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PubMed2006

Rhodococcus kroppenstedtii sp. nov., a novel actinobacterium isolated from a cold desert of the Himalayas, India.

The taxonomic position of an actinomycete, strain K07-23T, isolated from a cold desert of the Himalayas, India, was established by a polyphasic approach. The strain exhibited phenotypic characters that were typical of the genus Rhodococcus. 16S rRNA gene sequence (1467 bases) comparisons confirmed that strain K07-23T belongs to the genus Rhodococcus. 16S rRNA sequence similarity studies showed that the isolate is very closely related to Nocardia corynebacterioides DSM 20151T (98.6 %), which has been recently reclassified as Rhodococcus corynebacterioides. It showed 94.4-96.6 % sequence similarity with other species of the genus Rhodococcus. However, genomic relatedness between strain K07-23T and R. corynebacterioides as revealed by DNA-DNA hybridization was low (62 %). Based on polyphasic analysis, strain K07-23T could be clearly distinguished from other species. It is proposed that strain K07-23T (=MTCC 6634T=DSM 44908T=JCM 13011T) represents a novel species of Rhodococcus, Rhodococcus kroppenstedtii sp. nov.

Bacterial Typing Techniques↗

PubMed2006

N-acylhomoserine lactonase producing Rhodococcus spp. with different AHL-degrading activities.

N-acylhomoserine lactones (AHLs) are conserved signal molecules that control diverse biological activities in quorum sensing system of Gram-negative bacteria. Recently, several soil bacteria were found to degrade AHLs, thereby interfering with the quorum sensing system. Previously, Rhodococcus erythropolis W2 was reported to degrade AHLs by both oxido-reductase and AHL-acylase. In the present study, two AHL-utilizing bacteria, strains LS31 and PI33, were isolated and identified as the genus Rhodococcus. They exhibited different AHL-utilization abilities: Rhodococcus sp. strain LS31 rapidly degraded a wide range of AHLs, including N-3-oxo-hexanoyl-l-homoserine lactone (OHHL), whereas Rhodococcus sp. strain PI33 showed relatively less activity towards 3-oxo substituents. Coculture of strain LS31 with Erwinia carotovora effectively reduced the amount of OHHL and pectate lyase activity, compared with coculture of strain PI33 with E. carotovora. A mass spectrometry analysis indicated that both strains hydrolyzed the lactone ring of AHL to generate acylhomoserine, suggesting that AHL-lactonases (AHLases) from the two Rhodococcus strains are involved in the degradation of AHL, in contrast to R. erythropolis W2. To the best of our knowledge, this is the first report on AHLases of Rhodococcus spp.

4-Butyrolactone↗

PubMed1995

Cloning of the genes for degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine from Rhodococcus sp. strain TE1.

The degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine (2-chloro-4-ethyl-amino-6-isopropylamino-1,3,5-triazine) is associated with an indigenous plasmid in Rhodococcus sp. strain TE1. Plasmid DNA libraries of Rhodococcus sp. strain TE1 were constructed in a Rhodococcus-Escherichia coli shuttle vector, pBS305, and transferred into Rhodococcus sp. strain TE3, a derivative of Rhodococcus sp. strain TE1 lacking herbicide degradation activity, to select transformants capable of growing on EPTC as the sole source of carbon (EPTC+). Analysis of plasmids from the EPTC+ transformants indicated that the eptA gene, which codes for the enzyme required for EPTC degradation, residues on a 6.2-kb KpnI fragment. The cloned fragment also harbored the gene required for atrazine N dealkylation (atrA). The plasmid carrying the cloned fragment could be electroporated into a number of other Rhodococcus strains in which both eptA and atrA were fully expressed. No expression of the cloned genes was evident in E. coli strains. Subcloning of the 6.2-kb fragment to distinguish between EPTC- and atrazine-degrading genes was not successful.

Atrazine↗

PubMed1993

Characterization of nitrile hydratase genes cloned by DNA screening from Rhodococcus erythropolis.

Southern hybridization analysis using the genes encoding the alpha- and beta-subunits of nitrile hydratase (NHase) from Rhodococcus sp. N-774 as probe suggested that two R. erythropolis strains, JCM6823 and JCM2892, among 31 strains mainly from Japan Culture of Microorganisms (JCM) have NHase genes. Restriction analysis of DNA fragments showing positive hybridization showed that each fragment carried a nucleotide sequence very similar to that of the NHase genes from Rhodococcus sp. N-774. Nucleotide sequence analysis of the DNA fragment cloned from R. erythropolis JCM6823 showed the presence of the genes encoding the alpha- and beta-subunits of NHase, which show 94.7% and 96.2% identity in amino acid sequence to those of Rhodococcus sp. N-774, respectively, as well as a C-terminal portion of the amidase gene upstream from these genes. Despite the extremely high amino acid sequence similarity in both NHases and amidases from R. erythropolis JCM6823 and Rhodococcus sp. N-774, the NHases and amidases from R. erythropolis strains showed broader substrate specificity when compared to those from Rhodococcus sp. N-774. This suggests that a very limited number of amino acid residues are responsible for the difference in substrate specificity. Although the NHase of Rhodococcus sp. N-774 are constitutively produced, the NHases of both R. erythropolis strains were inducibly produced by addition of epsilon-caprolactam as an inducer.

Amino Acid Sequence↗

PubMed1991

Severe Rhodococcus equi pneumonia: case report and literature review.

Rhodococcus equi is an aerobic, gram-positive, non-motile pleomorphic bacillus infecting immunocompromised patients. Forty-nine cases of Rhodococcus equi infection have been reported, mainly in patients infected with the human immunodeficiency virus (HIV). A case in which Rhodococcus equi caused severe pulmonary infection, the most common presentation, is described. Clinically, patients have symptoms of pneumonia with hemoptysis as a prominent feature. X-ray will often show a cavitating upper-lobe infiltrate, resembling infection with mycobacteria. Rhodococcus equi is easily cultured from blood or sputum on standard media, but is frequently regarded as a contaminant. Mortality from Rhodococcus equi pneumonia is high (25%) and early surgical intervention has been recommended. Based on this review, the benefit of surgery seems dubious, whereas good results have been obtained using long-term antibiotic treatment with erythromycin plus rifampicin, or vancomycin in combination with either of these antibiotics.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101.

Rhodococcus opacus strain SAO101 was shown to degrade on various polycyclic aromatic hydrocarbons such as naphthalene, dibenzofuran (DF), and dibenzo-p-dioxin (DD). One of the unique traits of the strain SAO101 is its ability to oxidize DF compounds by lateral dioxygenation. To clone the lateral dioxygenase gene involved in compound degradation in strain SAO101, we identified a cosmid clone that oxidizes aromatic compounds by using SAO101 genomic DNA. Sequencing analysis revealed that isolated cosmid clone contained ring-hydroxylating dioxygenase genes (narAaAb) with homologies to indene dioxygenase genes of Rhodococcus strain I24 and naphthalene dioxygenase genes of Rhodococcus strain NCIMB12038. The NarAaAb-expressing Rhodococcus cells exhibited broad substrate specificity for bicyclic aromatic compounds and had high ability to degrade dibenzofuran and naphthalene. Metabolite analysis revealed that dihydrodiol compounds were detected as metabolites from dibenzofuran by the NarAaAb-expressing Rhodococcus strain, indicating that dibenzofuran was converted by lateral dioxygenase activity of NarA dioxygenase. Based on reverse transcriptase-polymerase chain reaction analysis, it was found that the narAaAb genes were cotranscribed and that their expression was induced in the presence of aromatic hydrocarbon compounds. It is likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by this strain. Strain SAO101 harbors three huge linear plasmids, pWK301 (1,100 kbp), pWK302 (1,000 kbp), and pWK303 (700 kbp), and the nar genes were found to be located on the pWK301 plasmid.

Benzofurans↗

PubMed1987

The taxonomic status of Rhodococcus equi.

The species Corynebacterium equi was proposed for strains isolated from foals suffering from purulent pneumonia. The taxon has had a confused history and is currently listed under both Corynebacterium and Rhodococcus in the Approved Lists of Bacterial Names. Data from modern taxonomic studies indicate that Corynebacterium equi Magnusson 1923 should be reduced to a synonym of Rhodococcus equi (Magnusson) Goodfellow and Alderson 1980. Rhodococcus equi has repeatedly been shown to be a good species on the basis of chemical, molecular biological, numerical phenetic and serological data. Improved methods are needed to differentiate Rhodococcus equi from closely related species of Rhodococcus.

Nocardiaceae↗

PubMed2006

A multipurpose transposon-based vector system mediates protein expression in Rhodococcus erythropolis.

In the current study we developed two transposon-based vectors; namely pTNR-KA and pTNR-TA and utilized them for expression of proteasome complex, derived from Streptomyces coelicolor, in Rhodococcus erythropolis. The two vectors can be transposed into Rhodococcus cells by means of electroporation, either individually in two consecutive processes or in combinations by a single step. During transposition, each of the two vectors liberates its transposable-marker gene, which integrated in a single copy into a random site in the Rhodococcus chromosomal DNA. Southern blot analysis indicated that the two transposable-marker genes of both vectors does not alter or knock out each other. To utilize these vectors for Streptomyces proteasome expression, two expression cassettes were constructed; each cassette comprised a constitutive promoter (P(nit)), the DNA fragment, prcA or prcB that encodes alpha- or beta-subunits of Streptomyces proteasome, and T(thcA) transcriptional terminator. The cassettes were then individually introduced into the multiple cloning sites that are located in the transposable-marker gene of the two vectors. The two cassettes-harboring vectors were subsequently co-transposed, in combinations, into the Rhodococcus genome by a single electroporation step and the Streptomyces proteasome was successfully expressed in the rodococcal host cell. The isolated proteasome was further characterized and the peptidase activity was confirmed and indicated that it was biologically active. The present study concluded that both pTNR-KA and pTNR-TA can be used as transposon-based protein expression systems in Rhodococcus species.

Animals↗

PubMed2005

Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources.

The aerobic degradation of phenol, chlorobenzene and dichlorobenzene as a sole carbon source has been observed in bacterial Gram-positive strain G2PT isolated from a wastewater bioprocessor. Cells display branching mycelia fragmenting into rod and coccoid elements when grown on TSA. Aerial hyphae formation occurs when grown on phenol and chlorinated aromatics as the sole carbon source. Growth was observed at up to 0.75% phenol as a sole carbon source, indicating a strong tolerance for the compound. The 16S rRNA gene sequence shares the greatest similarity with members of the Rhodococcus genus, with the closest shared nucleotide identity of 98% with the aromatic toxin degrading bacteria Rhodococcus zopfii DSM 44108T. Neighbor-joining and parsimony analysis of Corynebacterineae 16S rRNA gene sequences consistently places strain G2PT in a clade shared with R. zopfii within the Rhodococcus rhodochrous subclade. Based on a unique polyphasic profile involving phenotypic, ribosomal DNA sequence analysis, DNA-DNA hybridization, mol% DNA G+C content and fatty acid composition, G2PT is proposed to represent a previously uncharacterized, novel species in the genus Rhodococcus. The name Rhodococcus phenolicus is proposed for the isolate with the type strain G2PT (= DSM 44812) (= NRRL B-24323) [corrected]

Bioreactors↗

PubMed2000

Rhodococcus pyridinivorans sp. nov., a pyridine-degrading bacterium.

The taxonomic position of a bacterial strain (PDB9T) that is capable of degrading pyridine was clarified by a polyphasic taxonomic approach using phenotypic, chemotaxonomic and genetic methods. The cells, which are rods and branched filaments during the early growth phase, fragment into short rods or cocci, thereby completing the growth cycle. Strain PDB9T was found to have a cell wall of chemotype IV, MK-8(H2) as the predominant menaquinone, mycolic acids with 36-46 carbon atoms and C16:0' C18:1 cis9, 10-methyl-C18:0 (TBSA) as the major fatty acids. The G+C content of the DNA was 66 mol%. The phylogenetic tree showed that strain PDB9T falls within an evolutionary radiation comprising Rhodococcus species and is most closely related to the type strain of Rhodococcus rhodochrous, sharing 99% 16S rDNA similarity. The differences in some phenotypic characteristics and the genetic distinctiveness distinguish strain PDB9T from the Rhodococcus species described previously. Therefore, strain PDB9T should be placed in the genus Rhodococcus as a new species, for which the new name Rhodococcus pyridinivorans sp. nov. is proposed. The type strain of the new species is strain PDB9T (= KCTC 0647BPT = KCCM 80005T).

DNA, Ribosomal↗

PubMed2002

Rhodococcus jostii sp. nov., isolated from a medieval grave.

The taxonomic position of a bacterial strain isolated from the femur of the remains of Jost Lucemburský, margrave in Moravia, Brno (Czech Republic), was investigated by phenotypic, chemotaxonomic and molecular taxonomic methods. The chemotaxonomic characteristics, including the cell-wall amino acid and sugar compositions, the quinone system and the fatty acid profile, were in good agreement with those of the genus Rhodococcus. The G+C content of the DNA was 67.4 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unknown strain represents a distinct line of descent within the genus Rhodococcus. The nearest relatives of the bacterium were Rhodococcus opacus and Rhodococcus percolatus. The unknown bacterium was readily distinguished from these species by using phenotypic methods. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Rhodococcus jostii sp. nov. The type strain is strain IFO 16295T (= CCM 4760T).

Amino Acids↗

PubMed1989

Cloning and expression of Rhodococcus genes encoding pigment production in Escherichia coli.

Pigment was produced by Escherichia coli cells carrying recombinant plasmids pNIL100, pNIL200 and pNIL400 containing DNA from Rhodococcus sp. E. coli cells containing pNIL100 or pNIL200 (with DNA inserts from Rhodococcus sp. JL10 and Rhodococcus sp. ATCC 21145 respectively) produced both blue and pink pigments, while cells containing pNIL400 (with a DNA insert from Rhodococcus sp. ATCC 21145) produced only pink pigment. Colonies of E. coli(pNIL100) and E. coli(pNIL200) were dark blue, whereas E. coli(pNIL400) colonies were pink. No pigment was detected in Streptomyces griseus transformants containing pNIL100, pNIL200 or pNIL400. Restriction endonuclease mapping indicated that the cloned DNA fragments were different. The pigment gene(s) in pNIL200 producing both the blue and pink pigments were contained within a 2.8 kb DNA fragment. The pigments produced by E. coli transformants containing pNIL200 were characterized by visible and UV spectroscopy. No similar pigments were detected in Rhodococcus sp. ATCC 21145.

Cloning, Molecular↗

PubMed2001

Construction of Rhodococcus random mutagenesis libraries using Tn5 transposition complexes.

The ability to generate tagged mutants of Rhodococcus spp. will facilitate a deeper understanding of this medically and commercially important genus. The absence of efficient transposon systems in these organisms has here been overcome by the use of Tn5-based DNA-protein transposition complexes which can transpose at high efficiency. To achieve this, electroporation efficiencies and antibiotic selection were optimized. A Rhodococcus rhodochrous CW25 Tn5 insertion library of 1500 mutants was created. Southern blotting of 23 representative mutants demonstrated random insertion. A number of auxotrophic mutants were isolated and the disrupted regions involved were identified by inverse PCR and subsequent sequencing. Transposition of Tn5 was confirmed by the presence of 9 bp direct repeats of Rhodococcus DNA flanking the transposon insertion site. To further test this system, a Tn5 insertion library was constructed in a wild-type soil isolate of Rhodococcus spp. This is the first viable transposon knockout system reported for Rhodococcus.

Base Sequence↗

PubMed2004

Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil.

The taxonomic relationships of two actinomycetes provisionally assigned to the genus Rhodococcus were determined using a polyphasic taxonomic approach. The generic assignment was confirmed by 16S rRNA gene similarity data, as the organisms, strains MTCC 1534 and W 4937(T), were shown to belong to the Rhodococcus rhodochrous subclade. These organisms had phenotypic properties typical of rhodococci; they were aerobic, Gram-positive, weakly acid-fast actinomycetes that showed an elementary branching-rod-coccus growth cycle and contained meso-diaminopimelic acid, arabinose and galactose in whole-organism hydrolysates, N-glycolated muramic acid residues, dehydrogenated menaquinones with eight isoprene units as the predominant isoprenologue and mycolic acids that co-migrated with those extracted from the type strain of R. rhodochrous. The strains had identical phenotypic profiles and belong to the same genomic species, albeit one distinguished from Rhodococcus pyridinivorans, with which they formed a distinct phyletic line. They were also distinguished from representatives of all of the species classified in the R. rhodochrous 16S rRNA gene tree using a set of phenotypic features. The genotypic and phenotypic data show that the strains merit recognition as a novel species of Rhodococcus. The name proposed is Rhodococcus gordoniae sp. nov., with the type strain W 4937(T) (=DSM 44689(T)=NCTC 13296(T)).

DNA, Bacterial↗

PubMed2005

Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil.

A Gram-positive, aerobic, non-motile, mesophilic strain, designated YIM 70056(T), was isolated from a forest soil sample in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had less than 97.0 % similarity to any Rhodococcus species with validly published names, with the exception of Rhodococcus fascians (DSM 20669(T)), which was found to be its closest neighbour (98.9 % similarity). Chemotaxonomic data, including peptidoglycan type, diagnostic sugar compositions, fatty acid profiles, menaquinones, polar lipids and mycolic acids, were determined for this isolate; the results supported the affiliation of strain YIM 70056(T) to the genus Rhodococcus. The DNA G + C content was 63.5 mol%. The results of DNA-DNA hybridization with R. fascians DSM 20669(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate YIM 70056(T) represents a novel Rhodococcus species, for which the name Rhodococcus yunnanensis sp. nov. is proposed, with YIM 70056(T) (=CCTCC AA 204007(T) = KCTC 19021(T) = DSM 44837(T)) as the type strain.

Aerobiosis↗

PubMed1994

Chlorocatechol 1,2-dioxygenase from Rhodococcus erythropolis 1CP. Kinetic and immunochemical comparison with analogous enzymes from gram-negative strains.

Chlorocatechol 1,2-dioxygenase from Rhodococcus erythropolis 1CP was purified to homogeneity. In contrast to chlorocatechol 1,2-dioxygenase from Gram-negative strains which have a very broad substrate tolerance, the Rhodococcus enzyme was relatively more specific and had a distinct preference for 4-substituted catechols. Protein and metal analysis indicate an unusual stoichiometry of one atom each of iron and manganese/64-kDa homodimer. The N-terminal amino acid sequence (27 residues) of the Rhodococcus chlorocatechol 1,2-dioxygenase was determined and exhibited 15-22% identity to the published sequences of catechol 1,2-dioxygenases and other chlorocatechol 1,2-dioxygenases. Antiserum was raised in rabbits and antibodies against Rhodococcus chlorocatechol 1,2-dioxygenase were affinity purified. Dot-blot analysis revealed a very weak reaction between the antibodies and partially purified chlorocatechol 1,2-dioxygenases from Alcaligenes eutrophus JMP134 and Pseudomonas putida 87. No reaction between these antibodies and above enzymes was observed using Western blotting. Kinetic and immunochemical data as well as comparison of subunit molecular mass and suggest that the Rhodococcus enzyme differs significantly from the known highly similar chlorocatechol 1,2-dioxygenases of Gram-negative strains and seems to be only distantly related to them.

Amino Acid Sequence↗

PubMed2003

Biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a rabbit liver cytochrome P450: insight into the mechanism of RDX biodegradation by Rhodococcus sp. strain DN22.

A unique metabolite with a molecular mass of 119 Da (C(2)H(5)N(3)O(3)) accumulated during biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by Rhodococcus sp. strain DN22 (D. Fournier, A. Halasz, J. C. Spain, P. Fiurasek, and J. Hawari, Appl. Environ. Microbiol. 68:166-172, 2002). The structure of the molecule and the reactions that led to its synthesis were not known. In the present study, we produced and purified the unknown metabolite by biotransformation of RDX with Rhodococcus sp. strain DN22 and identified the molecule as 4-nitro-2,4-diazabutanal using nuclear magnetic resonance and elemental analyses. Furthermore, we tested the hypothesis that a cytochrome P450 enzyme was responsible for RDX biotransformation by strain DN22. A cytochrome P450 2B4 from rabbit liver catalyzed a very similar biotransformation of RDX to 4-nitro-2,4-diazabutanal. Both the cytochrome P450 2B4 and intact cells of Rhodococcus sp. strain DN22 catalyzed the release of two nitrite ions from each reacted RDX molecule. A comparative study of cytochrome P450 2B4 and Rhodococcus sp. strain DN22 revealed substantial similarities in the product distribution and inhibition by cytochrome P450 inhibitors. The experimental evidence led us to propose that cytochrome P450 2B4 can catalyze two single electron transfers to RDX, thereby causing double denitration, which leads to spontaneous hydrolytic ring cleavage and decomposition to produce 4-nitro-2,4-diazabutanal. Our results provide strong evidence that a cytochrome P450 enzyme is the key enzyme responsible for RDX biotransformation by Rhodococcus sp. strain DN22.

Aerobiosis↗

PubMed1995

Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase.

Determination of the N-terminal sequences of two EPTC (S-ethyl dipropylcarbamothioate)-induced proteins from thiocarbamate-degrading Rhodococcus sp. strain NI86/21 resolved by two-dimensional electrophoresis enabled the localization of the respective structural genes on two distinct DNA fragments. One of these strongly induced proteins is a NAD(+)-dependent dehydrogenase active on aliphatic aldehydes. The second protein was identified as a cytochrome P-450 enzyme. The cytochrome P-450 gene represents the first member of a new family, CYP116. Downstream of the cytochrome P-450 gene, two genes for a [2Fe-2S] ferredoxin (rhodocoxin) and a ferredoxin reductase are located. A putative regulatory gene encoding a new member of the AraC-XylS family of positive transcriptional regulators is divergently transcribed from the cytochrome P-450 gene. By hybridization, it was demonstrated that the aldehyde dehydrogenase gene is widespread in the Rhodococcus genus, but the components of the cytochrome P-450 system are unique to Rhodococcus sp. strain NI86/21. Overexpression in Escherichia coli was achieved for all of these proteins except for the regulatory protein. Evidence for the involvement of this cytochrome P-450 system in EPTC degradation and herbicide biosafening for maize was obtained by complementation experiments using EPTC-negative Rhodococcus erythropolis SQ1 and mutant FAJ2027 as acceptor strains. N dealkylation by cytochrome P-450 and conversion of the released aldehyde into the corresponding carboxylic acid by aldehyde dehydrogenase are proposed as the reactions initiating thiocarbamate catabolism in Rhodococcus sp. strain NI86/21. In addition to the major metabolite N-depropyl EPTC, another degradation product was identified, EPTC-sulfoxide.

Aldehyde Dehydrogenase↗