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PubMed2002

Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil.

A polyphasic study was undertaken to establish the taxonomic position of a soil isolate that had provisionally been assigned to the genus Rhodococcus. The organism showed a combination of phenotypic properties typical of rhodococci and formed a distinct phyletic line within the Rhodococcus erythropolis 165 rDNA subclade. The organism was readily distinguished from representatives of validly described species classified in this subclade on the basis of DNA-DNA relatedness and phenotypic data. Consequently, it is proposed that the organism be recognized as a novel species of Rhodococcus, Rhodococcus maanshanensis sp. nov. The type strain is strain M712(T) (= AS 4.1720(T) = JCM 11374(T)).

Base Composition↗

PubMed1992

Development of a host-vector system in a Rhodococcus strain and its use for expression of the cloned nitrile hydratase gene cluster.

Two different types of plasmid were isolated from strains of Rhodococcus rhodochrous. Two plasmids, of the same type but from different strains, were combined with Escherichia coli plasmids carrying antibiotic resistance markers to develop E. coli-Rhodococcus shuttle vectors. The ampicillin and kanamycin resistance markers served for selection in Rhodococcus. Electroporation was used to introduce recombinant plasmid DNA into R. rhodochrous ATCC 12674 at a frequency of 5 x 10(7) transformants per microgram DNA. With these host-vector and transformation systems, the nitrile hydratase and amidase genes of a Rhodococcus strain were introduced into the host strain and were efficiently expressed.

Acrylamides↗

PubMed1999

Characterization of IS2112, a new insertion sequence from Rhodococcus, and its relationship with mobile elements belonging to the IS110 family.

A new insertion sequence (IS2112) was identified in the genome of the 1-haloalkane-utilizing bacterium Rhodococcus rhodochrous NCIMB 13064. The insertion element is 1415 bp long, does not contain terminal inverted repeats, and is not flanked by directly repeated sequences. IS2112 belongs to the IS110 family of transposable elements, and forms a separate subfamily, along with IS116. Two copies of IS2112 were found in R. rhodochrous NCIMB 13064 and one, two or three copies of a similar sequence were detected in five other 1-haloalkane-degrading Rhodococcus strains. There were no sequences homologous to IS2112 found in the 1-haloalkane-degrading 'Pseudomonas pavonaceae' 170 and Rhodococcus sp. HA1 or in several Rhodococcus strains which do not utilize haloalkanes. IS2112 was originally found in plasmid pRTL1 of R. rhodochrous NCIMB 13064, which harbours genes encoding utilization of 1-haloalkanes, and was located 5 kbp upstream of the haloalkane dehalogenase gene (dhaA). Although the second copy of IS2112 in strain NCIMB 13064 was also present on the pRTL1 plasmid, these sequences do not apparently comprise a single composite transposon encoding haloalkane utilization. An analysis of derivatives of NCIMB 13064 revealed that IS2112 was involved in genome rearrangements. IS2112 appeared to change its location as a result of transposition and as a result of other rearrangements of the NCIMB 13064 genome.

Amino Acid Sequence↗

PubMed2005

Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.

The type strain of Nocardia corynebacterioides was the subject of a polyphasic taxonomic study. The 16S rRNA gene sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Mycobacterium, Nocardia, Rhodococcus, Skermania, Tsukamurella and Williamsia, and phylogenetic trees were constructed by using maximum-parsimony, maximum-likelihood and neighbour-joining methods. It was evident from the phylogenetic analysis that N. corynebacterioides represents a distinct phyletic line within the genus Rhodococcus. Menaquinone analysis showed that the organism contained dihydrogenated menaquinone with eight isoprene units, MK-8(H(2)), as the major isoprenologue. The genealogical evidence, together with chemotaxonomic and phenotypic data from this and previous studies, indicates that N. corynebacterioides DSM 20151(T) (= CIP 104510(T)) should be reclassified in the genus Rhodococcus as Rhodococcus corynebacterioides comb. nov.

Bacterial Typing Techniques↗

PubMed2004

Rhodococcus opacus expresses the xsc gene to utilize taurine as a carbon source or as a nitrogen source but not as a sulfur source.

The Gram-positive bacteria Rhodococcus opacus ISO-5 and Rhodococcus sp. RHA1 utilized taurine (2-aminoethanesulfonate) as the sole source of carbon or of nitrogen or of sulfur for growth. Different gene clusters and enzymes were active under these different metabolic situations. Under carbon- or nitrogen-limited conditions three enzymes were induced, though to different levels: taurine-pyruvate aminotransferase (Tpa), alanine dehydrogenase (Ald) and sulfoacetaldehyde acetyltransferase (Xsc). The specific activities of these enzymes in R. opacus ISO-5 were sufficient to explain the growth rates under the different conditions. These three enzymes were purified and characterized, and the nature of each reaction was confirmed. Analyses of the genome of Rhodococcus sp. RHA1 revealed a gene cluster, tauR-ald-tpa, putatively encoding regulation and oxidation of taurine, located 20 kbp from the xsc gene and separate from two candidate phosphotransacetylase (pta) genes, as well as many candidate ABC transporters (tauBC). PCR primers allowed the amplification and sequencing of the tauR-ald-tpa gene cluster and the xsc gene in R. opacus ISO-5. The N-terminal sequences of the three tested proteins matched the derived amino acid sequences of the corresponding genes. The sequences of the four genes found in each Rhodococcus strain shared high degrees of identity (>95 % identical positions). RT-PCR studies proved transcription of the xsc gene when taurine was the source of carbon or of nitrogen. Under sulfur-limited conditions no xsc mRNA was generated and no Xsc was detected. Taurine dioxygenase (TauD), the enzyme catalysing the anticipated desulfonative reaction when taurine sulfur is assimilated, was presumed to be present because oxygen-dependent taurine disappearance was demonstrated with taurine-grown cells only. A putative tauD gene (with three other candidates) was detected in strain ISO-5. Regulation of the different forms of metabolism of taurine remains to be elucidated.

Acetaldehyde↗

PubMed1995

Sequence and molecular characterization of a DNA region encoding the dibenzothiophene desulfurization operon of Rhodococcus sp. strain IGTS8.

Dibenzothiophene (DBT), a model compound for sulfur-containing organic molecules found in fossil fuels, can be desulfurized to 2-hydroxybiphenyl (2-HBP) by Rhodococcus sp. strain IGTS8. Complementation of a desulfurization (dsz) mutant provided the genes from Rhodococcus sp. strain IGTS8 responsible for desulfurization. A 6.7-kb TaqI fragment cloned in Escherichia coli-Rhodococcus shuttle vector pRR-6 was found to both complement this mutation and confer desulfurization to Rhodococcus fascians, which normally is not able to desulfurize DBT. Expression of this fragment in E. coli also conferred the ability to desulfurize DBT. A molecular analysis of the cloned fragment revealed a single operon containing three open reading frames involved in the conversion of DBT to 2-HBP. The three genes were designated dszA, dszB, and dszC. Neither the nucleotide sequences nor the deduced amino acid sequences of the enzymes exhibited significant similarity to sequences obtained from the GenBank, EMBL, and Swiss-Prot databases, indicating that these enzymes are novel enzymes. Subclone analyses revealed that the gene product of dszC converts DBT directly to DBT-sulfone and that the gene products of dszA and dszB act in concert to convert DBT-sulfone to 2-HBP.

Acid Rain↗

PubMed2000

Gene cloning and nucleotide sequencing and properties of a cocaine esterase from Rhodococcus sp. strain MB1.

A strain of Rhodococcus designated MB1, which was capable of utilizing cocaine as a sole source of carbon and nitrogen for growth, was isolated from rhizosphere soil of the tropane alkaloid-producing plant Erythroxylum coca. A cocaine esterase was found to initiate degradation of cocaine, which was hydrolyzed to ecgonine methyl ester and benzoate; both of these esterolytic products were further metabolized by Rhodococcus sp. strain MB1. The structural gene encoding a cocaine esterase, designated cocE, was cloned from Rhodococcus sp. strain MB1 genomic libraries by screening recombinant strains of Rhodococcus erythropolis CW25 for growth on cocaine. The nucleotide sequence of cocE corresponded to an open reading frame of 1,724 bp that codes for a protein of 574 amino acids. The amino acid sequence of cocaine esterase has a region of similarity with the active serine consensus of X-prolyl dipeptidyl aminopeptidases, suggesting that the cocaine esterase is a serine esterase. The cocE coding sequence was subcloned into the pCFX1 expression plasmid and expressed in Escherichia coli. The recombinant cocaine esterase was purified to apparent homogeneity and was found to be monomeric, with an M(r) of approximately 65,000. The apparent K(m) of the enzyme (mean +/- standard deviation) for cocaine was measured as 1.33 +/- 0.085 mM. These findings are of potential use in the development of a linked assay for the detection of illicit cocaine.

Amino Acid Sequence↗

PubMed2005

Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14.

o-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here Rhodococcus genes mediating oxygenation in the first step of o-xylene degradation. Rhodococcus opacus TKN14, isolated from soil contaminated with o-xylene, was able to utilize o-xylene as the sole carbon source and to metabolize it to o-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in Escherichia coli. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert o-xylene into o-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (nidABCD) that had been isolated from Rhodococcus sp. strain I24. Complementation studies, using E. coli expressing various combinations of individual open reading frames, revealed that a gene (named nidE) for rubredoxin (Rd) and a novel gene (named nidF) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of o-xylene, in addition to the dioxygenase iron-sulfur protein genes (nidAB). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding cis-dihydrodiols. All the nidABEF genes were transcriptionally induced in R. opacus TKN14 by the addition of o-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by Rhodococcus species as the first key enzyme.

Base Sequence↗

PubMed1992

The biology and genetics of the genus Rhodococcus.

The genus Rhodococcus is a unique taxon consisting of microorganisms that exhibit broad metabolic diversity, particularly to hydrophobic compounds such as hydrocarbons, chlorinated phenolics, steroids, lignin, coal, and petroleum. Advances in chemical, numerical, and molecular systematic methods have contributed greatly to the circumspection of the rhodococci, including the development of diagnostic fluoregenic probes for improved biochemical profiling and identification. Bioprocessing systems employing various Rhodococcus strains are operational for industrial and environmental applications. Such applications include production of acrylic acid and acrylamide, steroid conversions, and bioremediation of chlorinated hydrocarbons and phenolics. Progress on the genetic systems of the rhodococci is rather limited, although a number of plasmids, cloning vectors, and DNA transfer systems have been reported recently, such that progress should be rapid. Certain members of the genus Rhodococcus are known pathogens for humans, animals, and plants. Recent trends indicate that rhodococci of animal origin are opportunistic human pathogens, indicating the need for a greatly improved recognition and understanding of the virulence factors associated with the genus Rhodococcus.

Rhodococcus↗

PubMed1991

[Biosensors for the determination of phenol and benzoate on the basis of Rhodococcus cells and enzyme extracts].

An amperometric biosensor for determination of phenol, cresol, benzoate and 2-methyl-4-chlorophenol using Rhodococcus-cells and enzyme extracts of Rhodococcus has been developed. The influence of cultivation of Rhodococcus-cells and preincubation of the biosensor with desired substrate on sensibility and specificity was been investigated. In relation to cultivation and preincubation the Rhodococcus sensor was high specific to benzoate or phenol and cresol. A linear range was obtained for phenol and benzoate up to 80 mumol and for 2-methyl-4-chlorophenol up to 400 mumol. The biosensor using enzyme extracts show a higher specificity, it is but necessary NADPH. A further disadvantage is the little measuring range of this sensor.

Benzoates↗

PubMed1994

Rhodococcus equi pneumonia in an HIV-infected patient.

We report a case of a 46-year-old HIV-infected patient suffering Rhodococcus equi pneumonia and septicaemia. After the failure of an initial antibiotic treatment, the upper lobe of the right lung was resected due to a cavitating pneumonia. After that the patient stabilized for a period of 7 months by administration of a resistogram-adapted combination of tetracycline, erythromycin and clindamycin. Due to the patient's decision, antibiotic treatment was stopped when a cytomegalovirus retinitis was diagnosed. Six weeks later new pulmonary infiltrations were diagnosed and a Rhodococcus equi bacteraemia evolved. The patient died one year after the first diagnosis of the Rhodococcus equi infection. The present case suggests that the infection with Rhodococcus equi in patients with advanced HIV infection demands permanent antibiotic prophylaxis.

AIDS-Related Opportunistic Infections↗

PubMedDate not supplied

[Rhodococcus isolated from a gluteal abscess].

The pathogenic role of the genus Rhodococcus as an infectious agent in human beings is very small. Its taxonomic allocation may be difficult since there is no systematic description of this bacterial group. This paper summarizes the international literature on the microbiologic diagnosis of Rhodococcus and the small number of known cases of Rhodococcus infections. A description is given of the first case of a post-injection gluteal abscess caused by a Rhodococcus sp.

Abscess↗

PubMed1982

Is Rhodococcus equi a soil organism?

A total of 189 isolates of Rhodococcus equi and related organisms and 16 marker strains representing the genera Rhodococcus and Corynebacterium were screened for 160 unit characters in a numerical taxonomic study. Analysis of the data indicated that R. equi forms a relatively homogeneous cluster distinctly separated from the recognized species of Rhodococcus and Corynebacterium (sensu stricto). Other members of the genus Rhodococcus are soil organisms and R. equi appears to fit into the genus on ecological as well as taxonomic grounds. It seems unlikely that R. equi could be a gastrointestinal tract commensal because unlike members of the latter group it is an obligate aerobe with an optimum temperature requirement of 28-30 degrees C. It is capable of utilizing simple organic compounds as sources of carbon or carbon and nitrogen and is sensitive to bile salts. Furthermore, it appears that isolation of R. equi from the gut contents of animals is dependent on those animals having access to grazing. Taxonomic studies (backed-up by ecological studies) support the concept that R. equi is a soil organism.

Actinomycetales↗

PubMed2000

Multiple respiratory bursts as a response to veratrate stress in Rhodococcus erythropolis cells.

Although Rhodococcus spp. strains are able to degrade methoxyphenols by enzymatic means, the contact with veratric acid (3, 4-dimethoxybenzoic acid, hereafter called veratrate) is very stressful for the cells of Rhodococcus erythropolis DSM 1069 (Rh). Within 5 min of contact veratrate in phosphate buffer, the emergence of many vacuoles was observed in the cell body and respiratory bursts, with violent endogenous oxygen uptake, took place several times during the 24 h incubation. During these peaks (where the cells were in their MAX states), increased activity of NADH oxidase was noted, accompanied by maximal accumulation of vanillic and isovanillic acids (3-methoxy-4-hydroxybenzoic acid and 4-hydroxy-3-methoxybenzoic acid respectively, hereafter called vanillates) in the incubation medium, which appeared to be products of veratrate demethylation. At the troughs (cell in their MIN state), the vacuoles disappeared from the cell body, oxygen uptake was normal, and the pool of vanillates decreased while the veratrate level in the medium increased. The cells from MAX and MIN states reacted in opposite ways in the presence of either formaldehyde and GSH, or paraquate and cAMP. The NADH oxidase activity, measured as oxygen uptake against NADH in the membrane pellets of MAX and MIN stage cells, differed in their response to the exogenous presence of FAD, ATP, cAMP, catalase, GSH, H(2)O(2)and methoxyphenolic substrates. The periodic character of these events is described here. Co-operation between two multiprotein membrane complexes (NAD(P)H oxidase and 3-O/4-O-demethylases) in Rhodococcus erythropolis cells and their competition for two common substrates-NAD(P)H and O(2)-is proposed as an explanation for rhythmical nature of these reactions.

Biological Clocks↗

PubMed2001

Structure-activity relationship of mycoloyl glycolipids derived from Rhodococcus sp. 4306.

Novel mycoloyl glycolipids with short carbon chains were isolated and purified from Rhodococcus sp. 4306, a soil origin of Actinomycetales. Their chemical structures were identified as trehalose 6,6'-dimycolate (TDM), trehalose 6-monomycolate, glucose 6-monomycolate, mannose 6-monomycolate and fructose 6-monomycolate. The length of carbon chains and number of double bonds of mycolic acids were C(34), C(36)and C(38)saturated, monoenoic and dienoic molecular species, which were much shorter than those of Mycobacterium tuberculosis (C(78-88)monoenoic and dienoic). Among them, only TDM could induce prominent granulomatous inflammation of the lung and spleen in mice. By contrast, other mycoloyl glycolipids induced mild lesions. The small-sized TDM of Rhodococcus possessed granulomatogenic activity, however, the toxicity was much lower than that of M. tuberculosis. Rhodococcal TDM was composed of mycolic acid with the shortest carbon chains, when compared to granulomatogenic TDM of Mycobacterium, Nocardia and Rhodococcus reported previously. Our results imply that rhodococcal TDM is a pathogenetic factor similar to that of M. tuberculosis, although rhodococcal TDM exhibits low toxicity.

Actinomycetales Infections↗

PubMed1997

Acute mediastinitis due to Rhodococcus equi in a patient with human immunodeficiency virus infection.

A patient with human immunodeficiency virus infection developed anterior mediastinitis during antibiotic treatment for empyema due to Rhodococcus equi. This is the first reported case of infection with this organism in this setting. Despite an adequate course of therapy and maintenance treatment with antibiotics to which the isolate of Rhodococcus equi was susceptible in vitro, the patient experienced relapse of the infection into the mediastinum. Clinicians should consider this complication when Rhodococcus equi is present in pleural effusions.

AIDS-Related Opportunistic Infections↗

PubMed2003

A small cryptic plasmid from Rhodococcus erythropolis: characterization and utility for gene expression.

Exploration of metabolically diverse rhodococci is generally hampered by the lack of genetic tools. A small cryptic plasmid (pAN12) isolated from Rhodococcus erythropolis strain AN12 was sequenced. Plasmid pAN12 encodes proteins that share homology to replication proteins and putative cell division proteins. Based on in vitro transposon mutagenesis, we determined that the Rep protein of pAN12 is essential for plasmid replication in Rhodococcus spp., and the putative cell division protein Div is important for plasmid stability. The pAN12 replicon is able to replicate in R. erythropolis strains AN12 and CW23 (ATCC 47072) and is compatible with the nocardiophage Q4 replicon present on a Rhodococcus shuttle plasmid pDA71. pAN12 appears to belong to the pIJ101/pJV1 family of rolling circle replication plasmids. Expression of an isoprenoid pathway gene ( dxs) on the pAN12-derived multicopy shuttle vector increased production of carotenoid pigments in R. erythropolis ATCC 47072.

Adenosine Triphosphatases↗

PubMed2004

Indene bioconversion by a toluene inducible dioxygenase of Rhodococcus sp. I24.

Rhodococcus sp. I24 can oxygenate indene via at least three independent enzyme activities: (i) a naphthalene inducible monooxygenase (ii) a naphthalene inducible dioxygenase, and (iii) a toluene inducible dioxygenase (TID). Pulsed field gel analysis revealed that the I24 strain harbors two megaplasmids of approximately 340 and approximately 50 kb. Rhodococcus sp. KY1, a derivative of the I24 strain, lacks the approximately 340 kb element as well as the TID activity. Southern blotting and sequence analysis of an indigogenic, I24-derived cosmid suggested that an operon encoding a TID resides on the approximately 340 kb element. Expression of the tid operon was induced by toluene but not by naphthalene. In contrast, naphthalene did induce expression of the nid operon, encoding the naphthalene dioxygenase in I24. Cell free protein extracts of Escherichia coli cells expressing tidABCD were used in HPLC-based enzyme assays to characterize the indene bioconversion of TID in vitro. In addition to 1-indenol, indene was transformed to cis-indandiol with an enantiomeric excess of 45.2% of cis-(1S,2R)-indandiol over cis-(1R,2S)-indandiol, as revealed by chiral HPLC analysis. The Km of TID for indene was 380 microM. The enzyme also dioxygenated naphthalene to cis-dihydronaphthalenediol with an activity of 78% compared to the formation of cis-indandiol from indene. The Km of TID for naphthalene was 28 microM. TID converted only trace amounts of toluene to 1,2-dihydro-3-methylcatechol after prolonged incubation time. The results indicate the role of the tid operon in the bioconversion of indene to 1-indenol and cis-(1S,2R)-indandiol by Rhodococcus sp. I24.

Chromatography, High Pressure Liquid↗