Differential Degradation of Bicyclics with Aromatic and Alicyclic Rings by Rhodococcus sp. Strain DK17

Abstract

The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations.The ability of bacteria to use aromatic hydrocarbons for growth was first demonstrated over a century ago by isolating Bacillus hexacarborum on the basis of its ability to grow with toluene and xylene (22). Up until now, much research has centered on elucidating the bacterial metabolism of monocyclic and polycyclic aromatic hydrocarbons at the biochemical and molecular level, and the details of these metabolic pathways have been well documented (3,5,6,15,24). In contrast, little in-depth work has been reported regarding the degradation of bicyclics containing both aromatic and alicyclic moieties. Two different catabolic pathways, through either initial alicyclic or aromatic ring oxidation, have been proposed in several different bacteria, although the alicyclic ring oxidation route seems more common (1,4,11,12,13,16,18,23).Recently, we reported that Rhodococcus sp. strain DK17 uses indan as a growth substrate via the o-xylene pathway (9). Specifically, indan degradation by DK17 is initiated by o-xylene dioxygenase, leading to the formation of 4,5-indandiol, which then undergoes ring cleavage by a meta-cleavage dioxygenase (methylcatechol 2,3-dioxygenase, encoded by akbC). The fact that DK17 is the first example of a bacterial strain that metabolizes indan by aromatic oxidation led us to examine its ability to metabolize indan-related compounds such as indene, tetralin, and 1,2-dihydronaphthalene. Our preliminary growth tests showed that DK17 is able to grow on tetralin, while 1,2-dihydronaphthalene and indene failed to serve as sole carbon and energy sources.Considering their structural similarities to tetralin and indan, respectively, the inability ...

Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17

“…Rhodococcus sp. strain DK17 was isolated from a crude oilcontaminated site in Yeochon, South Korea, for the ability to grow on o-xylene as the sole source of carbon and energy and was later found to also have the ability to grow on benzene, toluene, ethylbenzene, isopropylbenzene, n-propyl-to n-hexylbenzenes, phenol, indan, tetralin, and phthalates (3,5,6). Strain DK17 possesses three linear megaplasmids (380-kb pDK1, 330-kb pDK2, and 750-kb pDK3).…”

Anthranilate degradation by a cold‐adapted Pseudomonas sp.

“…The amino acid sequence of the large subunit (AntA) of PAMC 25931 AntDO was aligned with those of close relatives of AntA, using the GenBank database by BLAST search and other representative aromatic dioxygenase large subunits. Currently, aromatic dioxygenase large subunits are phylogenetically classified in five groups . As shown in Fig.…”

Functional Identification of OphR, an IclR Family Transcriptional Regulator Involved in the Regulation of the Phthalate Catabolic Operon in Rhodococcus sp. Strain DK17

“…strains DK176 and KC810 were derived from DK17 by curing pDK2 [11] and pDK3 [7], respectively. Initially, DK176 and KC810 were grown overnight in 50 ml mineral salts basal (MSB) medium containing 20 mM glucose.…”

“…As explained in the Introduction, the pDK2-encoded and pDK3-encoded phthalate operons are equally functional in DK17. Accordingly, two previously constructed mutant strains, the pDK2-cured DK176 [11] and the pDK3-cured KC810 [7], were grown on glucose and phthalate, respectively, and the total cellular protein patterns were compared. The soluble cell extracts were separated on onedimensional SDS-PAGE (data not shown).…”

“…strain DK17 is also able to utilize phthalate as a growth substrate via the Gram-positive pathway [6,7]. DK17 possesses three megaplasmids (380 kb pDK1, 330 kb pDK2, and 750 kb pDK3), and the phthalate operons in DK17 are duplicated and are present on both pDK2 and pDK3 [6,8].…”