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PubMed2004

Degradation of hydrocarbons and alcohols at different temperatures and salinities by Rhodococcus erythropolis DCL14.

Rhodococcus erythropolis DCL14 cells were able to metabolise C5-C16 hydrocarbons and C1-C12 alcohols as sole carbon and energy sources, both at 15 and 28 degrees C. Metabolic activity was also observed at 1.00%, 1.95% and 2.50% sodium chloride. Almost complete degradation of n-, iso- and cyclo-alkanes and aromatic compounds present in fuel oil was achieved after 9 months, 60% being consumed in the first three months. The results from the conditions tested here suggest that this type of bacterium could be involved in bioremediation processes in marine environments such as the Atlantic, Pacific and Indian Ocean.

Alcohols↗

PubMed2005

Inhibition of diethyl ether degradation in Rhodococcus sp. strain DEE5151 by glutaraldehyde and ethyl vinyl ether.

Alkyl ether-degrading Rhodococcus sp. strain DEE5151, isolated from activated sewage sludge, has an activity for the oxidation of a variety of alkyl ethers, aralkyl ethers and dibenzyl ether. The whole cell activity for diethyl ether oxidation was effectively inhibited by 2,3-dihydrofurane, ethyl vinyl ether and glutaraldehyde. Glutaraldehyde of less than 30 microM inhibited the activity by a competitive manner with the inhibition constant, K(I) of 7.07+/-1.36 microM. The inhibition type became mixed at higher glutaraldehyde concentrations >30 microM, probably due to the inactivation of the cell activity by the Schiff-base formation. Structurally analogous ethyl vinyl ether inhibited the diethyl ether oxidation activity in a mixed manner with decreasing the apparent maximum oxidation rate, v(max)(app), and increasing the apparent Michaelis-Menten constant, K(M)(app). The mixed type inhibition by ethyl vinyl ether seemed to be introduced not only by the structure similarity with diethyl ether, but also by the reactivity of the vinyl ether with cellular components in the whole cell system.

Biodegradation, Environmental↗

PubMed2005

Molecular and biochemical analysis of phthalate and terephthalate degradation by Rhodococcus sp. strain DK17.

Alkylbenzene-degrading Rhodococcus sp. strain DK17 is able to utilize phthalate and terephthalate as growth substrates. The genes encoding the transformation of phthalate and terephthalate to protocatechuate are organized as two separate operons, located 6.7kb away from each other. Interestingly, both the phthalate and terephthalate operons are induced in response to terephthalate while expression of the terephthalate genes is undetectable in phthalate-grown cells. In addition to two known plasmids (380-kb pDK1 and 330-kb pDK2), a third megaplasmid (750-kb pDK3) was newly identified in DK17. The phthalate and terephthalate operons are duplicated and are present on both pDK2 and pDK3. RT-PCR experiments, coupled with sequence analysis, suggest that phthalate and terephthalate degradation in DK17 proceeds through oxygenation at carbons 3 and 4 and at carbons 1 and 2 to form 3,4-dihydro-3,4-dihydroxyphthalate and 1,2-dihydro-1,2-dihydroxyterephthalate, respectively. The 3,4-dihydroxyphthalate pathway was further corroborated through colorometric tests. Apparently, the two dihydrodiol metabolites are subsequently dehydrogenated and decarboxylated to form protocatechuate, which is further degraded by a protocatechuate 3,4-dioxygenase as confirmed by a ring-cleavage enzyme assay.

Biodegradation, Environmental↗

PubMed2005

Degradation of aflatoxin B(1) by cell-free extracts of Rhodococcus erythropolis and Mycobacterium fluoranthenivorans sp. nov. DSM44556(T).

Biological degradation of aflatoxin B(1) (AFB(1)) by Rhodococcus erythropolis was examined in liquid cultures and in cell-free extracts. Dramatic reduction of AFB(1) was observed during incubation in the presence of R. erythropolis cells (17% residual AFB(1) after 48 h and only 3-6% residual AFB(1) after 72 h). Cell-free extracts of four bacterial strains, R. erythropolis DSM 14,303, Nocardia corynebacterioides DSM 12,676, N. corynebacterioides DSM 20,151, and Mycobacterium fluoranthenivorans sp. nov. DSM 44,556(T) were produced by disrupting cells in a French pressure cell. The ability of crude cell-free extracts to degrade AFB(1) was studied under different incubation conditions. Aflatoxin B(1) was effectively degraded by cell free extracts of all four bacterial strains. N. corynebacterioides DSM 12,676 (formerly erroneously classified as Flavobacterium aurantiacum) showed the lowest degradation ability (60%) after 24 h, while >90% degradation was observed with N. corynebacterioides DSM 20,151 over the same time. R. erythropolis and M. fluoranthenivorans sp. nov. DSM 44,556(T) have shown more than 90% degradation of AFB(1) within 4 h at 30 degrees C, whilst after 8 h AFB(1) was practicably not detectable. The high degradation rate and wide temperature range for degradation by R. erythropolis DSM 14,303 and M. fluoranthenivorans sp. nov. DSM 44,556(T) indicate potential for application in food and feed processing.

Aflatoxin B1↗

PubMed2006

Biological degradation of aflatoxin B1 by Rhodococcus erythropolis cultures.

Aflatoxin contamination of food and grain poses a serious economic and health problem worldwide, but particularly in Africa. Aflatoxin B(1) (AFB(1)) is extremely mutagenic, toxic and a potent carcinogen to both humans and livestock and chronic exposure to low levels of AFB(1) is a concern. In this study, the biodegradation of aflatoxin B(1) (AFB(1)) by Rhodococcus erythropolis was examined in liquid cultures using thin layer chromatography (TLC), high performance liquid chromatography (HPLC), electro spray mass spectrometry (ESMS) and liquid chromatography mass spectrometry (LCMS). AFB(1) was effectively degraded by extracellular extracts from R. erythropolis liquid cultures. Results indicated that the degradation is enzymatic and that the enzymes responsible for the degradation of AFB(1) are extracellular and constitutively produced. Furthermore, the biodegradation of AFB(1) when treated with R. erythropolis extracellular fraction coincided with a loss of mutagenicity, as evaluated by the Ames test for mutagenicity.

Aflatoxin B1↗

PubMed2005

Immune response to vaccines based upon the VapA protein of the horse pathogen, Rhodococcus equi, in a murine model.

Rhodococcus equi is a significant pathogen in foals predominantly causing a pyogranulomatous bronchopneumonia. Many vaccine candidates have been tested for the prevention of R. equi disease in foals. However, none of these have been developed for widespread commercial use. Previous studies have shown that a Th1 immune response is imperative for the protection of foals against R. equi disease. In this study a DNA and a protein vaccine based upon the well-characterised R. equi virulence-associated protein VapA were developed. The vaccines were tested in the BALB/c murine model and the results showed that both vaccine candidates elicited a Th1-type response in the host. Upon coadministration of an IL-12 expression plasmid with the DNA vaccine, an increase in the Th1 response was observed. However, when mice were challenged with 1.5 x 10(7) virulent R. equi ATCC 33701 none of the vaccinated mice showed protection apart from the mice immunised with live R. equi. These results indicate that despite their immunogenicity the VapA-based DNA and recombinant protein vaccines developed in this study were unable to prevent bacterial replication following a high-dose systemic challenge with virulent R. equi in the BALB/c model.

Actinomycetales Infections↗

PubMed2006

Immunogenicity of synthetic Rhodococcus equi virulence-associated protein peptides in neonate foals.

Rhodococcus equi infection is considered the most common cause of pneumonia in foals less than 6 months of age. Immunization of foals and/or mares may become a procedure of choice for prevention. The present work documents the antibody response of neonate foals to R. equi virulence-associated protein (Vap) vaccine candidate peptides. A mixture of 4 R. equi (ATCC 33701) Vap peptides was selected based on their hydrophilicity and recognition by naturally acquired IgG antibodies from 13 adult horses and 33 neonate foals from France and Japan. They were combined with a water-based nanoparticular adjuvant to promote a protective immune response including both Th1 cytokine pattern and antibody response. A single intramuscular injection resulted in an IgG antibody response 30 days later, although inconsistently. In responding animals, no bias in IgG subclass distribution was observed, and antibody response was associated with enhanced serum opsonic activity. In conclusion, data indicate that synthetic Vap peptides combined with nanoparticular adjuvant were immunogenic and resulted in a significant increase in IgG antibodies against the corresponding virulent R. equi strain in a majority of foals.

Actinomycetales Infections↗

PubMed2006

Detection, isolation and partial characterization of an immunostimulating glycoprotein from Rhodococcus fascians.

In a search for novel immunostimulating substances we detected that culture supernatants of the gram-positive phytopathogenic bacterium, Rhodococcus fascians, were able to induce cytokine release (TNF(alpha)) from mouse peritoneal macrophages. Monoclonal antibodies were generated against the active principle, and were employed for its isolation and partial characterization as a high molecular (MW>100 kDa) glycoprotein. In addition, methods practicable for its biotechnological preparation and several ELISA variants for its determination were developed.

Animals↗

PubMed2004

Isolation and characterization of Rhodococcus sp. strains TMP2 and T12 that degrade 2,6,10,14-tetramethylpentadecane (pristane) at moderately low temperatures.

Branched alkanes including 2,6,10,14-tetramethylpentadecane (pristane) are more resistant to biological degradation than straight-chain alkanes especially under low-temperature conditions, such as 10 degrees C. Two bacterial strains, TMP2 and T12, that are capable of degrading pristane at 10 degrees C were isolated and characterized. Both strains grew optimally at 30 degrees C and were identified as Rhodococcus sp. based on the 16S rRNA gene sequences. Strain T12 degraded comparable amounts of pristane in a range of temperatures from 10 to 30 degrees C and strain TMP2 degraded pristane similarly at 10 and 20 degrees C but did not degrade it at 30 degrees C. These data suggest that the strains have adapted their pristane degradation system to moderately low-temperature conditions.

Adaptation, Physiological↗

PubMed2005

Gene expression analysis using a modified HiCEP method applicable to prokaryotes: a study of the response of Rhodococcus to isoniazid and ethambutol.

We established a novel method to analyze the gene expression of prokaryotes by modifying and optimizing the HiCEP (high coverage gene expression analysis) method, which was originally developed for eukaryotic gene expression profiling. Following the removal of abundant rRNA, the mRNA of prokaryotic cells was enzymatically polyadenylated and subjected to HiCEP analysis. This method was highly reproducible due to selective PCR that was performed by using adaptor specific primers. We confirmed induction of tipA and induction or suppression of cspA, which are genes that are obtained from distinctive actinomycetes and responded to thiostrepton and temperature stress, respectively. Further, we applied this method to explore the gene expression profile of Rhodococcus erythropolis in response to drugs that inhibit cell wall synthetic pathways, and we were able to identify 35 upregulated genes. Among these genes, we confirmed the upregulation of 22 genes by using RT-PCR (reverse transcriptase-polymerase chain reaction). Some of these genes are involved in the synthesis of mycolic acid and arabinogalactan, suggesting a cell response to drug treatment by regulation of the genes involved in cell wall synthesis. This method could prove to be a useful technique for gene expression analysis of prokaryotes, particularly nonmodel strains with unknown genome sequences.

Antitubercular Agents↗

PubMed2004

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.

Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.

Amino Acid Sequence↗

PubMed2006

Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol.

The crystal structure of the 3-chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III) ion-containing enzyme specialized in the aerobic biodegradation of 3-chloro- and methyl-substituted catechols, has been solved by molecular replacement techniques using the coordinates of 4-chlorocatechol 1,2-dioxygenase from the same organism (PDB code 1S9A) as a starting model and refined at 1.9 A resolution (R(free) 21.9%; R-factor 17.4%). The analysis of the structure and of the kinetic parameters for a series of different substrates, and the comparison with the corresponding data for the 4-chlorocatechol 1,2-dioxygenase isolated from the same bacterial strain, provides evidence of which active site residues are responsible for the observed differences in substrate specificity. Among the amino acid residues expected to interact with substrates, only three are altered Val53(Ala53), Tyr78(Phe78) and Ala221(Cys224) (3-chlorocatechol 1,2-dioxygenase(4-chlorocatechol 1,2-dioxygenase)), clearly identifying the substitutions influencing substrate selectivity in these enzymes. The crystallographic asymmetric unit contains eight subunits (corresponding to four dimers) that show heterogeneity in the conformation of a co-crystallized molecule bound to the catalytic non-heme iron(III) ion resembling a benzohydroxamate moiety, probably a result of the breakdown of recently discovered siderophores synthesized by Gram-positive bacteria. Several different modes of binding benzohydroxamate into the active site induce distinct conformations of the interacting protein ligands Tyr167 and Arg188, illustrating the plasticity of the active site origin of the more promiscuous substrate preferences of the present enzyme.

Amino Acid Sequence↗

PubMedDate not supplied

The N-terminal coiled coil of the Rhodococcus erythropolis ARC AAA ATPase is neither necessary for oligomerization nor nucleotide hydrolysis.

Deletion mutants of the Rhodococcus erythropolis ARC AAA ATPase were generated and characterized by biochemical analysis and electron microscopy. Based on sequence comparisons the ARC protein was divided into three consecutive regions, the N-terminal coiled coil, the central ARC-specific inter domain and the C-terminal AAA domain. When the ARC AAA domain was expressed separately it formed aggregates of undefined structure. However, when the AAA domain was expressed in conjunction with the preceeding inter domain, but without the N-terminal coiled coil, high-molecular weight-complexes were formed (ARC-DeltaCC) which showed an N-ethylmaleimide-sensitive ATPase activity. In 2D crystallization experiments the ARC-DeltaCC particles yielded crystals nearly identical to those formed by the wild-type ARC complexes. Thus, the N-terminal coiled coil, which was proposed to have a role in the assembly of and/or interaction between the eukaryotic AAA ATPases in the 26S proteasome, is neither essential for assembly nor for ATP hydrolysis of the ARC ATPase. The N-terminal domain of related AAA ATPases mediates the interaction with substrates or co-factors, suggesting a regulatory function for the N-terminal coiled coil of the ARC ATPase. Surprisingly, the mutant ARC protein ARC-DeltaAAA consisting of the N-terminal coiled coil and the central inter domain, but deleted for the C-terminal AAA domain, was shown to form a dodecameric complex with sixfold symmetry. This suggests an important role of the inter domain for the ordered assembly of the ARC ATPase.

Adenosine Triphosphatases↗

PubMed2006

Characterization of the mobilization determinants of pAN12, a small replicon from Rhodococcus erythropolis AN12.

Bacteria belonging to the Gram-positive actinomycete species, Rhodococcus erythropolis, are diverse not only in terms of metabolic potentials but the plasmids they encode. It was shown previously that the R. erythropolis AN12 genome harbors a 6.3kb cryptic plasmid called pAN12, which is a member of the pIJ101 family of plasmids. Here we show that pAN12 is conjugatively mobilizable into other rhodococcal strains. A series of plasmid deletion constructs were tested for loss of mobility to identify the pAN12 cis-acting conjugation requirement. In this way, an approximately 700bp region was found to be required for plasmid transmission. A small 61bp element within this region confers mobility to an otherwise non-mobilizable plasmid. Unlike pIJ101, which encodes all necessary factors for transfer, pAN12 mobility is dependent on the presence of an AN12 megaplasmid, pREA400.

Base Sequence↗

PubMedDate not supplied

Low-temperature biodegradation of high amounts of phenol by Rhodococcus spp. and basidiomycetous yeasts.

Four cold-adapted microbial strains able to degrade high amounts of phenol were isolated from hydrocarbon-contaminated alpine soils. Two of the strains were bacteria identified as Rhodococcus spp., and two strains were basidiomycetous yeasts. One of the yeasts was identified as Trichosporon dulcitum, while the second yeast strain belonged to the Urediniomycetes and probably represents a novel species. This strain was not able to grow at temperatures above 20 degrees C, while the other three strains were cold-tolerant and could grow at temperatures ranging from 1-25 degrees C (T. dulcitum) or 1-30 degrees C (rhodococci). The yeast strains were characterized by a substantially lower optimum temperature for growth and biodegradation compared to the bacteria. The urediniomycete strain degraded 5 mM phenol at 1 degrees C faster than the two bacteria at 10 degrees C. The optimum temperature for phenol degradation was 10 degrees C (novel yeast species), 20 degrees C (T. dulcitum), or 30 degrees C (rhodococci). Using fed-batch cultivation in mineral medium with phenol as the sole carbon source, high amounts of phenol were degraded at 10 degrees C. Both rhodococci degraded up to 12.5 mM phenol, while the two yeast strains even utilized as much as 15 mM phenol.

Basidiomycota↗

PubMed2005

Catabolism of Mesamoll, a technical formulation of alkylsulfonic acid phenyl esters, by two strains of Rhodococcus rhodochrous.

The bacterial catabolism of a technical formulation of alkylsulfonic acid phenyl esters employed as a general purpose plasticizer, Mesamoll, was elucidated. Two strains of the genus Rhodococcus were found able to utilize this substrate mixture as sole source of carbon and energy. Growth experiments along with enzymatic measurements indicated that both strains utilized the phenol that was released from the corresponding alkylsulfonic acid phenyl ester-probably by enzymatic hydrolysis catalyzed by esterases-via the ortho-pathway. By GC/MS analysis it was demonstrated that those alkyl chain homologues with substituents present at or close to the end of the aliphatic backbone (i.e., 2-tetradecylsulfonic acid phenyl ester) are degraded, while those with substituents close to the center of the alkyl chain (i.e., 7-tetradecylsulfonic acid phenyl ester) are rather persistent.

Bacterial Proteins↗

PubMed2005

Metabolites from the biodegradation of di-ester plasticizers by Rhodococcus rhodochrous.

The plasticizers di-2-ethylhexyl phthalate (DEHP) and di-2-ethylhexyl adipate (DEHA) are ubiquitous in the environment and undergo partial biodegradation in the presence of soil micro-organisms. The validity of a proposed pathway for the degradation of these plasticizers by Rhodococcus rhodochrous has been confirmed by the identification of 2-ethylhexanal in gas phase emissions. Complete analyses of the aqueous and gas phases were able to account for more than 98% of the 2-ethylhexanol component of the DEHA added at the beginning of a growth study. Of this, 25% was either 2-ethylhexanol or 2-ethylhexanal that had been stripped into the gas phase and, at most, only 2% of the 2-ethylhexanol component could have been removed by mineralization. It is concluded that plasticizers are of significant environmental concern due to the resistance of the metabolites to biodegradation and their known health impacts. Two of the metabolites are of added concern due to their volatility and their potential impact on indoor air quality.

Adipates↗

PubMed2004

Immunogenecity of synthetic peptides representing linear B-cell epitopes of VapA of Rhodococcus equi.

Amino acid 65-78 of membrane protein VapA of the facultative intracellular Rhodococcus equi contained an immunodominant N-terminal B-cell epitope (N15Y peptide). Safety and immunogenecity of a synthetic peptide consisting of the amino acid 65-78 of VapA (peptide N15Y) were evaluated first in mice and in healthy adult horses. A single dose of a peptide-VapA vaccine induced and only in presence of adjuvant, specific IgG antibodies in sera of mice. After challenge with virulent R. equi 3 weeks after immunization, tissue clearance was more delayed in immunized mice than in control mice. An antibody-mediated response (restricted to IgG1 and IgG2b subclasses) predominated in vaccinated mice sera and no specific lymphocytes proliferation was observed. Next, a total of 15 mares were given systemic inoculation of N15Y peptide with IMS3012 ( n = 4 ) or IMS2211 ( n = 4 ) or ISA35 ( n = 4 ) or placebo ( n = 2). Serological responses to the peptide vaccine were found in all but not in placebo group. A significant increase of IgGb subclass in sera of vaccinated mare with N15Y peptide in presence of IMS3012 was observed in comparison to IMS2211 or ISA35 or control group. Moreover, INF-gamma, IL-2 and IL-10 mRNA expression increased more significantly in peripheral blood lymphocytes of IMS3012 group than in IMS2211 or ISA35 group. Interestingly, a significant decrease of IL-4 mRNA expression (undetectable level) was observed with all adjuvants. These results support the use of peptide N15Y in presence of IMS3012 adjuvant in future studies of protection of foals against R. equi.

Actinomycetales Infections↗