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PubMed1996

Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase.

The 1.4-kb downstream region from a nitrilase gene (nitA) of an actinomycete Rhodococcus rhodochrous J1, which is industrially in use, was found to be required for the isovaleronitrile-dependent induction of nitrilase synthesis in experiments using a Rhodococcus-Escherichia coli shuttle vector pK4 in a Rhodococcus strain. Sequence analysis of the 1.4-kb region revealed the existence of an open reading frame (nitR) of 957 bp, which would encode a protein with a molecular mass of 35,100. Deletion of the central and 3'-terminal portion of nitR resulted in the complete loss of nitrilase activity, demonstrating that nitR codes for a transcriptional positive regulator in nitA expression. The deduced amino acid sequence of nitR showed similarity to a positive regulator family including XylS from Pseudomonas putida and AraC from E. coli. By Northern blot analysis, the 1.4-kb transcripts for nitA were detected in R. rhodochrous J1 cells cultured in the presence of isovaleronitrile, but not those cultured in the absence of isovaleronitrile. The transcriptional start site for nitA was mapped to a C residue located 26 bp upstream of its translational start site. Deletion analysis to define the nitA promoter region suggested the possible participation of an inverted repeat sequence, centered on base pair -52, in induction of nitA transcription.

Amino Acid Sequence↗

PubMed1996

A novel gene cluster including the Rhodococcus rhodochrous J1 nhlBA genes encoding a low molecular mass nitrile hydratase (L-NHase) induced by its reaction product.

The 3.5 kilobases (kb) of the 5'-upstream region from nhlBA encoding a cobalt-containing low molecular mass nitrile hydratase (L-NHase) from Rhodococcus rhodochrous J1 was found to be required for the amide-dependent expression of nhlBA in experiments using a Rhodococcus transformation system. Sequence analysis of the 3.5-kb fragment revealed the presence of two open reading frames (nhlD and nhlC) in this fragment. NhlD has similarity to regulators MerR, CadC, and ArsR. NhlC has similarity to the regulators AmiC, for the expression of an aliphatic amidase from Pseudomonas aeruginosa, and NhhC, for the expression of a high molecular mass nitrile hydratase from R. rhodochrous J1. Assays of NHase activity of transformants carrying nhlD deletion or nhlC deletion mutations suggest a negative regulatory role for nhlD and a positive regulatory role for nhlC in the process of the L-NHase formation. Assays of NHase and amidase activities and Western blot analyses of each Rhodococcus transformant carrying various deletion plasmids, have shown that nhlBA and amdA encoding an amidase, which is located 1.9 kb downstream of nhlBA, were regulated in the same manner. These findings present the genetic evidence for a novel gene cluster controlling the expression of L-NHase, which is induced by the reaction product (amide) in the "practical microorganism" R. rhodochrous J1.

Base Sequence↗

PubMed1992

Central venous catheter sepsis caused by unusual Gordona (Rhodococcus species: identification with a digoxigenin-labeled rDNA probe.

We describe central line sepsis caused by Gordona (Rhodococcus) species in two patients, which complicated receipt of long-term total parenteral nutrition at home. Species identification was attempted by conventional biochemical analysis and analysis of polymorphisms in the ribosomal RNA genes with use of a digoxigenin-labeled rDNA probe. Using these techniques, we identified our first patient's isolate as Gordona terrae. The isolate from our second patient was biochemically atypical and could not be reliably matched to any of the recognized Gordona (Rhodococcus) species. To our knowledge, these patients are the first to have been reported with systemic infection caused by Gordona (Rhodococcus) species. The first patient's infection resolved after 6 weeks of intravenous therapy with vancomycin with the catheter left in situ; however, infection in the second patient required catheter removal for cure. These cases show that immunocompetent patients receiving long-term parenteral nutrition may develop central line infections with these unusual species of microorganisms.

Actinomycetales Infections↗

PubMed2006

Rhodococcus ruber as a cause of keratitis.

PURPOSE: To report a case of suppurative keratitis caused by Rhodococcus ruber in a healthy 31-year-old male patient. METHODS: Ocular examination of the patient revealed a central corneal epithelial defect following trauma, with severe anterior chamber reaction hypopyon. Corneal scrapings were performed from the base of the ulcer and were subjected to routine microbiologic investigation including direct microscopic techniques (Gram stain and 10% KOH), and culture was done on blood agar and potato dextrose agar. Biochemical analysis and antibiotic sensitivity testing were done on the isolate, and additional confirmation was done by DNA sequencing. RESULTS: The isolate was identified as Rhodococcus ruber, an uncommon cause of suppurative keratitis. The isolate was found to be sensitive to augmentin, erythromycin, co-trimoxazole, tobramycin, amikacin, ciprofloxacin, ofloxacin, and sulfamethoxazole. CONCLUSION: We present a case of Rhodococcus ruber, which was successfully treated. Even if the clinical picture of ulcer is nonspecific, the need of a routine microbiologic examination and sequencing proves to be confirmatory in cases of suppurative keratitis, where the causative organisms are varied in nature.

Actinomycetales Infections↗

PubMed1994

Rhodococcus zopfii sp. nov., a toxicant-degrading bacterium.

A toluene-degrading bacterial strain isolated from bioreactors was identified as a member of the genus Rhodococcus on the basis of the following characteristics: meso-diaminopimelic acid, arabinose, galactose, and glucose are the diagnostic cellular sugars; the mycolic acids contain 33 to 36 carbon atoms; and the formation of a branching mycelium is followed by marked fragmentation of the mycelium into irregular rod-shaped to coccoid units. DNA-DNA hybridization analyses performed with type strains of Rhodococcus species showed that this strain is less than 70% related to other species that have similar phenotypic characteristics. On the basis of these findings, we propose that this strain should be described as a new species, Rhodococcus zopfii, in honor of Wilhelm Friedrich Zopf. The type strain is strain T1.

Base Composition↗

PubMed1999

Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276.

Rhodococcus corallinus (formerly Nocardia corallina) B-276, isolated with propene as sole carbon and energy source, is able to oxidize trichloroethene (TCE). Glucose- or propene-grown R. corallinus B-276 cells exhibited no difference in TCE degradation efficiency. TCE degradation was found to be growth-phase-dependent and maximum rates were monitored with stationary-phase cells. K(m) and Vmax values for TCE degradation of R. corallinus B-276 grown in nutrient broth medium in the presence of glucose were 187 microM and 2.4 nmol min-1 (mg protein)-1, respectively. Escherichia coli recombinants harbouring and expressing the alkene monooxygenase genes of R. corallinus B-276 exhibited the ability to degrade TCE. This result provides clear evidence that the alkene monooxygenase of R. corallinus B-276 catalyses TCE oxidation. R. corallinus B-276 was shown to contain four linear plasmids, pNC10 (70 kb), pNC20 (85 kb), pNC30 (185 kb) and pNC40 (235 kb). The observation that pNC30-deficient strains had lost the ability to grow on propene suggested that the genes of the propene degradation pathway are encoded by the linear plasmid pNC30. Southern blot analysis with cloned alkene monooxygenase genes from R. corallinus B-276 revealed a positive hybridization signal with the linear plasmid pNC30. This result clearly shows that the alkene monooxygenase is encoded by the linear plasmid pNC30. Eleven short-chain-alkene-oxidizing strains were screened for the presence of linear plasmids. Among these, four propene-oxidizing Rhodococcus strains and one ethene-oxidizing Mycobacterium strain were found to contain linear megaplasmids. Southern blot analysis with the alkene monooxygenase revealed positive signals with linear plasmids of two propene-oxidizing Rhodococcus ruber strains. These results indicate that homologous alkene monooxygenases are encoded by linear plasmids in R. ruber strains.

Alkenes↗

PubMed2003

Rhodococcus tukisamuensis sp. nov., isolated from soil.

A novel strictly aerobic, heterotrophic, mesophilic bacterium, strain Mb8(T), was isolated from soil in Sapporo City, Hokkaido, Japan. The G+C content of strain Mb8(T) was 66.0 mol%. It had mycolic acids with 44-52 carbon atoms and C16 : 0 and C18 : 1 (9) as the major fatty acids. The major isoprenoid quinone was MK-8(H(2)). The cell wall contained meso-diaminopimelic acid, arabinose and galactose. 16S rDNA, chemotaxonomic and morphological data indicated that this strain clearly belonged to the genus RHODOCOCCUS: Based on phenotypic properties and DNA-DNA hybridization data, strain Mb8(T) (=JCM 11308(T)=NCIMB 13903(T)) has been assigned to the genus Rhodococcus as the type strain of Rhodococcus tukisamuensis sp. nov.

Base Composition↗

PubMed2003

Structural and functional features of Rhodococcus ruber lipoarabinomannan.

The genus Rhodococcus is part of the phylogenetic group nocardioform actinomycetes, which also includes the genus MYCOBACTERIUM: Members of this phylogenetic group have a characteristic cell envelope structure, which is dominated by various complex lipids. Among these, lipoglycans are of particular interest since mycobacterial lipoarabinomannans are important immunomodulatory molecules that are likely to be involved in the subsequent fate of mycobacterial bacilli once inside phagocytic cells. Rhodococcus ruber is a species closely related to an established opportunistic human pathogen, Rhodococcus equi. This paper reports the isolation and characterization of R. ruber lipoarabinomannan, designated as RruLAM. SDS-PAGE and gas chromatography analyses revealed that RruLAM was of an intermediate size between Mycobacterium tuberculosis lipoarabinomannan and lipomannan. Using a combination of chemical degradation and (1)H, (13)C-NMR experiments, the carbohydrate structure of RruLAM was unambiguously shown to be composed of a linear (alpha1-->6)-Manp backbone substituted at some O-2 positions by a single t-alpha-Araf sugar unit. Integration of the anomeric proton signals provided an indication of the degree of branching as approximately 45 %. The RruLAM structure is much simpler than that established for M. tuberculosis lipoarabinomannan but is also different from that determined for the closely related species and opportunistic human pathogen, R. equi. RruLAM was unable to induce the production of TNF-alpha by either human or murine macrophage cell lines, suggesting that more sophisticated structures, such as phosphoinositol capping motifs, are required for such activity.

Animals↗

PubMed2003

Degradation of alkanes and highly chlorinated benzenes, and production of biosurfactants, by a psychrophilic Rhodococcus sp. and genetic characterization of its chlorobenzene dioxygenase.

Rhodococcus sp. strain MS11 was isolated from a mixed culture. It displays a diverse range of metabolic capabilities. During growth on 1,2,4-trichlorobenzene, 1,2,4,5-tetrachlorobenzene (1,2,4,5-TeCB) and 3-chlorobenzoate stoichiometric amounts of chloride were released. It also utilized all three isomeric dichlorobenzenes and 1,2,3-trichlorobenzene as the sole carbon and energy source. Furthermore, the bacterium grew well on a great number of n-alkanes ranging from n-heptane to n-triacontane and on the branched alkane 2,6,10,14-tetramethylpentadecane (pristane) and slowly on n-hexane and n-pentatriacontane. It was able to grow at temperatures from 5 to 30 degrees C, with optimal growth at 20 degrees C, and could tolerate 6 % NaCl in mineral salts medium. Genes encoding the initial chlorobenzene dioxygenase were detected by using a primer pair that was designed against the alpha-subunit (TecA1) of the chlorobenzene dioxygenase of Ralstonia (formerly Burkholderia) sp. strain PS12. The amino acid sequence of the amplified part of the alpha-subunit of the chlorobenzene dioxygenase of Rhodococcus sp. strain MS11 showed >99 % identity to the alpha-subunit of the chlorobenzene dioxygenase from Ralstonia sp. strain PS12 and the parts of both alpha-subunits responsible for substrate specificity were identical. The subsequent enzymes dihydrodiol dehydrogenase and chlorocatechol 1,2-dioxygenase were induced in cells grown on 1,2,4,5-TeCB. During cultivation on medium-chain-length n-alkanes ranging from n-decane to n-heptadecane, including 1-hexadecene, and on the branched alkane pristane, strain MS11 produced biosurfactants lowering the surface tension of the cultures from 72 to </=29 mN m(-1). Glycolipids were extracted from the supernatant of a culture grown on n-hexadecane and characterized by (1)H- and (13)C-NMR-spectroscopy and mass spectrometry. The two major components consisted of alpha,alpha-trehalose esterified at C-2 or C-4 with a succinic acid and at C-2' with a decanoic acid. They differed from one another in that one 2,3,4,2'-trehalosetetraester, found in higher concentration, was esterified at C-2, C-3 or C-4 with one octanoic and one decanoic acid and the other one, of lower concentration, with two octanoic acids. The results demonstrate that Rhodococcus sp. strain MS11 may be well suited for bioremediation of soils and sediments contaminated for a long time with di-, tri- and tetrachlorobenzenes as well as alkanes.

Alkanes↗

PubMed2002

Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038.

The three-component naphthalene dioxygenase (NDO) enzyme system carries out the first step in the aerobic degradation of naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene by Rhodococcus sp. strain NCIMB 12038. The terminal oxygenase component (naphthalene 1,2-dioxygenase) that catalyzes this reaction belongs to the aromatic ring hydroxylating dioxygenase family and has been crystallized. These enzymes utilize a mononuclear non-heme iron centre to catalyze the addition of dioxygen to their respective substrates. In this reaction, two electrons, two protons and a dioxygen molecule are consumed. The Rhodococcus enzyme has only 33 and 29% sequence identity to the corresponding alpha- and beta-subunits of the NDO system of Pseudomonas putida NCIMB 9816-4, for which the tertiary structure has been reported. In order to determine the three-dimensional structure of the Rhodococcus NDO, diffraction-quality crystals have been prepared by the hanging-drop method. The crystals belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 87.5, b = 144, c = 185.6 A, alpha = beta = gamma = 90 degrees, and diffract to 2.3 A resolution.

Crystallization↗

PubMed1989

Carotenoid pigments of genus Rhodococcus.

A study of carotenoid pigments of the genus Rhodococcus was carried out. According to carotenes contained, Rhodococcus species were divided into three groups: the first group of Rhodococcus luteus, R. coprophilus, R. lentifragmentus, and R. maris, which formed beta-carotene; the second group of R. equi, R. rubropertinctus, R. aichiensis, R. sputi, R. chubuensis, R. obuensis, R. bronchialis, R. roseus, R. rhodochrous, R. rhodnii, and R. terrae, which formed gamma-carotene-like substance; and the third group of R. aurantiacus, which formed neither carotene. Other carotenoid pigments were different according to the species.

Carotenoids↗

PubMed1989

Evidence for the pathogenic role of Rhodococcus species in pulmonary diseases.

Three hundred expectorated sputa from patients suffering from chest disorders were examined microscopically and cultured on various media. Among other micro-organisms isolated there were four strains of Rhodococcus aurantiacus (Gordona aurantiaca), one each of Rh. erythropolis, Rh. pellegrino, Rh. rubropertinctus and Rh. rhodnii. Suspensions in 5% hog gastric mucin were virulent for immuno-suppressed white mice and the pathology of their lungs was compatible with those produced in experimental nocardial and rhodococcus infections. The in-vitro antibiogram was similar to that of Nocardia asteroides. Two of the patients from whom Rh. aurantiacus and Rh. pellegrino were isolated responded bacteriologically and clinically to treatment with co-trimoxazole. The frequency with which these rhodococci were isolated and the clinical conditions of the patients strongly indicated a pathogenic role for some Rhodococcus species. It is suggested that rhodococci should be sought in chronic pulmonary infections, particularly in those who are immuno-compromised or debilitated, and their aetiologic role determined.

Actinomycetales Infections↗

PubMed1993

Amidase coupled with low-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1. Sequencing and expression of the gene and purification and characterization of the gene product.

The cloned 9.4-kb insert of plasmid pNHJ20L containing low-molecular-mass nitrile hydratase (L-NHase) gene from Rhodococcus rhodochrous J1 [Kobayashi, M. et al. (1991) Biochim. Biophys. Acta 1129, 23-33] was digested with various restriction enzymes, and the trimmed fragments were inserted into pUC18 or pUC19. A 1.96-kb EcoRI-SphI region located 1.9-kb downstream of the L-NHase gene was found to be essential for the expression of amidase activity in Escherichia coli; the gene arrangement of the amidase and the NHase in R. rhodochrous J1 differed from those in Rhodococcus species including N-774 and Pseudomonas chlororaphis B23. The nucleotide-determined sequence indicated that the amidase consists of 515 amino acids (54626 Da) and the deduced amino acid sequence of the amidase had high similarity to those of amidases from Rhodococcus species including N-774 and P. chlororaphis B23 and to indole-3-acetamide hydrolase from Pseudomonas savastanoi. The amidase gene modified in the nucleotide sequence upstream from its start codon expressed 8% of the total soluble protein in E. coli under the control of lac promoter. The level of amidase activity in cell-free extracts of E. coli was 0.468 unit/mg using benzamide as a substrate. This amidase was purified to homogeneity from extracts of the E. coli transformant with 30.4% overall recovery. The molecular mass of the enzyme estimated by HPLC was about 110 kDa and the enzyme consists of two subunits identical in molecular mass (55 kDa). The enzyme acted upon aliphatic amides such as propionamide and also upon aromatic amides such as benzamide. The apparent Km values for propionamide and benzamide were 0.48 mM and 0.15 mM, respectively. This amidase was highly specific for the S-enantiomer of 2-phenylpropionamide, but could not recognize the configuration of 2-chloropropionamide. It also catalyzed the transfer of an acyl group from an amide to hydroxylamine to produce the corresponding hydroxamate.

Amidohydrolases↗

PubMed2006

Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4.

Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.

Base Sequence↗

PubMed2001

Metabolism of anthracene by a Rhodococcus species.

A Rhodococcus sp. isolated from contaminated river sediment was investigated to determine if the isolate could degrade high molecular mass polycyclic aromatic hydrocarbons. The Rhodococcus sp. was able to utilize anthracene (53%), phenanthrene (31%), pyrene (13%), and fluoranthene (5%) as sole source of carbon and energy, but not naphthalene or chrysene. In a study of the degradation of anthracene by a Rhodococcus sp., the identification of ring-fission products indicated at least two ring-cleavage pathways. One results in the production of 6,7-benzocoumarin, previously shown to be produced chemically from the product of meta cleavage of 1,2-dihydroxyanthracene, a pathway which has been well established in Gram-negative bacteria. The second is an ortho cleavage of 1,2-dihydroxyanthracene that produces 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid, a dicarboxylic acid ring-fission product. This represents a novel metabolic pathway only identified in Gram-positive bacteria.

Anthracenes↗

PubMed2002

Sulfur-selective desulfurization of dibenzothiophene and diesel oil by newly isolated Rhodococcus sp. strains.

New desulfurizing bacteria able to convert dibenzothiophene into 2-hydroxybiphenyl and sulfate were isolated from contaminated soils collected in Mexican refineries. Random amplified polymorphic DNA analysis showed they were different from previously reported Rhodococcus erythropolis desulfurizing strains. According to 16S rRNA gene sequencing and fatty acid analyses, these new isolates belonged to the genus Rhodococcus. These strains could desulfurize 4,6-dimethyldibenzothiophene which is one of the most difficult dibenzothiophene derivatives to remove by hydrodesulfurization. A deeply hydrodesulfurized diesel oil containing significant amounts of 4,6-dimethyldibenzothiophene was treated with Rhodococcus sp. IMP-S02 cells. Up to 60% of the total sulfur was removed and all the 4,6-dimethyldibenzothiophene disappeared as a result of this treatment.

Biodegradation, Environmental↗

PubMed2006

Microbial desulfurization of gasoline by free whole-cells of Rhodococcus erythropolis XP.

Rhodococcus erythropolis XP could grow well with condensed thiophenes, mono-thiophenic compounds and mercaptans present in gasoline. Rhodococcus erythropolis XP was also capable of efficiently degrading the condensed thiophenes in resting cell as well as biphasic reactions in which n-octane served as a model oil phase. Free whole cells of R. erythropolis XP were adopted to desulfurize fluid catalytic cracking (FCC) and straight-run (SR) gasoline oils. About 30% of the sulfur content of FCC gasoline and 85% of sulfur in SR gasoline were reduced, respectively. Gas chromatography analysis with atomic emission detection also showed depletion of sulfur compounds in SR gasoline. Rhodococcus erythropolis XP could partly resist the toxicity of gasoline and had an application potential to biodesulfurization of gasoline.

Biodegradation, Environmental↗

PubMed1988

Degradation and O-methylation of chlorinated phenolic compounds by Rhodococcus and Mycobacterium strains.

Three polychlorophenol-degrading Rhodococcus and Mycobacterium strains were isolated independently from soil contaminated with chlorophenol wood preservative and from sludge of a wastewater treatment facility of a kraft pulp bleaching plant. Rhodococcus sp. strain CG-1 and Mycobacterium sp. strain CG-2, isolated from tetrachloroguaiacol enrichment, and Rhodococcus sp. strain CP-2, isolated from pentachlorophenol enrichment, mineralized pentachlorophenol and degraded several other polychlorinated phenols, guaiacols (2-methoxyphenols), and syringols (2,6-dimethoxyphenols) at micromolar concentrations and were sensitive to the toxic effects of pentachlorophenol. All three strains initiated degradation of the chlorophenols by para-hydroxylation, producing chlorinated para-hydroquinones, which were then further degraded. Parallel to degradation, strains CG-1, CG-2, and CP-2 also O-methylated nearly all chlorinated phenols, guaiacols, syringols, and hydroquinones. O-methylation of chlorophenols was a slow reaction compared with degradation. The preferred substrates of the O-methylating enzyme(s) were those with the hydroxyl group flanked by two chlorine substituents. O-methylation was constitutively expressed, whereas degradation of chlorinated phenolic compounds was inducible.

Anisoles↗