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PubMed2004

Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1.

Transcription of the bphA1A2A3A4C1B genes, which are responsible for the conversion of biphenyl and polychlorinated biphenyl to the meta-cleavage products in Rhodococcus sp. strain RHA1, was examined. The bphA1 promoter (P(bphA1)) was identified and was shown to promote transcription induction by biphenyl and ethylbenzene. An 8.8-kb HindIII fragment that promotes transcription induction of P(bphA1) in Rhodococcus erythropolis IAM1399 was isolated from the region downstream of bphB by using a reporter plasmid containing P(bphA1). Analysis of the nucleotide sequence of this fragment revealed a set of putative two-component regulatory system genes, which were designated bphS and bphT. Deletion analysis of the 8.8-kb HindIII fragment indicated that bphT is responsible for the basal activation of P(bphA1) and that both bphS and bphT are required for the elevated basal activation of and transcriptional induction by biphenyl of P(bphA1). These results support the notion that bphS and bphT encode a sensor kinase and a response regulator, respectively, of a two-component regulatory system. The bphS and bphT genes promote transcriptional induction by a variety of aromatic compounds, including biphenyl, benzene, alkylbenzenes, and chlorinated benzenes. A promoter activity assay and reverse transcription (RT)-PCR analysis revealed a weak constitutive promoter in the adjacent region upstream of bphS. RT-PCR analysis indicated that there is induced transcription of bphA1 through bphT, in which P(bphA1) is thought to take part. An insertionally inactivated bphS mutant, SDR1, did not grow on biphenyl. Growth was restored by introduction of an intact bphS gene into SDR1. These results indicate that at least bphS is indispensably responsible for the growth of RHA1 on biphenyl.

Amino Acid Sequence↗
PubMed2005

Rhodococcus equi brain abscess in a patient without HIV.

Rhodococcus equi, a Gram positive organism, is a cause of infections in immunocompromised individuals. In humans, it mainly causes disease in those infected with human immunodeficiency virus (HIV), and generally presents as chronic pulmonary infection. It may also cause intracranial infections, which manifest as brain abscesses. This report describes a case of rhodococcus brain and pulmonary infection in a patient who did not have HIV or another disorder of cell mediated immunity. He was treated with intravenous imipenem, vancomycin, and rifampin for eight weeks and recovered from the infection.

Actinomycetales Infections↗
PubMed1993

1,3,5-Trihydroxybenzene biodegradation by Rhodococcus sp. BPG-8.

The metabolic pathway used by Rhodococcus sp. BPG-8 isolated from oil-rich soil in Newfoundland for the degradation of 1,3,5-trihydroxybenzene (phloroglucinol) as a sole source of carbon and energy was determined. Culture filtrates of cells grown on phloroglucinol detected 1,2,3,5-tetrahydroxybenzene when extracted and analyzed using gas chromatography--mass spectrometry, thin-layer chromatography, and ultraviolet spectrophotometry. Nonaromatics were either derivatized with 2,4-dinitrophenylhydrazine and compared against authentic standards by the above methods, or detected by chemical and enzymatic methods. Extracts of cells grown on phloroglucinol contained phloroglucinol hydroxylase activity, and a dioxygenase that carried out ortho-cleavage of 1,2,3,5-tetrahydroxybenzene. The extract also showed inducible activity for further metabolism of acetopyruvate leading to accumulation of formate in the supernatant. A tentative degradative pathway for phloroglucinol by Rhodococcus sp. BPG--8 is proposed.

Biodegradation, Environmental↗
PubMed1994

Sequence of Rhodococcus gene cluster encoding the subunits of ethanolamine ammonia-lyase and an APC-like permease.

Sequence analysis of a 5173-bp genomic fragment from the nocardioform actinomycete Rhodococcus sp. strain NI86/21 revealed the presence of two genes, eutB and eutC, encoding the putative homologues of the large and small subunits of the ethanolamine ammonia-lyase, respectively, from Salmonella typhimurium. This is the first report of the characterization of these genes in a Gram-positive species. Immediately upstream of eutB, a gene encoding a putative permease of the APC (amino acids, polyamines, choline) transporter family was located. At present, no other Gram-positive members of this permease family are known. The translational coupling of these eut genes suggests an operon-like organization of the ethanolamine genes in Rhodococcus species. A truncated open reading frame downstream of eutC contained an N-terminal motif characteristic of membrane-anchored lipoproteins.

Amino Acid Sequence↗
PubMed2002

Hydrophobicity development, alkane oxidation, and crude-oil emulsification in a Rhodococcus species.

The relationship between the phenomena alkane oxidation, extreme hydrophobicity of the cell surface, and crude-oil emulsification in Rhodococcus sp. strain 094 was investigated. Compounds that induce the emulsifying ability simultaneously induced the cytochrome P450-containing alkane oxidizing system and the transition from low to high cell-surface hydrophobicity. Exposed to inducers of crude-oil emulsification, the cells developed a strong hydrophobic character during exponential growth, which was rapidly lost when entering stationary phase. The loss in hydrophobicity coincided in time with the crude-oil emulsification, indicating that the components responsible for the formation of cell-surface hydrophobicity act as excellent emulsion stabilisers only after release from the cells. Rhodococcus sp. strain 094 possessed three distinct levels of cell-surface hydrophobicity. One level of low hydrophobicity was characteristic of cells in late stationary phase and was independent of growth substrate. A second and more hydrophobic level was observed for cells in exponential phase grown on water-soluble substrates, while a third level, characterised by extreme cell hydrophobicity, was observed for cells in exponential phase cultivated on hydrophobic substrates such as hexadecane. The production of the oil-emulsifying agents seems to require external sources of nitrogen and phosphate.

Alkanes↗
PubMed2005

Identification of a carboxylesterase-producing Rhodococcus soil isolate.

Subtropical soil microbial isolates were screened for carbohydrate, tributyrin, or olive oil hydrolysis using agar plates supplemented with the corresponding substrates. A heterotrophic, aerobic, Gram-positive strain displaying activity on tributyrin was selected and further characterized. Analysis of the morphological and physiological traits of the strain placed it as a member of the genus Rhodococcus. Further 16S rDNA sequencing revealed a 99% identity to Rhodococcus erythropolis. The strain displayed lipolytic activity on fatty-acid-derivative substrates of short chain length, with cell extract fractions having highest activity, as confirmed by the presence, after zymogram analysis, of a ca. 60-kDa intracellular protein band with activity on 4-methylumbelliferone-butyrate substrate. The presence of such a lipolytic enzyme, similar to those found in other Gram-positive bacteria, indicates that the strain could be of interest for certain biotechnological applications, like the synthesis of pharmaceuticals or biocide detoxification.

Bacterial Typing Techniques↗
PubMed2001

Prevalence of virulent Rhodococcus equi in soil from five R. equi-endemic horse-breeding farms and restriction fragment length polymorphisms of virulence plasmids in isolates from soil and infected foals in Texas.

Rhodococcus equi isolates (462) obtained from 64 soil samples collected on 5 R. equi-endemic horse-breeding farms and isolates from 100 infected foals in Texas were examined to determine the prevalence and genotypic diversity of virulence-associated plasmids. Isolates were tested for the presence of 15-17-kDa virulence-associated protein antigens (VapA) by immunoblotting and virulence-associated plasmids by PCR. Plasmid DNAs were isolated and analyzed by digestion with restriction endonucleases for estimation of size and comparison of polymorphisims. Rhodococcus equi were isolated from soil of all 5 farms; however, virulent R. equi were only isolated from 3 of the 5 farms and represented 18.8% (87 of 462) of total isolates. Of the 87 virulent soil isolates, 56 (64.5%) contained an 85-kb type I plasmid, 23 (26.4%) an 87-kb type I plasmid, 7 (8%) a newly defined 85-kb type III plasmid (Tx 43), and 1 (1.1%) a newly defined 85-kb type IV plasmid (Tx 47). Of the 100 isolates from infected foals, 96 were virulent. Of the 96 virulent isolates, 51 (53.1%) contained an 85-kb type I plasmid, 39 (40.6%) an 87-kb type I plasmid, 4 (4.2%) an 85-kb type III plasmid (Tx 43), and 2 (2.1%) an 85-kb type IV plasmid (Tx 47). There are at least 4 different R. equi virulence-associated plasmids in Texas, 2 of which have not previously been described. Based upon virulence plasmid typing, there is geographic diversity among isolates of R. equi from clinical and environmental samples on horse-breeding farms in Texas. There is not a strong correlation between the presence of virulent R. equi in farm soils and the R. equi disease status of those farms.

Actinomycetales Infections↗
PubMed2002

Detection of Rhodococcus equi by polymerase chain reaction using species-specific nonproprietary primers.

Species-specific primers for the polymerase chain reaction (PCR) for the detection of Rhodococcus equi were developed. These primers were based on unique DNA fragments produced from R. equi reference strains and field isolates. Following random amplification of polymorphic DNA from R. equi and R. rhodochrous with a set of 40 arbitrary 10-base pair (bp) primers, a pair of species-specific primers was designed to detect a unique 700-bp fragment of R. equi chromosomal DNA. This PCR product was limited to R. equi and was not detectable in other Rhodococcus species or in a panel of additional gram-positive and gram-negative bacteria.

Actinomycetales Infections↗
PubMed1994

Nitrile hydratase gene from Rhodococcus sp. N-774 requirement for its downstream region for efficient expression.

For improvement of the production of nitrile hydratase (NHase) from Rhodococcus sp. N-774 by recombinant DNA techniques, several plasmids, each of which had a deletion of the upstream or downstream region of the genes encoding the alpha and beta subunits of NHase, were constructed. Enzyme assays of recombinant R. rhodochrous and Escherichia coli cells showed that a downstream region of the NHase genes was indispensable for the production of active NHase in both cells, but for the production of the active amidase, no genes other than the amidase structural gene were required. The nucleotide sequence of the downstream region contained a single open reading frame (Orf1188) with 396 amino acids. Orf1188 showed similarity in amino acid sequence to P47K, an open reading frame found downstream of the NHase genes from Pseudomonas chlororaphis B23, and also to the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. Because the distance between the TGA stop codon for the NHase beta-subunit and the ATG codon for Orf1188 is only 98 bp, and because production of both Orf1188 and NHase is dependent on a promoter upstream of the amidase gene, these genes appear to be co-transcribed in a polycistronic manner, forming an operon. By optimization of the culture conditions of R. rhodochrous carrying pKRNH2, which contained the amidase, NHase, and Orf1188 genes, the transformant showed the NHase activity 6-fold higher than that of the original strain, Rhodococcus sp. N-774.

Amino Acid Sequence↗
PubMed2000

Alkylated benzothiophene desulfurization by Rhodococcus sp. strain T09.

A benzothiophene desulfurizing bacterium was isolated and identified as Rhodococcus sp. strain T09. Growth assays revealed that this strain assimilated, as the sole sulfur source, various organosulfur compounds that cannot be assimilated by the well-studied dibenzothiophene-desulfurizing Rhodococcus sp. IGTS8. The cellular growth rate of strain T09 for the alkylated benzothiophenes depended on the alkylated position and the length of the alkyl moiety.

Alkylation↗
PubMed2001

Improvement of desulfurization activity in Rhodococcus erythropolis KA2-5-1 by genetic engineering.

Rhodococcus erythropolis KA2-5-1 can desulfurize dibenzothiophene (DBT) into 2-hydroxybiphenyl. A cryptic plasmid, pRC4, which was derived from R. rhodochrous IFO3338, was combined with an Escherichia coli vector to construct an E. coli-Rhodococcus shuttle vector. The complete nucleotide sequence of 2582-bp pRC4 was analyzed. Based on the characteristics of its putative replication genes, pRC4 was assigned to the family of pAL5000-related replicons. The desulfurization gene cluster, dszABC, and the related reductase gene, dszD, cloned from KA2-5-1, were reintroduced into KA2-5-1 and efficiently expressed. The DBT desulfurization ability of the transformant carrying two dszABC clusters and one dszD on the vector was about 4-fold higher than that of the parent strain, and the transformant also showed improved desulfurization activity for light gas oil (LGO). Sulfur components in LGO before and after the reaction were analyzed with gas chromatography-atomic emission detection.

Amino Acid Sequence↗
PubMed2002

Isolation and characterization of dibenzofuran-degrading actinomycetes: analysis of multiple extradiol dioxygenase genes in dibenzofuran-degrading Rhodococcus species.

Sixteen actinomycetes capable of utilizing dibenzofuran as a sole source of carbon and energy were isolated, including Rhodococcus, Microbacterium, and Terrabacter genera. Heretofore, no dibenzofuran-utilizing strain belonging to the genus Microbacterium has been reported. Five extradiol dioxygenase genes (dfdB, and edil to 4) of the strain Rhodococcus sp. YK2 were cloned and analyzed. The nucleotide sequence of dfdB gene was almost identical to the bphC1 gene of Terrabacter sp. DPO360, which was involved in dibenzofuran metabolism in this strain. Southern and Northern hybridization analyses using these extradiol dioxygenase genes as probes suggest that the dfdB gene in YK2 was conserved in diverse dibenzofuran-utilizing actinomycetes; also, the dfdB gene was the only expressed gene among five extradiol dioxygenase genes in the medium containing DF as a sole carbon source. These results suggest that the dfdB gene is important for dibenzofuran metabolism not only in the strain YK2, but also in diverse dibenzofuran-degrading actinomycetes.

Actinobacteria↗
PubMed1998

Improved electroporation of Rhodococcus equi.

The condition of an electroporation method was re-evaluated for the introduction of foreign plasmid DNA into Rhodococcus equi. The method is based on an electroporation of the bacteria made competent by culturing in a broth containing glycine and by heat shock at 50 degrees C. Transformation of R. equi could be achieved with a chloramphenicol-resistant shuttle vector originating from Rhodococcus fascians at an efficiency of about 10(4) transformants/microgram DNA. The bacteria were also shown to become competent when they were incubated with a chemical transformation buffer prior to washing with an electroporation buffer.

Culture Media↗
PubMed1989

Microbial metabolism of quinoline and related compounds. II. Degradation of quinoline by Pseudomonas fluorescens 3, Pseudomonas putida 86 and Rhodococcus spec. B1.

Quinoline catabolism was investigated with different bacterial strains, able to use quinoline as sole source of carbon, nitrogen and energy. Some degradation products of quinoline were isolated from the culture fluids and identified. With Pseudomonas fluorescens and Pseudomonas putida we found 2-oxo-1,2-dihydroquinoline, 8-hydroxy-2-oxo-1,2-dihydroquinoline, 8-hydroxycoumarin and 2,3-dihydroxyphenylpropionic acid as intermediates. With a Rhodococcus strain 2-oxo-1,2-dihydroquinoline, 6-hydroxy-2-oxo-1,2-dihydroquinoline, a red meta-cleavage product and a blue fluorescent compound were isolated. The red compound was identified as 5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridone. From this the blue fluorescent azacoumarin 2H-pyrano-2-one-[3,2b]-5H-6-pyridone is formed by chemical decomposition. Therefore it can be considered a by-product of quinoline-degradation in Rhodococcus spec. With the present results two different degradation pathways for quinoline in different microorganisms are proposed.

Chemical Phenomena↗
PubMed1991

Microbial metabolism of quinoline and related compounds. XII. Isolation and characterization of the quinoline oxidoreductase from Rhodococcus spec. B1 compared with the quinoline oxidoreductase from Pseudomonas putida 86.

Quinoline oxidoreductase from Rhodococcus spec. B1 was purified 39-fold to apparent homogeneity in a 5-step procedure with a recovery of 26%. The Mr of the native enzyme as determined by gel chromatography was 300,000. SDS polyacrylamide gel electrophoresis of the enzyme revealed 3 protein bands corresponding to Mr 82,000, 32,000, and 18,000. The enzyme contains 1.3 atoms of molybdenum, 8 atoms of iron, 8 atoms of acid-labile sulphur, 2 molecules of FAD and 2 molecules of molybdopterin cytosine dinucleotide. Cyanide, 4-hydroxymercuribenzoate and methanol were effective as inhibitors. The amino-terminal protein sequences of the 3 subunits of quinoline oxidoreductase from Rhodococcus B1 compared to those of quinoline oxidoreductase from Pseudomonas putida 86 revealed no difference among 71 amino acids examined.

Amino Acid Sequence↗
PubMed2000

Association of disease with isolation and virulence of Rhodococcus equi from farm soil and foals with pneumonia.

OBJECTIVE: To determine whether isolation and virulence of Rhodococcus equi from soil and infected foals are associated with clinical disease. DESIGN: Cross-sectional and case-control study. SAMPLE POPULATION: R equi isolates from 50 foals with pneumonia and soil samples from 33 farms with and 33 farms without a history of R equi infection (affected and control, respectively). PROCEDURE: R equi was selectively isolated from soil samples. Soil and clinical isolates were evaluated for virulence-associated protein antigen plasmids (VapA-P) and resistance to the beta-lactam antibiotics penicillin G and cephalothin. Microbiologic cultures and VapA-P assays were performed at 2 independent laboratories. RESULTS: VapA-P was detected in 49 of 50 (98%) clinical isolates; there was complete agreement between laboratories. Rhodococcus equi was isolated from soil on 28 of 33 (84.8%) affected farms and 24 of 33 (72.7%) control farms, but there was poor agreement between laboratories. Virulence-associated protein antigen plasmids were detected on 14 of 66 (21.2%) farms by either laboratory, but results agreed for only 1 of the 14 VapA-P-positive farms. We did not detect significant associations between disease status and isolation of R equi from soil, detection of VapA-P in soil isolates, or resistance of soil isolates to beta-lactam antibiotics. No association between beta-lactam antibiotic resistance and presence of VapA-P was detected. CONCLUSIONS AND CLINICAL RELEVANCE: On the basis of soil microbiologic culture and VapA-P assay results, it is not possible to determine whether foals on a given farm are at increased risk of developing disease caused by R equi.

Actinomycetales Infections↗
PubMed2003

Evaluation of equine breeding farm management and preventative health practices as risk factors for development of Rhodococcus equi pneumonia in foals.

OBJECTIVE: To determine whether foal management practices, environmental management, and preventative health practices are risk factors for development of Rhodococcus equi pneumonia in foals. DESIGN: Prospective matched case-control study. ANIMALS: 2,764 foals on 64 equine breeding farms with 9,991 horses. PROCEDURE: During 1997, participating veterinarians completed paired data collection forms for comparison; 1 for an affected farm (containing > or = 1 foal with pneumonia caused by R equi) and 1 for a control farm. Information collected pertained to stabling facilities, environmental management, foal husbandry, and preventative equine health practices. RESULTS: Matched farm data compared by use of conditional logistic regression indicated that personnel on affected farms were more likely to attend foal births, test foals for adequacy of passive immunity, administer plasma or other treatments to foals to supplement serum immunoglobulin concentrations, administer hyperimmune plasma prophylactically to foals, vaccinate mares and foals against Streptococcus equi infection, and use multiple anthelmintics in deworming programs. Affected farms were also more likely to have foals that developed other respiratory tract disorders and were approximately 4 times as likely to have dirt floors in stalls used for housing foals as were control farms. CONCLUSIONS AND CLINICAL RELEVANCE: Rhodococcus equi pneumonia does not appear to be associated with poor farm management or a lack of attention to preventative health practices. Housing foals in stalls with dirt floors may increase the risk for development of R equi pneumonia.

Actinomycetales Infections↗