAa from P. resinovorans CA10 as an outgroup. [36], S. yanoikuyae B1 (BphA1c and XylX) [40,41] and Sphingobium sp. CHY-1 (PhnA1a and PhnA1b) [42] were reported to have the same gene arrangement with 63-97% sequence identity when compared to F199.…”

Section: Discussionmentioning

confidence: 99%

A New Classification System for Bacterial Rieske Non-Heme Iron Aromatic Ring-Hydroxylating Oxygenases

Kweon¹,

Kim²,

Baek³

et al. 2011

Recent Advances in Biochemistry

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Background: Rieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components.

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Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m -xylene degradation by Sphingomonas yanoikuyae B1

Cited by 92 publications

References 43 publications

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Reclassification of a parathione-degrading Flavobacterium sp. ATCC 27551 as Sphingobium fuliginis

A New Classification System for Bacterial Rieske Non-Heme Iron Aromatic Ring-Hydroxylating Oxygenases

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