Plasmid-encoded degradation of p-nitrophenol and 4-nitrocatechol by Arthrobacter protophormiae

Novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A6

Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

Characterization of methylhydroquinone-metabolizing oxygenase genes encoded on plasmid in Burkholderia sp. NF100

Methylhydroquinone is an intermediate in the degradation of fenitrothion by Burkholderia sp. NF100. The catabolic gene (mhq) for methylhydroquinone degradation encoded on the plasmid pNF1 in the strain was cloned and sequenced. The mhq clone contained two ORFs, mhqA and mhqB, of which the deduced amino acid sequence shared significant homology with NAD(P)H-dependent flavoprotein monooxygenases and extradiol dioxygenases, respectively. Parts of the consensus sequences of the monooxygenase gene and dioxygenase gene have been identified in MhqA and MhqB from strain NF100, respectively. MhqA was overexpressed in Escherichia coli, and partially purified MhqA catalyzed the NADPH-dependent hydroxylation of methylhydroquinone. MhqB was also overexpressed in E. coli, and the purified enzyme showed an extradiol ring cleavage activity toward 3-methylcatechol but a very low activity was observed toward 4-methylcatechol.

Monitoring Arthrobacter protophormiae RKJ100 in a 'tag and chase' method during p-nitrophenol bio-remediation in soil microcosms

Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation.

Crystal Structure of the Hydroxyquinol 1,2-Dioxygenase from Nocardioides simplex 3E, a Key Enzyme Involved in Polychlorinated Aromatics Biodegradation

Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a central intermediate in the degradation of aromatic compounds including a variety of particularly recalcitrant polychloro- and nitroaromatic pollutants. We report here the primary sequence determination and the analysis of the crystal structure of the 1,2-HQD from Nocardioides simplex 3E solved at 1.75 A resolution using the multiple wavelength anomalous dispersion of the two catalytic irons (1 Fe/293 amino acids). The catalytic Fe(III) coordination polyhedron composed by the side chains of Tyr164, Tyr197, His221, and His223 resembles that of the other known intradiol-cleaving dioxygenases, but several of the tertiary structure features are notably different. One of the most distinctive characteristics of the present structure is the extensive openings and consequent exposure to solvent of the upper part of the catalytic cavity arranged to favor the binding of hydroxyquinols but not catechols. A co-crystallized benzoate-like molecule is also found bound to the metal center forming a distinctive hydrogen bond network as observed previously also in 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP. This is the first structure of an intradiol dioxygenase specialized in hydroxyquinol ring cleavage to be investigated in detail.

Pot and field studies on bioremediation of p-nitrophenol contaminated soil using Arthrobacter protophormiae RKJ100

Biodegradation of p-nitrophenol (PNP), a priority pollutant, was studied as a model system for bioremediation of sites contaminated with nitroaromatic/organic compounds. Bioremediation of PNP-containing soil was first carried out in pots using immobilized and free cells of Arthrobacter protophormiae RKJ100 in order to ascertain the role of a suitable carrier material. Results showed that stability of the introduced strain was enhanced upon immobilization and that the rate of PNP depletion decreased with increasing depth of soil. Small-scale field studies (in one square meter plots) were then conducted in which PNP-contaminated soil from an agricultural field was bioaugmented with strain RKJ100 under natural environmental conditions. PNP was totally depleted in 5 days by immobilized cells, whereas free cells were able to deplete 75% of PNP in the same time period. The fate of the released strain as monitored by plate counts, hybridization studies, and real-time polymerase chain reaction revealed fairly stable population of the cells upon immobilization on corncob powder throughout the period of study.

Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate

Arthrobacter nitroguajacolicus Rü61a, which utilizes quinaldine as sole source of carbon and energy, was shown to contain a conjugative linear plasmid of approximately 110 kb, named pAL1. It exhibits similarities with other linear plasmids from Actinomycetales in that it has proteins covalently attached to its 5' ends. Southern hybridization with probes for the genes encoding quinaldine 4-oxidase and N-acetylanthranilate amidase indicated that pAL1 contains the gene cluster encoding the degradation of quinaldine to anthranilate. A mutant of strain Rü61a that had lost pAL1 indeed could not convert quinaldine, but was still able to grow on anthranilate. Conjugative transfer of pAL1 to the plasmid-less mutant of strain Rü61a and to Arthrobacter nicotinovorans DSM 420 (pAO1) occurred at frequencies of 5.4x10(-4) and 2.0x10(-4) per recipient, respectively, and conferred the ability to utilize quinaldine. Five other quinaldine-degrading Gram-positive strains were isolated from soil samples; 16S rDNA sequence analysis suggested the closest relationship to different Arthrobacter species. Except for strain K2-29, all isolates contained a pAL1-like linear plasmid carrying genes encoding quinaldine conversion. A 478 bp fragment that on pAL1 represents an intergenic region showed 100 % sequence identity in all isolates harbouring a pAL1-like plasmid, suggesting horizontal dissemination of the linear plasmid among the genus Arthrobacter.

A microcosm study on bioremediation of p-nitrophenol-contaminated soil using Arthrobacter protophormiae RKJ100

p-Nitrophenol (PNP), a toxic nitroaromatic compound, can build up in soils due to extensive usage of nitrophenolic pesticides and hence needs to be removed. Arthrobacter protophormiae RKJ100, a PNP-degrading organism, was used in this work to study factors affecting its growth, and then evaluated for its capacity to degrade PNP in soil microcosms. Molasses (10%) treated with 0.1% potassium hexacyanoferrate was found to be a suitable and cheap carbon source for inoculum preparation. Induction studies showed that PNP depletion was quicker when cells were induced by pre-exposure to PNP. The efficiency of PNP degradation in soil by strain RKJ100 was seen to be dependent on pH, temperature, initial PNP concentration and inoculum size. Microcosm studies performed with varying concentrations (1.4-210 ppm) of PNP-spiked soils showed that strain RKJ100 could effectively degrade PNP over the range 1.4-140 ppm. A cell density of 2x10(8) colony forming units/g soil was found to be suitable for PNP degradation over a temperature range of 20-40 degrees C and at a slightly alkaline pH (7.5). Our results indicate that strain RKJ100 has potential for use in in situ bioremediation of PNP-contaminated sites. This is a model study that could be used for decontamination of sites contaminated also with other compounds.

Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli

Arthrobacter aurescens strain TC1 metabolizes atrazine to cyanuric acid via TrzN, AtzB, and AtzC. The complete sequence of a 160-kb bacterial artificial chromosome clone indicated that trzN, atzB, and atzC are linked on the A. aurescens genome. TrzN, AtzB, and AtzC were shown to be functional in Escherichia coli. Hybridization studies localized trzN, atzB, and atzC to a 380-kb plasmid in A. aurescens strain TC1.

A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101

p-Nitrophenol (4-NP) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated; however, the genetic information remains very limited. In this study, a novel 4-NP degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101, was identified and characterized. The deduced amino acid sequences of npcB, npcA, and npcC showed identity with phenol 2-hydroxylase component B (reductase, PheA2) of Geobacillus thermoglucosidasius A7 (32%), with 2,4,6-trichlorophenol monooxygenase (TcpA) of Ralstonia eutropha JMP134 (44%), and with hydroxyquinol 1,2-dioxygenase (ORF2) of Arthrobacter sp. strain BA-5-17 (76%), respectively. The npcB, npcA, and npcC genes were cloned into pET-17b to construct the respective expression vectors pETnpcB, pETnpcA, and pETnpcC. Conversion of 4-NP was observed when a mixture of crude cell extracts of Escherichia coli containing pETnpcB and pETnpcA was used in the experiment. The mixture converted 4-NP to hydroxyquinol and also converted 4-nitrocatechol (4-NCA) to hydroxyquinol. Furthermore, the crude cell extract of E. coli containing pETnpcC converted hydroxyquinol to maleylacetate. These results suggested that npcB and npcA encode the two-component 4-NP/4-NCA monooxygenase and that npcC encodes hydroxyquinol 1,2-dioxygenase. The npcA and npcC mutant strains, SDA1 and SDC1, completely lost the ability to grow on 4-NP as the sole carbon source. These results clearly indicated that the cloned npc genes play an essential role in 4-NP mineralization in R. opacus SAO101.

Chemotaxis and biodegradation of 3-methyl- 4-nitrophenol by Ralstonia sp. SJ98

3-Methyl-4-nitrophenol is one of the major breakdown products of fenitrothion [O,O-dimethyl O-(3-methyl-4-nitrophenyl) thiophosphate], a recalcitrant organophosphate insecticide used in agriculture. Being the non-polar methylated aromatic compound, 3-methyl-4-nitrophenol is highly toxic and, therefore, a complete degradation of this compound is important for environmental decontamination/bioremediation purposes. A gram negative, motile Ralstonia sp. SJ98 was isolated by selective screening from a soil sample contaminated with pesticides. The microorganism was capable of utilizing 3-methyl-4-nitrophenol as the sole source of carbon and energy. Thin layer chromatography (TLC), gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), and high performance liquid chromatography (HPLC) were performed to determine the possible intermediates in the degradative pathway of this compound. Taken together, catechol was found to be one of the major intermediate of the pathway. Furthermore, the chemotactic behavior of Ralstonia sp. SJ98 towards 3-methyl-4-nitrophenol was tested using three different methods i.e., drop assay, swarm plate assay and capillary assay, which were found to be positive towards this compound. This is the first report clearly indicating the involvement of a microorganism in the chemotaxis and biodegradation of methyl-4-nitrophenol and formation of catechol as an intermediate in the degradative pathway.

Kinetics of biodegradation of p-nitrophenol by different bacteria

Three bacterial species, i.e., Ralstonia sp. SJ98, Arthrobacter protophormiae RKJ100, and Burkholderia cepacia RKJ200, have been examined for their efficiency and kinetics behavior toward PNP degradation. All the three bacteria utilized PNP as the sole source of carbon, nitrogen, and energy. The rates of radiolabeled [U-(14)C]PNP degradation by all the bacteria were higher in the nitrogen-free medium compared to the medium with nitrogen. The apparent K(m) values of PNP degradation by SJ98, RKJ100, and RKJ200 were 0.32, 0.28, and 0.23 mM, respectively, as determined from the Michaelis-Menten curves. The maximum rates of PNP degradation (V(max)) according to Lineweaver-Burk's plots were 11.76, 7.81, and 3.84 micromol PNP degraded/min/mg dry biomass, respectively. The interpretation drawn from the Lineweaver-Burk's plots showed that the PNP degradation by SJ98 was stimulated by 4-nitrocatechol and 1, 2,4-benzenetriol. Benzoquinone and hydroquinone inhibited PNP degradation by RKJ100 noncompetitively and competitively, respectively, whereas in the case of RKJ200, benzoquinone and hydroquinone inhibited PNP degradation in an uncompetitive manner. beta-Ketoadipate did not affect the rate of PNP degradation in any case.