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Expression of glutathione S-transferase and peptide methionine sulphoxide reductase in Ochrobactrum anthropi is correlated to the production of reactive oxygen species caused by aromatic substrates.

Peptide methionine sulphoxide reductase (MsrA) and glutathione S-transferases (GSTs) are considered as detoxification enzymes. In the xenobiotics-degrading bacterium Ochrobactrum anthropi the two enzymes are co-induced by toxic concentrations of aromatic substrates such as phenol and 4-chlorophenol. In aerobic organisms, degradation of aromatic substrates by mono- and dioxygenases leads to a generation of oxidative stress that causes the occurrence of reactive oxygen species (ROS). A capillary electrophoretic method, using the intracellular conversion of dihydrorhodamine-123 into rhodamine-123, was developed to measure the content of ROS in the bacteria. The presence of toxic concentrations of the aromatic substrate 4-chlorophenol, an inducer of GST and MsrA, leads to a significant increase in the production of ROS. These results strongly suggest that GST and MsrA enzymes are part of the bacterial defence mechanism against particular oxidative stress conditions. As oxidative stress is known to be present predominantly close to the cytoplasmic membrane, we investigated the subcellular distribution of both MsrA and GST enzymes in this bacterium grown in the presence of 4-chlorophenol. By Western blotting, MsrA and GST was assayed in the cytoplasm as well as in the periplasm. Moreover, immunolocalisation by colloidal gold immunoelectron microscopy identified the two proteins associated with the cell envelope.

Chlorophenols↗

A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.

BACKGROUND: The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. RESULTS: The crystal structure of the enzyme has been determined to 1.82 A resolution using the multiple isomorphous replacement method. The heterodimer folds into a single domain organised as an alphabetabetaalpha sandwich in which two mixed beta sheets are flanked on both sides by two alpha helices. CONCLUSIONS: DmpA shows no similarity to other known aminopeptidases in either fold or catalytic mechanism, and thus represents the first example of a novel family of aminopeptidases. The protein fold of DmpA does, however, show structural homology to members of the N-terminal nucleophile (Ntn) hydrolase superfamily. DmpA presents functionally equivalent residues in the catalytic centre when compared with other Ntn hydrolases, and is therefore likely to use the same catalytic mechanism. In spite of this homology, the direction and connectivity of the secondary structure elements differ significantly from the consensus Ntn hydrolase topology. The DmpA structure thus characterises a new subfamily, but supports the common catalytic mechanism for these enzymes suggesting an evolutionary relationship.

Aminopeptidases↗

Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis. The most common bacterial resistance mechanism against beta-lactam compounds is the synthesis of beta-lactamases that hydrolyse beta-lactam rings. These enzymes are believed to have evolved from cell-wall DD-peptidases. Understanding the biochemical and mechanistic features of the beta-lactam targets is crucial because of the increasing number of resistant bacteria. DAP is a D-aminopeptidase produced by Ochrobactrum anthropi. It is inhibited by various beta-lactam compounds and shares approximately 25% sequence identity with the R61 DD-carboxypeptidase and the class C beta-lactamases. RESULTS: The crystal structure of DAP has been determined to 1.9 A resolution using the multiple isomorphous replacement (MIR) method. The enzyme folds into three domains, A, B and C. Domain A, which contains conserved catalytic residues, has the classical fold of serine beta-lactamases, whereas domains B and C are both antiparallel eight-stranded beta barrels. A loop of domain C protrudes into the substrate-binding site of the enzyme. CONCLUSIONS: Comparison of the biochemical properties and the structure of DAP with PBPs and serine beta-lactamases shows that although the catalytic site of the enzyme is very similar to that of beta-lactamases, its substrate and inhibitor specificity rests on residues of domain C. DAP is a new member of the family of penicillin-recognizing proteins (PRPs) and, at the present time, its enzymatic specificity is clearly unique.

Amino Acid Sequence↗

Liquid chromatography-electrospray mass spectrometry study of cysteine-10 S-glutathiolation in recombinant glutathione S-transferase of Ochrobactrum anthropi.

Glutathione S-transferase of Ochrobactrum anthropi (OaGST), a bacterium isolated from soils contaminated by xenobiotic pollutants, was recently purified, cloned and characterised in our laboratories. The recombinant OaGST (rOaGST), highly expressed in Escherichia coli, when purified by glutathione-affinity chromatography and then analysed by electrospray ionisation mass spectrometry (ESI-MS), has evidenced a disulphide bond with glutathione (S-glutathiolation), which was removable by reduction with 2-mercaptoethanol. Enzymatic digestion of rOaGST with endoproteinase Glu-C, followed by liquid chromatography (LC)-ESI-MS analyses of the peptide mixtures under both reducing and not reducing conditions, have shown that glutathione was covalently bound to the Cys10 residue of rOaGST. Furthermore, LC-ESI-MS analyses of overexpressed rOaGST in Escherichia coli crude extracts, with and without incubation with glutathione, have not shown any S-glutathiolation of the recombinant enzyme.

Amino Acid Sequence↗

Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi.

We report the first large-scale gel-free proteomic analysis of the soluble subproteome of the emerging pathogen Ochrobactrum anthropi. Utilizing our robust offline multidimensional protein identification protocol, a total of 57 280 peptides were initially identified utilizing automated MS/MS analysis software. We describe our investigation of the heuristic protein validation tool PROVALT and demonstrate its ability to increase the speed and accuracy of the curation process of large-scale proteomic datasets. PROVALT reduced our peptide list to 8517 identified peptides and further manual curation of these peptides led to a final list of 984 uniquely identified peptides that resulted in the positive identification of 249 proteins. These identified proteins were functionally classified and physiochemically characterized. A variety of typical "housekeeping" functions identified within the proteome included nucleic acid, amino and fatty acid anabolism and catabolism, glycolysis, TCA cycle, and pyruvate and selenoamino acid metabolism. In addition, a number of potential virulence factors of relevance to both plant and human disease were identified.

Amino Acid Sequence↗

Ammonium and methylammonium uptake in a fertilizer-degrading strain of Ochrobactrum anthropi.

The transport of ammonium and methylammonium was studied in a strain of Ochrobactrum anthropi, a microorganism isolated from garden soil and able to degrade methyleneureas which are used as slow-release nitrogen fertilizer. The activity of both transport systems was determined using [14C]methylammonium. Differences between the two transport systems were observed with regard to their pH- and temperature dependence as well as their kinetic parameters and regulation during growth with various nitrogen sources. Ammonium transport was subject to repression by ammonium and to derepression in its absence, while the methylammonium carrier was induced in the presence of methylamine. The ammonium but not the methylammonium transport system was severely inhibited by ammonium, and metabolic poisons inhibited both uptake systems. The analysis of intracellular metabolites using thin-layer chromatography and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry indicated that methylammonium was rapidly metabolized to N-methylglutamate via gamma-N-methylglutamine.

Biodegradation, Environmental↗

Role of Ser11 in the stabilization of the structure of Ochrobactrum anthropi glutathione transferase.

GSTs (glutathione transferases) are a multifunctional group of enzymes, widely distributed and involved in cellular detoxification processes. In the xenobiotic-degrading bacterium Ochrobactrum anthropi, GST is overexpressed in the presence of toxic concentrations of aromatic compounds such as 4-chlorophenol and atrazine. We have determined the crystal structure of the GST from O. anthropi (OaGST) in complex with GSH. Like other bacterial GSTs, OaGST belongs to the Beta class and shows a similar binding pocket for GSH. However, in contrast with the structure of Proteus mirabilis GST, GSH is not covalently bound to Cys10, but is present in the thiolate form. In our investigation of the structural basis for GSH stabilization, we have identified a conserved network of hydrogen-bond interactions, mediated by the presence of a structural water molecule that links Ser11 to Glu198. Partial disruption of this network, by mutagenesis of Ser11 to alanine, increases the K(m) for GSH 15-fold and decreases the catalytic efficiency 4-fold, even though Ser11 is not involved in GSH binding. Thermal- and chemical-induced unfolding studies point to a global effect of the mutation on the stability of the protein and to a central role of these residues in zippering the terminal helix of the C-terminal domain to the starting helix of the N-terminal domain.

Circular Dichroism↗

D,L-Hydantoinase activity of an Ochrobactrum anthropi strain.

AIMS: A microorganism with the ability to release methionine from D,L-(2-methylthioethyl) hydantoin (strain 245) was isolated from soil. The aim of this study was the identification of the strain and the adjustment of the conditions of growth and of the enzymatic reaction, in order to achieve high specific activities of bioconversion of the hydantoin. METHODS AND RESULTS: Strain 245 was identified as Ochrobactrum anthropi. The strain grew at alkaline pH (up to 10.0) and its hydantoinase activity was found to be inducible by the substrate D,L-(2-methylthioethyl) hydantoin. The enzyme is also alkalostable, with a pH optimum of 9.0. Under these conditions, hydantoinase activity was significantly enhanced and its half life prolonged when 200 mmol l-1 ammonium and phosphate were added. The addition of Ca2+, Na+, Cu2+, Co2+, Mg2+, Zn2+ or Fe3+ (0.5 mmol l-1) to the reaction mixture increased the hydantoinase activity of strain 245 up to tenfold after 24 h of incubation, compared with unamended controls. CONCLUSION: The adequate adjustment of some environmental parameters (pH, addition of inducer, presence of ammonium, phosphate, heavy metals and other ions) can considerably increase the D, L-hydantoinase activity of strain 245. SIGNIFICANCE AND IMPACT OF THE STUDY: The findings reported here set up the initial conditions for a further application of strain 245 in the production of methionine from hydantoine.

Amidohydrolases↗

Gene cloning, nucleotide sequencing, and purification and characterization of the D-stereospecific amino-acid amidase from Ochrobactrum anthropi SV3.

The gene encoding the D-stereospecific amino-acid amidase from Ochrobactrum anthropi SV3 was cloned and sequenced. Analysis of 7.3 kb of genomic DNA revealed the presence of six ORFs, one of which (daaA) encodes the D-amino-acid amidase. This enzyme, DaaA, is composed of 363 amino-acid residues (molecular mass 40 082 Da), and the deduced amino-acid sequence exhibits homology to alkaline D-peptidase from Bacillus cereus DF4-B (32% identity), DD-peptidase from Streptomyces R61 (29% identity), and other penicillin-recognizing proteins. The DaaA protein contains the typical SXXK, YXN, and H(K)XG active-site motifs identified in the penicillin-binding proteins and beta-lactamases. The daaA gene modified in the nucleotide sequence upstream from its start codon was overexpressed in Escherichia coli. The activity of the recombinant DaaA enzyme in cell-free extracts of E. coli was 33.6 U. mg-1 with D-phenylalaninamide as substrate, which is about 350-fold higher than in extracts of O. anthropi SV3. This enzyme was purified to electrophoretic homogeneity by ammonium sulfate fractionation and three column chromatography steps. On gel-filtration chromatography, DaaA appeared to be a monomer with a molecular mass of 40 kDa. It had maximal activity at 45 degrees C and pH 9.0, and was completely inactivated in the presence of phenylmethanesulfonyl fluoride or Zn2+. DaaA had hydrolyzing activity toward D-amino-acid amides with aromatic or hydrophobic side chains, but did not act on the substrates for the DD-peptidase and beta-lactamase, despite their sequence similarity to DaaA. The characteristics of the recombinant DaaA are similar to those found for the native enzyme partially purified from O. anthropi SV3.

Amidohydrolases↗

Ochrobactrum anthropi bloodstream infection complicating hemodialysis.

We report two cases of bacteremia with Ochrobactrum anthropi in patients on hemodialysis. Bacteremia became clinically manifest by recurrent febrile episodes during and after dialysis. In one patient, bacteremia persisted after ciprofloxacin therapy and was cleared only by removal of the dialysis catheter and a 3-week course of gentamicin. The second patient remained intermittently bacteremic for more than 3 months, although the dialysis catheter had been replaced. A MEDLINE search revealed only one previous report of O anthropi bloodstream infection in a patient on hemodialysis, but the pathogen is recognized increasingly as a causative agent of human disease, most importantly in debilitated patients. In contrast to most previously described cases, the two patients reported here had no malignancies and were not on immunosuppressive therapy. Treatment of O anthropi infection is challenging because of widespread and unpredictable resistance to antimicrobial agents and discrepancies between in vitro susceptibility and in vivo efficacy.

Aged↗

Epidemiological investigation of Ochrobactrum anthropi strains isolated from a haematology unit.

Ochrobactrum anthropi is an oxidase-producing gram-negative bacillus preferring aqueous environments. It is an opportunist of low pathogenicity with a wide and unpredictable antibiotic resistance. We observed bacteraemia caused by this organism in two immunocompromized patients hospitalized in the same haematology unit and catheter-associated sepsis was recognized within two days. Another isolate was obtained from the stools of a third patient of the same unit. Environmental investigations recovered an isolate from a tap-water sample of the unit. Pulsed-field gel electrophoresis analysis of these four isolates and two others isolates previously found in the same ward, showed identical restriction patterns for the two blood isolates and confirmed that the two bacteraemia were epidemiologically related.

Adult↗

Infective endocarditis and septic embolization with Ochrobactrum anthropi: case report and review of literature.

Ochrobactrum anthropi, previously known as CDC group Vd, is an aerobic, Gram-negative bacillus of low virulence that occasionally causes human infection. We describe a case of infective endocarditis with O. anthropi complicated by septic embolization. A review of all the literature reported cases of O. anthropi infection is presented and categorized into 'Central line related', 'Transplant related' and "Other pyogenic infections". Mortality appears to be related to the underlying disease state, rather than the organism.

Adult↗

Ochrobactrum anthropi bacteraemia in immunocompetent children.

Ochrobactrum anthropi is an emerging pathogen in immunocompromised patients but infections with the bacterium have very rarely been documented in normal hosts. We report the characteristics of O. anthropi bacteraemia in 11 immunocompetent children, aged 2 months to 7 y, hospitalized in a general hospital during a 5-y period. Children commonly presented with fever, non-specific respiratory or gastrointestinal manifestations, leukocytosis and neutrophilia and had a rapid recovery, even when they did not receive a specific treatment. In 10 cases positive blood cultures were obtained on admission and in all cases subsequent cultures were sterile. In conclusion, O. anthropi may cause bacteraemia in immunocompetent hosts, although further studies are required to clarify whether these isolates represent pseudobacteraemia or whether O. anthropi is a potential pathogen of low virulence.

Anti-Bacterial Agents↗

Beneficial role of hydrophytes in removing Cr(VI) from wastewater in association with chromate-reducing bacterial strains Ochrobactrum intermedium and Brevibacterium.

This study deals with the use of three chromium-resistant bacterial strains (Ochrobactrum intermedium CrT-1, Brevibacterium CrT-13, and CrM-1) in conjunction with Eichornia crassipes for the removal of toxic chromium from wastewater. Bacterial strains resulted in reduced uptake of chromate into inoculated plants as compared to noninoculated control plants. In the presence of different heavy metals, chromium uptake into the plants was 28.7 and 7.15% less at an initial K2CrO4 concentration of 100 and 500 microg ml(-1) in comparison to a metal free chromium solution. K2CrO4 uptake into the plant occurred at different pHs tested, but maximum uptake was observed at pH 5. Nevertheless, the bacterial strains caused some decrease in chromate uptake into the plants, but the combined effect of plants and bacterial strains conduce more removal of Cr(VI) from the solution.

Brevibacterium↗

Physical map and gene survey of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs.

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes research aimed at determining the genome structure of Ochrobactrum anthropi, an opportunistic human pathogen that has potential applications in biodegradation of hazardous organic compounds. A BAC library for O. anthropi was constructed that provides a 70-fold genome coverage based on an estimated genome size of 4.8 Mb. The library contains 3072 clones with an average insert size of 112 kb. High-density colony filters of the library were made, and a physical map of the genome was constructed using a hybridization without replacement strategy. In addition, 1536 BAC clones were fingerprinted with HindIII and analyzed using IMAGE and Fingerprint Contig software (FPC, Sanger Centre, U.K.). The FPC results supported the hybridization data, resulting in the formation of two major contigs representing the two major replicons of the O. anthropi genome. After determining a reduced tiling path, 138 BAC ends from the reduced tile were sequenced for a preliminary gene survey. A search of the public databases with the BLASTX algorithm resulted in 77 strong hits (E-value < 0.001), of which 89% showed similarity to a wide variety of prokaryotic genes. These results provide a contig-based physical map to assist the cloning of important genomic regions and the potential sequencing of the O. anthropi genome.

Chromosomes, Bacterial↗

Characterization, cloning and sequence analysis of the inducible Ochrobactrum anthropi AmpC beta-lactamase.

Ochrobactrum anthropi is resistant to most cephalosporins and penicillins due, at least in part, to the inducible expression of a single beta-lactamase. The beta-lactamase gene has been cloned and sequenced. It encodes an AmpC-type class 1 serine active-site enzyme that hydrolyses mainly cephalosporins and is resistant to inhibition by clavulanic acid. Expression of the ampC gene is inducible via a typical AmpR regulator, which is encoded upstream of ampC. Inducible expression is retained following cloning of O. anthropi ampR-ampC into Escherichia coli, confirming that the signal for AmpR activation in O. anthropi is the same as that used in the Enterobacteriaceae. This is the first reported example of an AmpC beta-lactamase outside of the gamma-subdivision of the bacterial kingdom. Genomic searches of other non-gamma-subdivision bacteria revealed a homologous ampR-ampC cluster in the plant symbiont, Sinorhizobium meliloti.

Amino Acid Sequence↗

Ochrobactrum anthropi bacteremia in pediatric oncology patients.

Ochrobactrum anthropi is an emerging pathogen in immunocompromised hosts, particularly in patients with indwelling catheters. We report the characteristics of 14 O. anthropi bacteremic episodes in 11 children with Hickman-type central catheters. Children presented with fever and nonspecific clinical manifestations. Bacteremia was successfully treated with antibiotics, but catheter removal was necessary to achieve cure in four cases.

Anti-Bacterial Agents↗

Optimization of a medium for enhancing nicotine biodegradation by Ochrobactrum intermedium DN2.

AIMS: To optimize a medium for nicotine degradation by Ochrobactrum intermedium DN2 in presence of yeast extract, glucose and Tween 80 using response surface methodology (RSM). METHODS AND RESULTS: In this study, the effects of yeast extract, glucose and Tween 80 on nicotine degradation were investigated in flasks using a novel nicotine-degrading bacterium, O. intermedium DN2. A full factorial central composite design was applied in the design of experiments and in the analysis of the experimental data. The results showed that the most significant variable influencing nicotine degradation was yeast extract, followed by glucose, and then Tween 80. Moreover these three factors interacted with each other and combined to produce positive effects on nicotine degradation. The experimental data also allowed the development of an empirical model (P < 0.0001) describing the inter-relationship between independent and dependent variables. By solving the regression equation, the optimal values of the variables were determined as: yeast extracts 0.094%, glucose 0.101% and Tween 80 0.080%. Using the medium obtained, about 1,220 mg l(-1) of nicotine was degraded (95.55%) within 10 h at the specific biodegradation of 116.59 mg l(-1) h(-1) in 30-l bioreactor containing 25-l tobacco extract. CONCLUSIONS: An optimal medium of nicotine degradation by the strain DN2 was obtained. SIGNIFICANCE AND IMPACT OF THE STUDY: RSM proved to be reliable in developing the model, optimizing factors and analysing interaction effects. The results provide better understanding on the interactions between yeast extract, glucose and Tween 80 for nicotine biodegradation.

Biodegradation, Environmental↗